Nutrient loading and consumers: Agents of change in open-coast macrophyte assemblages

PubMed Central

Nielsen, Karina J.

2003-01-01

Human activities are significantly altering nutrient regimes and the abundance of consumers in coastal ecosystems. A field experiment in an open-coast, upwelling ecosystem showed that small increases in nutrients increased the biomass and evenness of tide pool macrophytes where consumer abundance and nutrient loading rates were low. Consumers, when abundant, had negative effects on the diversity and biomass of macrophytes. Nutrient loading increases and consumers are less abundant and efficient as wave exposure increases along open coastlines. Experimentally reversing the natural state of nutrient supply and consumer pressure at a wave-protected site to match wave-exposed sites caused the structure of the macrophyte assemblage to converge on that found naturally in wave-exposed pools. The increases in evenness and abundance were driven by increases in structurally complex functional groups. In contrast, increased nutrient loading in semienclosed marine or estuarine ecosystems is typically associated with declines in macrophyte diversity because of increases in structurally simple and opportunistic functional groups. If nutrient concentration of upwelled waters changes with climatic warming or increasing frequency of El Niños, as predicted by some climate models, these results suggest that macrophyte abundance and evenness along wave-swept open-coasts will also change. Macrophytes represent a significant fraction of continental shelf production and provide important habitat for many marine species. The combined effects of shifting nutrient regimes and overexploitation of consumers may have unexpected consequences for the structure and functioning of open-coast communities. PMID:12796509

Nutrient loading and consumers: agents of change in open-coast macrophyte assemblages.

PubMed

Nielsen, Karina J

2003-06-24

Human activities are significantly altering nutrient regimes and the abundance of consumers in coastal ecosystems. A field experiment in an open-coast, upwelling ecosystem showed that small increases in nutrients increased the biomass and evenness of tide pool macrophytes where consumer abundance and nutrient loading rates were low. Consumers, when abundant, had negative effects on the diversity and biomass of macrophytes. Nutrient loading increases and consumers are less abundant and efficient as wave exposure increases along open coastlines. Experimentally reversing the natural state of nutrient supply and consumer pressure at a wave-protected site to match wave-exposed sites caused the structure of the macrophyte assemblage to converge on that found naturally in wave-exposed pools. The increases in evenness and abundance were driven by increases in structurally complex functional groups. In contrast, increased nutrient loading in semienclosed marine or estuarine ecosystems is typically associated with declines in macrophyte diversity because of increases in structurally simple and opportunistic functional groups. If nutrient concentration of upwelled waters changes with climatic warming or increasing frequency of El Niños, as predicted by some climate models, these results suggest that macrophyte abundance and evenness along wave-swept open-coasts will also change. Macrophytes represent a significant fraction of continental shelf production and provide important habitat for many marine species. The combined effects of shifting nutrient regimes and overexploitation of consumers may have unexpected consequences for the structure and functioning of open-coast communities.

Pollinators of the Rocky Mountain columbine: temporal variation, functional groups and associations with floral traits

PubMed Central

Brunet, Johanne

2009-01-01

Background and Aims Pollinators together with other biotic and some abiotic factors can select for floral traits. However, variation in pollinator abundance over time and space can weaken such selection. In the present study, the variation in pollinator abundance over time and space was examined in populations of the Rocky Mountain columbine. The variation in three floral traits is described and correlations between pollinator type, functional pollinator groups or altitude and floral traits are examined. Methods Pollinator observations took place in six Aquilegia coerulea populations over 1–4 years and spur length, flower colour and sepal length were measured in 12 populations. Pollinator abundance, measured as visits per flower per hour, was compared among populations and years. Pollinators were grouped into two functional groups: pollen or nectar collectors. The following associations were examined: annual presence of hawkmoths and whiter flowers with longer spurs; the presence of Sphinx vashti and longer spurs; and higher altitudes and whiter flowers. The study looked at whether an increase in the proportion of hawkmoths in a population was associated with whiter and larger flowers with longer spurs. Key Results The abundance of different pollinator groups varied over time and space. Floral traits varied among populations. Higher altitude was correlated with bluer flowers. Whiter flowers were associated with the annual presence of hawkmoths. Populations visited by Sphinx vashti had longer spurs than populations visited only by Hyles lineata. Populations with greater percentage of nectar-collecting pollinators did not have whiter, larger flowers with longer spurs. Conclusions Despite the large variation in pollinator abundance over time and space, one species of bumble-bee or hawkmoth tended to predominate in each population each year. Future studies of Aquilegia coerulea should examine the specific influences of pollinators and the environment on flower colour and of hawkmoth species on spur length. PMID:19414518

Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli.

PubMed

Gao, Jie; Lan, Ting

2016-01-19

Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty-three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers.

Instability of copronecrophagous beetle assemblages (Coleoptera: Scarabaeinae) in a mountainous tropical landscape of Mexico.

PubMed

Halffter, Gonzalo; Pineda, Eduardo; Arellano, Lucrecia; Escobar, Federico

2007-12-01

We analyzed changes over time in species composition and functional guild structure (temporal beta diversity) for natural assemblages and those modified by humans in a fragmented, tropical mountain landscape. The assemblages belong to cloud forests (the original vegetation type), secondary forests, traditional shaded coffee plantations, commercial shaded coffee plantations, and a cattle pasture. Copronecrophagous beetles, subfamily Scarabaeinae (Insecta: Coleoptera: Scarabaeidae), were used as the indicator group. This group has been used in previous studies and other tropical forests and has been found to be a good indicator of the effects of anthropogenic change. For each assemblage, we compared samples that were collected several years apart. Changes were found in species composition, order of abundance, and in the proportion that a given species is present in the different functional groups. The changes that occurred between samplings affected the less abundant species in the cloud forest and in the pasture. In the other vegetation types, both abundant and less abundant species were affected. Their order of abundance and proportion in the different guilds also changed. This study shows that, although landscape richness remains relatively constant, richness at the local level (alpha diversity) changes notably even over short lapses of time. This could be a characteristic of landscapes with intermediate degrees of disturbance (such as those that have been partially modified for human use), where assemblage composition is very fluid.

Recovery of biological soil crust richness and cover 12-16 years after wildfires in Idaho, USA

NASA Astrophysics Data System (ADS)

Root, Heather T.; Brinda, John C.; Dodson, E. Kyle

2017-09-01

Changing fire regimes in western North America may impact biological soil crust (BSC) communities that influence many ecosystem functions, such as soil stability and C and N cycling. However, longer-term effects of wildfire on BSC abundance, species richness, functional groups, and ecosystem functions after wildfire (i.e., BSC resilience) are still poorly understood. We sampled BSC lichen and bryophyte communities at four sites in Idaho, USA, within foothill steppe communities that included wildfires from 12 to 16 years old. We established six plots outside each burn perimeter and compared them with six plots of varying severity within each fire perimeter at each site. BSC cover was most strongly negatively impacted by wildfire at sites that had well-developed BSC communities in adjacent unburned plots. BSC species richness was estimated to be 65 % greater in unburned plots compared with burned plots, and fire effects did not vary among sites. In contrast, there was no evidence that vascular plant functional groups or fire severity (as measured by satellite metrics differenced normalized burn ratio (dNBR) or relativized differenced normalized burn ratio (RdNBR)) significantly affected longer-term BSC responses. Three large-statured BSC functional groups that may be important in controlling wind and water erosion (squamulose lichens, vagrant lichens, and tall turf mosses) exhibited a significant decrease in abundance in burned areas relative to adjacent unburned areas. The decreases in BSC cover and richness along with decreased abundance of several functional groups suggest that wildfire can negatively impact ecosystem function in these semiarid ecosystems for at least 1 to 2 decades. This is a concern given that increased fire frequency is predicted for the region due to exotic grass invasion and climate change.

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea.

PubMed

Wemheuer, Bernd; Wemheuer, Franziska; Meier, Dimitri; Billerbeck, Sara; Giebel, Helge-Ansgar; Simon, Meinhard; Scherber, Christoph; Daniel, Rolf

2017-11-05

Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria . Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.

Experimental Manipulation of Grassland Plant Diversity Induces Complex Shifts in Aboveground Arthropod Diversity

PubMed Central

Hertzog, Lionel R.; Meyer, Sebastian T.; Weisser, Wolfgang W.; Ebeling, Anne

2016-01-01

Changes in producer diversity cause multiple changes in consumer communities through various mechanisms. However, past analyses investigating the relationship between plant diversity and arthropod consumers focused only on few aspects of arthropod diversity, e.g. species richness and abundance. Yet, shifts in understudied facets of arthropod diversity like relative abundances or species dominance may have strong effects on arthropod-mediated ecosystem functions. Here we analyze the relationship between plant species richness and arthropod diversity using four complementary diversity indices, namely: abundance, species richness, evenness (equitability of the abundance distribution) and dominance (relative abundance of the dominant species). Along an experimental gradient of plant species richness (1, 2, 4, 8, 16 and 60 plant species), we sampled herbivorous and carnivorous arthropods using pitfall traps and suction sampling during a whole vegetation period. We tested whether plant species richness affects consumer diversity directly (i), or indirectly through increased productivity (ii). Further, we tested the impact of plant community composition on arthropod diversity by testing for the effects of plant functional groups (iii). Abundance and species richness of both herbivores and carnivores increased with increasing plant species richness, but the underlying mechanisms differed between the two trophic groups. While higher species richness in herbivores was caused by an increase in resource diversity, carnivore richness was driven by plant productivity. Evenness of herbivore communities did not change along the gradient in plant species richness, whereas evenness of carnivores declined. The abundance of dominant herbivore species showed no response to changes in plant species richness, but the dominant carnivores were more abundant in species-rich plant communities. The functional composition of plant communities had small impacts on herbivore communities, whereas carnivore communities were affected by forbs of small stature, grasses and legumes. Contrasting patterns in the abundance of dominant species imply different levels of resource specialization for dominant herbivores (narrow food spectrum) and carnivores (broad food spectrum). That in turn could heavily affect ecosystem functions mediated by herbivorous and carnivorous arthropods, such as herbivory or biological pest control. PMID:26859496

The structure evolution of biochar from biomass pyrolysis and its correlation with gas pollutant adsorption performance.

PubMed

Chen, Yingquan; Zhang, Xiong; Chen, Wei; Yang, Haiping; Chen, Hanping

2017-12-01

Biochar is carbon-rich, porous and with a great potential in gas pollutant controlling. The physical-chemical structure of biochar is important for the application. This paper firstly reviewed the evolution behavior of physical-chemical structure for biochar during pyrolysis. At lower temperature (<500°C), biomass firstly transformed to "3D network of benzene rings" with abundant functional groups. With temperature increasing (500-700°C), it converted to "2D structure of fused rings" with abundant porosity. As temperature increasing further (>700°C), it may transit into a "graphite microcrystalline structure", the porosity and functional groups were diminished correspondingly. The modification of biochar and its application as sorbent for gas pollutant were also reviewed. Activation and doping can significantly increase the porosity and special functional groups in biochar, which is favorable for gas pollutant adsorption. With a higher porosity, the adsorption capacity of gas pollutant is bigger, however, the functional groups determined the sorption stability of gas pollutant. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota.

PubMed

Weber, Eva B; Lehtovirta-Morley, Laura E; Prosser, James I; Gubry-Rangin, Cécile

2015-03-01

Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. © FEMS 2015.

High-throughput sequencing technology to reveal the composition and function of cecal microbiota in Dagu chicken.

PubMed

Xu, Yunhe; Yang, Huixin; Zhang, Lili; Su, Yuhong; Shi, Donghui; Xiao, Haidi; Tian, Yumin

2016-11-04

The chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. The coding capacity of microbiome vastly surpasses that of the host's genome, encoding biochemical pathways that the host has not developed. An optimal gut microbiota can increase agricultural productivity. This study aims to explore the composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range (outdoor, OD) and cage (indoor, ID) raising. Cecal samples were collected from 24 chickens across 4 groups (12-w OD, 12-w ID, 18-w OD, and 18-w ID). We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions to characterize the cecal microbiota of Dagu chicken and compare the difference of cecal microbiota between free-range and cage raising chickens. It was found that 34 special operational taxonomic units (OTUs) in OD groups and 4 special OTUs in ID groups. 24 phyla were shared by the 24 samples. Bacteroidetes was the most abundant phylum with the largest proportion, followed by Firmicutes and Proteobacteria. The OD groups showed a higher proportion of Bacteroidetes (>50 %) in cecum, but a lower Firmicutes/Bacteroidetes ratio in both 12-w old (0.42, 0.62) and 18-w old groups (0.37, 0.49) compared with the ID groups. Cecal microbiota in the OD groups have higher abundance of functions involved in amino acids and glycan metabolic pathway. The composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range and cage raising are different. The cage raising mode showed a lower proportion of Bacteroidetes in cecum, but a higher Firmicutes/Bacteroidetes ratio compared with free-range mode. Cecal microbiota in free-range mode have higher abundance of functions involved in amino acids and glycan metabolic pathway.

A molecular investigation of soil organic carbon composition across a subalpine catchment

USGS Publications Warehouse

Hsu, Hsiao-Tieh; Lawrence, Corey R.; Winnick, Matthew J.; Bargar, John R.; Maher, Katharine

2018-01-01

The dynamics of soil organic carbon (SOC) storage and turnover are a critical component of the global carbon cycle. Mechanistic models seeking to represent these complex dynamics require detailed SOC compositions, which are currently difficult to characterize quantitatively. Here, we address this challenge by using a novel approach that combines Fourier transform infrared spectroscopy (FT-IR) and bulk carbon X-ray absorption spectroscopy (XAS) to determine the abundance of SOC functional groups, using elemental analysis (EA) to constrain the total amount of SOC. We used this SOC functional group abundance (SOC-fga) method to compare variability in SOC compositions as a function of depth across a subalpine watershed (East River, Colorado, USA) and found a large degree of variability in SOC functional group abundances between sites at different elevations. Soils at a lower elevation are predominantly composed of polysaccharides, while soils at a higher elevation have more substantial portions of carbonyl, phenolic, or aromatic carbon. We discuss the potential drivers of differences in SOC composition between these sites, including vegetation inputs, internal processing and losses, and elevation-driven environmental factors. Although numerical models would facilitate the understanding and evaluation of the observed SOC distributions, quantitative and meaningful measurements of SOC molecular compositions are required to guide such models. Comparison among commonly used characterization techniques on shared reference materials is a critical next step for advancing our understanding of the complex processes controlling SOC compositions.

Nanoplankton and picoplankton in the Western English Channel: abundance and seasonality from 2007-2013

NASA Astrophysics Data System (ADS)

Tarran, Glen A.; Bruun, John T.

2015-09-01

The nano- and picoplankton community at Station L4 in the Western English Channel was studied between 2007 and 2013 by flow cytometry to quantify abundance and investigate seasonal cycles within these communities. Nanoplankton included both photosynthetic and heterotrophic eukaryotic single-celled organisms while the picoplankton included picoeukaryote phytoplankton, Synechococcus sp. cyanobacteria and heterotrophic bacteria. A Box-Jenkins Transfer Function climatology analysis of surface data revealed that Synechococcus sp., cryptophytes, and heterotrophic flagellates had bimodal annual cycles. Nanoeukaryotes and both high and low nucleic acid-containing bacteria (HNA and LNA, respectively) groups exhibited unimodal annual cycles. Phaeocystis sp., whilst having clearly defined abundance maxima in spring was not detectable the rest of the year. Coccolithophores exhibited a weak seasonal cycle, with abundance peaks in spring and autumn. Picoeukaryotes did not exhibit a discernable seasonal cycle at the surface. Timings of maximum group abundance varied through the year. Phaeocystis sp. and heterotrophic flagellates peaked in April/May. Nanoeukaryotes and HNA bacteria peaked in June/July and had relatively high abundance throughout the summer. Synechococcus sp., cryptophytes and LNA bacteria all peaked from mid to late September. The transfer function model techniques used represent a useful means of identifying repeating annual cycles in time series data with the added ability to detect trends and harmonic terms at different time scales from months to decades.

Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome.

PubMed

Dudek, Magda; Adams, Jessica; Swain, Martin; Hegarty, Matthew; Huws, Sharon; Gallagher, Joe

2014-10-20

This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed.

Modeling wetland blackbird populations as a function of waterfowl abundance in the prairie pothole region of the United States and Canada

USGS Publications Warehouse

Forcey, G.M.; Linz, G.M.; Thogmartin, W.E.; Bleier, W.J.

2008-01-01

Blackbirds share wetland habitat with many waterfowl species in Bird Conservation Region 11 (BCR 11), the prairie potholes. Because of similar habitat preferences, there may be associations between blackbird populations and populations of one or more species of waterfowl in BCR11. This study models populations of red-winged blackbirds and yellow-headed blackbirds as a function of multiple waterfowl species using data from the North American Breeding Bird Survey within BCR11. For each blackbird species, we created a global model with blackbird abundance modeled as a function of 11 waterfowl species; nuisance effects (year, route, and observer) also were included in the model. Hierarchical Poisson regression models were fit using Markov chain Monte Carlo methods in WinBUGS 1.4.1. Waterfowl abundances were weakly associated with blackbird numbers, and no single waterfowl species showed a strong correlation with any blackbird species. These findings suggest waterfowl abundance from a single species is not likely a good bioindicator of blackbird abundance; however, a global model provided good fit for predicting red-winged blackbird abundance. Increased model complexity may be required for accurate predictions of blackbird abundance; the amount of data required to construct appropriate models may limit this approach for predicting blackbird abundance in the prairie potholes. Copyright ?? Taylor & Francis Group, LLC.

Logging cuts the functional importance of invertebrates in tropical rainforest

PubMed Central

Ewers, Robert M.; Boyle, Michael J. W.; Gleave, Rosalind A.; Plowman, Nichola S.; Benedick, Suzan; Bernard, Henry; Bishop, Tom R.; Bakhtiar, Effendi Y.; Chey, Vun Khen; Chung, Arthur Y. C.; Davies, Richard G.; Edwards, David P.; Eggleton, Paul; Fayle, Tom M.; Hardwick, Stephen R.; Homathevi, Rahman; Kitching, Roger L.; Khoo, Min Sheng; Luke, Sarah H.; March, Joshua J.; Nilus, Reuben; Pfeifer, Marion; Rao, Sri V.; Sharp, Adam C.; Snaddon, Jake L.; Stork, Nigel E.; Struebig, Matthew J.; Wearn, Oliver R.; Yusah, Kalsum M.; Turner, Edgar C.

2015-01-01

Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests. PMID:25865801

Logging cuts the functional importance of invertebrates in tropical rainforest.

PubMed

Ewers, Robert M; Boyle, Michael J W; Gleave, Rosalind A; Plowman, Nichola S; Benedick, Suzan; Bernard, Henry; Bishop, Tom R; Bakhtiar, Effendi Y; Chey, Vun Khen; Chung, Arthur Y C; Davies, Richard G; Edwards, David P; Eggleton, Paul; Fayle, Tom M; Hardwick, Stephen R; Homathevi, Rahman; Kitching, Roger L; Khoo, Min Sheng; Luke, Sarah H; March, Joshua J; Nilus, Reuben; Pfeifer, Marion; Rao, Sri V; Sharp, Adam C; Snaddon, Jake L; Stork, Nigel E; Struebig, Matthew J; Wearn, Oliver R; Yusah, Kalsum M; Turner, Edgar C

2015-04-13

Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010.

PubMed

Schipper, Aafke M; Belmaker, Jonathan; de Miranda, Murilo Dantas; Navarro, Laetitia M; Böhning-Gaese, Katrin; Costello, Mark J; Dornelas, Maria; Foppen, Ruud; Hortal, Joaquín; Huijbregts, Mark A J; Martín-López, Berta; Pettorelli, Nathalie; Queiroz, Cibele; Rossberg, Axel G; Santini, Luca; Schiffers, Katja; Steinmann, Zoran J N; Visconti, Piero; Rondinini, Carlo; Pereira, Henrique M

2016-12-01

Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5-year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Functional trait responses to grazing are mediated by soil moisture and plant functional group identity

PubMed Central

Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

2015-01-01

Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance–resistance strategies to grazing and mixed acquisitive–conservative strategies in resource utilization. PMID:26655858

Functional trait responses to grazing are mediated by soil moisture and plant functional group identity.

PubMed

Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

2015-12-11

Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization.

Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota

PubMed Central

Weber, Eva B.; Lehtovirta-Morley, Laura E.; Prosser, James I.; Gubry-Rangin, Cécile

2015-01-01

Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. PMID:25764563

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss).

PubMed

Gonçalves, A T; Gallardo-Escárate, C

2017-05-01

This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout (Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both. A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets. Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance. This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary modulation with functional feeds in aquatic organisms. © 2017 The Society for Applied Microbiology.

Community structure of rare methanogenic archaea: insight from a single functional group

PubMed Central

Winkel, Matthias; Wagner, Dirk

2017-01-01

Abstract The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups. PMID:29029047

Comparative diversity of arthropods on Bt maize and non-Bt maize in two different cropping systems in South Africa.

PubMed

Truter, J; Van Hamburg, H; Van Den Berg, J

2014-02-01

The biodiversity of an agroecosystem is not only important for its intrinsic value but also because it influences ecological functions that are vital for crop production in sustainable agricultural systems and the surrounding environment. A concern about genetically modified (GM) crops is the potential negative impact that such crops could have on diversity and abundance of nontarget organisms, and subsequently on ecosystem functions. Therefore, it is essential to assess the potential environmental risk of the release of a GM crop and to study its effect on species assemblages within that ecosystem. Assessment of the impact of Bt maize on the environment is hampered by the lack of basic checklists of species present in maize agroecosystems. The aims of the study were to compile a checklist of arthropods that occur on maize in South Africa and to compare the diversity and abundance of arthropods and functional groups on Bt maize and non-Bt maize. Collections of arthropods were carried out during two growing seasons on Bt maize and non-Bt maize plants at two localities. Three maize fields were sampled per locality during each season. Twenty plants, each of Bt maize and non-Bt maize, were randomly selected from the fields at each site. The arthropods collected during this study were classified to morphospecies level and grouped into the following functional groups: detritivores, herbivores, predators, and parasitoids. Based on feeding strategy, herbivores and predators were further divided into sucking herbivores or predators (piercing-sucking mouthparts) and chewing herbivores or predators (chewing mouthparts). A total of 8,771 arthropod individuals, comprising 288 morphospecies and presenting 20 orders, were collected. Results from this short-term study indicated that abundance and diversity of arthropods in maize and the different functional guilds were not significantly affected by Bt maize, either in terms of diversity or abundance.

Matrix Intensification Alters Avian Functional Group Composition in Adjacent Rainforest Fragments

PubMed Central

Deikumah, Justus P.; McAlpine, Clive A.; Maron, Martine

2013-01-01

Conversion of farmland land-use matrices to surface mining is an increasing threat to the habitat quality of forest remnants and their constituent biota, with consequences for ecosystem functionality. We evaluated the effects of matrix type on bird community composition and the abundance and evenness within avian functional groups in south-west Ghana. We hypothesized that surface mining near remnants may result in a shift in functional composition of avifaunal communities, potentially disrupting ecological processes within tropical forest ecosystems. Matrix intensification and proximity to the remnant edge strongly influenced the abundance of members of several functional guilds. Obligate frugivores, strict terrestrial insectivores, lower and upper strata birds, and insect gleaners were most negatively affected by adjacent mining matrices, suggesting certain ecosystem processes such as seed dispersal may be disrupted by landscape change in this region. Evenness of these functional guilds was also lower in remnants adjacent to surface mining, regardless of the distance from remnant edge, with the exception of strict terrestrial insectivores. These shifts suggest matrix intensification can influence avian functional group composition and related ecosystem-level processes in adjacent forest remnants. The management of matrix habitat quality near and within mine concessions is important for improving efforts to preserveavian biodiversity in landscapes undergoing intensification such as through increased surface mining. PMID:24058634

Matrix intensification alters avian functional group composition in adjacent rainforest fragments.

PubMed

Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

2013-01-01

Conversion of farmland land-use matrices to surface mining is an increasing threat to the habitat quality of forest remnants and their constituent biota, with consequences for ecosystem functionality. We evaluated the effects of matrix type on bird community composition and the abundance and evenness within avian functional groups in south-west Ghana. We hypothesized that surface mining near remnants may result in a shift in functional composition of avifaunal communities, potentially disrupting ecological processes within tropical forest ecosystems. Matrix intensification and proximity to the remnant edge strongly influenced the abundance of members of several functional guilds. Obligate frugivores, strict terrestrial insectivores, lower and upper strata birds, and insect gleaners were most negatively affected by adjacent mining matrices, suggesting certain ecosystem processes such as seed dispersal may be disrupted by landscape change in this region. Evenness of these functional guilds was also lower in remnants adjacent to surface mining, regardless of the distance from remnant edge, with the exception of strict terrestrial insectivores. These shifts suggest matrix intensification can influence avian functional group composition and related ecosystem-level processes in adjacent forest remnants. The management of matrix habitat quality near and within mine concessions is important for improving efforts to preserveavian biodiversity in landscapes undergoing intensification such as through increased surface mining.

Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System

PubMed Central

Li, Shuqing; Song, Lina; Gao, Xiang; Jin, Yaguo; Liu, Shuwei; Shen, Qirong; Zou, Jianwen

2017-01-01

Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models. PMID:28373862

Leaf litter arthropod responses to tropical forest restoration.

PubMed

Cole, Rebecca J; Holl, Karen D; Zahawi, Rakan A; Wickey, Philipp; Townsend, Alan R

2016-08-01

Soil and litter arthropods represent a large proportion of tropical biodiversity and perform important ecosystem functions, but little is known about the efficacy of different tropical forest restoration strategies in facilitating their recovery in degraded habitats. We sampled arthropods in four 7- to 8-year-old restoration treatments and in nearby reference forests. Sampling was conducted during the wet and dry seasons using extractions from litter and pitfall samples. Restoration treatments were replicated in 50 × 50-m plots in four former pasture sites in southern Costa Rica: plantation - trees planted throughout the plot; applied nucleation/islands - trees planted in patches of different sizes; and natural regeneration - no tree planting. Arthropod abundance, measures of richness and diversity, and a number of functional groups were greater in the island treatment than in natural regeneration or plantation treatments and, in many cases, were similar to reference forest. Litter and pitfall morphospecies and functional group composition in all three restoration treatments were significantly different than reference sites, but island and plantation treatments showed more recovery than natural regeneration. Abundance and functional group diversity showed a much greater degree of recovery than community composition. Synthesis and applications: The less resource-intensive restoration strategy of planting tree islands was more effective than tree plantations in restoring arthropod abundance, richness, and functional diversity. None of the restoration strategies, however, resulted in similar community composition as reference forest after 8 years of recovery, highlighting the slow rate of recovery of arthropod communities after disturbance, and underscoring the importance of conservation of remnant forests in fragmented landscapes.

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome

PubMed Central

Dudek, Magda; Adams, Jessica; Swain, Martin; Hegarty, Matthew; Huws, Sharon; Gallagher, Joe

2014-01-01

This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed. PMID:25334059

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

PubMed Central

Taylor, Joe D; Cunliffe, Michael

2016-01-01

Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

PubMed Central

Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

2014-01-01

Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

[Effects of different soil and water loss control measures on the dung beetle assemblages in Huangfuchuan watershed, Inner Mongolia of North China].

PubMed

Liu, Wei; Wang, Run-Run; Liu, Xin-Min

2013-03-01

By using pitfall trap method, and taking the croplands and natural grasslands under different soil and water loss control measures as sampling plots, an investigation was conducted on the dung beetle assemblages in the Huangfuchuan watershed of Inner Mongolia from September 2007 to September 2008, aimed to understand the effects of different soil and water loss control measures on the dung beetle assemblages in the watershed. A total of 6169 dung beetles were captured, belonging to 15 species, 5 genus, and 2 families. The dominant species were Aphodius rectus and Onthophagus gibbulus, accounting for 66. 54% and 13. 26% of the total captured beetles, respectively. A lack of the species suitable for living in woodland habitats was the basic feature of the dung beetle assemblages. As compared with the control, all test soil and water loss control measures did not cause an obvious increase of species richness, biomass, and abundance of the dung beetle assemblages. The biomass and species richness of the assemblages as well as the abundance of the functional groups II and III had a significant negative correlation with the average tree (grass) height. Under the effects of long-term agricultural cultivation and the lack of large herbivores, the species richness and abundance of the functional group I (larger paracoprids and telocoprids) were lower than those of the functional groups II (relatively smaller paracoprids) and II (endocoprids), the main components of the dung beetle assemblages in the watershed. The faeces of the residents and livestock in the study region provided abundant foods for the dung beetle assemblages, inducing the relatively high abundance and spices richness of the assemblages occurred in the croplands nearby the villages. Our results suggested that natural grasslands were the suitable habitats for the dung beetles in Huangfuchuan watershed. At regional scale, to popularize the successful experiences of comprehensive soil and water loss control, preserve natural grasslands, and feed appropriate number of livestock (especially larger herbivores) could be the effective approaches for maintaining the diversity of dung beetles and the ecosystem functions.

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.

PubMed

Cai, Wei; Li, Yi; Niu, Lihua; Zhang, Wenlong; Wang, Chao; Wang, Peifang; Meng, Fangang

2017-10-15

The composition and distribution characteristics of bacterial communities in biofilms attached to hydraulic concrete structure (HCS) surfaces were investigated for the first time in four reservoirs in the middle and lower reaches of the Yangtze River Basin using 16S rRNA Miseq sequencing. High microbial diversity was found in HCS biofilms, and notable differences were observed in different types of HCS. Proteobacteria, Cyanobacteria and Chloroflexi were the predominant phyla, with respective relative abundances of 35.3%, 25.4% and 13.0%. The three most abundant genera were Leptolyngbya, Anaerolineaceae and Polynucleobacter. The phyla Beta-proteobacteria and Firmicutes and genus Lyngbya were predominant in CGP, whereas the phyla Cyanobacteria and Chloroflexi and genera Leptolyngbya, Anaerolinea and Polynucleobacter survived better in land walls and bank slopes. Dissolved oxygen, ammonia nitrogen and temperature were characterized as the main factors driving the bacterial community composition. The most abundant groups of metabolic functions were also identified as ammonia oxidizers, sulphate reducers, and dehalogenators. Additionally, functional groups related to biocorrosion were found to account for the largest proportion (14.0% of total sequences) in gate piers, followed by those in land walls (11.5%) and bank slopes (10.2%). Concrete gate piers were at the greatest risk of biocorrosion with the most abundant negative bacterial groups, especially for sulphate reducers. Thus, it should be paid high attention to the biocorrosion prevention of concrete gate piers. Overall, this study contributed to the optimization of microbial control and the improvement of the safety management for water conservation structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understory plant communities and the functional distinction between savanna trees, forest trees, and pines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veldman, Joseph W.; Mattingly, W. Brett; Brudvig, Lars A.

Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in firemore » frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are more fire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity.« less

The Influence of Coral Reef Benthic Condition on Associated Fish Assemblages

PubMed Central

Chong-Seng, Karen M.; Mannering, Thomas D.; Pratchett, Morgan S.; Bellwood, David R.; Graham, Nicholas A. J.

2012-01-01

Accumulative disturbances can erode a coral reef’s resilience, often leading to replacement of scleractinian corals by macroalgae or other non-coral organisms. These degraded reef systems have been mostly described based on changes in the composition of the reef benthos, and there is little understanding of how such changes are influenced by, and in turn influence, other components of the reef ecosystem. This study investigated the spatial variation in benthic communities on fringing reefs around the inner Seychelles islands. Specifically, relationships between benthic composition and the underlying substrata, as well as the associated fish assemblages were assessed. High variability in benthic composition was found among reefs, with a gradient from high coral cover (up to 58%) and high structural complexity to high macroalgae cover (up to 95%) and low structural complexity at the extremes. This gradient was associated with declining species richness of fishes, reduced diversity of fish functional groups, and lower abundance of corallivorous fishes. There were no reciprocal increases in herbivorous fish abundances, and relationships with other fish functional groups and total fish abundance were weak. Reefs grouping at the extremes of complex coral habitats or low-complexity macroalgal habitats displayed markedly different fish communities, with only two species of benthic invertebrate feeding fishes in greater abundance in the macroalgal habitat. These results have negative implications for the continuation of many coral reef ecosystem processes and services if more reefs shift to extreme degraded conditions dominated by macroalgae. PMID:22870294

The influence of coral reef benthic condition on associated fish assemblages.

PubMed

Chong-Seng, Karen M; Mannering, Thomas D; Pratchett, Morgan S; Bellwood, David R; Graham, Nicholas A J

2012-01-01

Accumulative disturbances can erode a coral reef's resilience, often leading to replacement of scleractinian corals by macroalgae or other non-coral organisms. These degraded reef systems have been mostly described based on changes in the composition of the reef benthos, and there is little understanding of how such changes are influenced by, and in turn influence, other components of the reef ecosystem. This study investigated the spatial variation in benthic communities on fringing reefs around the inner Seychelles islands. Specifically, relationships between benthic composition and the underlying substrata, as well as the associated fish assemblages were assessed. High variability in benthic composition was found among reefs, with a gradient from high coral cover (up to 58%) and high structural complexity to high macroalgae cover (up to 95%) and low structural complexity at the extremes. This gradient was associated with declining species richness of fishes, reduced diversity of fish functional groups, and lower abundance of corallivorous fishes. There were no reciprocal increases in herbivorous fish abundances, and relationships with other fish functional groups and total fish abundance were weak. Reefs grouping at the extremes of complex coral habitats or low-complexity macroalgal habitats displayed markedly different fish communities, with only two species of benthic invertebrate feeding fishes in greater abundance in the macroalgal habitat. These results have negative implications for the continuation of many coral reef ecosystem processes and services if more reefs shift to extreme degraded conditions dominated by macroalgae.

Effect of Habitat Size, Quality, and Isolation on Functional Groups of Beetles in Hollow Oaks

PubMed Central

Pilskog, Hanne Eik; Birkemoe, Tone; Framstad, Erik; Sverdrup-Thygeson, Anne

2016-01-01

One of the largest threats to biodiversity is land use change and habitat loss. Hollow oaks (Quercus spp. L.) are well-defined patches that are hotspots for biodiversity and red-listed species, but they are often rare and fragmented in the landscape. We investigated the effect of patch size, habitat quality, and isolation on functional groups and red-listed saproxylic beetles in hollow oaks (n = 40) in Norway. The groups were defined by host tree association, trophic grouping, and red-listed status. Habitat quality, represented by tree form was most important in explaining species richness for most groups. Patch size, represented by circumference and amount of dead branches, was most important in explaining abundance. Isolation, that is single oaks compared with oaks in groups, had a negative effect on the abundance of beetles feeding both on wood and fungi (xylomycethopagous), as well as on species associated with broadleaved trees (oak semi-specialists), but did not affect species richness. This indicates that at this scale and in this landscape, isolated oaks are as species rich and valuable for conservation as other oaks, although some functional groups may be more vulnerable to isolation than others. The red-listed species only responded to patch size, indicating that oaks with large circumference and many dead branches are especially important for red-listed species and for conservation. PMID:26945089

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

PubMed Central

Carrick, Hunter J.; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H.; Vanderploeg, Henry A.

2017-01-01

ABSTRACT One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. We show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation. PMID:28593195

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.

PubMed

Denef, Vincent J; Carrick, Hunter J; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H; Vanderploeg, Henry A

2017-01-01

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. We show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denef, Vincent J.; Carrick, Hunter J.; Cavaletto, Joann

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptiblemore » to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions.Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. Here, we show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.« less

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

DOE PAGES

Denef, Vincent J.; Carrick, Hunter J.; Cavaletto, Joann; ...

2017-05-31

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptiblemore » to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions.Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. Here, we show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.« less

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils.

PubMed

Wu, Ruo-Nan; Meng, Han; Wang, Yong-Feng; Lan, Wensheng; Gu, Ji-Dong

2017-11-01

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al 3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH 3 /NH 4 + equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al 3+ . Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.

Population Abundance and Ecosystem Service Provision: The Case of Birds

PubMed Central

Gaston, Kevin J; Cox, Daniel T C; Canavelli, Sonia B; García, Daniel; Hughes, Baz; Maas, Bea; Martínez, Daniel; Ogada, Darcy; Inger, Richard

2018-01-01

Abstract Although there is a diversity of concerns about recent persistent declines in the abundances of many species, the implications for the associated delivery of ecosystem services to people are surprisingly poorly understood. In principle, there are a broad range of potential functional relationships between the abundance of a species or group of species and the magnitude of ecosystem-service provision. Here, we identify the forms these relationships are most likely to take. Focusing on the case of birds, we review the empirical evidence for these functional relationships, with examples of supporting, regulating, and cultural services. Positive relationships between abundance and ecosystem-service provision are the norm (although seldom linear), we found no evidence for hump-shaped relationships, and negative ones were limited to cultural services that value rarity. Given the magnitude of abundance declines among many previously common species, it is likely that there have been substantial losses of ecosystem services, providing important implications for the identification of potential tipping points in relation to defaunation resilience, biodiversity conservation, and human well-being. PMID:29686433

Bidentate, monoanionic auxiliary-directed functionalization of carbon-hydrogen bonds.

PubMed

Daugulis, Olafs; Roane, James; Tran, Ly Dieu

2015-04-21

In recent years, carbon-hydrogen bond functionalization has evolved from an organometallic curiosity to a tool used in mainstream applications in the synthesis of complex natural products and drugs. The use of C-H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C-H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C-H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp(3) C-H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp(2) C-H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C-H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp(2) and sp(3) C-H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon-hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C-H bond functionalization step. Second, the directing groups can be removed, enabling their use in synthesis and functionalization of natural products and medicinally relevant substances. While the development of these directing groups presents a significant advance, several limitations of this methodology are apparent. The use of expensive second-row transition metal catalysts is still required for efficient sp(3) C-H bond functionalization. Furthermore, the need to install and subsequently remove the relatively expensive directing group is a disadvantage.

Bidentate, Monoanionic Auxiliary-Directed Functionalization of Carbon–Hydrogen Bonds

PubMed Central

Daugulis, Olafs; Roane, James; Tran, Ly Dieu

2015-01-01

CONSPECTUS In recent years, carbon–hydrogen bond functionalization has evolved from an organometallic curiosity to mainstream applications in the synthesis of complex natural products and drugs. The use of C–H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C–H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C–H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp3 C–H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp2 C–H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C–H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp2 and sp3 C–H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon–hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C–H bond functionalization step. Second, the directing groups can be removed, enabling their use in synthesis and functionalization of natural products and medicinally relevant substances. While the development of these directing groups presents a significant advance, several limitations of this methodology are apparent. The use of expensive second-row transition metal catalysts is still required for efficient sp3 C–H bond functionalization. Furthermore, a disadvantage is the need to install and subsequently remove the relatively expensive directing group. PMID:25756616

Maintenance of soil functioning following erosion of microbial diversity.

PubMed

Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Freitag, Thomas; Guillaumaud, Nadine; Roux, Xavier Le

2006-12-01

The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.

Social Insects Dominate Eastern US Temperate Hardwood Forest Macroinvertebrate Communities in Warmer Regions

PubMed Central

King, Joshua R.; Warren, Robert J.; Bradford, Mark A.

2013-01-01

Earthworms, termites, and ants are common macroinvertebrates in terrestrial environments, although for most ecosystems data on their abundance and biomass is sparse. Quantifying their areal abundance is a critical first step in understanding their functional importance. We intensively sampled dead wood, litter, and soil in eastern US temperate hardwood forests at four sites, which span much of the latitudinal range of this ecosystem, to estimate the abundance and biomass m−2 of individuals in macroinvertebrate communities. Macroinvertebrates, other than ants and termites, differed only slightly among sites in total abundance and biomass and they were similar in ordinal composition. Termites and ants were the most abundant macroinvertebrates in dead wood, and ants were the most abundant in litter and soil. Ant abundance and biomass m−2 in the southernmost site (Florida) were among the highest values recorded for ants in any ecosystem. Ant and termite biomass and abundance varied greatly across the range, from <1% of the total macroinvertebrate abundance (in the northern sites) to >95% in the southern sites. Our data reveal a pronounced shift to eusocial insect dominance with decreasing latitude in a temperate ecosystem. The extraordinarily high social insect relative abundance outside of the tropics lends support to existing data suggesting that ants, along with termites, are globally the most abundant soil macroinvertebrates, and surpass the majority of other terrestrial animal (vertebrate and invertebrate) groups in biomass m−2. Our results provide a foundation for improving our understanding of the functional role of social insects in regulating ecosystem processes in temperate forest. PMID:24116079

New aerial survey and hierarchical model to estimate manatee abundance

USGS Publications Warehouse

Langimm, Cahterine A.; Dorazio, Robert M.; Stith, Bradley M.; Doyle, Terry J.

2011-01-01

Monitoring the response of endangered and protected species to hydrological restoration is a major component of the adaptive management framework of the Comprehensive Everglades Restoration Plan. The endangered Florida manatee (Trichechus manatus latirostris) lives at the marine-freshwater interface in southwest Florida and is likely to be affected by hydrologic restoration. To provide managers with prerestoration information on distribution and abundance for postrestoration comparison, we developed and implemented a new aerial survey design and hierarchical statistical model to estimate and map abundance of manatees as a function of patch-specific habitat characteristics, indicative of manatee requirements for offshore forage (seagrass), inland fresh drinking water, and warm-water winter refuge. We estimated the number of groups of manatees from dual-observer counts and estimated the number of individuals within groups by removal sampling. Our model is unique in that we jointly analyzed group and individual counts using assumptions that allow probabilities of group detection to depend on group size. Ours is the first analysis of manatee aerial surveys to model spatial and temporal abundance of manatees in association with habitat type while accounting for imperfect detection. We conducted the study in the Ten Thousand Islands area of southwestern Florida, USA, which was expected to be affected by the Picayune Strand Restoration Project to restore hydrology altered for a failed real-estate development. We conducted 11 surveys in 2006, spanning the cold, dry season and warm, wet season. To examine short-term and seasonal changes in distribution we flew paired surveys 1–2 days apart within a given month during the year. Manatees were sparsely distributed across the landscape in small groups. Probability of detection of a group increased with group size; the magnitude of the relationship between group size and detection probability varied among surveys. Probability of detection of individual manatees within a group also differed among surveys, ranging from a low of 0.27 on 11 January to a high of 0.73 on 8 August. During winter surveys, abundance was always higher inland at Port of the Islands (POI), a manatee warm-water aggregation site, than in the other habitat types. During warm-season surveys, highest abundances were estimated in offshore habitat where manatees forage on seagrass. Manatees continued to use POI in summer, but in lower numbers than in winter, possibly to drink freshwater. Abundance in other inland systems and inshore bays was low compared to POI in winter and summer, possibly because of low availability of freshwater. During cold weather, maps of patch abundance of paired surveys showed daily changes in manatee distribution associated with rapid changes in air and water temperature as manatees sought warm water with falling temperatures and seagrass areas with increasing temperatures. Within a habitat type, some patches had higher manatee abundance suggesting differences in quality, possibly due to freshwater flow. If hydrological restoration alters the location of quality habitat, postrestoration comparisons using our methods will document how manatees adjust to new resources, providing managers with information on spatial needs for further monitoring or management. Total abundance for the entire area was similar among survey dates. Credible intervals however were large on a few surveys, and may limit our ability to statistically detect trends in total abundance. Additional modeling of abundance with time- and patch-specific covariates of salinity, water temperature, and seagrass abundance will directly link manatee abundance with physical and biological changes due to restoration and should decrease uncertainty of estimates.

Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects.

PubMed

Edwards, C B; Friedlander, A M; Green, A G; Hardt, M J; Sala, E; Sweatman, H P; Williams, I D; Zgliczynski, B; Sandin, S A; Smith, J E

2014-01-07

On coral reefs, herbivorous fishes consume benthic primary producers and regulate competition between fleshy algae and reef-building corals. Many of these species are also important fishery targets, yet little is known about their global status. Using a large-scale synthesis of peer-reviewed and unpublished data, we examine variability in abundance and biomass of herbivorous reef fishes and explore evidence for fishing impacts globally and within regions. We show that biomass is more than twice as high in locations not accessible to fisheries relative to fisheries-accessible locations. Although there are large biogeographic differences in total biomass, the effects of fishing are consistent in nearly all regions. We also show that exposure to fishing alters the structure of the herbivore community by disproportionately reducing biomass of large-bodied functional groups (scraper/excavators, browsers, grazer/detritivores), while increasing biomass and abundance of territorial algal-farming damselfishes (Pomacentridae). The browser functional group that consumes macroalgae and can help to prevent coral-macroalgal phase shifts appears to be most susceptible to fishing. This fishing down the herbivore guild probably alters the effectiveness of these fishes in regulating algal abundance on reefs. Finally, data from remote and unfished locations provide important baselines for setting management and conservation targets for this important group of fishes.

Locally rare species influence grassland ecosystem multifunctionality

PubMed Central

Manning, Peter; Prati, Daniel; Gossner, Martin M.; Alt, Fabian; Arndt, Hartmut; Baumgartner, Vanessa; Binkenstein, Julia; Birkhofer, Klaus; Blaser, Stefan; Blüthgen, Nico; Boch, Steffen; Böhm, Stefan; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Heinze, Johannes; Hölzel, Norbert; Jung, Kirsten; Klaus, Valentin H.; Klein, Alexandra-Maria; Kleinebecker, Till; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Morris, E. Kathryn; Müller, Jörg; Oelmann, Yvonne; Overmann, Jörg; Pašalić, Esther; Renner, Swen C.; Rillig, Matthias C.; Schaefer, H. Martin; Schloter, Michael; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Sikorski, Johannes; Socher, Stephanie A.; Solly, Emily F.; Sonnemann, Ilja; Sorkau, Elisabeth; Steckel, Juliane; Steffan-Dewenter, Ingolf; Stempfhuber, Barbara; Tschapka, Marco; Türke, Manfred; Venter, Paul; Weiner, Christiane N.; Weisser, Wolfgang W.; Werner, Michael; Westphal, Catrin; Wilcke, Wolfgang; Wolters, Volkmar; Wubet, Tesfaye; Wurst, Susanne; Fischer, Markus; Allan, Eric

2016-01-01

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity–multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities. PMID:27114572

Locally rare species influence grassland ecosystem multifunctionality.

PubMed

Soliveres, Santiago; Manning, Peter; Prati, Daniel; Gossner, Martin M; Alt, Fabian; Arndt, Hartmut; Baumgartner, Vanessa; Binkenstein, Julia; Birkhofer, Klaus; Blaser, Stefan; Blüthgen, Nico; Boch, Steffen; Böhm, Stefan; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Heinze, Johannes; Hölzel, Norbert; Jung, Kirsten; Klaus, Valentin H; Klein, Alexandra-Maria; Kleinebecker, Till; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Morris, E Kathryn; Müller, Jörg; Oelmann, Yvonne; Overmann, Jörg; Pašalić, Esther; Renner, Swen C; Rillig, Matthias C; Schaefer, H Martin; Schloter, Michael; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Sikorski, Johannes; Socher, Stephanie A; Solly, Emily F; Sonnemann, Ilja; Sorkau, Elisabeth; Steckel, Juliane; Steffan-Dewenter, Ingolf; Stempfhuber, Barbara; Tschapka, Marco; Türke, Manfred; Venter, Paul; Weiner, Christiane N; Weisser, Wolfgang W; Werner, Michael; Westphal, Catrin; Wilcke, Wolfgang; Wolters, Volkmar; Wubet, Tesfaye; Wurst, Susanne; Fischer, Markus; Allan, Eric

2016-05-19

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity-multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities. © 2016 The Author(s).

In situ formation of pyridyl-functionalized poly(3-hexylthiophene)s via quenching of the Grignard metathesis polymerization: Toward ligands for semiconductor quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kochemba, William Michael; Pickel, Deanna L.; Sumpter, Bobby G.

The synthesis of well-defined, end-functional poly(3-hexylthiophene)s (P3HTs) by in situ quenching of the Grignard metathesis (GRIM) polymerization is complicated by the extreme tendency to favor difunctional products in all but a few cases. A facile one-pot method for preparing 2-pyridyl and 3-pyridyl P3HTs with high abundance of monofunctional products is established via an examination of the kinetics of the end-functionalization quenching reaction with lithium chloride complexes of 2- and 3-pyridyl Grignard reagents. Density functional theory calculations guide the selection of pyridine as the end group, which provides the capacity to ligate cadmium selenide (CdSe) nanocrystals and arrests aggregation upon thermalmore » annealing when dispersed in a P3HT matrix. The relative abundances of various end-functional products, as ascertained by high-resolution matrix assisted laser desorption ionization time-of-flight mass spectrometry, can be altered through the use of 1-pentene as an additive: GRIM polymerizations quenched with 3-pyridyl and 2-pyridyl Grignard reagents show 5% and 18% abundances of difunctional, pyridyl-capped P3HTs, respectively, when 1-pentene is present at 1000:1 relative to the nickel catalyst. This represents a significant improvement compared to quenching with aryl Grignard reagents, where difunctional products predominate. Furthermore, the ability to manipulate end group compositions coupled with the propensity of pyridyl-functionalized P3HTs to ligate semiconductor quantum dots (SQDs) opens new possibilities for tuning the morphology of conjugated polymer/SQD blends.« less

Exploiting the functional and taxonomic structure of genomic data by probabilistic topic modeling.

PubMed

Chen, Xin; Hu, Xiaohua; Lim, Tze Y; Shen, Xiajiong; Park, E K; Rosen, Gail L

2012-01-01

In this paper, we present a method that enable both homology-based approach and composition-based approach to further study the functional core (i.e., microbial core and gene core, correspondingly). In the proposed method, the identification of major functionality groups is achieved by generative topic modeling, which is able to extract useful information from unlabeled data. We first show that generative topic model can be used to model the taxon abundance information obtained by homology-based approach and study the microbial core. The model considers each sample as a “document,” which has a mixture of functional groups, while each functional group (also known as a “latent topic”) is a weight mixture of species. Therefore, estimating the generative topic model for taxon abundance data will uncover the distribution over latent functions (latent topic) in each sample. Second, we show that, generative topic model can also be used to study the genome-level composition of “N-mer” features (DNA subreads obtained by composition-based approaches). The model consider each genome as a mixture of latten genetic patterns (latent topics), while each functional pattern is a weighted mixture of the “N-mer” features, thus the existence of core genomes can be indicated by a set of common N-mer features. After studying the mutual information between latent topics and gene regions, we provide an explanation of the functional roles of uncovered latten genetic patterns. The experimental results demonstrate the effectiveness of proposed method.

The Origin and Distribution of Heavy Elements in HCG 62

NASA Technical Reports Server (NTRS)

Vrtilek, Jan; Lavoie, Anthony R. (Technical Monitor)

2000-01-01

We present recent data on the compact group HCG 62 taken with AXAF CCD Imaging Spectrometer-S (ACIS-S) on Chandra. The sparseness of groups and their relatively simple dynamical history allow the properties of the Intergalatic Medium (IGM) to be more directly related to galaxy evolution than may be possible in clusters, and their lower gas temperatures produce strong lines from a broader range of elements than is the case in hotter clusters. This observation exploits the high X-ray brightness of HCG 62 to determine accurately the abundances of heavy elements as a function of position in the group, to test whether abundance variations are associated with individual galaxies, and to trace the origin of the enrichment.

Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea.

PubMed

Hu, Anyi; Jiao, Nianzhi; Zhang, Chuanlun L

2011-10-01

Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the "shallow" cluster was exclusively derived from epipelagic water and the "deep" cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.

Functional roles affect diversity-succession relationships for boreal beetles.

PubMed

Gibb, Heloise; Johansson, Therese; Stenbacka, Fredrik; Hjältén, Joakim

2013-01-01

Species diversity commonly increases with succession and this relationship is an important justification for conserving large areas of old-growth habitats. However, species with different ecological roles respond differently to succession. We examined the relationship between a range of diversity measures and time since disturbance for boreal forest beetles collected over a 285 year forest chronosequence. We compared responses of "functional" groups related to threat status, dependence on dead wood habitats, diet and the type of trap in which they were collected (indicative of the breadth of ecologies of species). We examined fits of commonly used rank-abundance models for each age class and traditional and derived diversity indices. Rank abundance distributions were closest to the Zipf-Mandelbrot distribution, suggesting little role for competition in structuring most assemblages. Diversity measures for most functional groups increased with succession, but differences in slopes were common. Evenness declined with succession; more so for red-listed species than common species. Saproxylic species increased in diversity with succession while non-saproxylic species did not. Slopes for fungivores were steeper than other diet groups, while detritivores were not strongly affected by succession. Species trapped using emergence traps (log specialists) responded more weakly to succession than those trapped using flight intercept traps (representing a broader set of ecologies). Species associated with microhabitats that accumulate with succession (fungi and dead wood) thus showed the strongest diversity responses to succession. These clear differences between functional group responses to forest succession should be considered in planning landscapes for optimum conservation value, particularly functional resilience.

Will anticipated future climatic conditions affect belowground C utilization? - Insights into the role of microbial functional groups in a temperate heath/grassland.

NASA Astrophysics Data System (ADS)

Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa; Egsgaard, Helge; Kappel Schmidt, Inger; Jakobsen, Iver; Ambus, Per

2013-04-01

The global terrestrial soil organic matter stock is the biggest terrestrial carbon pool (1500 Pg C) of which about 4 % is turned over annually. Thus, terrestrial ecosystems have the potential to accelerate or diminish atmospheric climate change effects via belowground carbon processes. We investigated the effect of elevated CO2 (510 ppm), prolonged spring/summer droughts and increased temperature (1 ˚C) on belowground carbon allocation and on the recovery of carbon by the soil microbial community. An in-situ 13C-carbon pulse-labeling experiment was carried out in a temperate heath/grassland (Denmark) in May 2011. Recently assimilated 13C-carbon was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in microbial functional groups on the basis of phospholipid fatty acids (PLFAs) in roots. Gram-negative and gram-positive bacteria were distinguished from the decomposer groups of actinomycetes (belonging to the group of gram-positive bacteria) and saprophytic fungi. Mycorrhizal fungi specific PLFAs were not detected probably due to limited sample size in combination with restricted sensitivity of the used GC-c-IRMS setup. Climate treatments did not affect 13C allocation into roots, soil and microbial biomass carbon and also the total microbial biomass size stayed unchanged as frequently observed. However, climate treatments changed the composition of the microbial community: elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy) but did not affect the abundance of decomposers. Drought favored the bacterial community whereas increased temperatures showed reduced abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). However, not only the microbial community composition was affected by the applied climatic conditions, but also the activity of microbial functional groups in their utilization of recently assimilated carbon. Particularly the negative effect of the future treatment combination (CO2×T×D) on actinomycetes activity was surprising. By means of activity patterns of gram-negative bacteria, we observed the fastest carbon turnover rate under elevated CO2, and the slowest under extended drought conditions. A changed soil microbial community in combination with altered activities of different microbial functional groups leads to the conclusion that carbon allocation belowground was different under ambient and future climatic conditions and indicated reduced utilization of soil organic matter in the future due to a change of actinomycetes abundance and activity.

What´s in the tank? Nematodes and other major components of the meiofauna of bromeliad phytotelms in lowland Panama.

PubMed

Zotz, Gerhard; Traunspurger, Walter

2016-03-15

Nematodes are a very diverse and extremely abundant group of animals, but their occurrence in the tropics is surprisingly little understood. We investigated the meiofauna of epiphytic tank bromeliads in the lowlands of Panama with particular emphasis on nematodes. We encountered 89 morphospecies of nematodes in 54 bromeliad tanks, which were sampled in the wet and the dry season. Rotifers were by far the most abundant group in both the dry and the wet season (with up to 960 individual ml(-1)), followed by nematodes, annelids and harpacticoid copepods. Individual plants hosted up to 25 nematode species. These nematodes represented a diversity of feeding guilds, suction-feeders and deposit-feeders being most abundant. The relative abundances of feeding-types of nematodes differed considerably in the wet and dry season. Both species richness and abundance were strongly correlated with the size of the phytotelms and the season, while species diversity assessed with the Shannon-index was affected by neither of the two. This is the first study with a particular focus on the diversity of nematodes in tank bromeliads. We document a meiofauna of considerable abundance and diversity, which suggests important functional roles in ecological processes such as decomposition, which in turn warrants further study.

Establishing a molecular relationship between chondritic and cometary organic solids

PubMed Central

Cody, George D.; Heying, Emily; Alexander, Conel M. O.; Nittler, Larry R.; Kilcoyne, A. L. David; Sandford, Scott A.

2011-01-01

Multidimensional solid-state NMR spectroscopy is used to refine the identification and abundance determination of functional groups in insoluble organic matter (IOM) isolated from a carbonaceous chondrite (Murchison, CM2). It is shown that IOM is composed primarily of highly substituted single ring aromatics, substituted furan/pyran moieties, highly branched oxygenated aliphatics, and carbonyl groups. A pathway for producing an IOM-like molecular structure through formaldehyde polymerization is proposed and tested experimentally. Solid-state 13C NMR analysis of aqueously altered formaldehyde polymer reveals considerable similarity with chondritic IOM. Carbon X-ray absorption near edge structure spectroscopy of formaldehyde polymer reveals the presence of similar functional groups across certain Comet 81P/Wild 2 organic solids, interplanetary dust particles, and primitive IOM. Variation in functional group concentration amongst these extraterrestrial materials is understood to be a result of various degrees of processing in the parent bodies, in space, during atmospheric entry, etc. These results support the hypothesis that chondritic IOM and cometary refractory organic solids are related chemically and likely were derived from formaldehyde polymer. The fine-scale morphology of formaldehyde polymer produced in the experiment reveals abundant nanospherules that are similar in size and shape to organic nanoglobules that are ubiquitous in primitive chondrites. PMID:21464292

Identifying ecological "sweet spots" underlying cyanobacteria functional group dynamics from long-term observations using a statistical machine learning approach

NASA Astrophysics Data System (ADS)

Nelson, N.; Munoz-Carpena, R.; Phlips, E. J.

2017-12-01

Diversity in the eco-physiological adaptations of cyanobacteria genera creates challenges for water managers who are tasked with developing appropriate actions for controlling not only the intensity and frequency of cyanobacteria blooms, but also reducing the potential for blooms of harmful taxa (e.g., toxin producers, N2 fixers). Compounding these challenges, the efficacy of nutrient management strategies (phosphorus-only versus nitrogen-and-phosphorus) for cyanobacteria bloom abatement is the subject of an ongoing debate, which increases uncertainty associated with bloom mitigation decision-making. In this work, we analyze a unique long-term (17-year) dataset composed of monthly observations of cyanobacteria genera abundances, zooplankton abundances, water quality, and flow from Lake George, a bloom-impacted flow-through lake of the St. Johns River (FL, USA). Using the Random Forests machine learning algorithm, an assumption-free ensemble modeling approach, the dataset was evaluated to quantify and characterize relationships between environmental conditions and seven cyanobacteria groupings: five genera (Anabaena, Cylindrospermopsis, Lyngbya, Microcystis, and Oscillatoria) and two functional groups (N2 fixers and non-fixers). Results highlight the selectivity of nitrogen in describing genera and functional group dynamics, and potential for physical effects to limit the efficacy of nutrient management as a mechanism for cyanobacteria bloom mitigation.

An experimental analysis of granivory in a desert ecosystem: Progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, J.H.

1987-03-01

Controlled, replicated experiments are revealing the network of interactions that determine structure, dynamics, and energy transfer in a desert community that is functionally interconnected by the consumption of seeds (granivory). This community includes seed-eating rodents, ants, and birds, seed-producing annual and perennial plants, and other kinds of organisms that interact with these. The experiments entail removal of important species or functional groups of granivores or plants and supplementation of seed resources. The results demonstrate a large number of direct and indirect interactions that have important effects on the abundance of species and functional groups, the structure of the community, andmore » the dynamics of energy flow. The results suggest that networks of interaction are structured with sufficient overlap in resource requirements and interconnections through indirect pathways that community- and ecosystem-level processes, such as energy flow, are relatively insensitive to major perturbations in the abundance of particular species or functional groups. This preliminary finding has important implications for understanding the response of ecosystems to natural and human-caused perturbations, for the management of agricultural and other human-modified ecosystems, and for the design of perturbation-resistant networks for acquisition and distribution of human resources such energy and information. 44 refs.« less

Water availability not fruitfall modulates the dry season distribution of frugivorous terrestrial vertebrates in a lowland Amazon forest

PubMed Central

Paredes, Omar Stalin Landázuri; Norris, Darren; de Oliveira, Tadeu Gomes

2017-01-01

Terrestrial vertebrate frugivores constitute one of the major guilds in tropical forests. Previous studies show that the meso-scale distribution of this group is only weakly explained by variables such as altitude and tree basal area in lowland Amazon forests. For the first time we test whether seasonally limiting resources (water and fallen fruit) affect the dry season distribution in 25 species of terrestrial vertebrates. To examine the effects of the spatial availability of fruit and water on terrestrial vertebrates we used a standardized, regularly spaced arrangement of camera-traps within 25km2 of lowland Amazon forest. Generalized linear models (GLMs) were then used to examine the influence of four variables (altitude, distance to large rivers, distance to nearest water, and presence vs absence of fruits) on the number of photos on five functional groups (all frugivores, small, medium, large and very large frugivores) and on seven of the most abundant frugivore species (Cuniculus paca, Dasyprocta leporina, Mazama americana, Mazama nemorivaga, Myoprocta acouchy, Pecari tajacu and Psophia crepitans). A total of 279 independent photos of 25 species were obtained from 900 camera-trap days. For most species and three functional groups, the variation in the number of photos per camera was significantly but weakly explained by the GLMs (deviance explained ranging from 6.2 to 48.8%). Generally, we found that the presence of water availability was more important than the presence of fallen fruit for the groups and species studied. Medium frugivores, large-bodied frugivores, and two of the more abundant species (C. paca and P. crepitans) were recorded more frequently closer to water bodies; while none of the functional groups nor the most abundant species showed any significant relationship with the presence of fallen fruit. Two functional groups and two of the seven most common frugivore species assessed in the GLMs showed significant results with species-specific responses to altitude. Our findings provide a more detailed understanding of how frugivorous vertebrates cope with periods of water and fruit scarcity in lowland Amazon forests. PMID:28301589

Water availability not fruitfall modulates the dry season distribution of frugivorous terrestrial vertebrates in a lowland Amazon forest.

PubMed

Paredes, Omar Stalin Landázuri; Norris, Darren; Oliveira, Tadeu Gomes de; Michalski, Fernanda

2017-01-01

Terrestrial vertebrate frugivores constitute one of the major guilds in tropical forests. Previous studies show that the meso-scale distribution of this group is only weakly explained by variables such as altitude and tree basal area in lowland Amazon forests. For the first time we test whether seasonally limiting resources (water and fallen fruit) affect the dry season distribution in 25 species of terrestrial vertebrates. To examine the effects of the spatial availability of fruit and water on terrestrial vertebrates we used a standardized, regularly spaced arrangement of camera-traps within 25km2 of lowland Amazon forest. Generalized linear models (GLMs) were then used to examine the influence of four variables (altitude, distance to large rivers, distance to nearest water, and presence vs absence of fruits) on the number of photos on five functional groups (all frugivores, small, medium, large and very large frugivores) and on seven of the most abundant frugivore species (Cuniculus paca, Dasyprocta leporina, Mazama americana, Mazama nemorivaga, Myoprocta acouchy, Pecari tajacu and Psophia crepitans). A total of 279 independent photos of 25 species were obtained from 900 camera-trap days. For most species and three functional groups, the variation in the number of photos per camera was significantly but weakly explained by the GLMs (deviance explained ranging from 6.2 to 48.8%). Generally, we found that the presence of water availability was more important than the presence of fallen fruit for the groups and species studied. Medium frugivores, large-bodied frugivores, and two of the more abundant species (C. paca and P. crepitans) were recorded more frequently closer to water bodies; while none of the functional groups nor the most abundant species showed any significant relationship with the presence of fallen fruit. Two functional groups and two of the seven most common frugivore species assessed in the GLMs showed significant results with species-specific responses to altitude. Our findings provide a more detailed understanding of how frugivorous vertebrates cope with periods of water and fruit scarcity in lowland Amazon forests.

Neonicotinoid insecticides negatively affect performance measures of non‐target terrestrial arthropods: a meta‐analysis

USGS Publications Warehouse

Main, Anson; Webb, Elisabeth B.; Goyne, Keith W.; Mengel, Doreen C.

2018-01-01

Neonicotinoid insecticides are currently the fastest‐growing and most widely used insecticide class worldwide. Valued for their versatility in application, these insecticides may cause deleterious effects in a range of non‐target (beneficial) arthropods. However, it remains unclear whether strong patterns exist in terms of their major effects, if broad measures of arthropod performance are negatively affected, or whether different functional groups are equally vulnerable. Here, we present a meta‐analysis of 372 observations from 44 field and laboratory studies that describe neonicotinoid effects on 14 arthropod orders across five broad performance measures: abundance, behavior, condition, reproductive success, and survival. Across studies, neonicotinoids negatively affected all performance metrics evaluated; however, magnitude of the effects varied. Arthropod behavior and survival were the most negatively affected and abundance was the least negatively affected. Effects on arthropod functional groups were inconsistent. Pollinator condition, reproductive success, and survival were significantly lower in neonicotinoid treatments compared to untreated controls; whereas, neonicotinoid effects on detritivores were not significant. Although magnitude of arthropod response to neonicotinoids varied among performance measures and functional groups, we documented a consistent negative relationship between exposure to neonicotinoid insecticides in published studies and beneficial arthropod performance.

Oxygen-rich hierarchical porous carbon derived from artemia cyst shells with superior electrochemical performance.

PubMed

Zhao, Yufeng; Ran, Wei; He, Jing; Song, Yanfang; Zhang, Chunming; Xiong, Ding-Bang; Gao, Faming; Wu, Jinsong; Xia, Yongyao

2015-01-21

In this study, three-dimensional (3D) hierarchical porous carbon with abundant functional groups is produced through a very simple low-cost carbonization of Artemia cyst shells. The unique hierarchical porous structure of this material, combining large numbers of micropores and macropores, as well as reasonable amount of mesopores, is proven favorable to capacitive behavior. The abundant oxygen functional groups from the natural carbon precursor contribute stable pseudocapacitance. As-prepared sample exhibits high specific capacitance (369 F g(-1) in 1 M H2SO4 and 349 F g(-1) in 6 M KOH), excellent cycling stability with capacitance retention of 100% over 10 000 cycles, and promising rate performance. This work not only describes a simple way to produce high-performance carbon electrode materials for practical application, but also inspires an idea for future structure design of porous carbon.

The abundance of ultra-diffuse galaxies from groups to clusters. UDGs are relatively more common in more massive haloes

NASA Astrophysics Data System (ADS)

van der Burg, Remco F. J.; Hoekstra, Henk; Muzzin, Adam; Sifón, Cristóbal; Viola, Massimo; Bremer, Malcolm N.; Brough, Sarah; Driver, Simon P.; Erben, Thomas; Heymans, Catherine; Hildebrandt, Hendrik; Holwerda, Benne W.; Klaes, Dominik; Kuijken, Konrad; McGee, Sean; Nakajima, Reiko; Napolitano, Nicola; Norberg, Peder; Taylor, Edward N.; Valentijn, Edwin

2017-11-01

In recent years, many studies have reported substantial populations of large galaxies with low surface brightness in local galaxy clusters. Various theories that aim to explain the presence of such ultra-diffuse galaxies (UDGs) have since been proposed. A key question that will help to distinguish between models is whether UDGs have counterparts in host haloes with lower masses, and if so, what their abundance as a function of halo mass is. We here extend our previous study of UDGs in galaxy clusters to galaxy groups. We measure the abundance of UDGs in 325 spectroscopically selected groups from the Galaxy And Mass Assembly (GAMA) survey. We make use of the overlapping imaging from the ESO Kilo-Degree Survey (KiDS), from which we can identify galaxies with mean surface brightnesses within their effective radii down to 25.5 mag arcsec-2 in the r band. We are able to measure a significant overdensity of UDGs (with sizes reff ≥ 1.5 kpc) in galaxy groups down to M200 = 1012 M⊙, a regime where approximately only one in ten groups contains a UDG that we can detect. We combine measurements of the abundance of UDGs in haloes that cover three orders of magnitude in halo mass, finding that their numbers scale quite steeply with halo mass: NUDG(R < R200) ∝ M2001.11±0.07. To better interpret this, we also measure the mass-richness relation for brighter galaxies down to Mr* + 2.5 in the same GAMA groups, and find a much shallower relation of NBright(R < R200) ∝ M2000.78±0.05. This shows that compared to bright galaxies, UDGs are relatively more abundant in massive clusters than in groups. We discuss the implications, but it is still unclear whether this difference is related to a higher destruction rate of UDGs in groups or if massive haloes have a positive effect on UDG formation.

Root colonization and spore abundance of arbuscular mycorrhizal fungi in distinct successional stages from an Atlantic rainforest biome in southern Brazil.

PubMed

Zangaro, Waldemar; Rostirola, Leila Vergal; de Souza, Priscila Bochi; de Almeida Alves, Ricardo; Lescano, Luiz Eduardo Azevedo Marques; Rondina, Artur Berbel Lírio; Nogueira, Marco Antonio; Carrenho, Rosilaine

2013-04-01

The influence of plant functional groups and moderate seasonality on arbuscular mycorrhizal (AM) fungal status (root colonization and spore density) was investigated during 13 consecutive months in a chronosequence of succession in southern Brazil, consisting of grassland field, scrub vegetation, secondary forest and mature forest, in a region of transition from tropical to subtropical zones. AM root colonization and spore density decreased with advancing succession and were highest in early successional sites with grassland and scrub vegetation, intermediary in the secondary forest and lowest in the mature forest. They were little influenced by soil properties, but were sufficiently influenced by the fine root nutrient status and fine root traits among different functional plant groups. AM root colonization and spore density were higher during the favourable plant growth season (spring and summer) than during the less favourable plant growth season (autumn and winter). Spore density displayed significant seasonal variation at all sites, whilst root colonization displayed significant seasonal variation in grassland, scrub and secondary forest, but not in mature forest. The data suggest that (1) different plant functional groups display different relationships with AM fungi, influencing their abundance differentially; (2) plant species from early successional phases are more susceptible to AM root colonization and maintain higher AM sporulation than late successional species; (3) fine root traits and nutrient status influence these AM fungal attributes; and (4) higher AM spore production and root colonization is associated with the season of higher light incidence and temperature, abundant water in soil and higher plant metabolic activity.

Annual grass invasion in sagebrush-steppe: The relative importance of climate, soil properties and biotic interactions

USGS Publications Warehouse

Bansal, Sheel; Sheley, Roger L.

2016-01-01

The invasion by winter-annual grasses (AGs) such as Bromus tectorum into sagebrush steppe throughout the western USA is a classic example of a biological invasion with multiple, interacting climate, soil and biotic factors driving the invasion, although few studies have examined all components together. Across a 6000-km2 area of the northern Great Basin, we conducted a field assessment of 100 climate, soil, and biotic (functional group abundances, diversity) factors at each of 90 sites that spanned an invasion gradient ranging from 0 to 100 % AG cover. We first determined which biotic and abiotic factors had the strongest correlative relationships with AGs and each resident functional group. We then used regression and structural equation modeling to explore how multiple ecological factors interact to influence AG abundance. Among biotic interactions, we observed negative relationships between AGs and biodiversity, perennial grass cover, resident species richness, biological soil crust cover and shrub density, whereas perennial and annual forb cover, tree cover and soil microbial biomass had no direct linkage to AG. Among abiotic factors, AG cover was strongly related to climate (increasing cover with increasing temperature and aridity), but had weak relationships with soil factors. Our structural equation model showed negative effects of perennial grasses and biodiversity on AG cover while integrating the negative effects of warmer climate and positive influence of belowground processes on resident functional groups. Our findings illustrate the relative importance of biotic interactions and climate on invasive abundance, while soil properties appear to have stronger relationships with resident biota than with invasives.

Associations between regional moisture gradient, tree species dominance, and downed wood abundance

NASA Astrophysics Data System (ADS)

Johnson, A. C.; Mills, J.

2007-12-01

Downed wood functions as a source of nurse logs, physical structure in streams, food, and carbon. Because downed wood is important in upland and aquatic habitats, an understanding of wood recruitment along a continuum from wet to dry landscapes is critical for both preservation of biodiversity and restoration of natural ecosystem structure and function. We assessed downed wood in public and private forests of Washington and Oregon by using a subset of the Forest Inventory and Analysis (FIA) database including 15,842 sampled conditions. Multivariate regression trees, ANOVA, and t-tests were used to discern environmental conditions most closely associated with abundance of woody debris. Of the 16 parameters included in the analysis, rainfall, forest ownership, number of damaged standing trees, and forest elevation were most indicative of woody debris abundance. The Hemlock/spruce Group, including hemlock, spruce, cedar, and white pine, most associated with wetter soils, had significantly more downed wood than 12 other forest groups. The Ponderosa Pine Group, indicative of drier sites with higher fire frequencies, included ponderosa pine, sugar pine, and incense cedar, and had significantly less downed wood volume. Overall, the amount of woody debris in either the Spruce/hemlock Group or the Ponderosa Pine Group did not change significantly as tree age increased from 5 to 350 years. Plots within the Hemlock/spruce with greater standing tree volume also had significantly greater downed wood volume. In contrast, greater downed wood volume was not associated with greater standing tree volume in the Ponderosa Pine Group. Knowledge of linkages among environmental variables and stand characteristics are useful in development of regional forest models aimed at understanding the effects of climate change and disturbance on forest succession.

Comparison of 13C Nuclear Magnetic Resonance and Fourier Transform Infrared spectroscopy for estimating humification and aromatization of soil organic matter

NASA Astrophysics Data System (ADS)

Rogers, K.; Cooper, W. T.; Hodgkins, S. B.; Verbeke, B. A.; Chanton, J.

2017-12-01

Solid state direct polarization 13C NMR spectroscopy (DP-NMR) is generally considered the most quantitatively reliable method for soil organic matter (SOM) characterization, including determination of the relative abundances of carbon functional groups. These functional abundances can then be used to calculate important soil parameters such as degree of humification and extent of aromaticity that reveal differences in reactivity or compositional changes along gradients (e.g. thaw chronosequence in permafrost). Unfortunately, the 13C NMR DP-NMR experiment is time-consuming, with a single sample often requiring over 24 hours of instrument time. Alternatively, solid state cross polarization 13C NMR (CP-NMR) can circumvent this problem, reducing analyses times to 4-6 hours but with some loss of quantitative reliability. Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) is a quick and relatively inexpensive method for characterizing solid materials, and has been suggested as an alternative to NMR for analysis of soil organic matter and determination of humification (HI) and aromatization (AI) indices. However, the quantitative reliability of ATR-FTIR for SOM analyses has never been verified, nor have any ATR-FTIR data been compared to similar measurements by NMR. In this work we focused on FTIR vibrational bands that correspond to the three functional groups used to calculate HI and AI values: carbohydrates (1030 cm-1), aromatics (1510, 1630 cm-1), and aliphatics (2850, 2920 cm-1). Data from ATR-FTIR measurements were compared to analogous quantitation by DP- and CP-NMR using peat samples from Sweden, Minnesota, and North Carolina. DP- and CP-NMR correlate very strongly, although the correlations are not always 1:1. Direct comparison of relative abundances of the three functional groups determined by NMR and ATR-FTIR yielded satisfactory results for carbohydrates (r2= 0.78) and aliphatics (r2=0.58), but less so for aromatics (r2= 0.395). ATR-FTIR has to this point been used primarily for relative abundance analyses (e.g. calculating HI and AI values), but these results suggest FTIR can provide quantitative reliability that approaches that of NMR.

Probing satellite galaxies in the Local Group by using FAST

NASA Astrophysics Data System (ADS)

Li, Jing; Wang, You-Gang; Kong, Min-Zhi; Wang, Jie; Chen, Xuelei; Guo, Rui

2018-01-01

The abundance of neutral hydrogen (HI) in satellite galaxies in the local group is important for studying the formation history of our local group. In this work, we generated mock HI satellite galaxies in the Local Group using the high mass-resolution hydrodynamic APOSTLE simulation. The simulated HI mass function agrees with the ALFALFA survey very well above 106 M ⊙, although there is a discrepancy below this scale because of the observed flux limit. After carefully checking various systematic elements in the observations, including fitting of line width, sky coverage, integration time and frequency drift due to uncertainty in a galaxy’s distance, we predicted the abundance of HI in galaxies in a future survey that will be conducted by FAST. FAST has a larger aperture and higher sensitivity than the Arecibo telescope. We found that the HI mass function could be estimated well around 105 M ⊙ if the integration time is 40 minutes. Our results indicate that there are 61 HI satellites in the Local Group and 36 in the FAST field above 105 M ⊙. This estimation is one order of magnitude better than the current data, and will put a strong constraint on the formation history of the Local Group. Also more high resolution simulated samples are needed to achieve this target.

Functional group diversity of bee pollinators increases crop yield

PubMed Central

Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

2008-01-01

Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees. PMID:18595841

Nitrogen Addition Regulates Soil Nematode Community Composition through Ammonium Suppression

PubMed Central

Wei, Cunzheng; Zheng, Huifen; Li, Qi; Lü, Xiaotao; Yu, Qiang; Zhang, Haiyang; Chen, Quansheng; He, Nianpeng; Kardol, Paul; Liang, Wenju; Han, Xingguo

2012-01-01

Nitrogen (N) enrichment resulting from anthropogenic activities has greatly changed the composition and functioning of soil communities. Nematodes are one of the most abundant and diverse groups of soil organisms, and they occupy key trophic positions in the soil detritus food web. Nematodes have therefore been proposed as useful indicators for shifts in soil ecosystem functioning under N enrichment. Here, we monitored temporal dynamics of the soil nematode community using a multi-level N addition experiment in an Inner Mongolia grassland. Measurements were made three years after the start of the experiment. We used structural equation modeling (SEM) to explore the mechanisms regulating nematode responses to N enrichment. Across the N enrichment gradient, significant reductions in total nematode abundance, diversity (H' and taxonomic richness), maturity index (MI), and the abundance of root herbivores, fungivores and omnivores-predators were found in August. Root herbivores recovered in September, contributing to the temporal variation of total nematode abundance across the N gradient. Bacterivores showed a hump-shaped relationship with N addition rate, both in August and September. Ammonium concentration was negatively correlated with the abundance of total and herbivorous nematodes in August, but not in September. Ammonium suppression explained 61% of the variation in nematode richness and 43% of the variation in nematode trophic group composition. Ammonium toxicity may occur when herbivorous nematodes feed on root fluid, providing a possible explanation for the negative relationship between herbivorous nematodes and ammonium concentration in August. We found a significantly positive relationship between fungivores and fungal phospholipid fatty acids (PLFA), suggesting bottom-up control of fungivores. No such relationship was found between bacterivorous nematodes and bacterial PLFA. Our findings contribute to the understanding of effects of N enrichment in semiarid grassland on soil nematode trophic groups, and the cascading effects in the detrital soil food web. PMID:22952671

Post-entry and volcanic contaminant abundances of zinc, copper, selenium, germanium and gallium in stratospheric micrometeorites

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1995-01-01

Some fraction of Zn, Cu, Se, Ga and Ge in chondritic interplanetary dust particles (IDPs) collected in the lower stratosphere between 1981 May and 1984 June has a volcanic origin. I present a method to evaluate the extent of this unavoidable type of stratospheric contamination for individual particles. The mass-normalized abundances for Cu and Ge as a function of mass-normalized stratospheric residence time show their time-integrated stratospheric aerosol abundances. The Zn, Se and Ga abundances show a subdivision into two groups that span approximately two-year periods following the eruptions of the Mount St. Helens (1980 May) and El Chichon (1982 April) volcanoes. Elemental abundances in particles collected at the end of each two-year period indicate low, but not necessarily ambient, volcanic stratospheric abundances. Using this time-integrated baseline, I calculate the straospheric contaminant fractions in nine IDPs and show that Zn, SE and Ga abundances in chondritic IDPs derive in part from stratospheric aerosol contaminants. Post-entry elemental abundances (i.e., the amount that survived atmospheric entry heating of the IDP) show enrichments relative to the CI abundances but in a smaller number of particles than previously suggested.

The effects of mass and metallicity upon planetary nebula formation

NASA Astrophysics Data System (ADS)

Papp, K. A.; Purton, C. R.; Kwok, S.

1983-05-01

A parameterized function is constructed which describes the possible dependence of planetary nebula formation upon metal abundance and stellar mass. Data on galaxies in the Local Group compared with predictions made from the parameterized function indicate that heavy element abundance is the principal agent influencing the formation of planetary nebulae; stars which are rich in heavy elements are the progenitors of planetary nebulae. This analysis, when compared with the observations, argues for a modest degree of pre-enrichment in a few of the sample galaxies. The heavy element dependence of planetary nebula formation also accounts for the deficit of planetary nebulae in the nuclei of NGC 221 and NGC 224, and in the bulge of our Galaxy.

Testing functional trait-based mechanisms underpinning plant responses to grazing and linkages to ecosystem functioning in grasslands

NASA Astrophysics Data System (ADS)

Zheng, S. X.; Li, W. H.; Lan, Z. C.; Ren, H. Y.; Wang, K. B.; Bai, Y. F.

2014-09-01

Abundant evidence has shown that grazing alters plant functional traits, ecological strategies, community structure, and ecosystem functioning of grasslands. Few studies, however, have examined how plant responses to grazing are mediated by resource availability and functional group identity. We test functional trait-based mechanisms underlying the responses of different life forms to grazing and linkages to ecosystem functioning along a soil moisture gradient in the Inner Mongolia grassland. A principal component analysis (PCA) based on 9 traits × 276 species matrix showed that the plant size spectrum (i.e., individual biomass), leaf economics spectrum (leaf N content and leaf density), and light competition spectrum (height and stem-leaf biomass ratio) distinguished plant species responses to grazing. The three life forms exhibited differential strategies as indicated by trait responses to grazing. The annuals and biennials adopted grazing-tolerant strategies associated with high growth rate, reflected by high leaf N content and specific leaf area. The perennial grasses exhibited grazing-tolerant strategies associated with great regrowth capacity and high palatability scores, whereas perennial forbs showed grazing-avoidant strategies with short stature and low palatability scores. In addition, the dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization. Grazing increased the relative abundance of perennial forbs with low palatability in the wet and fertile meadow, but it promoted perennial grasses with high palatability in the dry and infertile typical steppe. Our findings suggest that the effects of grazing on plant functional traits are dependent on both the abiotic (e.g., soil moisture) and biotic (e.g., plant functional group identity and composition) factors. Grazing-induced shifts in functional group composition are largely dependent on resource availability, particularly water availability.

Tissue-Specific Venom Composition and Differential Gene Expression in Sea Anemones

PubMed Central

Macrander, Jason; Broe, Michael; Daly, Marymegan

2016-01-01

Cnidarians represent one of the few groups of venomous animals that lack a centralized venom transmission system. Instead, they are equipped with stinging capsules collectively known as nematocysts. Nematocysts vary in abundance and type across different tissues; however, the venom composition in most species remains unknown. Depending on the tissue type, the venom composition in sea anemones may be vital for predation, defense, or digestion. Using a tissue-specific RNA-seq approach, we characterize the venom assemblage in the tentacles, mesenterial filaments, and column for three species of sea anemone (Anemonia sulcata, Heteractis crispa, and Megalactis griffithsi). These taxa vary with regard to inferred venom potency, symbiont abundance, and nematocyst diversity. We show that there is significant variation in abundance of toxin-like genes across tissues and species. Although the cumulative toxin abundance for the column was consistently the lowest, contributions to the overall toxin assemblage varied considerably among tissues for different toxin types. Our gene ontology (GO) analyses also show sharp contrasts between conserved GO groups emerging from whole transcriptome analysis and tissue-specific expression among GO groups in our differential expression analysis. This study provides a framework for future characterization of tissue-specific venom and other functionally important genes in this lineage of simple bodied animals. PMID:27389690

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia

PubMed Central

Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M

2015-01-01

Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n=38), Aves (n=8) and Reptilia (n=8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity <90%) demonstrating a large ‘unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild. PMID:25343515

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.

PubMed

Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M

2015-03-17

Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n = 38), Aves (n = 8) and Reptilia (n = 8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity <90%) demonstrating a large 'unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild.

[Salivary microbiome in people with obesity: a pilot study].

PubMed

Wu, Y J; Chi, X P; Chen, F; Deng, X L

2018-02-18

To investigate the characterization of the salivary microbiome in people with obesity and the differences in microbial composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight controls. The study was carried out in people with obesity and age- and sex-matched normal weight controls. None of these selected participants had the systemic disease, oral mucosal disease or periodontal disease. Unstimulated saliva samples were collected and oral examination was conducted. DNAs from saliva samples were extracted and sequenced in an Illumina NextSeq 500 platform. Community composition, linear discriminant analysis of taxonomic differences,gene prediction, gene set construction and annotation of gene function were performed. The classified bacterial reads of the samples were 2 630 428 for each sample. A total of 11 phyla, 19 classes, 26 orders, 41 families, 62 genera and 164 species were detected ultimately. All samples had the same predominant phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria). There were statistical differences between the groups at the class, order, family, genus and species levels. At the class level, Negativicutes and Erysipelotrichia were more abundant in the obesity group, while Flavobacteriia and Bateroidetes dominated in normal weight group (P<0.05). At the species level, 16 showed significant differences in relative abundance among the groups, in which Prevotella melaninogenica,Prevotella salivae,Solobacterium moorei and Atopobium parvulum ware more abundant in the obesity group, whereas Streptococcus sanguinis dominated in normal weight group (P<0.05). The people with obesity had a higher number of salivary microbial genes (P<0.05). We produced statistics on gene prediction and found salivary microbiome of obesity group had a higher number of genes (P < 0.05). Genes associated with the pathways of metabolism and environmental information processing and human diseases were significantly enriched in the saliva samples of people with obesity (P < 0.01). Significant differences were seen in composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight people. We hope to go on further study with larger sample size in the near future.

Modelling chemical abundance distributions for dwarf galaxies in the Local Group: the impact of turbulent metal diffusion

NASA Astrophysics Data System (ADS)

Escala, Ivanna; Wetzel, Andrew; Kirby, Evan N.; Hopkins, Philip F.; Ma, Xiangcheng; Wheeler, Coral; Kereš, Dušan; Faucher-Giguère, Claude-André; Quataert, Eliot

2018-02-01

We investigate stellar metallicity distribution functions (MDFs), including Fe and α-element abundances, in dwarf galaxies from the Feedback in Realistic Environment (FIRE) project. We examine both isolated dwarf galaxies and those that are satellites of a Milky Way-mass galaxy. In particular, we study the effects of including a sub-grid turbulent model for the diffusion of metals in gas. Simulations that include diffusion have narrower MDFs and abundance ratio distributions, because diffusion drives individual gas and star particles towards the average metallicity. This effect provides significantly better agreement with observed abundance distributions in dwarf galaxies in the Local Group, including small intrinsic scatter in [α/Fe] versus [Fe/H] of ≲0.1 dex. This small intrinsic scatter arises in our simulations because the interstellar medium in dwarf galaxies is well mixed at nearly all cosmic times, such that stars that form at a given time have similar abundances to ≲0.1 dex. Thus, most of the scatter in abundances at z = 0 arises from redshift evolution and not from instantaneous scatter in the ISM. We find similar MDF widths and intrinsic scatter for satellite and isolated dwarf galaxies, which suggests that environmental effects play a minor role compared with internal chemical evolution in our simulations. Overall, with the inclusion of metal diffusion, our simulations reproduce abundance distribution widths of observed low-mass galaxies, enabling detailed studies of chemical evolution in galaxy formation.

Ecology of ephemeroptera, plecoptera and trichoptera (insecta) in rivers of the gunung jerai forest reserve: diversity and distribution of functional feeding groups.

PubMed

Hamid, Suhaila Ab; Md Rawi, Che Salmah

2014-08-01

A field study was performed to describe the functional feeding groups (FFGs) of Ephemeroptera, Plecoptera and Trichoptera (EPT) in the Tupah, Batu Hampar and Teroi Rivers in the Gunung Jerai Forest Reserve (GJFR), Kedah, Malaysia. Twenty-nine genera belonging to 19 families were identified. The EPTs were classified into five FFGs: collector-gatherers (CG), collector-filterers (CF), shredders (SH), scrapers (SC) and predators (P). In this study, CG and CF were the dominant groups inhabiting all three rivers. Ephemeroptera dominated these rivers due to their high abundance, and they were also the CG (90.6%). SC were the lowest in abundance among all groups. Based on the FFGs, the Teroi River was suitable for CG, whereas the Tupah and Batu Hampar Rivers were suitable for CG and CF. The distribution of FFGs differed among the rivers (CG, χ(2) = 23.6, p = 0.00; SH, χ(2) = 10.02, p = 0.007; P, χ(2) = 25.54, p = 0.00; CF, χ(2) = 21.95, p = 0.00; SC, χ(2) = 9.31, p = 0.01). These findings indicated that the FFGs found in rivers of the GJFR represent high river quality.

L-Glutamine Supplementation Alleviates Constipation during Late Gestation of Mini Sows by Modifying the Microbiota Composition in Feces

PubMed Central

Lu, Taofeng; Han, Lingxia; Zhao, Lili; Niu, Yinjie

2017-01-01

Constipation occurs frequently in both sows and humans, particularly, during late gestation. The microbial community of the porcine gut, the enteric microbiota, plays a critical role in functions that sustain intestinal health. Hence, microbial regulation during pregnancy may be important to prevent host constipation. The present study was conducted to determine whether L-glutamine (Gln) supplementation improved intestinal function and alleviated constipation by regulation of enteric microbiota. 16S rRNA sequences obtained from fecal samples from 9 constipated sows (3 in the constipation group and 6 in the 1.0% Gln group) were assessed from gestational day 70 to 84. Comparative analysis showed that the abundance of intestinal-friendly microbiota, that is, Bacteroidetes (P = 0.007) and Actinobacteria (P = 0.037), was comparatively increased in the 1.0% Gln group, while the abundance of pernicious bacteria, Oscillospira (P < 0.001) and Treponema (P = 0.011), was decreased. Dietary supplementation with 1.0% Gln may ameliorate constipation of sows by regulated endogenous gut microbiota. PMID:28386552

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

PubMed

Bouskill, Nicholas J; Eveillard, Damien; Chien, Diana; Jayakumar, Amal; Ward, Bess B

2012-03-01

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens

PubMed Central

Deusch, Oliver; O’Flynn, Ciaran; Colyer, Alison; Morris, Penelope; Allaway, David; Jones, Paul G.; Swanson, Kelly S.

2014-01-01

Background Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome. Methodology & Principal Findings Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome. Conclusions These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life. PMID:25010839

Identifying Common Patterns in Diverse Systems: Effects of Exurban Development on Birds of the Adirondack Park and the Greater Yellowstone Ecosystem, USA

NASA Astrophysics Data System (ADS)

Glennon, Michale J.; Kretser, Heidi E.; Hilty, Jodi A.

2015-02-01

We examined the impacts of exurban development on bird communities in Essex County, New York and Madison County, Montana by comparing differences in abundance of songbirds between subdivisions and control sites in both regions. We hypothesized that impacts to bird communities would be greater in the relatively homogeneous, closed canopy Adirondack forest of northern New York State than they would be in the more naturally heterogeneous grasslands interspersed with trees and shrubs of the Greater Yellowstone Ecosystem. We examined birds in five functional groups expected to be responsive to exurban development, and determined relative abundance within subdivisions and control sites across these two distinct regions. We found little support for our hypothesis. For birds in the area-sensitive, low nesting, and Neotropical migrant functional groups, relative abundance was lower in subdivisions in the Adirondacks and in Madison County, while relative abundance of edge specialists was greater in subdivisions in both regions. The direction and magnitude of change in the avian communities between subdivisions and controls was similar in both regions for all guilds except microhabitat specialists. These similarities across diverse ecosystems suggest that the ecological context of the encompassing region may be less important than other elements in shaping avian communities in exurban systems. This finding suggests that humans and their specific behaviors and activities in exurban areas may be underappreciated but potentially important drivers of change in these regions.

The potential role of habitat-forming seaweeds in modeling benthic ecosystem properties

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Díez, Isabel; Saiz-Salinas, José Ignacio

2017-12-01

Canopy-forming seaweeds provide specific habitats with key ecological properties and are facing severe declines worldwide with unforeseeable consequences for ecosystem processes. Investigating the loss of such natural habitats in order to develop management strategies for conservation is a major challenge in marine ecological research. This study investigated the shallow rocky bottoms of the southern Bay of Biscay at two sampling times with a view to identifying the effect of canopy seaweed availability on the taxonomic and functional properties of invertebrate multivariate structure, abundance, density, diversity and evenness. The multivariate taxonomic and functional structure of assemblages changed significantly according to canopy availability in terms of taxa and functional groups abundance, but no substantial change was observed in composition. Biogenic habitat simplification resulted in a decrease in total invertebrate abundance and in taxonomic and functional density and diversity, whilst no effects were observed in taxonomic and functional evenness. Loss of canopy involved an impoverishment of the whole community particularly for epiphytic colonial sessile suspension-feeders, but it also extended to non-epiphytic forms. Our results emphasize the importance of canopy decline as a major driver of changes in benthic ecosystem properties and highlight that biogenic space provided by canopy is a limiting resource for the development of rocky subtidal invertebrates.

Maize opaque5 Encodes Monogalactosyldiacylglycerol Synthase and Specifically Affects Galactolipids Necessary for Amyloplast and Chloroplast Function[C][W][OA

PubMed Central

Myers, Alan M.; James, Martha G.; Lin, Qiaohui; Yi, Gibum; Stinard, Philip S.; Hennen-Bierwagen, Tracie A.; Becraft, Philip W.

2011-01-01

The maize (Zea mays) opaque5 (o5) locus was shown to encode the monogalactosyldiacylglycerol synthase MGD1. Null and point mutations of o5 that affect the vitreous nature of mature endosperm engendered an allelic series of lines with stepwise reductions in gene function. C18:3/C18:2 galactolipid abundance in seedling leaves was reduced proportionally, without significant effects on total galactolipid content. This alteration in polar lipid composition disrupted the organization of thylakoid membranes into granal stacks. Total galactolipid abundance in endosperm was strongly reduced in o5- mutants, causing developmental defects and changes in starch production such that the normal simple granules were replaced with compound granules separated by amyloplast membrane. Complete loss of MGD1 function in a null mutant caused kernel lethality owing to failure in both endosperm and embryo development. The data demonstrate that low-abundance galactolipids with five double bonds serve functions in plastid membranes that are not replaced by the predominant species with six double bonds. Furthermore, the data identify a function of amyloplast membranes in the development of starch granules. Finally, the specific changes in lipid composition suggest that MGD1 can distinguish the constituency of acyl groups on its diacylglycerol substrate based upon the degree of desaturation. PMID:21685260

A common scaling rule for abundance, energetics, and production of parasitic and free-living species

USGS Publications Warehouse

Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

2011-01-01

The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the - 3/4 power. This result indicates "production equivalence," where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic.

Analysis of the Plasma Proteome in COPD: Novel Low Abundance Proteins Reflect the Severity of Lung Remodeling

PubMed Central

Merali, Salim; Barrero, Carlos A.; Bowler, Russell P.; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G.

2015-01-01

The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers. PMID:24111704

Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling.

PubMed

Merali, Salim; Barrero, Carlos A; Bowler, Russell P; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G

2014-04-01

The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.

Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

PubMed Central

Feris, Kevin; Ramsey, Philip; Frazar, Chris; Moore, Johnnie N.; Gannon, James E.; Holben, William E.

2003-01-01

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities. PMID:12957946

Fruit traits and temporal abundance shape plant-frugivore interaction networks in a seasonal tropical forest.

PubMed

Ramos-Robles, Michelle; Dáttilo, Wesley; Díaz-Castelazo, Cecilia; Andresen, Ellen

2018-04-02

Interactions between fleshy fruited plants and frugivores are crucial for the structuring and functioning of biotic communities, particularly in tropical forests where both groups are diverse and play different roles in network organization. However, it remains poorly understood how different groups of frugivore species and fruit traits contribute to network structure. We recorded interactions among 28 plant species and three groups of frugivores (birds, bats, and non-flying mammals) in a seasonal forest in Mexico to determine which species contribute more to network structure and evaluate the importance of each species. We also determined whether fruit abundance, water content, morphology traits, and fruiting phenology are related to network parameters: the number of interactions, species contribution to nestedness, and species strength. We found that plants did not depend on a single group of frugivores, but rather on one species of each group: the bird Pitangus sulphuratus, the bat Sturnira parvidens, and the non-flying mammal Procyon lotor. The abundance, size, and water content of the fruits were significantly related to the contribution to nestedness, number of interactions, and species strength index of plant species. Tree species and birds contributed mainly to the nested structure of the network. We show that the structure of plant-frugivore networks in this seasonal forest is non-random and that fruit traits (i.e., abundance, phenology, size, and water content) are important factors shaping plant-frugivore networks. Identification of the key species and their traits that maintain the complex structure of species interactions is therefore fundamental for the integral conservation of tropical forests.

Bacterial community initial development in proglacial soils of Larsemann hill, East Antarctica

NASA Astrophysics Data System (ADS)

Ma, H.; Yan, W.; Shi, G.; Sun, B.; Zhang, Y.; Xiao, X.

2016-12-01

Glacial forefields are considered ideal places to explore how microbial communities will response to climate-driven environmental changes. Our knowledge of how the bacterial community activities and structure was influenced by changing environment due to glacier retreat is still very limited, especially at the initial stage of glacier retreat. The short gradient soil samples including the ice free and ice covered sites were sampled in the forehead of East Antarctica ice sheet, in Larsemann Hills. By employing the Miseq sequencing methods, 1.8 x104 high-quality sequences were gotten for each sample and the bacterial diversity including abundant bacteria and rare bacteria were studied and compared between the gradient samples. Even though in such an extreme stress condition, the bacterial diversity was high. The coefficient of variance between the five sites of abundant group was 0.886 which was higher than that of the top 20 rare group (0.159) significantly (unpaired t test, p-value<0.0001) suggesting that the abundant bacterial communities were more sensitive to the ice sheet change in the initial stage than rare bacteria did. And the abundant bacteria contributed the community structure more than the rare bacteria did. The rare group acted more like seed bank to keep the community functionality in the forehead of sheet. And the ice thickness was the major factor to affect the abundant bacterial community. Given the fact that Antarctica environment was more sensitive to the global warming, the study about abundant and rare bacteria response to condition change will be helpful to precisely predict community response to climate change in polar region. This finding will improve the understanding about the relationship between community structure and environment condition in extreme stress condition.

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

PubMed Central

Wessén, Ella; Söderström, Mats; Stenberg, Maria; Bru, David; Hellman, Maria; Welsh, Allana; Thomsen, Frida; Klemedtson, Leif; Philippot, Laurent; Hallin, Sara

2011-01-01

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers. PMID:21228891

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

2016-12-05

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Abundance and Diversity of Soil Arthropods in the Olive Grove Ecosystem

PubMed Central

Gonçalves, Maria Fátima; Pereira, José Alberto

2012-01-01

Arthropods are part of important functional groups in soil food webs. Recognizing these arthropods and understanding their function in the ecosystem as well as when they are active is essential to understanding their roles. In the present work, the abundance and diversity of soil arthropods is examined in olive groves in the northeast region of Portugal during the spring. Five classes of arthropods were found: Chilopoda, Malacostraca, Entognatha, Insecta, and Arachnida. Captures were numerically dominated by Collembola within Entognatha, representing 70.9% of total captures. Arachnida and Insecta classes represented about 20.4 and 9.0%, respectively. Among the predatory arthropods, the most representative groups were Araneae and Opiliones from Arachnida, and Formicidae, Carabidae, and Staphylinidae from Insecta. From the Formicidae family, Tetramorium semilaeve (Andre 1883), Tapinoma nigerrimum (Nylander 1856), and Crematogaster scutellaris (Olivier 1792) were the most representative ant species. Arthropods demonstrated preference during the day, with 74% of the total individuals recovered in this period, although richness and similarity were analogous during the day and night. PMID:22943295

Loss of soil (macro)fauna due to the expansion of Brazilian sugarcane acreage.

PubMed

Franco, André L C; Bartz, Marie L C; Cherubin, Maurício R; Baretta, Dilmar; Cerri, Carlos E P; Feigl, Brigitte J; Wall, Diana H; Davies, Christian A; Cerri, Carlos C

2016-09-01

Land use changes (LUC) from pasture to sugarcane (Saccharum spp.) crop are expected to add 6.4Mha of new sugarcane land by 2021 in the Brazilian Cerrado and Atlantic Forest biomes. We assessed the effects of these LUC on the abundance and community structure of animals that inhabit soils belowground through a field survey using chronosequences of land uses comprising native vegetation, pasture, and sugarcane along a 1000-km-long transect across these two major tropical biomes in Brazil. Macrofauna community composition differed among land uses. While most groups were associated with samples taken in native vegetation, high abundance of termites and earthworms appeared associated with pasture soils. Linear mixed effects analysis showed that LUC affected total abundance (X(2)(1)=6.79, p=0.03) and taxa richness (X(2)(1)=6.08, p=0.04) of soil macrofauna. Abundance increased from 411±70individualsm(-2) in native vegetation to 1111±202individualsm(-2) in pasture, but decreased sharply to 106±24individualsm(-2) in sugarcane soils. Diversity decreased 24% from native vegetation to pasture, and 39% from pasture to sugarcane. Thus, a reduction of ~90% in soil macrofauna abundance, besides a loss of ~40% in the diversity of macrofauna groups, can be expected when sugarcane crops replace pasture in Brazilian tropical soils. In general, higher abundances of major macrofauna groups (ants, coleopterans, earthworms, and termites) were associated with higher acidity and low contents of macronutrients and organic matter in soil. This study draws attention for a significant biodiversity loss belowground due to tropical LUC in sugarcane expansion areas. Given that many groups of soil macrofauna are recognized as key mediators of ecosystem processes such as soil aggregation, nutrients cycling and soil carbon storage, our results warrant further efforts to understand the impacts of altering belowground biodiversity and composition on soil functioning and agriculture performance across LUC in the tropics. Copyright © 2016 Elsevier B.V. All rights reserved.

Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function.

PubMed

Hemingway, Cheryl; Berk, Maurice; Anderson, Suzanne T; Wright, Victoria J; Hamilton, Shea; Eleftherohorinou, Hariklia; Kaforou, Myrsini; Goldgof, Greg M; Hickman, Katy; Kampmann, Beate; Schoeman, Johan; Eley, Brian; Beatty, David; Pienaar, Sandra; Nicol, Mark P; Griffiths, Michael J; Waddell, Simon J; Newton, Sandra M; Coin, Lachlan J; Relman, David A; Montana, Giovanni; Levin, Michael

2017-01-01

The WHO estimates around a million children contract tuberculosis (TB) annually with over 80 000 deaths from dissemination of infection outside of the lungs. The insidious onset and association with skin test anergy suggests failure of the immune system to both recognise and respond to infection. To understand the immune mechanisms, we studied genome-wide whole blood RNA expression in children with TB meningitis (TBM). Findings were validated in a second cohort of children with TBM and pulmonary TB (PTB), and functional T-cell responses studied in a third cohort of children with TBM, other extrapulmonary TB (EPTB) and PTB. The predominant RNA transcriptional response in children with TBM was decreased abundance of multiple genes, with 140/204 (68%) of all differentially regulated genes showing reduced abundance compared to healthy controls. Findings were validated in a second cohort with concordance of the direction of differential expression in both TBM (r2 = 0.78 p = 2x10-16) and PTB patients (r2 = 0.71 p = 2x10-16) when compared to a second group of healthy controls. Although the direction of expression of these significant genes was similar in the PTB patients, the magnitude of differential transcript abundance was less in PTB than in TBM. The majority of genes were involved in activation of leucocytes (p = 2.67E-11) and T-cell receptor signalling (p = 6.56E-07). Less abundant gene expression in immune cells was associated with a functional defect in T-cell proliferation that recovered after full TB treatment (p<0.0003). Multiple genes involved in T-cell activation show decreased abundance in children with acute TB, who also have impaired functional T-cell responses. Our data suggest that childhood TB is associated with an acquired immune defect, potentially resulting in failure to contain the pathogen. Elucidation of the mechanism causing the immune paresis may identify new treatment and prevention strategies.

Distribution of mesopredatory fish determined by habitat variables in a predator-depleted coastal system.

PubMed

Bergström, Lena; Karlsson, Martin; Bergström, Ulf; Pihl, Leif; Kraufvelin, Patrik

Shallow nearshore habitats are highly valued for supporting marine ecosystems, but are subject to intense human-induced pressures. Mesopredatory fish are key components in coastal food webs, and alterations in their abundance may have evident effects also on other parts of the ecosystem. The aim of this study was to clarify the relationship between the abundance of coastal mesopredatory fish, defined as mid-trophic level demersal and benthic species with a diet consisting predominantly of invertebrates, and ambient environmental variables in a fjord system influenced by both eutrophication and overfishing. A field survey was conducted over a coastal gradient comprising 300 data points sampled consistently for fish community and environmental data. Results from multivariate and univariate analyses supported each other, demonstrating that mesopredatory fish abundance at species and functional group level was positively related to the cover of structurally complex vegetation and negatively related to eutrophication, as measured by water transparency. Contrary to other studies showing an inverse relationship to piscivore abundance over time, the spatial distribution of mesopredatory fish was not locally regulated by the abundance of piscivorous fish, probably attributed to piscivores being at historically low levels due to previous overfishing. Mesopredatory fish abundance was highest in areas with high habitat quality and positively related to the abundance of piscivores, suggesting a predominance of bottom-up processes. We conclude that, in parallel with ongoing regulations of fishing pressure, measures to restore habitat function and food web productivity are important for the recovery of coastal fish communities in the area.

Bacterial gene abundances as indicators of greenhouse gas emission in soils.

PubMed

Morales, Sergio E; Cosart, Theodore; Holben, William E

2010-06-01

Nitrogen fixing and denitrifying bacteria, respectively, control bulk inputs and outputs of nitrogen in soils, thereby mediating nitrogen-based greenhouse gas emissions in an ecosystem. Molecular techniques were used to evaluate the relative abundances of nitrogen fixing, denitrifying and two numerically dominant ribotypes (based on the > or =97% sequence similarity at the 16S rRNA gene) of bacteria in plots representing 10 agricultural and other land-use practices at the Kellogg biological station long-term ecological research site. Quantification of nitrogen-related functional genes (nitrite reductase, nirS; nitrous oxide reductase, nosZ; and nitrogenase, nifH) as well as two dominant 16S ribotypes (belonging to the phyla Acidobacteria, Thermomicrobia) allowed us to evaluate the hypothesis that microbial community differences are linked to greenhouse gas emissions under different land management practices. Our results suggest that the successional stages of the ecosystem are strongly linked to bacterial functional group abundance, and that the legacy of agricultural practices can be sustained over decades. We also link greenhouse gas emissions with specific compositional responses in the soil bacterial community and assess the use of denitrifying gene abundances as proxies for determining nitrous oxide emissions from soils.

The velocity ellipsoid in the Galactic disc using Gaia DR1

NASA Astrophysics Data System (ADS)

Anguiano, Borja; Majewski, Steven R.; Freeman, Kenneth C.; Mitschang, Arik W.; Smith, Martin C.

2018-02-01

The stellar velocity ellipsoid of the solar neighbour (d < 200 pc) is re-examined using intermediate-old mono-abundance stellar groups with high-quality chemistry data together with parallaxes and proper motions from Gaia DR1. We find the average velocity dispersion values for the three space velocity components for the thin and thick discs of (σU, σV, σW)thin = (33 ± 4, 28 ± 2, 23 ± 2) and (σU, σV, σW)thick = (57 ± 6, 38 ± 5, 37 ± 4) km s-1, respectively. The mean values of the ratio between the semi-axes of the velocity ellipsoid for the thin disc are found to be σV/σU = 0.70 ± 0.13 and σW/σU is 0.64 ± 0.08, while for the thick disc σV/σU = 0.67 ± 0.11 and σW/σU is 0.66 ± 0.11. Inputting these dispersions into the linear Strömberg relation for the thin disc groups, we find the Sun's velocity with respect to the Local Standard of Rest in Galactic rotation to be V⊙ = 13.9 ± 3.4 km s-1. A relation is found between the vertex deviation and the chemical abundances for the thin disc, ranging from -5 to +40° as iron abundance increases. For the thick disc we find a vertex deviation of luv ˜- 15°. The tilt angle (luw) in the U-W plane for the thin disc groups ranges from -10 to +15°, but there is no evident relation between luw and the mean abundances. However, we find a weak relation for luw as a function of iron abundances and α-elements for most of the groups in the thick disc, where the tilt angle decreases from -5 to -20° when [Fe/H] decreases and [α/Fe] increases. The velocity anisotropy parameter is independent of the chemical group abundances and its value is nearly constant for both discs (β ˜ 0.5), suggesting that the combined disc is dynamically relaxed.

Diversity of bacterioplankton in the surface seawaters of Drake Passage near the Chinese Antarctic station.

PubMed

Xing, Mengxin; Li, Zhao; Wang, Wei; Sun, Mi

2015-07-01

The determination of relative abundances and distribution of different bacterial groups is a critical step toward understanding the functions of various bacteria and its surrounding environment. Few studies focus on the taxonomic composition and functional diversity of microbial communities in Drake Passage. In this study, marine bacterioplankton communities from surface seawaters at five locations in Drake Passage were examined by 16S rRNA gene sequence analyses. The results indicated that psychrophilic bacteria were the most abundant group in Drake Passage, and mainly made up of Bacillus, Aeromonas, Psychrobacter, Pseudomonas and Halomonas. Diversity analysis showed that surface seawater communities had no significant correlation with latitudinal gradient. Additionally, a clear difference among five surface seawater communities was evident, with 1.8% OTUs (only two) belonged to Bacillus consistent across five locations and 71% OTUs (80) existed in only one location. However, the few cosmopolitans had the largest population sizes. Our results support the hypothesis that the dominant bacterial groups appear to be analogous between geographical sites, but significant differences may be detected among rare bacterial groups. The microbial diversity of surface seawaters would be liable to be affected by environmental factors. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ecology of Ephemeroptera, Plecoptera and Trichoptera (Insecta) in Rivers of the Gunung Jerai Forest Reserve: Diversity and Distribution of Functional Feeding Groups

PubMed Central

Hamid, Suhaila Ab; Md Rawi, Che Salmah

2014-01-01

A field study was performed to describe the functional feeding groups (FFGs) of Ephemeroptera, Plecoptera and Trichoptera (EPT) in the Tupah, Batu Hampar and Teroi Rivers in the Gunung Jerai Forest Reserve (GJFR), Kedah, Malaysia. Twenty-nine genera belonging to 19 families were identified. The EPTs were classified into five FFGs: collector-gatherers (CG), collector-filterers (CF), shredders (SH), scrapers (SC) and predators (P). In this study, CG and CF were the dominant groups inhabiting all three rivers. Ephemeroptera dominated these rivers due to their high abundance, and they were also the CG (90.6%). SC were the lowest in abundance among all groups. Based on the FFGs, the Teroi River was suitable for CG, whereas the Tupah and Batu Hampar Rivers were suitable for CG and CF. The distribution of FFGs differed among the rivers (CG, χ2 = 23.6, p = 0.00; SH, χ2 = 10.02, p = 0.007; P, χ2 = 25.54, p = 0.00; CF, χ2 = 21.95, p = 0.00; SC, χ2 = 9.31, p = 0.01). These findings indicated that the FFGs found in rivers of the GJFR represent high river quality. PMID:25210588

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Distribution of Bathyarchaeota (MCG) archaea in the South China Sea sediments and implication of its ecological roles

NASA Astrophysics Data System (ADS)

Tiantian, Y.; Wang, F.; MingYang, N.

2015-12-01

Tiantian Yu1,2, Mingyang Niu1,2 and Fengping Wang1,2 1State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai, 200240, China; 2State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China ABSTRACT: Archaea of Bathyarchaeota Phylum (Miscellaneous Crenarchaeotal Group, MCG) are widespread and abundant in various marine and continental environments. However, very little is understood on the metabolisms and ecological roles of this cosmopolitan sedimentary archaea , partly due to obstacles of cultivation. Bathyarchaeota could be divided into large members of subgroups with potentially high genetic heterogeneity, implying different metabolic capabilities and functions in different subgroups. Here, we report our work on investigating Bathyarchaeota abundance and types of subgroups in the South China Sea(SCS) sediments, aim to understand their ecological roles in the carbon cycling. Bathyarchaeota were found the most dominant archaeal group in the sediments of SCS , most of which belong to subgroups MCG-8, MCG-15, MCG-17 and MCG-3. A new pair of 16S rRNA gene primers was designed as the published primers could not cover MCG-15 and MCG-17, which are the most dominant subgroups in the SCS sediments. Comparing with previous primers which used for quantifying the abundance of Bathyarchaeota via Q-PCR, the new primer revealed about an order of magnitude higher abundance in all South China Sea sediments. The relationship of geochemical parameters and MCG subgroups will further be explored to provide the basis for further understanding the metabolic function and biogeochemical roles of these poor-understood sedimentary archaea.

Effects of an oil spill on leafpack-inhabiting macroinvertebrates in the Chariton river, Missouri

USGS Publications Warehouse

Poulton, B.C.; Callahan, E.V.; Hurtubise, R.D.; Mueller, B.G.

1998-01-01

Artificial leaf packs were used to determine the effects of an oil spill on stream macroinvertebrate communities in the Chariton River, Missouri. Plastic mesh leaf retainers with approximately 10 g of leaves from five tree species were deployed at five sites (two upstream of the spill and three downstream) immediately after the spill and one year later. Four macroinvertebrate species dominating the community at upstream sites were virtually eliminated below the spill, including the stonefly Isoperla bilineata, the caddisfly Potamyia flava, the midge Thienemanniella xena, and blackfly larvae (Simulium sp.). Density of collector and shredder functional groups, and number of shredder taxa differed between upstream sites and the two furthest downstream sites during the 1990 sample period (Kruskal-Wallis w/Bonferroni paired comparisons, experiment wise error rate = 0.05). With one exception, no differences between sites were detected in the 1991-1992 sample period, indicating that the benthic community had at least partially recovered from the oil spill after one year. The odds of obtaining a sample with a small abundance of shredders (abundance < median) in 1990 was significantly greater downstream of the spill than upstream, and the odds of obtaining a sample with a small abundance of shredders at downstream sites was greater in 1990 than in 1991-1992. A similar pattern was observed in abundance and taxa richness of the collector functional group. No significant differences between the two sampling periods were detected at upstream sites. Observed effects appeared to be associated with oil sorption and substrate coating, creating conditions unsuitable for successful colonization.

The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups.

PubMed

Yin, Guangjun; Xu, Hongliang; Xiao, Shuyang; Qin, Yajuan; Li, Yaxuan; Yan, Yueming; Hu, Yingkao

2013-10-03

WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species. We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.

Intestinal microecology associated with fluoride resistance capability of the silkworm (Bombyx mori L.).

PubMed

Li, Guan-Nan; Xia, Xue-Juan; Tang, Wen-Chao; Zhu, Yong

2016-08-01

The silkworm (Bombyx mori L.) is an ideal model of Lepidoptera. However, the diversity and function of the intestinal microbiota in the gut of silkworm remain largely unknown. Changes in the intestinal microecology in fluoride-resistant strain T6 and fluoride-susceptible strain 734 of the silkworm in response to fluoride exposure were investigated. T6 and 734 were treated with 200 mg/kg fluoride (designated as T6-T and 734-T groups) and deionized water (designated as T6-C and 734-C groups). Culture-dependent approach revealed that the numbers of intestinal bacteria in the 734-T group significantly decreased compared with that in the 734-C group (4.8 ± 0.6 × 10(7) CFU/mL vs. 7.5 ± 0.7 × 10(7) CFU/mL; P < 0.05). Analyses of the intestinal content pH showed that the pH decreased in the 734-T group only. Additionally, SCFA concentrations significantly decreased in both treatment groups compared with the control groups. High-throughput sequencing indicated that the intestinal microbiota in the 734-T group was significantly more diverse than those in the other groups. The bacterial community was composed of two dominant groups (Firmicutes and Proteobacteria). Principal component analyses revealed a significant difference in the composition of the intestinal microbiota in the 734-T group compared with those in the other groups. Thaumarchaeota and Euryarchaeota were more abundant in the 734-T group, but they were less abundant in the other groups. This study enhances our understanding about the diversity and function of silkworm intestinal microbiota in response to fluoride exposure among silkworm strains with diverse resistance.

Spatial scaling patterns and functional redundancies in a changing boreal lake landscape

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Uden, Daniel R.; Johnson, Richard K.

2015-01-01

Global transformations extend beyond local habitats; therefore, larger-scale approaches are needed to assess community-level responses and resilience to unfolding environmental changes. Using longterm data (1996–2011), we evaluated spatial patterns and functional redundancies in the littoral invertebrate communities of 85 Swedish lakes, with the objective of assessing their potential resilience to environmental change at regional scales (that is, spatial resilience). Multivariate spatial modeling was used to differentiate groups of invertebrate species exhibiting spatial patterns in composition and abundance (that is, deterministic species) from those lacking spatial patterns (that is, stochastic species). We then determined the functional feeding attributes of the deterministic and stochastic invertebrate species, to infer resilience. Between one and three distinct spatial patterns in invertebrate composition and abundance were identified in approximately one-third of the species; the remainder were stochastic. We observed substantial differences in metrics between deterministic and stochastic species. Functional richness and diversity decreased over time in the deterministic group, suggesting a loss of resilience in regional invertebrate communities. However, taxon richness and redundancy increased monotonically in the stochastic group, indicating the capacity of regional invertebrate communities to adapt to change. Our results suggest that a refined picture of spatial resilience emerges if patterns of both the deterministic and stochastic species are accounted for. Spatially extensive monitoring may help increase our mechanistic understanding of community-level responses and resilience to regional environmental change, insights that are critical for developing management and conservation agendas in this current period of rapid environmental transformation.

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class

PubMed Central

Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

2015-01-01

Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10–11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did not always result from major changes in microbiota and vice versa. PMID:26691591

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class.

PubMed

Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

2015-01-01

Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10-11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did not always result from major changes in microbiota and vice versa.

A Group 6 Late Embryogenesis Abundant Protein from Common Bean Is a Disordered Protein with Extended Helical Structure and Oligomer-forming Properties*

PubMed Central

Rivera-Najera, Lucero Y.; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O.; García-Hernández, Enrique; Solórzano, Rosa M.; Reyes, José L.; Covarrubias, Alejandra A.

2014-01-01

Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance.

PubMed

Leles, S G; Mitra, A; Flynn, K J; Stoecker, D K; Hansen, P J; Calbet, A; McManus, G B; Sanders, R W; Caron, D A; Not, F; Hallegraeff, G M; Pitta, P; Raven, J A; Johnson, M D; Glibert, P M; Våge, S

2017-08-16

This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e. non-constitutive mixotrophs, NCMs), acquire their phototrophic potential through either integration of prey-plastids or through endosymbiotic associations with photosynthetic microbes. Analysis of field data reveals that 40-60% of plankton traditionally labelled as (non-phototrophic) microzooplankton are actually NCMs, employing acquired phototrophy in addition to phagotrophy. Specialist NCMs acquire chloroplasts or endosymbionts from specific prey, while generalist NCMs obtain chloroplasts from a variety of prey. These contrasting functional types of NCMs exhibit distinct seasonal and spatial global distribution patterns. Mixotrophs reliant on 'stolen' chloroplasts, controlled by prey diversity and abundance, dominate in high-biomass areas. Mixotrophs harbouring intact symbionts are present in all waters and dominate particularly in oligotrophic open ocean systems. The contrasting temporal and spatial patterns of distribution of different mixotroph functional types across the oceanic provinces, as revealed in this study, challenges traditional interpretations of marine food web structures. Mixotrophs with acquired phototrophy (NCMs) warrant greater recognition in marine research. © 2017 The Author(s).

Functional and structural responses to marine urbanisation

NASA Astrophysics Data System (ADS)

Mayer-Pinto, M.; Cole, V. J.; Johnston, E. L.; Bugnot, A.; Hurst, H.; Airoldi, L.; Glasby, T. M.; Dafforn, K. A.

2018-01-01

Urban areas have broad ecological footprints with complex impacts on natural systems. In coastal areas, growing populations are advancing their urban footprint into the ocean through the construction of seawalls and other built infrastructure. While we have some understanding of how urbanisation might drive functional change in terrestrial ecosystems, coastal systems have been largely overlooked. This study is one of the first to directly assess how changes in diversity relate to changes in ecosystem properties and functions (e.g. productivity, filtration rates) of artificial and natural habitats in one of the largest urbanised estuaries in the world, Sydney Harbour. We complemented our surveys with an extensive literature search. We found large and important differences in the community structure and function between artificial and natural coastal habitats. However, differences in diversity and abundance of organisms do not necessarily match observed functional changes. The abundance and composition of important functional groups differed among habitats with rocky shores having 40% and 70% more grazers than seawalls or pilings, respectively. In contrast, scavengers were approximately 8 times more abundant on seawalls than on pilings or rocky shores and algae were more diverse on natural rocky shores and seawalls than on pilings. Our results confirm previous findings in the literature. Oysters were more abundant on pilings than on rocky shores, but were also smaller. Interestingly, these differences in oyster populations did not affect in situ filtration rates between habitats. Seawalls were the most invaded habitats while pilings supported greater secondary productivity than other habitats. This study highlights the complexity of the diversity-function relationship and responses to ocean sprawl in coastal systems. Importantly, we showed that functional properties should be considered independently from structural change if we are to design and manage artificial habitats in ways to maximise the services provided by urban coastal systems and minimise their ecological impacts.

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

PubMed Central

Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M.; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G.; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

2015-01-01

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. PMID:25567651

Zooplankton From a Reef System Under the Influence of the Amazon River Plume.

PubMed

Neumann-Leitão, Sigrid; Melo, Pedro A M C; Schwamborn, Ralf; Diaz, Xiomara F G; Figueiredo, Lucas G P; Silva, Andrea P; Campelo, Renata P S; de Melo Júnior, Mauro; Melo, Nuno F A C; Costa, Alejandro E S F; Araújo, Moacyr; Veleda, Dóris R A; Moura, Rodrigo L; Thompson, Fabiano

2018-01-01

At the mouth of the Amazon River, a widespread carbonate ecosystem exists below the river plume, generating a hard-bottom reef (∼9500 km 2 ) that includes mainly large sponges but also rhodolith beds. The mesozooplankton associated with the pelagic realm over the reef formation was characterized, considering the estuarine plume and oceanic influence. Vertical hauls were carried out using a standard plankton net with 200 μm mesh size during September 2014. An indicator index was applied to express species importance as ecological indicators in community. Information on functional traits was gathered for the most abundant copepod species. Overall, 179 zooplankton taxa were recorded. Copepods were the richest (92 species), most diverse and most abundant group, whereas meroplankton were rare and less abundant. Species diversity (>3.0 bits.ind -1 ) and evenness (>0.6) were high, indicating a complex community. Small holoplanktonic species dominated the zooplankton, and the total density varied from 107.98 ind. m -3 over the reef area to 2,609.24 ind. m -3 in the estuarine plume, with a significant difference between coastal and oceanic areas. The most abundant copepods were the coastal species ithona plumifera and Clausocalanus furcatus and early stages copepodites of Paracalanidae. The holoplanktonic Oikopleura , an important producer of mucous houses, was very abundant on the reefs. The indicator species index revealed three groups: (1) indicative of coastal waters under the influence of the estuarine plume [ Euterpina acutifrons, Parvocalanus crassirostris, Oikopleura (Vexillaria) dioica and Hydromedusae]; (2) characterized coastal and oceanic conditions ( Clausocalanus ); (3) characterized the reef system ( O. plumifera ). Two major copepods functional groups were identified and sorted according to their trophic strategy and coastal-oceanic distribution. The species that dominated the coastal area and the area over the rhodolith beds are indicators of the estuarine plume and are mixed with species of the North Brazil Current. These species practically disappear offshore, where occur oceanic species commonly found in other oligotrophic tropical areas. This ecosystem shows a mixture of estuarine, coastal and oceanic communities coexisting in the waters over the Amazon reefs, with no significant differences among these areas. However, the MDS clearly separated the communities along the salinity gradient in the plume.

Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan

NASA Astrophysics Data System (ADS)

Shakir, Muhammad Mussadiq; Ahmed, Sohail

2015-05-01

Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops ( p < 0.05). Cluster analysis revealed four categories of soil arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface arthropods were the major contributors of variation in overall abundance in extreme temperature months while microarthropods in low-temperature months. CCA analysis revealed the occurrence of different arthropod groups in correspondence with different abiotic variables. Results are discussed in view of position of these arthropods as useful indicators under changing environmental conditions impacting agroecosystems in the study area.

Patterns of rare and abundant marine microbial eukaryotes.

PubMed

Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angélique; Kooistra, Wiebe H C F; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sébastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A; de Vargas, Colomban; Massana, Ramon

2014-04-14

Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Shift in community structure in an early-successional Mediterranean shrubland driven by long-term experimental warming and drought and natural extreme droughts.

PubMed

Liu, Daijun; Estiarte, Marc; Ogaya, Romà; Yang, Xiaohong; Peñuelas, Josep

2017-10-01

Global warming and recurring drought are expected to accelerate water limitation for plant communities in semiarid Mediterranean ecosystems and produce directional shifts in structure and composition that are not easily detected, and supporting evidence is scarce. We conducted a long-term (17 years) nocturnal-warming (+0.6°C) and drought (-40% rainfall) experiments in an early-successional Mediterranean shrubland to study the changes in community structure and composition, contrasting functional groups and dominant species, and the superimposed effects of natural extreme drought. Species richness decreased in both the warming and drought treatments. Responses to the moderate warming were associated with decreases in herb abundance, and responses to the drought were associated with decreases in both herb and shrub abundances. The drought also significantly decreased community diversity and evenness. Changes in abundance differed between herbs (decreases) and shrubs (increases or no changes). Both warming and drought, especially drought, increased the relative species richness and abundance of shrubs, favoring the establishment of shrubs. Both warming and drought produced significant shifts in plant community composition. Experimental warming shifted the community composition from Erica multiflora toward Rosmarinus officinalis, and drought consistently shifted the composition toward Globularia alypum. The responses in biodiversity (e.g., community biodiversity, changes of functional groups and compositional shifts) were also strongly correlated with atmospheric drought (SPEI) in winter-spring and/or summer, indicating sensitivity to water limitation in this early-successional Mediterranean ecosystem, especially to natural extreme droughts. Our results suggest that the shifts in species assembles and community diversity and composition are accelerated by the long-term nocturnal-warming and drought, combined with natural severe droughts, and that the magnitude of the impacts of climate change is also correlated with the successional status of ecosystem. The results thus highlight the necessity for assessing the impacts on ecosystemic functioning and services and developing effective measures for conserving biodiversity. © 2017 John Wiley & Sons Ltd.

Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus).

PubMed

Wang, Wen; Zheng, Sisi; Sharshov, Kirill; Sun, Hao; Yang, Fang; Wang, Xuelian; Li, Laixing; Xiao, Zhixiong

2017-04-01

Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

A normal abundance of faint satellites in the fossil group NGC 6482

NASA Astrophysics Data System (ADS)

Lieder, S.; Mieske, S.; Sánchez-Janssen, R.; Hilker, M.; Lisker, T.; Tanaka, M.

2013-11-01

A fossil group is considered the end product in a galaxy group's evolution. It is a massive central galaxy that dominates the luminosity budget of the group, and is the outcome of efficient merging between intermediate-luminosity members. Little is known, however, about the faint satellite systems of fossil groups. Here we present a Subaru/Suprime-Cam wide-field, deep imaging study in the B - and R -bands of the nearest fossil group NGC 6482 (Mtot ~ 4 × 1012M⊙), covering the virial radius out to 310 kpc. We performed detailed completeness estimations and selected group member candidates by a combination of automated object detection and visual inspection. A fiducial sample of 48 member candidates down to MR ~ -10.5 mag is detected, making this study the deepest of a fossil group to now. We investigate the photometric scaling relations, the color-magnitude relation, and the luminosity function of our galaxy sample. We find evidence of recent and ongoing merger events among bright group galaxies. The color-magnitude relation is comparable to that of nearby galaxy clusters, and it exhibits significant scatter at the faintest luminosities. The completeness-corrected luminosity function is dominated by early-type dwarfs and is characterized by a faint end slope α = -1.32 ± 0.05. We conclude that the NGC 6482 fossil group shows photometric properties consistent with those of regular galaxy clusters and groups, including a normal abundance of faint satellites. Appendix A is available in electronic form at http://www.aanda.orgThe reduced data are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/559/A76

Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis

PubMed Central

Borgdorff, Hanneke; Armstrong, Stuart D.; Tytgat, Hanne L. P.; Xia, Dong; Ndayisaba, Gilles F.; Wastling, Jonathan M.; van de Wijgert, Janneke H. H. M.

2016-01-01

Background A Lactobacillus-dominated cervicovaginal microbiota (VMB) protects women from adverse reproductive health outcomes, but the role of L. iners in the VMB is poorly understood. Our aim was to explore the association between the cervicovaginal L. iners and L. crispatus proteomes and VMB composition. Methods The vaginal proteomes of 50 Rwandan women at high HIV risk, grouped into four VMB groups (based on 16S rDNA microarray results), were investigated by mass spectrometry using cervicovaginal lavage (CVL) samples. Only samples with positive 16S results for L. iners and/or L. crispatus within each group were included in subsequent comparative protein analyses: Lactobacillus crispatus-dominated VMB cluster (with 16S-proven L. iners (ni) = 0, and with 16S-proven L. crispatus (nc) = 5), L. iners-dominated VMB cluster (ni = 11, nc = 4), moderate dysbiosis (ni = 12, nc = 2); and severe dysbiosis (ni = 8, nc = 2). The relative abundances of proteins that were considered specific for L. iners and L. crispatus were compared among VMB groups. Results Forty Lactobacillus proteins were identified of which 7 were specific for L. iners and 11 for L. crispatus. The relative abundances of L. iners DNA starvation/stationary phase protection protein (DPS), and the glycolysis enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glucose-6-phosphate isomerase (GPI), were significantly decreased in women with L. iners-containing dysbiosis compared to women with a L. iners-dominated VMB, independent of vaginal pH and L. iners abundance. Furthermore, L. iners DPS, GAPDH, GPI, and fructose-bisphosphate aldolase (ALDO) were significantly negatively associated with vaginal pH. Glycolysis enzymes of L. crispatus showed a similar negative, but nonsignificant, trend related to dysbiosis. Conclusions Most identified Lactobacillus proteins had conserved intracellular functions, but their high abundance in CVL supernatant might imply an additional extracellular (moonlighting) role. Our findings suggest that these proteins can be important in maintaining a Lactobacillus-dominated VMB. Functional studies are needed to investigate their roles in vaginal bacterial communities and whether they can be used to prevent vaginal dysbiosis. PMID:26963809

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes.

PubMed

Boivin, Vincent; Deschamps-Francoeur, Gabrielle; Couture, Sonia; Nottingham, Ryan M; Bouchard-Bourelle, Philia; Lambowitz, Alan M; Scott, Michelle S; Abou-Elela, Sherif

2018-07-01

Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. S tructured n on c oding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing. © 2018 Boivin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Functional consequences of climate change-induced plant species loss in a tallgrass prairie.

PubMed

Craine, Joseph M; Nippert, Jesse B; Towne, E Gene; Tucker, Sally; Kembel, Steven W; Skibbe, Adam; McLauchlan, Kendra K

2011-04-01

Future climate change is likely to reduce the floristic diversity of grasslands. Yet the potential consequences of climate-induced plant species losses for the functioning of these ecosystems are poorly understood. We investigated how climate change might alter the functional composition of grasslands for Konza Prairie, a diverse tallgrass prairie in central North America. With species-specific climate envelopes, we show that a reduction in mean annual precipitation would preferentially remove species that are more abundant in the more productive lowland positions at Konza. As such, decreases in precipitation could reduce productivity not only by reducing water availability but by also removing species that inhabit the most productive areas and respond the most to climate variability. In support of this prediction, data on species abundance at Konza over 16 years show that species that are more abundant in lowlands than uplands are preferentially reduced in years with low precipitation. Climate change is likely to also preferentially remove species from particular functional groups and clades. For example, warming is forecast to preferentially remove perennials over annuals as well as Cyperaceae species. Despite these predictions, climate change is unlikely to unilaterally alter the functional composition of the tallgrass prairie flora, as many functional traits such as physiological drought tolerance and maximum photosynthetic rates showed little relationship with climate envelope parameters. In all, although climatic drying would indirectly alter grassland productivity through species loss patterns, the insurance afforded by biodiversity to ecosystem function is likely to be sustained in the face of climate change.

The Functional Implications of Bottom Up and Top Down Controls on Marine Bacteria in Arthur Harbor, a Highly Productive Coastal Setting on the West Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Bowman, J. S.; Amaral-Zettler, L. A.; Rich, J. J.; Luria, C.; Ducklow, H. W.

2016-02-01

Marine bacteria can be broadly classified into two groups based on their ecology; slow growing oligotrophic specialists and fast growing copiotrophs. These ecological strategies are associated with specific taxonomic and functional groups, making it possible to use 16S rRNA gene amplicon and shotgun metagenomic data to qualitatively, and possibly quantitatively, identify the contribution of each strategy to marine biogeochemical cycles. We leveraged a 5-year (2009 to 2014) time series of 16S rRNA gene amplicon data for Arthur Harbor, located near Palmer Station, Antarctica, to identify trends in the abundance of taxa associated with each ecological strategy. Using emergent self-organizing maps, we identified four recurring "modes" in bacterial community structure based on the relative abundance of the ubiquitous SAR11 clade. A different bacterial genus was dominant in each mode; Pelagibacter, Polaribacter, Roseobacter, and Colwellia. To explore the functional implications of these different modes we applied shotgun metagenomics and functional predictions using the newly available tool PAPRICA, in combination with flow cytometry and estimates of bacterial production. Our annotation and assembly of binned contigs corresponding to the dominant genera illuminate the succession of metabolic functions across the 2013-2014 austral summer and inform the timing of autotrophic and mixotrophic (putatively bacterivorous) phytoplankton blooms. Surprisingly, while the abundance of Pelagibacter 16S rRNA gene reads was negatively correlated with the concentration of chlorophyll a, the ratio of Pelagibacter to Polaribacter and Roseobacter was poorly correlated with the ratio of high nucleic acid (HNA) to low nucleic acid (LNA) bacteria as determined by flow cytometry, and the relative size of the HNA population at times contrasted sharply with chlorophyll a. These findings suggest that the physiological state of bacterial cells and top down controls play a strong role in HNA: LNA dynamics.

Scavenging efficiency and red fox abundance in Mediterranean mountains with and without vultures

NASA Astrophysics Data System (ADS)

Morales-Reyes, Zebensui; Sánchez-Zapata, José A.; Sebastián-González, Esther; Botella, Francisco; Carrete, Martina; Moleón, Marcos

2017-02-01

Vertebrate scavenging assemblages include two major functional groups: obligate scavengers (i.e., vultures), which depend totally on carrion and are undergoing severe declines around the globe, and facultative scavengers, which exploit carrion opportunistically and are generally ubiquitous. Our goal was to investigate the hypothesis that vultures can indirectly regulate the abundance of mesopredators (i.e., facultative scavengers) through modulating their access to carrion resources. We studied scavenging efficiency and red fox (Vulpes vulpes) abundance in two neighbouring areas of South-eastern Spain where vultures (mainly griffon vultures Gyps fulvus) are present (Cazorla) and absent (Espuña). To do so, we monitored ungulate carcasses consumption during winter and summer, and counted red fox scats along walking transects as a proxy of fox density. Our results confirmed that scavenging efficiency was higher in Cazorla and in carcasses visited by vultures. This resulted in increasing scavenging opportunities for facultative scavengers where vultures were absent. Accordingly, mean red fox abundance was higher in Espuña. These results suggest the existence of a vulture-mediated mesopredator release (i.e., an increase of mesopredator numbers following vulture loss), which could trigger important indirect ecological effects. Also, our study demonstrates that facultative scavengers are hardly able to functionally replace vultures, mainly because the former exploit carrion on a slower time scale.

Disturbance influences oyster community richness and evenness, but not diversity.

PubMed

Kimbro, David L; Grosholz, Edwin D

2006-09-01

Foundation species in space-limited systems can increase diversity by creating habitat, but they may also reduce diversity by excluding primary space competitors. These contrasting forces of increasing associate diversity and suppressing competitor diversity have rarely been examined experimentally with respect to disturbance. In a benthic marine community in central California, where native oysters are a foundation species, we tested how disturbance influenced overall species richness, evenness, and diversity. Surprisingly, overall diversity did not peak across a disturbance gradient because, as disturbance decreased, decreases in overall species evenness opposed increases in overall species richness. Decreasing disturbance intensity (high oyster abundance) led to increasing species richness of sessile and mobile species combined. This increase was due to the facilitation of secondary sessile and mobile species in the presence of oysters. In contrast, decreasing disturbance intensity and high oyster abundance decreased the evenness of sessile and mobile species. Three factors likely contributed to this decreased evenness: oysters reduced abundances of primary sessile species due to space competition; oysters supported more rare mobile species; and oysters disproportionately increased the relative abundance of a few common mobile species. Our results highlight the need for further studies on how disturbance can differentially affect the evenness and richness of different functional groups, and ultimately how these differences affect the relationship between overall diversity and ecosystem function.

Proteomic analysis of early-stage embryos: implications for egg quality in hapuku (Polyprion oxygeneios).

PubMed

Kohn, Yair Y; Symonds, Jane E; Kleffmann, Torsten; Nakagawa, Shinichi; Lagisz, Malgorzata; Lokman, P Mark

2015-12-01

In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function/pathway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice.

PubMed

Dong, Hui; Song, Weiwei; Wang, Chunlin; Mu, Changkao; Li, Ronghua

2017-07-03

By the search for new natural compounds with beneficial health effects, cephalopod ink has been considered as an attempt to develop new drugs and functional foods, which is an especially active field in Asia, where cephalopods are a major fishery catch, for which ink sacs are a bi-product and where homeopathic medicine has deep roots. There is a demand to evaluate the safety and influence to the organism. The specific composition and relative abundance of the gut microbiota, which is potentially a major modulator of host metabolism, drives the interaction between functional foods and host health. We explore the effects of melanin from Sepiella Maindroni, most common cuttlefish in China, on the intestinal microbiome of mice. ICR mice were randomly divided four groups, which were normal group (S), low melanin dose group (D; 120 mg/kg), medium melanin dose group (Z; 240 mg/kg), and high melanin dose group (G; 480 mg/kg). Melanin was delivered for 28 consecutive days. Fecal samples were used to generate 7715 operational taxonomic units (OTUs) via high-throughput sequencing. There were significant shifts in relative abundance of the dominant taxa at the phylum, class, order, family, and genus levels following melanin treatment. MSMI had no significant effect on the structure of intestinal flora in mice. The main effect was in the proportion of dominant bacterial communities. The effect positively correlated with the dose. From a health point of view, the use of melanin does not cause intestinal flora disorder. Our results may have important implications for MSMI as functional food component and potential therapeutic for manipulating gut microbiota.

Characterization of the salivary microbiome in people with obesity

PubMed Central

Zhang, Qian

2018-01-01

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases. PMID:29576948

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

PubMed Central

Thompson, Luke R; Williams, Gareth J; Haroon, Mohamed F; Shibl, Ahmed; Larsen, Peter; Shorenstein, Joshua; Knight, Rob; Stingl, Ulrich

2017-01-01

Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways—at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75–79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology. PMID:27420030

Intracellular localization of a group II chaperonin indicates a membrane-related function

NASA Technical Reports Server (NTRS)

Trent, Jonathan D.; Kagawa, Hiromi K.; Paavola, Chad D.; McMillan, R. Andrew; Howard, Jeanie; Jahnke, Linda; Lavin, Colleen; Embaye, Tsegereda; Henze, Christopher E.

2003-01-01

Chaperonins are protein complexes that are believed to function as part of a protein folding system in the cytoplasm of the cell. We observed, however, that the group II chaperonins known as rosettasomes in the hyperthermophilic archaeon Sulfolobus shibatae, are not cytoplasmic but membrane associated. This association was observed in cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C by using immunofluorescence microscopy and in thick sections of rapidly frozen cells grown at 76 degrees C by using immunogold electron microscopy. We observed that increased abundance of rosettasomes after heat shock correlated with decreased membrane permeability at lethal temperature (92 degrees C). This change in permeability was not seen in cells heat-shocked in the presence of the amino acid analogue azetidine 2-carboxylic acid, indicating functional protein synthesis influences permeability. Azetidine experiments also indicated that observed heat-induced changes in lipid composition in S. shibatae could not account for changes in membrane permeability. Rosettasomes purified from cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C bind to liposomes made from either the bipolar tetraether lipids of Sulfolobus or a variety of artificial lipid mixtures. The presence of rosettasomes did not significantly change the transition temperature of liposomes, as indicated by differential scanning calorimetry, or the proton permeability of liposomes, as indicated by pyranine fluorescence. We propose that these group II chaperonins function as a structural element in the natural membrane based on their intracellular location, the correlation between their functional abundance and membrane permeability, and their potential distribution on the membrane surface.

Molecular Characterization of the Gas-Particle Interface of Soot Sampled from a Diesel Engine Using a Titration Method.

PubMed

Tapia, A; Salgado, M S; Martín, María Pilar; Lapuerta, M; Rodríguez-Fernández, J; Rossi, M J; Cabañas, B

2016-03-15

Surface functional groups of two different types of combustion aerosols, a conventional diesel (EN 590) and a hydrotreated vegetable oil (HVO) soot, have been investigated using heterogeneous chemistry (i.e., gas-particle surface reactions). A commercial sample of amorphous carbon (Printex XE2-B) was analyzed as a reference substrate. A Knudsen flow reactor was used to carry out the experiments under molecular flow conditions. The selected gases for the titration experiments were: N(CH3)3 for the identification of acidic sites, NH2OH for the presence of carbonyl groups, CF3COOH and HCl for basic sites of different strength, and O3 and NO2 for reducing groups. Reactivity with N(CH3)3 indicates a lower density of acidic functionalities for Printex XE2-B in relation to diesel and HVO soot. Results for NH2OH experiments indicates that commercial amorphous carbon exhibits a lower abundance of available carbonyl groups at the interface compared to the results from diesel and HVO soot, the latter being the one with the largest abundance of carbonyl functions. Reactions with acids indicate the presence of weak basic oxides on the particle surface that preferentially interact with the strong acid CF3COOH. Finally, reactions with O3 and NO2 reveal that diesel and especially HVO have a significantly higher reactivity with both oxidizers compared to that of Printex XE2-B because they have more reducing sites by roughly a factor of 10 and 30, respectively. The kinetics of titration reactions have also been investigated.

Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR

PubMed Central

Thorn, Kevin A.; Cox, Larry G.

2015-01-01

Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected. PMID:26556054

Ant Abundance along a Productivity Gradient: Addressing Two Conflicting Hypotheses

PubMed Central

Segev, Udi; Kigel, Jaime; Lubin, Yael; Tielbörger, Katja

2015-01-01

The number of individuals within a population or community and their body size can be associated with changes in resource supply. While these relationships may provide a key to better understand the role of abiotic vs. biotic constraints in animal communities, little is known about the way size and abundance of organisms change along resource gradients. Here, we studied this interplay in ants, addressing two hypotheses with opposite predictions regarding variation in population densities along resource gradients- the ‘productivity hypothesis’ and the ‘productivity-based thinning hypothesis’. The hypotheses were tested in two functional groups of ground-dwelling ants that are directly primary consumers feeding on seeds: specialized seed-eaters and generalist species. We examined variations in colony density and foraging activity (a size measurement of the forager caste) in six ant assemblages along a steep productivity gradient in a semi-arid region, where precipitation and plant biomass vary 6-fold over a distance of 250km. An increase in the density or foraging activity of ant colonies along productivity gradients is also likely to affect competitive interactions among colonies, and consequently clinal changes in competition intensity were also examined. Ant foraging activity increased with productivity for both functional groups. However, colony density revealed opposing patterns: it increased with productivity for the specialized seed-eaters, but decreased for the generalist species. Competition intensity, evaluated by spatial partitioning of species at food baits and distribution of colonies, was uncorrelated with productivity in the specialized seed-eaters, but decreased with increasing productivity in the generalists. Our results provide support for two contrasting hypotheses regarding the effect of resource availability on the abundance of colonial organisms- the ‘productivity hypothesis’ for specialized seed-eaters and the ‘productivity-based thinning hypothesis’ for generalist species. These results also stress the importance of considering the role of functional groups in studies of community structure. PMID:26176853

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices.

PubMed

Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

2015-02-22

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Incorporating detection probability into northern Great Plains pronghorn population estimates

USGS Publications Warehouse

Jacques, Christopher N.; Jenks, Jonathan A.; Grovenburg, Troy W.; Klaver, Robert W.; DePerno, Christopher S.

2014-01-01

Pronghorn (Antilocapra americana) abundances commonly are estimated using fixed-wing surveys, but these estimates are likely to be negatively biased because of violations of key assumptions underpinning line-transect methodology. Reducing bias and improving precision of abundance estimates through use of detection probability and mark-resight models may allow for more responsive pronghorn management actions. Given their potential application in population estimation, we evaluated detection probability and mark-resight models for use in estimating pronghorn population abundance. We used logistic regression to quantify probabilities that detecting pronghorn might be influenced by group size, animal activity, percent vegetation, cover type, and topography. We estimated pronghorn population size by study area and year using mixed logit-normal mark-resight (MLNM) models. Pronghorn detection probability increased with group size, animal activity, and percent vegetation; overall detection probability was 0.639 (95% CI = 0.612–0.667) with 396 of 620 pronghorn groups detected. Despite model selection uncertainty, the best detection probability models were 44% (range = 8–79%) and 180% (range = 139–217%) greater than traditional pronghorn population estimates. Similarly, the best MLNM models were 28% (range = 3–58%) and 147% (range = 124–180%) greater than traditional population estimates. Detection probability of pronghorn was not constant but depended on both intrinsic and extrinsic factors. When pronghorn detection probability is a function of animal group size, animal activity, landscape complexity, and percent vegetation, traditional aerial survey techniques will result in biased pronghorn abundance estimates. Standardizing survey conditions, increasing resighting occasions, or accounting for variation in individual heterogeneity in mark-resight models will increase the accuracy and precision of pronghorn population estimates.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry.

PubMed

Blincoe, William D; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A; Joyce, Leo A; Mangion, Ian; Sheng, Huaming

2018-04-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS 1 ). Significant water/alcohol loss (>30% abundance in MS 1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. Graphical Abstract ᅟ.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Blincoe, William D.; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A.; Joyce, Leo A.; Mangion, Ian; Sheng, Huaming

2018-02-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS1). Significant water/alcohol loss (>30% abundance in MS1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. [Figure not available: see fulltext.

An observer's guide to the (Local Group) dwarf galaxies: predictions for their own dwarf satellite populations

NASA Astrophysics Data System (ADS)

Dooley, Gregory A.; Peter, Annika H. G.; Yang, Tianyi; Willman, Beth; Griffen, Brendan F.; Frebel, Anna

2017-11-01

A recent surge in the discovery of new ultrafaint dwarf satellites of the Milky Way has inspired the idea of searching for faint satellites, 103 M⊙ 99 per cent chance that at least one satellite with stellar mass M* > 105 M⊙ exists around the combined five Local Group field dwarf galaxies with the largest stellar mass. When considering satellites with M* > 104 M⊙, we predict a combined 5-25 satellites for the five largest field dwarfs, and 10-50 for the whole Local Group field dwarf population. Because of the relatively small number of predicted dwarfs, and their extended spatial distribution, a large fraction each Local Group dwarf's virial volume will need to be surveyed to guarantee discoveries. We compute the predicted number of satellites in a given field of view of specific Local Group galaxies, as a function of minimum satellite luminosity, and explicitly obtain such values for the Solitary Local dwarfs survey. Uncertainties in abundance-matching and reionization models are large, implying that comprehensive searches could lead to refinements of both models.

Functional insights into the late embryogenesis abundant (LEA) protein family from Dendrobium officinale (Orchidaceae) using an Escherichia coli system

PubMed Central

Ling, Hong; Zeng, Xu; Guo, Shunxing

2016-01-01

Late embryogenesis abundant (LEA) proteins, a diverse family, accumulate during seed desiccation in the later stages of embryogenesis. LEA proteins are associated with tolerance to abiotic stresses, such as drought, salinity and high or cold temperature. Here, we report the first comprehensive survey of the LEA gene family in Dendrobium officinale, an important and widely grown medicinal orchid in China. Based on phylogenetic relationships with the complete set of Arabidopsis and Oryza LEA proteins, 17 genes encoding D. officinale LEAs (DofLEAs) were identified and their deduced proteins were classified into seven groups. The motif composition of these deduced proteins was correlated with the gene structure found in each LEA group. Our results reveal the DofLEA genes are widely distributed and expressed in tissues. Additionally, 11 genes from different groups were introduced into Escherichia coli to assess the functions of DofLEAs. Expression of 6 and 7 DofLEAs in E. coli improved growth performance compared with the control under salt and heat stress, respectively. Based on qPCR data, all of these genes were up-regulated in various tissues following exposure to salt and heat stresses. Our results suggest that DofLEAs play an important role in responses to abiotic stress. PMID:28004781

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

PubMed Central

Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

2013-01-01

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

Dividing up the pie: Whales, fish, and humans as competitors

NASA Astrophysics Data System (ADS)

Ruzicka, James J.; Steele, John H.; Ballerini, Tosca; Gaichas, Sarah K.; Ainley, David G.

2013-09-01

Similarly structured food web models of four coastal ecosystems (Northern California Current, Central Gulf of Alaska, Georges Bank, southwestern Antarctic Peninsula) were used to investigate competition among whales, fishes, pinnipeds, and humans. Two analysis strategies simulated the effects of historic baleen and odontocete whale abundances across all trophic levels: food web structure scenarios and time-dynamic scenarios. Direct competition between whales and commercial fisheries is small at current whale abundances; whales and fisheries each take similar proportions of annual pelagic fish production (4-7%). Scenarios show that as whale populations grow, indirect competition between whales and fish for zooplankton would more likely impact fishery production than would direct competition for fish between whales and commercial fisheries. Increased baleen whale abundance would have greater and broader indirect effects on upper trophic levels and fisheries than a similar increase in odontocete abundance. Time-dynamic scenarios, which allow for the evolution of compensatory mechanisms, showed more modest impacts than structural scenarios, which show the immediate impacts of altered energy pathways. Structural scenarios show that in terms of energy availability, there is potential for large increases in whale abundance without major changes to existing food web structures and without substantial reduction of fishery production. For each ecosystem, a five-fold increase in baleen whale abundance could be supported with minor disruptions to existing energy flow pathways. However, such an increase would remain below historical population levels for many cetaceans. A larger expansion (20X) could be accommodated only with large reductions in energy flow to competitor groups. The scope for odontocete expansion varies between ecosystems but may be more restricted than the scope for baleen expansion because they feed at higher, less productive trophic levels. Egestion: unassimilated consumption, feces; directed to detritus pools. Metabolism: basal metabolism, specific dynamic action, and activity costs in terms of ammonium excretion NH4+; directed to recycled nutrient pools. Predation: a production term; production directed to grazing or predation by other functional groups. “Other” mortality: a production term; “other” mortality is unconsumed production; principally unconsumed phytoplankton; directed to detritus pools. Export (losses): a production term; export of plankton and pelagic detritus by physical transport; export losses are handled as a reduction of group transfer efficiency (the fraction of consumption that is passed to higher trophic level groups through grazing or predation). “Consumption” for phytoplankton is the uptake of new nitrate NO3- input and recycled ammonium NH4+ produced by consumer metabolism. Nitrate input was rescaled to carbon based upon the Redfield ratio (6.625 mmole C mmole N-1) and to wet weight based upon the estimated carbon content of fish (8.8 mg wet weight mg C-1) (Steele et al., 2007).The E2E trophic network matrices for each region are provided as Supplementary material. The E2E network models for the Northern California Current (NCC), Central Gulf of Alaska (CGoA), and southwestern Antarctic Peninsula (sWAP) ecosystems were derived following the techniques of Steele and Ruzicka (2011) from solutions for biomasses, consumption rates, and predation pressure upon each functional group calculated using ECOPATH algorithms (Christensen and Walters, 2004). The NCC model was modified from Ruzicka et al. (2012), the CGoA model was modified as noted in the Supplementary material from the full Gulf of Alaska model documented in Aydin et al. (2007), and the sWAP model was modified from Ballerini et al. (submitted for publication). A quantitative assessment of the Georges Bank (GB) food web is given in Steele et al. (2007) and Collie et al. (2009). Top predators (seabirds, baleen whales, odontocetes) were implicit in the original GB model. These components have now been explicitly defined using information from Link et al. (2006) to provide estimates of the abundance, diets, and consumption rates of birds and mammals on Georges Bank. (ECOPATH parameters and diet matrices for all four regional models are provided in the Supplementary material).Each regional model was developed by a different team of researchers with different emphasis of purpose but was re-structured so that each shared similar functional group aggregations. Functional groups were aggregated using production-weighted mean values of physiological parameters and diets and the sums of group biomasses and fishery harvests. Model currencies also differed between regional models: wet weight biomass (NCC, CGoA), nitrogen biomass (GB), and carbon biomass (sWAP). However, all analyses are expressed as comparable dimensionless metrics: relative changes in production rate (E2E network scenarios) and relative changes in biomass (time-dynamic scenarios).

Microbial Nitrogen Cycling Associated with the Early Diagenesis of Organic Matter in Subseafloor Sediments

NASA Astrophysics Data System (ADS)

Zhao, R.

2015-12-01

The early diagenesis of organic matter is the major energy source of marine sedimentary biosphere and thus controls its population size; however, the vertical distribution of any functional groups along with the diagenesis of organic matter is remained unclear, especially for those microbes involved in nitrogen transformation which serve as a major control on the nitrogen flux between reservoirs. Here we investigated the vertical distributions of various functional groups in five sediment cores retrieved from Arctic Mid-Ocean Ridge (AMOR), with emphasis on the nitrifiers, denitrifiers and anaerobic ammonium oxidizing bacteria (anammox). We observed the clear geochemical zonation associated with organic matter diagenesis in the sediments based on the pore water profiles of oxygen, nitrate, ammonium, manganese and sulfate, with distinct geochemical transition zones at the boundaries of geochemical zones, including oxic-anoxic transition zone (OATZ) and nitrate-manganese reduction zone (NMTZ). Nitrate was produced in surface oxygenated sediments and nitrate consumption mainly took place at the NMTZ, splitted between re-oxidation of ammonium and manganese (II). Abundances of ammonia oxidizers, nitrite oxidizers, and denitrifiers, estimated through quantitative PCR targeting their respective functional genes, generally decrease with depth, but constantly elevated around the OATZ, NMTZ, and manganese-reduction zone as well. Anammox bacteria were only detected around the NMTZ where both nitrate/nitrite and ammonium are available. These depth profiles of functional groups were also confirmed by the community structure profiling by prokaryotic 16S rRNA gene tag pyrosequencing. Cell-specific rates of nitrification and denitrification, calculated from the bulk net reaction rates divided by functional group abundances, were similar to those values from oligotrophic sediments like North Pond and thus suggested that nitrifiers and denitirifiers populations were in maintenance state. This study illustrated the microbial nitrogen transformation accompanying the early diagenesis of organic matter in marine sediments, which scenario might be occurring in a wide range of stratified environments on Earth.

Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes

PubMed Central

García-Morales, Rodrigo; Badano, Ernesto I.; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E.; Ávila-Gómez, Eva S.

2016-01-01

Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others. PMID:27926923

Assemblage patterns of fish functional groups relative to habitat connectivity and conditions in floodplain lakes

USGS Publications Warehouse

Miyazono, S.; Aycock, J.N.; Miranda, L.E.; Tietjen, T.E.

2010-01-01

We evaluated the influences of habitat connectivity and local environmental factors on the distribution and abundance patterns of fish functional groups in 17 floodplain lakes in the Yazoo River Basin, USA. The results of univariate and multivariate analyses showed that species-environmental relationships varied with the functional groups. Species richness and assemblage structure of periodic strategists showed strong and positive correlations with habitat connectivity. Densities of most equilibrium and opportunistic strategists decreased with habitat connectivity. Densities of certain equilibrium and opportunistic strategists increased with turbidity. Forested wetlands around the lakes were positively related to the densities of periodic and equilibrium strategists. These results suggest that decreases in habitat connectivity, forested wetland buffers and water quality resulting from environmental manipulations may cause local extinction of certain fish taxa and accelerate the dominance of tolerant fishes in floodplain lakes. ?? 2010 John Wiley & Sons A/S.

Distribution of cavity trees in midwestern old-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Distribution of cavity trees in midwesternold-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R., III Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus

DOE PAGES

Prestat, Emmanuel; David, Maude M.; Hultman, Jenni; ...

2014-09-26

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associatedmore » functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.« less

Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers.

PubMed

Stern, Joshua M; Moazami, Saman; Qiu, Yunping; Kurland, Irwin; Chen, Zigui; Agalliu, Ilir; Burk, Robert; Davies, Kelvin P

2016-10-01

The trillions of microbes that colonize our adult intestine are referred to as the gut microbiome (GMB). Functionally it behaves as a metabolic organ that communicates with, and complements, our own human metabolic apparatus. While the relationship between the GMB and kidney stone disease (KSD) has not been investigated, dysbiosis of the GMB has been associated with diabetes, obesity and cardiovascular disease. In this pilot study we sought to identify unique changes in the GMB of kidney stone patients compared to patients without KSD. With an IRB-approved protocol we enrolled 29 patients into our pilot study. 23 patients were kidney stone formers and six were non-stone forming controls. Specimens were collected after a 6h fast and were flash frozen in dry ice and then stored at -80 °C. Microbiome: determination of bacterial abundance was by analysis of 16 s rRNA marker gene sequences using next generation sequencing. Sequencing of the GMB identified 178 bacterial genera. The five most abundant enterotypes within each group made up to greater than 50 % of the bacterial abundance identified. Bacteroides was 3.4 times more abundant in the KSD group as compared to control (34.9 vs 10.2 %; p = 0.001). Prevotella was 2.8 times more abundant in the control group as compared to the KSD group (34.7 vs 12.3 %; p = 0.005). In a multivariate analysis including age, gender, BMI, and DM, kidney stone disease remained an increased risk for high prevalence for Bacteroides (OR = 3.26, p = 0.033), whereas there was an inverse association with Prevotella (OR = 0.37, p = 0.043). There were no statistically significant differences in bacterial abundance levels for Bacteroides or Prevotella when comparing patients with and without DM, obesity (BMI >30), HTN or HLD. 11 kidney stone patients completed 24 h urine analysis at the time of this writing. Looking at the bacterial genuses with at least 4 % abundance in the kidney stone group, Eubacterium was inversely correlated with oxalate levels (r = -0.60, p < 0.06) and Escherichia trended to an inverse correlation with citrate (r = -0.56, p < 0.08). We also compared bacterial abundance between uric acid (UA) stone formers (n = 5) and non UA stone formers (n = 18) and found no significant difference between them. We identified two genus of bacteria in the GMB that had significant association with KSD. Interestingly, components of the 24-h urine appear to be correlated to bacterial abundance. These preliminary studies for the first time associate differences in the GMB with kidney stone formation. Further studies are warranted to evaluate the potential causative role of preexisting dysbiosis in kidney stone disease.

Bacterial and fungal community composition and functioning of two different peatlands in China

NASA Astrophysics Data System (ADS)

Wang, Meng; Tian, Jianqing; Bu, Zhaojun; Chen, Huai; Zhu, Qiuan; Peng, Changhui

2017-04-01

Peatlands are important carbon sinks which store one third of the global soil carbon ( 550 Gt) with only 3% of the land surface. The slow rate of organic matter decomposition associated with low microbial diversity and limited functioning under cold, acidic and anoxic condition is of critical importance in controlling biogeochemical cycles in northern peatlands. To evaluate the variation in microbial community composition and functionality can advance our understanding of the underlying mechanisms of the biogeochemical processes and interactions. However, there is still a lack of information for Chinese peatlands. Here, we sampled peat profiles at three different depths (10-20, 30-40 and 60-70 cm) from two typical peatlands in China: a rich fen in Qinghai-Tibet Plateau (QTP) and a poor fen in the Changbai Mountains (CBM). We investigated the bacterial (16S rRNA) and fungal (ITS2) community composition and diversity with high-throughput sequencing and predicted the metagenome functioning with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). The results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most abundant bacterial phyla in the upper peat layer (10-20 cm) for both sites, with increasing abundance of Chloroflexi and Bacteroidetes down to the saturated zone (60-70 cm in CMB; 30-40 and 60-70 cm in QTP). For fungi, Ascomycota, Ciliophora and Basidiomycota were the most abundant phyla in both sites, with decreasing Ciliophora abundance down to the saturated zone. The α-diversity of both bacterial and fungal showed a decreasing trend with depth in QTP, with the largest diversity occurring at the depth of 30-40 cm in CMB. Regardless of sampling sites, the bacterial communities at the depth of 60-70 cm were more similar than the other depths. The fungal community was clustered into two groups, corresponding to two sampling sites. The variation in fungal community with depth was larger in QTP than in CBM. The predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of amino acid, lipid and xenobiotics, as well as environmental adaptation, were decreased with depth in CBM, with energy metabolism showing the opposite trend. In contrast, the KO abundances of amino acid and lipid metabolism and environmental adaptation were the highest in the middle layer (30-40 cm) in QTP, where the KO abundance of energy metabolism was the lowest. In general, the difference in predicted metagenome functioning between sites was less obvious than between depths. These results highlight the important role of hydrology in shaping the microbial community in minerotrophic peatlands. The effect of environmental drivers on microbial diversity and functioning may be mediated by shifting in hydrological dynamics (e.g. land use change and desiccation) which should be considered under future global change condition.

Reef fish communities are spooked by scuba surveys and may take hours to recover

PubMed Central

Cheal, Alistair J.; Miller, Ian R.

2018-01-01

Ecological monitoring programs typically aim to detect changes in the abundance of species of conservation concern or which reflect system status. Coral reef fish assemblages are functionally important for reef health and these are most commonly monitored using underwater visual surveys (UVS) by divers. In addition to estimating numbers, most programs also collect estimates of fish lengths to allow calculation of biomass, an important determinant of a fish’s functional impact. However, diver surveys may be biased because fishes may either avoid or are attracted to divers and the process of estimating fish length could result in fish counts that differ from those made without length estimations. Here we investigated whether (1) general diver disturbance and (2) the additional task of estimating fish lengths affected estimates of reef fish abundance and species richness during UVS, and for how long. Initial estimates of abundance and species richness were significantly higher than those made on the same section of reef after diver disturbance. However, there was no evidence that estimating fish lengths at the same time as abundance resulted in counts different from those made when estimating abundance alone. Similarly, there was little consistent bias among observers. Estimates of the time for fish taxa that avoided divers after initial contact to return to initial levels of abundance varied from three to 17 h, with one group of exploited fishes showing initial attraction to divers that declined over the study period. Our finding that many reef fishes may disperse for such long periods after initial contact with divers suggests that monitoring programs should take great care to minimise diver disturbance prior to surveys. PMID:29844998

[Vital traits of woody species in High Andean forest edges of the Cogua Forest Reserve (Colombia)].

PubMed

Montenegro, Alba Lucía; Vargas, Orlando

2008-06-01

The Cogua Forest Reserve was studied throughout eight months to detect the existence of functional species-groups associated with edge wood forest. A second goal was to determine which species were the most successful in edge areas and their particular vital traits. The regeneration and growth of the forest patches to the adjacent matrix depends on the establishment of these species and their tolerance to both habitats. Three types of High Andean edge forest were studied. Two forest patches were chosen for each of the three edge types: Chusquea scandens edge, "paramune" and old-edge; the name of the latter was given because of its advanced successional state. In each patch, the vegetation was evaluated in two 60 m transects perpendicular to the edge and along the matrix-edge-interior gradient of the forest. All woody species were identified and counted to determine their abundance. A total of nine species were chosen as representative of High Andean forest edges in the reserve, because of their high abundance in this environment, their presence in both patches of each edge type and their ability to colonize the adjacent matrix. Each species was evaluated using 20 vital attributes of individual, leaf, and reproductive traits. Six species groups were found through a Correspondence Analysis. However, all nine species have high variation and plasticity levels for the attributes, even inside the groups. This trend suggests that while they are not clearly differentiated functional groups, they probably are representing different strategies within a single functional group of great plasticity. Tibouchina grossa and Pentacalia Pulchella are found in all edge and matrix types; the other species are found in all edge types, except by Gaiadendron punctatum and Weinmannia tomentosa, absent in the Chusquea scandens edge. All nine species are important elements in the restoration of forest edges, mainly where they are more abundant, evidencing their success in the particular conditions of an edge type. Miconia ligustrina and M. squamulosa are the most relevant species in the Chusquea scandens edge and matrix; while G. punctatum, P. pulchella, W. tomentosa, W. balbisiana and especially Macleania rupestris, are more important in the paramune edge and matrix; Hedyosmum bonplandianum is more important in the edge than in the matrix regeneration, while T. grossa is the most successful edge and matrix regeneration species, because it is the most abundant and has high levels of tolerance, vegetative reproduction and litter production. These features are related with a high rate of tissue replacement, as well as a persistent seed bank with smaller and more numerous seeds, evidence of its high fecundity.

The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups

PubMed Central

2013-01-01

Background WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species. Results We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. Conclusions In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. PMID:24088323

Zooplankton From a Reef System Under the Influence of the Amazon River Plume

PubMed Central

Neumann-Leitão, Sigrid; Melo, Pedro A. M. C.; Schwamborn, Ralf; Diaz, Xiomara F. G.; Figueiredo, Lucas G. P.; Silva, Andrea P.; Campelo, Renata P. S.; de Melo Júnior, Mauro; Melo, Nuno F. A. C.; Costa, Alejandro E. S. F.; Araújo, Moacyr; Veleda, Dóris R. A.; Moura, Rodrigo L.; Thompson, Fabiano

2018-01-01

At the mouth of the Amazon River, a widespread carbonate ecosystem exists below the river plume, generating a hard-bottom reef (∼9500 km2) that includes mainly large sponges but also rhodolith beds. The mesozooplankton associated with the pelagic realm over the reef formation was characterized, considering the estuarine plume and oceanic influence. Vertical hauls were carried out using a standard plankton net with 200 μm mesh size during September 2014. An indicator index was applied to express species importance as ecological indicators in community. Information on functional traits was gathered for the most abundant copepod species. Overall, 179 zooplankton taxa were recorded. Copepods were the richest (92 species), most diverse and most abundant group, whereas meroplankton were rare and less abundant. Species diversity (>3.0 bits.ind-1) and evenness (>0.6) were high, indicating a complex community. Small holoplanktonic species dominated the zooplankton, and the total density varied from 107.98 ind. m-3 over the reef area to 2,609.24 ind. m-3 in the estuarine plume, with a significant difference between coastal and oceanic areas. The most abundant copepods were the coastal species ithona plumifera and Clausocalanus furcatus and early stages copepodites of Paracalanidae. The holoplanktonic Oikopleura, an important producer of mucous houses, was very abundant on the reefs. The indicator species index revealed three groups: (1) indicative of coastal waters under the influence of the estuarine plume [Euterpina acutifrons, Parvocalanus crassirostris, Oikopleura (Vexillaria) dioica and Hydromedusae]; (2) characterized coastal and oceanic conditions (Clausocalanus); (3) characterized the reef system (O. plumifera). Two major copepods functional groups were identified and sorted according to their trophic strategy and coastal-oceanic distribution. The species that dominated the coastal area and the area over the rhodolith beds are indicators of the estuarine plume and are mixed with species of the North Brazil Current. These species practically disappear offshore, where occur oceanic species commonly found in other oligotrophic tropical areas. This ecosystem shows a mixture of estuarine, coastal and oceanic communities coexisting in the waters over the Amazon reefs, with no significant differences among these areas. However, the MDS clearly separated the communities along the salinity gradient in the plume. PMID:29545783

Consistent patterns of variation in macrobenthic assemblages and environmental variables over multiple spatial scales using taxonomic and functional approaches.

PubMed

Veiga, Puri; Torres, Ana Catarina; Aneiros, Fernando; Sousa-Pinto, Isabel; Troncoso, Jesús S; Rubal, Marcos

2016-09-01

Spatial variability of environmental factors and macrobenthos, using species and functional groups, was examined over the same scales (100s of cm to >100 km) in intertidal sediments of two transitional water systems. The objectives were to test if functional groups were a good species surrogate and explore the relationship between environmental variables and macrobenthos. Environmental variables, diversity and the multivariate assemblage structure showed the highest variability at the scale of 10s of km. However, abundance was more variable at 10s of m. Consistent patterns were achieved using species and functional groups therefore, these may be a good species surrogate. Total carbon, salinity and silt/clay were the strongest correlated with macrobenthic assemblages. Results are valuable for design and interpretation of future monitoring programs including detection of anthropogenic disturbances in transitional systems and propose improvements in environmental variable sampling to refine the assessment of their relationship with biological data across spatial scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

Book review: A new view on the species abundance distribution

USGS Publications Warehouse

DeAngelis, Donald L.

2018-01-01

The sampled relative abundances of species of a taxonomic group, whether birds, trees, or moths, in a natural community at a particular place vary in a way that suggests a consistent underlying pattern, referred to as the species abundance distribution (SAD). Preston [1] conjectured that the numbers of species, plotted as a histogram of logarithmic abundance classes called octaves, seemed to fit a lognormal distribution; that is, the histograms look like normal distributions, although truncated on the left-hand, or low-species-abundance, end. Although other specific curves for the SAD have been proposed in the literature, Preston’s lognormal distribution is widely cited in textbooks and has stimulated attempts at explanation. An important aspect of Preston’s lognormal distribution is the ‘veil line’, a vertical line drawn exactly at the point of the left-hand truncation in the distribution, to the left of which would be species missing from the sample. Dewdney rejects the lognormal conjecture. Instead, starting with the long-recognized fact that the number of species sampled from a community, when plotted as histograms against population abundance, resembles an inverted J, he presents a mathematical description of an alternative that he calls the ‘J distribution’, a hyperbolic density function truncated at both ends. When multiplied by species richness, R, it becomes the SAD of the sample.

Microorganisms associated with feathers of barn swallows in radioactively contaminated areas around chernobyl.

PubMed

Czirják, Gábor Arpád; Møller, Anders Pape; Mousseau, Timothy A; Heeb, Philipp

2010-08-01

The Chernobyl catastrophe provides a rare opportunity to study the ecological and evolutionary consequences of low-level, environmental radiation on living organisms. Despite some recent studies about negative effects of environmental radiation on macroorganisms, there is little knowledge about the effect of radioactive contamination on diversity and abundance of microorganisms. We examined abundance patterns of total cultivable bacteria and fungi and the abundance of feather-degrading bacterial subset present on feathers of barn swallows (Hirundo rustica), a colonial migratory passerine, around Chernobyl in relation to levels of ground level environmental radiation. After controlling for confounding variables, total cultivable bacterial loads were negatively correlated with environmental radioactivity, whereas abundance of fungi and feather-degrading bacteria was not significantly related to contamination levels. Abundance of both total and feather-degrading bacteria increased with barn swallow colony size, showing a potential cost of sociality. Males had lower abundance of feather-degrading bacteria than females. Our results show the detrimental effects of low-level environmental radiation on total cultivable bacterial assemblage on feathers, while the abundance of other microorganism groups living on barn swallow feathers, such as feather-degrading bacteria, are shaped by other factors like host sociality or host sex. These data lead us to conclude that the ecological effects of Chernobyl may be more general than previously assumed and may have long-term implications for host-microbe interactions and overall ecosystem functioning.

Decomposition Dynamics and Changes in Chemical Composition of Wheat Straw Residue under Anaerobic and Aerobic Conditions

PubMed Central

Gao, Hongjian; Chen, Xi; Wei, Junling; Zhang, Yajie; Zhang, Ligan; Chang, Jiang; Thompson, Michael L.

2016-01-01

Soil aeration is a crucial factor that regulates crop residue decomposition, and the chemical composition of decomposing crop residues may change the forms and availability of soil nutrients, such as N and P. However, to date, differences in the chemical composition of crop straw residues after incorporation into soil and during its decomposition under anaerobic vs. aerobic conditions have not been well documented. The objective of the present study was to assess changes in the C-containing functional groups of wheat straw residue during its decomposition in anaerobic and aerobic environments. A 12-month incubation experiment was carried out to investigate the temporal variations of mass, carbon, and nitrogen loss, as well as changes in the chemical composition of wheat (Triticum aestivum L) straw residues under anaerobic and aerobic conditions by measuring C-containing functional groups using solid state nuclear magnetic resonance (NMR) spectroscopy. The residual mass, carbon content, and nitrogen content of the straw residue sharply declined during the initial 3 months, and then slowly decreased during the last incubation period from 3 to 12 months. The decomposition rate constant (k) for mass loss under aerobic conditions (0.022 d-1) was higher than that under anaerobic conditions (0.014 d-1). The residual mass percentage of cellulose and hemicellulose in the wheat straw gradually declined, whereas that of lignin gradually increased during the entire 12-month incubation period. The NMR spectra of C-containing functional groups in the decomposing straw under both aerobic and anaerobic conditions were similar at the beginning of the incubation as well as at 1 month, 6 months, and 12 months. The main alterations in C-containing functional groups during the decomposition of wheat straw were a decrease in the relative abundances of O-alkyl C and an increase in the relative abundances of alkyl C, aromatic C and COO/N-C = O functional groups. The NMR signals of alkyl C and aromatic C in decomposing wheat straw residues under anaerobic condition were higher than those under aerobic conditions. The higher mass percentages of lignin and the higher signals of aromatic C and alkyl C functional groups in decomposing wheat residues under anaerobic conditions than under aerobic conditions were due to the slower decomposition rates of aryl C and alkyl C in wheat straw residues under anaerobic conditions. PMID:27380023

Finger millet bran supplementation alleviates obesity-induced oxidative stress, inflammation and gut microbial derangements in high-fat diet-fed mice.

PubMed

Murtaza, Nida; Baboota, Ritesh K; Jagtap, Sneha; Singh, Dhirendra P; Khare, Pragyanshu; Sarma, Siddhartha M; Podili, Koteswaraiah; Alagesan, Subramanian; Chandra, T S; Bhutani, K K; Boparai, Ravneet K; Bishnoi, Mahendra; Kondepudi, Kanthi Kiran

2014-11-14

Several epidemiological studies have shown that the consumption of finger millet (FM) alleviates diabetes-related complications. In the present study, the effect of finger millet whole grain (FM-WG) and bran (FM-BR) supplementation was evaluated in high-fat diet-fed LACA mice for 12 weeks. Mice were divided into four groups: control group fed a normal diet (10 % fat as energy); a group fed a high-fat diet; a group fed the same high-fat diet supplemented with FM-BR; a group fed the same high-fat diet supplemented with FM-WG. The inclusion of FM-BR at 10 % (w/w) in a high-fat diet had more beneficial effects than that of FM-WG. FM-BR supplementation prevented body weight gain, improved lipid profile and anti-inflammatory status, alleviated oxidative stress, regulated the expression levels of several obesity-related genes, increased the abundance of beneficial gut bacteria (Lactobacillus, Bifidobacteria and Roseburia) and suppressed the abundance of Enterobacter in caecal contents (P≤ 0·05). In conclusion, FM-BR supplementation could be an effective strategy for preventing high-fat diet-induced changes and developing FM-BR-enriched functional foods.

Atom-efficient regioselective 1,2-dearomatization of functionalized pyridines by an earth-abundant organolanthanide catalyst

NASA Astrophysics Data System (ADS)

Dudnik, Alexander S.; Weidner, Victoria L.; Motta, Alessandro; Delferro, Massimiliano; Marks, Tobin J.

2014-12-01

Developing earth-abundant, non-platinum metal catalysts for high-value chemical transformations is a critical challenge to contemporary chemical synthesis. Dearomatization of pyridine derivatives is an important transformation to access a wide range of valuable nitrogenous natural products, pharmaceuticals and materials. Here, we report an efficient 1,2-regioselective organolanthanide-catalysed pyridine dearomatization process using pinacolborane, which is compatible with a broad range of pyridines and functional groups and employs equimolar reagent stoichiometry. Regarding the mechanism, derivation of the rate law from NMR spectroscopic and kinetic measurements suggests first order in catalyst concentration, fractional order in pyridine concentration and inverse first order in pinacolborane concentration, with C=N insertion into the La-H bond as turnover-determining. An energetic span analysis affords a more detailed understanding of experimental activity trends and the unusual kinetic behaviour, and proposes the catalyst ‘resting’ state and potential deactivation pathways.

Hunting for low abundant redox proteins in plant plasma membranes.

PubMed

Lüthje, Sabine; Hopff, David; Schmitt, Anna; Meisrimler, Claudia-Nicole; Menckhoff, Ljiljana

2009-04-13

Nowadays electron transport (redox) systems in plasma membranes appear well established. Members of the flavocytochrome b family have been identified by their nucleotide acid sequences and characterized on the transcriptional level. For their gene products functions have been demonstrated in iron uptake and oxidative stress including biotic interactions, abiotic stress factors and plant development. In addition, NAD(P)H-dependent oxidoreductases and b-type cytochromes have been purified and characterized from plasma membranes. Several of these proteins seem to belong to the group of hypothetical or unknown proteins. Low abundance and the lack of amino acid sequence data for these proteins still hamper their functional analysis. Consequently, little is known about the physiological function and regulation of these enzymes. In recent years evidence has been presented for the existence of microdomains (so-called lipid rafts) in plasma membranes and their interaction with specific membrane proteins. The identification of redox systems in detergent insoluble membranes supports the idea that redox systems may have important functions in signal transduction, stress responses, cell wall metabolism, and transport processes. This review summarizes our present knowledge on plasma membrane redox proteins and discusses alternative strategies to investigate the function and regulation of these enzymes.

Severe plant invasions can increase mycorrhizal fungal abundance and diversity.

PubMed

Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

2013-07-01

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)--but not cheatgrass (Bromus tectorum)--support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance.

Severe plant invasions can increase mycorrhizal fungal abundance and diversity

PubMed Central

Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

2013-01-01

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)—but not cheatgrass (Bromus tectorum)—support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance. PMID:23486251

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

PubMed Central

Li, Fuyong

2017-01-01

ABSTRACT Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation. IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions. PMID:28235871

Letrozole, an aromatase inhibitor, reduces post-peak age-related regression of rooster reproductive performance.

PubMed

Ali, Emad Abdulgabbar; Zhandi, Mahdi; Towhidi, Armin; Zaghari, Mojtaba; Ansari, Mahdi; Najafi, Mojtaba; Deldar, Hamid

2017-08-01

This study was designed to evaluate orally administrated Letrozole (Lz) on reproductive performance, plasma testosterone and estradiol concentrations and relative abundance of mRNA of GnRH, FSH and LH in roosters. Ross 308 roosters (n=32) that were 40-weeks of age were individually housed and received a basal standard diet supplemented different amounts of capsulated Lz [0 (Lz-0), 0.5 (Lz-0.5), 1 (Lz-1) or 1.5 (Lz-1.5), mg Lz/bird/day] for 12 weeks. Sperm quality variables and plasma testosterone and estradiol concentrations were assessed from the first to the tenth week of the treatment period. Semen samples from the 11th to 12th week were used for artificial insemination and eggs were collected and allotted to assess fertility and hatchability rates. Relative abundance of hypothalamic and pituitary GnRH, LH and FSH mRNA was evaluated at the end of 12th week. The results indicated that total and forward sperm motility as well as egg hatchability rate were greater in the Lz-0.5 group. Greater sperm concentrations, ejaculate volume, sperm plasma membrane integrity, testis index and fertility rates were recorded for both Lz-0.5 and Lz-1 groups compared with the Lz-0 group (P<0.05). Body weight, percentage of sperm abnormalities, and sperm plasma membrane functionality were not affected by treatment. Testosterone and estradiol concentrations were negatively related with greater testosterone concentrations in the Lz-1.5 group which had lesser estradiol concentrations. Relative mRNA transcript abundance for GnRH, LH and FSH was Lz dose responsive being greater in the treated groups; however, this trend plateaued for GnRH and for the relative abundance of both LH and FSH mRNA was less in the Lz-1.5 group than the other treatment groups. It is concluded that Lz may be an effective treatment to improve age related post-peak reproductive performance of roosters. Copyright © 2017 Elsevier B.V. All rights reserved.

Probing the carbonyl functionality of a petroleum resin and asphaltene through oximation and schiff base formation in conjunction with N-15 NMR

USGS Publications Warehouse

Thorn, Kevin A.; Cox, Larry G.

2015-01-01

Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock.

PubMed

Jiao, Shengyin; Cao, Hui; Dai, Yue; Wu, Junhui; Lv, Jia; Du, Renjia; Han, Bei

2017-11-01

This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets. Fecal samples were collected from 6-, 12-, 18- and 24-month cattle fed high-fat diet, and healthy female parents fed regular diet. Total DNA was amplified (V3-V4 of 16S rRNA) and submitted to barcode-DNA pyrosequencing. Intestinal microbiota profiles and functions were then analyzed. A total of 114 512 operational taxonomic units were detected from the 1 802 243 sequences obtained. In 6-month-old and female parent groups, the top three abundant phyla were Bacteroidetes (37.6%, 32.2%), Firmicutes (34.4%, 48.2%) and Proteobacteria (9.1%, 6.3%); in the 12-, 18- and 24-month groups, they were Proteobacteria (45.5%, 47.1%, 38.8%), Firmicutes (27.4%, 22.2%, 20.1%) and Bacteroidetes (14.9%, 19.4%, 17.7%), respectively. Paludibacter and Desulfopila in abundance showed negative (P < 0.001) and positive (P < 0.05) correlation, respectively, to cattle weight gain through metagenomic functional prediction of methane, cysteine and methionine metabolism. Meanwhile, cofactor/vitamin and amino acid metabolic processes were significantly higher in bacteria from the regular diet group than high-fat diet groups, with markedly lower cellular processes and signaling, and reduced glycan biosynthesis and metabolism (P < 0.01). The 6-month cattle and female parents shared similar intestinal bacteria; the community structure of fecal microbiota was significantly affected by high-fat diet in older cattle. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Development of a diverse epiphyte community in response to phosphorus fertilization.

PubMed

Benner, Jon W; Vitousek, Peter M

2007-07-01

The role of terrestrial soil nutrient supply in determining the composition and productivity of epiphyte communities has been little investigated. In a montane Hawaiian rainforest, we documented dramatic increases in the abundance and species richness of canopy epiphytes in a forest that had been fertilized annually with phosphorus (P) for 15 years; there was no response in forest that had been fertilized with nitrogen (N) or other nutrients. The response of N-fixing lichens to P fertilization was particularly strong, although mosses and non-N-fixing lichens also increased in abundance and diversity. We show that enhancement of canopy P availability is the most likely factor driving the bloom in epiphytes. These results provide strong evidence that terrestrial soil fertility may structure epiphyte communities, and in particular that the abundance of N-fixing lichens--a functionally important epiphyte group--may be particularly sensitive to ecosystem P availability.

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

Impacts of an Invasive Non-Native Annual Weed, Impatiens glandulifera, on Above- and Below-Ground Invertebrate Communities in the United Kingdom

PubMed Central

Tanner, Robert A.; Varia, Sonal; Eschen, René; Wood, Suzy; Murphy, Sean T.; Gange, Alan C.

2013-01-01

Vegetation community composition and the above- and below-ground invertebrate communities are linked intrinsically, though few studies have assessed the impact of non-native plants on both these parts of the community together. We evaluated the differences in the above- (foliage- and ground-dwelling) and below-ground invertebrate communities in nine uninvaded plots and nine plots invaded by the annual invasive species Impatiens glandulifera, in the UK during 2007 and 2008. Over 139,000 invertebrates were identified into distinct taxa and categorised into functional feeding groups. The impact of I. glandulifera on the vegetation and invertebrate community composition was evaluated using multivariate statistics including principal response curves (PRC) and redundancy analysis (RDA). In the foliage-dwelling community, all functional feeding groups were less abundant in the invaded plots, and the species richness of Coleoptera and Heteroptera was significantly reduced. In the ground-dwelling community, herbivores, detritivores, and predators were all significantly less abundant in the invaded plots. In contrast, these functional groups in the below-ground community appeared to be largely unaffected, and even positively associated with the presence of I. glandulifera. Although the cover of I. glandulifera decreased in the invaded plots in the second year of the study, only the below-ground invertebrate community showed a significant response. These results indicate that the above- and below-ground invertebrate communities respond differently to the presence of I. glandulifera, and these community shifts can potentially lead to a habitat less biologically diverse than surrounding native communities; which could have negative impacts on higher trophic levels and ecosystem functioning. PMID:23840648

Pollen Deposition Is More Important than Species Richness for Seed Set in Luffa Gourd.

PubMed

Ali, M; Saeed, S; Sajjad, A

2016-10-01

In the context of global biodiversity decline, it is imperative to understand the different aspects of bee communities for sustaining the vital ecosystem service of pollination. Bee species can be assigned to functional groups (average difference among species in functionally related traits) on the basis of complementarity (trait variations exhibited by individual organisms) in their behavior but is not yet known which functional group trait is most important for seed set. In this study, first, the functional groups of bees were made based on their five selected traits (pollen deposition, visitation rate, stay time, visiting time of the day, body size) and then related to the seed set of obligate cross-pollinated Luffa gourd (Luffa aegyptiaca). We found that bee diversity and abundance differed significantly among the studied plots, but only the bee species richness was positively related to the seed set. Functional group diversity in terms of pollen deposition explained even more of the variance in seed set (r 2  = 0.74) than did the species richness (r 2  = 0.53) making it the most important trait of bee species for predicting the crop reproductive success.

Is Response to Fire Influenced by Dietary Specialization and Mobility? A Comparative Study with Multiple Animal Assemblages

PubMed Central

Bros, Vicenç; Brotons, Lluís; De Mas, Eva; Herraiz, Joan A.; Herrando, Sergi; Miño, Àngel; Olmo-Vidal, Josep M.; Quesada, Javier; Ribes, Jordi; Sabaté, Santiago; Sauras-Yera, Teresa; Serra, Antoni; Vallejo, V. Ramón; Viñolas, Amador

2014-01-01

Fire is a major agent involved in landscape transformation and an indirect cause of changes in species composition. Responses to fire may vary greatly depending on life histories and functional traits of species. We have examined the taxonomic and functional responses to fire of eight taxonomic animal groups displaying a gradient of dietary and mobility patterns: Gastropoda, Heteroptera, Formicidae, Coleoptera, Araneae, Orthoptera, Reptilia and Aves. The fieldwork was conducted in a Mediterranean protected area on 3 sites (one unburnt and two burnt with different postfire management practices) with five replicates per site. We collected information from 4606 specimens from 274 animal species. Similarity in species composition and abundance between areas was measured by the Bray-Curtis index and ANOSIM, and comparisons between animal and plant responses by Mantel tests. We analyze whether groups with the highest percentage of omnivorous species, these species being more generalist in their dietary habits, show weak responses to fire (i.e. more similarity between burnt and unburnt areas), and independent responses to changes in vegetation. We also explore how mobility, i.e. dispersal ability, influences responses to fire. Our results demonstrate that differences in species composition and abundance between burnt and unburnt areas differed among groups. We found a tendency towards presenting lower differences between areas for groups with higher percentages of omnivorous species. Moreover, taxa with a higher percentage of omnivorous species had significantly more independent responses of changes in vegetation. High- (e.g. Aves) and low-mobility (e.g. Gastropoda) groups had the strongest responses to fire (higher R scores of the ANOSIM); however, we failed to find a significant general pattern with all the groups according to their mobility. Our results partially support the idea that functional traits underlie the response of organisms to environmental changes caused by fire. PMID:24516616

Is response to fire influenced by dietary specialization and mobility? A comparative study with multiple animal assemblages.

PubMed

Santos, Xavier; Mateos, Eduardo; Bros, Vicenç; Brotons, Lluís; De Mas, Eva; Herraiz, Joan A; Herrando, Sergi; Miño, Àngel; Olmo-Vidal, Josep M; Quesada, Javier; Ribes, Jordi; Sabaté, Santiago; Sauras-Yera, Teresa; Serra, Antoni; Vallejo, V Ramón; Viñolas, Amador

2014-01-01

Fire is a major agent involved in landscape transformation and an indirect cause of changes in species composition. Responses to fire may vary greatly depending on life histories and functional traits of species. We have examined the taxonomic and functional responses to fire of eight taxonomic animal groups displaying a gradient of dietary and mobility patterns: Gastropoda, Heteroptera, Formicidae, Coleoptera, Araneae, Orthoptera, Reptilia and Aves. The fieldwork was conducted in a Mediterranean protected area on 3 sites (one unburnt and two burnt with different postfire management practices) with five replicates per site. We collected information from 4606 specimens from 274 animal species. Similarity in species composition and abundance between areas was measured by the Bray-Curtis index and ANOSIM, and comparisons between animal and plant responses by Mantel tests. We analyze whether groups with the highest percentage of omnivorous species, these species being more generalist in their dietary habits, show weak responses to fire (i.e. more similarity between burnt and unburnt areas), and independent responses to changes in vegetation. We also explore how mobility, i.e. dispersal ability, influences responses to fire. Our results demonstrate that differences in species composition and abundance between burnt and unburnt areas differed among groups. We found a tendency towards presenting lower differences between areas for groups with higher percentages of omnivorous species. Moreover, taxa with a higher percentage of omnivorous species had significantly more independent responses of changes in vegetation. High- (e.g. Aves) and low-mobility (e.g. Gastropoda) groups had the strongest responses to fire (higher R scores of the ANOSIM); however, we failed to find a significant general pattern with all the groups according to their mobility. Our results partially support the idea that functional traits underlie the response of organisms to environmental changes caused by fire.

Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates

PubMed Central

Szabó, Enikö; Liébana, Raquel; Hermansson, Malte; Modin, Oskar; Persson, Frank; Wilén, Britt-Marie

2017-01-01

The granular sludge process is an effective, low-footprint alternative to conventional activated sludge wastewater treatment. The architecture of the microbial granules allows the co-existence of different functional groups, e.g., nitrifying and denitrifying communities, which permits compact reactor design. However, little is known about the factors influencing community assembly in granular sludge, such as the effects of reactor operation strategies and influent wastewater composition. Here, we analyze the development of the microbiomes in parallel laboratory-scale anoxic/aerobic granular sludge reactors operated at low (0.9 kg m-3d-1), moderate (1.9 kg m-3d-1) and high (3.7 kg m-3d-1) organic loading rates (OLRs) and the same ammonium loading rate (0.2 kg NH4-N m-3d-1) for 84 days. Complete removal of organic carbon and ammonium was achieved in all three reactors after start-up, while the nitrogen removal (denitrification) efficiency increased with the OLR: 0% at low, 38% at moderate, and 66% at high loading rate. The bacterial communities at different loading rates diverged rapidly after start-up and showed less than 50% similarity after 6 days, and below 40% similarity after 84 days. The three reactor microbiomes were dominated by different genera (mainly Meganema, Thauera, Paracoccus, and Zoogloea), but these genera have similar ecosystem functions of EPS production, denitrification and polyhydroxyalkanoate (PHA) storage. Many less abundant but persistent taxa were also detected within these functional groups. The bacterial communities were functionally redundant irrespective of the loading rate applied. At steady-state reactor operation, the identity of the core community members was rather stable, but their relative abundances changed considerably over time. Furthermore, nitrifying bacteria were low in relative abundance and diversity in all reactors, despite their large contribution to nitrogen turnover. The results suggest that the OLR has considerable impact on the composition of the granular sludge communities, but also that the granule communities can be dynamic even at steady-state reactor operation due to high functional redundancy of several key guilds. Knowledge about microbial diversity with specific functional guilds under different operating conditions can be important for engineers to predict the stability of reactor functions during the start-up and continued reactor operation. PMID:28507540

Technical note: Relating functional group measurements to carbon types for improved model-measurement comparisons of organic aerosol composition

NASA Astrophysics Data System (ADS)

Takahama, Satoshi; Ruggeri, Giulia

2017-04-01

Functional group (FG) analysis provides a means by which functionalization in organic aerosol can be attributed to the abundances of its underlying molecular structures. However, performing this attribution requires additional, unobserved details about the molecular mixture to provide constraints in the estimation process. We present an approach for conceptualizing FG measurements of organic aerosol in terms of its functionalized carbon atoms. This reformulation facilitates estimation of mass recovery and biases in popular carbon-centric metrics that describe the extent of functionalization (such as oxygen to carbon ratio, organic mass to organic carbon mass ratio, and mean carbon oxidation state) for any given set of molecules and FGs analyzed. Furthermore, this approach allows development of parameterizations to more precisely estimate the organic carbon content from measured FG abundance. We use simulated photooxidation products of α-pinene secondary organic aerosol previously reported by Ruggeri et al. (2016) and FG measurements by Fourier transform infrared (FT-IR) spectroscopy in chamber experiments by Sax et al. (2005) to infer the relationships among molecular composition, FG composition, and metrics of organic aerosol functionalization. We find that for this simulated system, ˜ 80 % of the carbon atoms should be detected by FGs for which calibration models are commonly developed, and ˜ 7 % of the carbon atoms are undetectable by FT-IR analysis because they are not associated with vibrational modes in the infrared. Estimated biases due to undetected carbon fraction for these simulations are used to make adjustments in these carbon-centric metrics such that model-measurement differences are framed in terms of unmeasured heteroatoms (e.g., in hydroperoxide and nitrate groups for the case studied in this demonstration). The formality of this method provides framework for extending FG analysis to not only model-measurement but also instrument intercomparisons in other chemical systems.

Stellar Abundances for Galactic Archaeology Database. IV. Compilation of stars in dwarf galaxies

NASA Astrophysics Data System (ADS)

Suda, Takuma; Hidaka, Jun; Aoki, Wako; Katsuta, Yutaka; Yamada, Shimako; Fujimoto, Masayuki Y.; Ohtani, Yukari; Masuyama, Miyu; Noda, Kazuhiro; Wada, Kentaro

2017-10-01

We have constructed a database of stars in Local Group galaxies using the extended version of the SAGA (Stellar Abundances for Galactic Archaeology) database that contains stars in 24 dwarf spheroidal galaxies and ultra-faint dwarfs. The new version of the database includes more than 4500 stars in the Milky Way, by removing the previous metallicity criterion of [Fe/H] ≤ -2.5, and more than 6000 stars in the Local Group galaxies. We examined the validity of using a combined data set for elemental abundances. We also checked the consistency between the derived distances to individual stars and those to galaxies as given in the literature. Using the updated database, the characteristics of stars in dwarf galaxies are discussed. Our statistical analyses of α-element abundances show that the change of the slope of the [α/Fe] relative to [Fe/H] (so-called "knee") occurs at [Fe/H] = -1.0 ± 0.1 for the Milky Way. The knee positions for selected galaxies are derived by applying the same method. The star formation history of individual galaxies is explored using the slope of the cumulative metallicity distribution function. Radial gradients along the four directions are inspected in six galaxies where we find no direction-dependence of metallicity gradients along the major and minor axes. The compilation of all the available data shows a lack of CEMP-s population in dwarf galaxies, while there may be some CEMP-no stars at [Fe/H] ≲ -3 even in the very small sample. The inspection of the relationship between Eu and Ba abundances confirms an anomalously Ba-rich population in Fornax, which indicates a pre-enrichment of interstellar gas with r-process elements. We do not find any evidence of anti-correlations in O-Na and Mg-Al abundances, which characterizes the abundance trends in the Galactic globular clusters.

Decreased Functional Diversity and Biological Pest Control in Conventional Compared to Organic Crop Fields

PubMed Central

Krauss, Jochen; Gallenberger, Iris; Steffan-Dewenter, Ingolf

2011-01-01

Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid densities but long-term negative effects on biological pest control. Therefore conventional farmers should restrict insecticide applications to situations where thresholds for pest densities are reached. PMID:21611171

Decreased functional diversity and biological pest control in conventional compared to organic crop fields.

PubMed

Krauss, Jochen; Gallenberger, Iris; Steffan-Dewenter, Ingolf

2011-01-01

Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid densities but long-term negative effects on biological pest control. Therefore conventional farmers should restrict insecticide applications to situations where thresholds for pest densities are reached.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

More than 75 percent decline over 27 years in total flying insect biomass in protected areas

PubMed Central

Sorg, Martin; Jongejans, Eelke; Siepel, Henk; Hofland, Nick; Schwan, Heinz; Stenmans, Werner; Müller, Andreas; Sumser, Hubert; Hörren, Thomas; Goulson, Dave; de Kroon, Hans

2017-01-01

Global declines in insects have sparked wide interest among scientists, politicians, and the general public. Loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. Our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. Here, we used a standardized protocol to measure total insect biomass using Malaise traps, deployed over 27 years in 63 nature protection areas in Germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. Our analysis estimates a seasonal decline of 76%, and mid-summer decline of 82% in flying insect biomass over the 27 years of study. We show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. This yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the European landscape. PMID:29045418

Changes in fungal communities along a boreal forest soil fertility gradient.

PubMed

Sterkenburg, Erica; Bahr, Adam; Brandström Durling, Mikael; Clemmensen, Karina E; Lindahl, Björn D

2015-09-01

Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Maternal diets deficient in folic acid and related methyl donors modify mechanisms associated with lipid metabolism in the fetal liver of the rat.

PubMed

McNeil, Christopher J; Hay, Susan M; Rucklidge, Garry J; Reid, Martin D; Duncan, Gary J; Rees, William D

2009-11-01

Previously we have examined the effects of diets deficient in folic acid ( - F) or folate deficient with low methionine and choline ( - F LM LC) on the relative abundance of soluble proteins in the liver of the pregnant rat. In the present study we report the corresponding changes in the fetal liver at day 21 of gestation. The abundance of eighteen proteins increased when dams were fed the - F diet. When dams were fed the - F LM LC diet, thirty-three proteins increased and eight decreased. Many of the differentially abundant proteins in the fetal liver could be classified into the same functional groups as those previously identified in the maternal liver, namely protein synthesis, metabolism, lipid metabolism and proteins associated with the cytoskeleton and endoplasmic reticulum. The pattern was consistent with reduced cell proliferation in the - F LM LC group but not in the - F group. Metabolic enzymes associated with lipid metabolism changed in both the - F and - F LM LC groups. The mRNA for carnitine palmitoyl transferase were up-regulated and CD36 (fatty acid translocase) down-regulated in the - F group, suggesting increased mitochondrial oxidation of fatty acids as an indirect response to altered maternal lipid metabolism. In the - F LM LC group the mRNA for acetyl CoA carboxylase was down-regulated, suggesting reduced fatty acid synthesis. The mRNA for transcriptional regulators including PPARalpha and sterol response element-binding protein-1c were unchanged. These results suggest that an adequate supply of folic acid and the related methyl donors may benefit fetal development directly by improving lipid metabolism in fetal as well as maternal tissues.

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

PubMed

Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

2015-10-01

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

Chitosan-based multifunctional nanomedicines and theranostics for targeted therapy of cancer.

PubMed

Fathi, Marziyeh; Majidi, Sima; Zangabad, Parham Sahandi; Barar, Jaleh; Erfan-Niya, Hamid; Omidi, Yadollah

2018-05-30

Nanotechnology as an emerging field has established inevitable impacts on nano-biomedicine and treatment of formidable diseases, inflammations, and malignancies. In this regard, substantial advances in the design of systems for delivery of therapeutic agents have emerged magnificent and innovative pathways in biomedical applications. Chitosan (CS) is derived via deacetylation of chitin as the second most abundant polysaccharide. Owing to the unique properties of CS (e.g., biocompatibility, biodegradability, bioactivity, mucoadhesion, cationic nature and functional groups), it is an excellent candidate for diverse biomedical and pharmaceutical applications such as drug/gene delivery, transplantation of encapsulated cells, tissue engineering, wound healing, antimicrobial purposes, etc. In this review, we will document, discuss, and provide some key insights toward design and application of miscellaneous nanoplatforms based on CS. The CS-based nanosystems (NSs) can be employed as advanced drug delivery systems (DDSs) in large part due to their remarkable physicochemical and biological characteristics. The abundant functional groups of CS allow the facile functionalization in order to engineer multifunctional NSs, which can simultaneously incorporate therapeutic agents, molecular targeting, and diagnostic/imaging capabilities in particular against malignancies. These multimodal NSs can be literally translated into clinical applications such as targeted diagnosis and therapy of cancer because they offer minimal systemic toxicity and maximal cytotoxicity against cancer cells and tumors. The recent developments in the CS-based NSs functionalized with targeting and imaging agents prove CS as a versatile polymer in targeted imaging and therapy. © 2018 Wiley Periodicals, Inc.

Hybrid Amine-Functionalized Graphene Oxide as a Robust Bifunctional Catalyst for Atmospheric Pressure Fixation of Carbon Dioxide using Cyclic Carbonates.

PubMed

Saptal, Vitthal B; Sasaki, Takehiko; Harada, Kei; Nishio-Hamane, Daisuke; Bhanage, Bhalchandra M

2016-03-21

An environmentally-benign carbocatalyst based on amine-functionalized graphene oxide (AP-GO) was synthesized and characterized. This catalyst shows superior activity for the chemical fixation of CO2 into cyclic carbonates at the atmospheric pressure. The developed carbocatalyst exhibits superior activity owing to its large surface area with abundant hydrogen bonding donor (HBD) capability and the presence of well-defined amine functional groups. The presence of various HBD and amine functional groups on the graphene oxide (GO) surface yields a synergistic effect for the activation of starting materials. Additionally, this catalyst shows high catalytic activity to synthesize carbonates at 70 °C and at 1 MPa CO2 pressure. The developed AP-GO could be easily recovered and used repetitively in up to seven recycle runs with unchanged catalyst activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

PubMed Central

Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; McKain, Nest; Ross, Dave W.; Hyslop, Jimmy J.; Waterhouse, Anthony; Freeman, Tom C.

2016-01-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome. PMID:26891056

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

PubMed

Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

2016-02-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.

Potential functions of LEA proteins from the brine shrimp Artemia franciscana - anhydrobiosis meets bioinformatics.

PubMed

Janis, Brett; Uversky, Vladimir N; Menze, Michael A

2017-10-23

Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins, which are commonly found in plants and some animals. The brine shrimp Artemia franciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the Artemia LEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins. We show here that A. franciscana LEA proteins from different groups are more similar to each other than one originally expected, while functional differences among members of group three are possibly larger than commonly anticipated. Our data show that although these proteins are characterized by a large variety of forms and possible functions, as a general strategy, A. franciscana utilizes glassy matrix forming LEAs concurrently with proteins that more readily interact with binding partners. It is likely that the function(s) of both types, the matrix-forming and partner-binding LEA proteins, are regulated by changing water availability during desiccation.

Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria ▿†

PubMed Central

Constant, Philippe; Chowdhury, Soumitra Paul; Hesse, Laura; Pratscher, Jennifer; Conrad, Ralf

2011-01-01

Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H2 possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H2-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H2 oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 106 to 108 hhyL gene copies g (dry weight)−1. Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H2-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H2 oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H2 by soil, because high-affinity H2 oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur. PMID:21742924

Assessing the Response of Nematode Communities to Climate Change-Driven Warming: A Microcosm Experiment.

PubMed

Gingold, Ruth; Moens, Tom; Rocha-Olivares, Axayácatl

2013-01-01

Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for alternative diversity-ecosystem functioning relationships, such as the Rivets and the Idiosyncrasy Model.

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation

PubMed Central

Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

2016-01-01

Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface. PMID:26140532

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization

PubMed Central

Meneghine, Aylan K.; Nielsen, Shaun; Thomas, Torsten; Carareto Alves, Lucia Maria

2017-01-01

Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem. PMID:29267397

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

PubMed

Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

2016-02-01

Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

Distributions of ectomycorrhizal and foliar endophytic fungal communities associated with Pinus ponderosa along a spatially constrained elevation gradient.

PubMed

Bowman, Elizabeth A; Arnold, A Elizabeth

2018-04-01

Understanding distributions of plant-symbiotic fungi is important for projecting responses to environmental change. Many coniferous trees host ectomycorrhizal fungi (EM) in association with roots and foliar endophytic fungi (FE) in leaves. We examined how EM and FE associated with Pinus ponderosa each vary in abundance, diversity, and community structure over a spatially constrained elevation gradient that traverses four plant communities, 4°C in mean annual temperature, and 15 cm in mean annual precipitation. We sampled 63 individuals of Pinus ponderosa in 10 sites along a 635 m elevation gradient that encompassed a geographic distance of 9.8 km. We used standard methods to characterize each fungal group (amplified and sequenced EM from root tips; isolated and sequenced FE from leaves). Abundance and diversity of EM were similar across sites, but community composition and distributions of the most common EM differed with elevation (i.e., with climate, soil chemistry, and plant communities). Abundance and composition of FE did not differ with elevation, but diversity peaked in mid-to-high elevations. Our results suggest relatively tight linkages between EM and climate, soil chemistry, and plant communities. That FE appear less linked with these factors may speak to limitations of a culture-based approach, but more likely reflects the small spatial scale encompassed by our study. Future work should consider comparable methods for characterizing these functional groups, and additional transects to understand relationships of EM and FE to environmental factors that are likely to shift as a function of climate change. © 2018 Botanical Society of America.

LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles.

PubMed

Wise, Michael J

2003-10-29

The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties. Previous research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins. There is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones, via a role in DNA-binding. In general, non-globular and low-complexity proteins, such as the LEA proteins, pose particular challenges in determining their functions and modes of action. Rather than masking off and ignoring low-complexity domains, novel tools and tool combinations are needed which are capable of analysing such proteins in their entirety.

Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.

2013-10-01

To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differencesmore » in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.« less

[Functional diversity characteristics of canopy tree species of Jianfengling tropical montane rainforest on Hainan Island, China.

PubMed

Xu, Ge Xi; Shi, Zuo Min; Tang, Jing Chao; Liu, Shun; Ma, Fan Qiang; Xu, Han; Liu, Shi Rong; Li, Yi de

2016-11-18

Based on three 1-hm 2 plots of Jianfengling tropical montane rainforest on Hainan Island, 11 commom used functional traits of canopy trees were measured. After combining with topographical factors and trees census data of these three plots, we compared the impacts of weighted species abundance on two functional dispersion indices, mean pairwise distance (MPD) and mean nearest taxon distance (MNTD), by using single- and multi-dimensional traits, respectively. The relationship between functional richness of the forest canopies and species abundance was analyzed. We used a null model approach to explore the variations in standardized size effects of MPD and MNTD, which were weighted by species abundance and eliminated the influences of species richness diffe-rences among communities, and assessed functional diversity patterns of the forest canopies and their responses to local habitat heterogeneity at community's level. The results showed that variation in MPD was greatly dependent on the dimensionalities of functional traits as well as species abundance. The correlations between weighted and non-weighted MPD based on different dimensional traits were relatively weak (R=0.359-0.628). On the contrary, functional traits and species abundance had relatively weak effects on MNTD, which brought stronger correlations between weighted and non-weighted MNTD based on different dimensional traits (R=0.746-0.820). Functional dispersion of the forest canopies were generally overestimated when using non-weighted MPD and MNTD. Functional richness of the forest canopies showed an exponential relationship with species abundance (F=128.20; R 2 =0.632; AIC=97.72; P＜0.001), which might exist a species abundance threshold value. Patterns of functional diversity of the forest canopies based on different dimensional functional traits and their habitat responses showed variations in some degree. Forest canopies in the valley usually had relatively stronger biological competition, and functional diversity was higher than expected functional diversity randomized by null model, which indicated dispersed distribution of functional traits among canopy tree species in this habitat. However, the functional diversity of the forest canopies tended to be close or lower than randomization in the other habitat types, which demonstrated random or clustered distribution of the functional traits among canopy tree species.

Environmental Effects on the Metallicities of Early-Type Galaxies

NASA Technical Reports Server (NTRS)

Jones, Christine; Oliversen, Ronald J. (Technical Monitor)

2003-01-01

We have completed and published two papers based on research from this grant. Our first paper "SN IA Enrichment in Virgo Early-type Galaxies from ROSAT and ASCA Observations" was published in the Astrophysical Journal (vol 539,603) reported on the properties of nine X-ray bright elliptical galaxies in the Virgo cluster observed by ROSAT and ASCA. We measured iron abundance gradients as a function of radius in three galaxies. We found that the magnesium and silicon abundance gradients were in general flatter than those of iron. We suggest this is due to a metallicity dependence in the metal production rates of SN Ia's. We calculate SN Ia rates in the center of these galaxies that are comparable to those measured optically. Our second paper "ASCA Observations of Groups at Radii of Low Overdensity: Implications for Cosmic Preheating" also was published in the Astrophysical Journal (vol 578, 74). This paper reported on the ASCA spectroscopy of nine groups of galaxies. We found that the entropy profile in groups is driven by nongravitational heating processes, and could be explained by a short period of preheating by galactic winds.

Suppression of savanna ants alters invertebrate composition and influences key ecosystem processes.

PubMed

Parr, C L; Eggleton, P; Davies, A B; Evans, T A; Holdsworth, S

2016-06-01

In almost every ecosystem, ants (Hymenoptera: Formicidae) are the dominant terrestrial invertebrate group. Their functional value was highlighted by Wilson (1987) who famously declared that invertebrates are the "little things that run the world." However, while it is generally accepted that ants fulfil important functions, few studies have tested these assumptions and demonstrated what happens in their absence. We report on a novel large-scale field experiment in undisturbed savanna habitat where we examined how ants influence the abundance of other invertebrate taxa in the system, and affect the key processes of decomposition and herbivory. Our experiment demonstrated that ants suppressed the abundance and activity of beetles, millipedes, and termites, and also influenced decomposition rates and levels of herbivory. Our study is the first to show that top-down control of termites by ants can have important ecosystem consequences. Further studies are needed to elucidate the effects ant communities have on other aspects of the ecosystem (e.g., soils, nutrient cycling, the microbial community) and how their relative importance for ecosystem function varies among ecosystem types (e.g., savanna vs. forest).

Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.

PubMed

Perez-Rueda, Ernesto; Hernandez-Guerrero, Rafael; Martinez-Nuñez, Mario Alberto; Armenta-Medina, Dagoberto; Sanchez, Israel; Ibarra, J Antonio

2018-01-01

Gene regulation at the transcriptional level is a central process in all organisms, and DNA-binding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: the DNA-binding domain (DBD) and an extra domain, which in this work we have named "companion domain" (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: i) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as "promiscuous" families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.

Investigating the link between fish community structure and environmental state in deep-time

NASA Astrophysics Data System (ADS)

Sibert, E. C.

2017-12-01

In the modern ocean, a bottom-up ecological viewpoint posits that the composition of plankton communities is often a function of ambient oceanographic conditions, including nutrient concentrations and water temperature. Thus, certain plankton species or communities can be associated with specific oceanographic conditions, giving them potential as carriers of paleoceanographic information. Furthermore, consumer groups, such as fish, depend on the structure and composition of these plankton, and therefore different plankton communities will support different types of fish. In addition, fish have their own physiological constraints for surviving in particular environments, such as oxygen demand, and metabolic rate, causing certain clades to be selectively associated with different water mass characteristics. Thus, the relative or absolute abundances of different fish species or groups could shed light on shifting oxygen concentrations, temperature, or primary productivity in the past. To assess whether fish communities have sufficient environmental control to provide paleoceanographic insights, I use a variety of morphological, phylogenetic, and ecological statistical approaches, to correlate modern fish communities from around the world with environmental variables. I then apply these principles to a series of ichthyolith assemblages from the Cretaceous and Cenozoic, across both space and time, to assess whether fish community composition, abundance, or other characteristics can be predictive of ocean temperature or export productivity. I find that while the abundance of fish fossils in deep-sea cores is often, though not always, correlated with certain export production and temperature proxies, community composition appears to vary independently of these variables on long timescales, driven more by evolutionary processes. However, there are distinct differences in contemporary communities in different locations, suggesting that there is potential in using fish community composition in well-constrained systems. Furthermore, when fish community structure or abundance diverges from the expected state, this may provide significant insight into the structure and functioning of marine ecosystems.

Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA

Treesearch

Jozsef Geml; Gary A. Laursen; Ina Timling; Jack M. McFarland; Michael G. Booth; Niall Lennon; Chad Nusbaum; D. Lee Taylor

2009-01-01

Despite the critical roles fungi play in the functioning of ecosystems, especially as symbionts of plants and recyclers of organic matter, their biodiversity is poorly known in high-latitude regions. In this paper, we discuss the molecular diversity of one of the most diverse and abundant groups of ectomycorrhizal fungi: the genus Lactarius Pers....

Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

PubMed Central

Sauder, Laura A; Peterse, Francien; Schouten, Stefan; Neufeld, Josh D

2012-01-01

The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creating an ammonia gradient along the flowpath. This RBC system provides a valuable experimental system for testing the hypothesis that ammonia concentration determines the relative abundance of AOA and AOB. The results demonstrate that AOA increased as ammonium decreased across the RBC flowpath, as indicated by qPCR for thaumarchaeal amoA and 16S rRNA genes, and core lipid (CL) and intact polar lipid (IPL) crenarchaeol abundances. Overall, there was a negative logarithmic relationship (R2 = 0.51) between ammonium concentration and the relative abundance of AOA amoA genes. A single AOA population was detected in the RBC biofilms; this phylotype shared low amoA and 16S rRNA gene homology with existing AOA cultures and enrichments. These results provide evidence that ammonia availability influences the relative abundances of AOA and AOB, and that AOA are abundant in some municipal wastewater treatment systems. PMID:22639927

Abundance matters: a field experiment testing the more individuals hypothesis for richness–productivity relationships

PubMed Central

Yee, D. A.; Juliano, S. A.

2007-01-01

The more individuals hypothesis (MIH) postulates that productivity increases species richness by increasing mean equilibrium population size, thereby reducing the probability of local extinction. We tested the MIH for invertebrates colonizing microcosms that simulated tree holes by manipulating productivity through additions of leaf or animal detritus and subsequently determining the relationships among richness, total abundance, abundance per species, and measures of productivity. We quantified productivity as the rate of microorganism protein synthesis, microorganism metabolic rate, nutrient ion concentration, and type and amount of detritus. Microcosms with animal detritus attracted more species, more individuals per species, and more total individuals than did microcosms with similar amounts of leaf detritus. Relationships between richness or abundance and productivity varied with date. Richness in June increased as a linear function of productivity, whereas the power function predicted by the MIH fit best in July. Abundance in June and July was best described by a power function of productivity, but the linear function predicted by the MIH fit best in September. Abundance per species was best described by a power function of productivity in June and July. Path analysis showed that the indirect effect of productivity through abundance on richness that is predicted by MIH was important in all months, and that direct links between productivity and richness were unnecessary. Our results support many of the predictions of the MIH, but they also suggest that the effects of abundance on richness may be more complex than expected. PMID:17401581

The microbial diversity, distribution, and ecology of permafrost in China: a review.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

2015-07-01

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

PubMed

Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

2016-01-01

Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally stressful conditions.

Temporal and spatial distribution of phytoplankton functional groups and role of environment factors in a deep subtropical reservoir

NASA Astrophysics Data System (ADS)

Li, Lei; Li, Qiuhua; Chen, Jing'an; Wang, Jingfu; Jiao, Shulin; Chen, Fengfeng

2017-09-01

Phytoplankton and environment factors were investigated in 2015 and phytoplankton functional groups were used to understand their temporal and spatial distribution and their driving factors in Wanfeng Reservoir. Seventeen functional groups (B, D, E, F, G, J, Lo, MP, P, S1, T, W1, W2, X1, X2, Xph, Y) were identified based on 34 species. The dominant groups were: J/B/P/D in dry season, X1/J/Xph/G/T in normal season and J in flood season. Phytoplankton abundance ranged from 5.33×104 cells/L to 3.65×107 cells/L, with the highest value occurring in flood season and lowest in dry season. The vertical profile of dominant groups showed little differentiation except for P, which dominated surface layers over 20 m as a result of mixing water masses and higher transparency during dry season. However, the surface waters presented higher values of phytoplankton abundance than other layers, possibly because of greater irradiance. The significant explaining variables and their ability to describe the spatial distribution of the phytoplankton community in RDA differed seasonally as follows: dry season, NH4-N, NO3-N, NO2-N, TN:TP ratio and transparency (SD); normal season, temperature (WT), water depth, TN, NH4-N and NO3-N; flood season, WT, water depth, NO3-N and NO2-N. Furthermore, nitrogen, water temperature, SD and water depth were significant variables explaining the variance of phytoplankton communities when datasets included all samples. The results indicated that water physical conditions and hydrology were important in phytoplankton community dynamics, and nitrogen was more important than phosphorus in modifying phytoplankton communities. Seasonal differences in the relationship between the environment and phytoplankton community should be considered in water quality management.

A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries

PubMed Central

Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

2014-01-01

The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm−2). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance. PMID:25366060

More than mere numbers: the impact of lethal control on the social stability of a top-order predator.

PubMed

Wallach, Arian D; Ritchie, Euan G; Read, John; O'Neill, Adam J

2009-09-02

Population control of socially complex species may have profound ecological implications that remain largely invisible if only their abundance is considered. Here we discuss the effects of control on a socially complex top-order predator, the dingo (Canis lupus dingo). Since European occupation of Australia, dingoes have been controlled over much of the continent. Our aim was to investigate the effects of control on their abundance and social stability. We hypothesized that dingo abundance and social stability are not linearly related, and proposed a theoretical model in which dingo populations may fluctuate between three main states: (A) below carrying capacity and socially fractured, (B) above carrying capacity and socially fractured, or (C) at carrying capacity and socially stable. We predicted that lethal control would drive dingoes into the unstable states A or B, and that relaxation of control would allow recovery towards C. We tested our predictions by surveying relative abundance (track density) and indicators of social stability (scent-marking and howling) at seven sites in the arid zone subject to differing degrees of control. We also monitored changes in dingo abundance and social stability following relaxation and intensification of control. Sites where dingoes had been controlled within the previous two years were characterized by low scent-marking activity, but abundance was similar at sites with and without control. Signs of social stability steadily increased the longer an area was allowed to recover from control, but change in abundance did not follow a consistent path. Comparison of abundance and stability among all sites and years demonstrated that control severely fractures social groups, but that the effect of control on abundance was neither consistent nor predictable. Management decisions involving large social predators must therefore consider social stability to ensure their conservation and ecological functioning.

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume.

PubMed

Li, Meng; Jain, Sunit; Baker, Brett J; Taylor, Chris; Dick, Gregory J

2014-01-01

Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

A Transgenic Transcription Factor (TaDREB3) in Barley Affects the Expression of MicroRNAs and Other Small Non-Coding RNAs

PubMed Central

Hackenberg, Michael; Shi, Bu-Jun; Gustafson, Perry; Langridge, Peter

2012-01-01

Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (|log2| >1). Furthermore, TaDREB3-derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley. PMID:22870277

Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

PubMed

Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

2013-10-01

The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

Few apparent short-term effects of elevated soil temperature and increased frequency of summer precipitation on the abundance and taxonomic diversity of desert soil micro- and meso-fauna

USGS Publications Warehouse

Darby, B.J.; Neher, D.A.; Housman, D.C.; Belnap, J.

2011-01-01

Frequent hydration and drying of soils in arid systems can accelerate desert carbon and nitrogen mobilization due to respiration, microbial death, and release of intracellular solutes. Because desert microinvertebrates can mediate nutrient cycling, and the autotrophic components of crusts are known to be sensitive to rapid desiccation due to elevated temperatures after wetting events, we studied whether altered soil temperature and frequency of summer precipitation can also affect the composition of food web consumer functional groups. We conducted a two-year field study with experimentally-elevated temperature and frequency of summer precipitation in the Colorado Plateau desert, measuring the change in abundance of nematodes, protozoans, and microarthropods. We hypothesized that microfauna would be more adversely affected by the combination of elevated temperature and frequency of summer precipitation than either effect alone, as found previously for phototrophic crust biota. Microfauna experienced normal seasonal fluctuations in abundance, but the effect of elevated temperature and frequency of summer precipitation was statistically non-significant for most microfaunal groups, except amoebae. The seasonal increase in abundance of amoebae was reduced with combined elevated temperature and increased frequency of summer precipitation compared to either treatment alone, but comparable with control (untreated) plots. Based on our findings, we suggest that desert soil microfauna are relatively more tolerant to increases in ambient temperature and frequency of summer precipitation than the autotrophic components of biological soil crust at the surface.

Functional variation in the gut microbiome of wild Drosophila populations.

PubMed

Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

2018-05-26

Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Distribution and function of carbamate hydrolase genes cehA and mcd in soils: the distinct role of soil pH.

PubMed

Rousidou, Constantina; Karaiskos, Dionysis; Myti, Despoina; Karanasios, Evangelos; Karas, Panagiotis A; Tourna, Maria; Tzortzakakis, Emmanuel A; Karpouzas, Dimitrios G

2017-01-01

Synthetic carbamates constitute a significant pesticide group with oxamyl being a leading compound in the nematicide market. Oxamyl degradation in soil is mainly microbially mediated. However, the distribution and function of carbamate hydrolase genes (cehA, mcd, cahA) associated with the soil biodegradation of carbamates is not yet clear. We studied oxamyl degradation in 16 soils from a potato monoculture area in Greece where oxamyl is regularly used. Oxamyl showed low persistence (DT50 2.4-26.7 days). q-PCR detected the cehA and mcd genes in 10 and three soils, respectively. The abundance of the cehA gene was positively correlated with pH, while both cehA abundance and pH were negatively correlated with oxamyl DT50. Amongst the carbamates used in the study region, oxamyl stimulated the abundance and expression only of the cehA gene, while carbofuran stimulated the abundance and expression of both genes. The cehA gene was also detected in pristine soils upon repeated treatments with oxamyl and carbofuran and only in soils with pH ≥7.2, where the most rapid degradation of oxamyl was observed. These results have major implications regarding the maintenance of carbamate hydrolase genes in soils, have practical implications regarding the agricultural use of carbamates, and provide insights into the evolution of cehA. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The non-linear relationship between body size and function in parrotfishes

NASA Astrophysics Data System (ADS)

Lokrantz, J.; Nyström, M.; Thyresson, M.; Johansson, C.

2008-12-01

Parrotfishes are a group of herbivores that play an important functional role in structuring benthic communities on coral reefs. Increasingly, these fish are being targeted by fishermen, and resultant declines in biomass and abundance may have severe consequences for the dynamics and regeneration of coral reefs. However, the impact of overfishing extends beyond declining fish stocks. It can also lead to demographic changes within species populations where mean body size is reduced. The effect of reduced mean body size on population dynamics is well described in literature but virtually no information exists on how this may influence important ecological functions. The study investigated how one important function, scraping (i.e., the capacity to remove algae and open up bare substratum for coral larval settlement), by three common species of parrotfishes ( Scarus niger, Chlorurus sordidus, and Chlorurus strongylocephalus) on coral reefs at Zanzibar (Tanzania) was influenced by the size of individual fishes. There was a non-linear relationship between body size and scraping function for all species examined, and impact through scraping was also found to increase markedly when fish reached a size of 15 20 cm. Thus, coral reefs which have a high abundance and biomass of parrotfish may nonetheless be functionally impaired if dominated by small-sized individuals. Reductions in mean body size within parrotfish populations could, therefore, have functional impacts on coral reefs that previously have been overlooked.

Surface chemical structure of poly(ethylene naphthalate) films during degradation in low-pressure high-frequency plasma treatments

NASA Astrophysics Data System (ADS)

Kamata, Noritsugu; Yuji, Toshifumi; Thungsuk, Nuttee; Arunrungrusmi, Somchai; Chansri, Pakpoom; Kinoshita, Hiroyuki; Mungkung, Narong

2018-06-01

The surface chemical structure of poly(ethylene naphthalate) (PEN) films treated with a low-pressure, high-frequency plasma was investigated by storing in a box at room temperature to protect the PEN film surface from dust. The functional groups on the PEN film surface changed over time. The functional groups of –C=O, –COH, and –COOH were abundant in the Ar + O2 mixture gas plasma-treated PEN samples as compared with those in untreated PEN samples. The changes occurred rapidly after 2 d following the plasma treatment, reaching steady states 8 d after the treatment. Hydrophobicity had an inverse relationship with the concentration of these functional groups on the surface. Thus, the effect of the low-pressure high-frequency plasma treatment on PEN varies as a function of storage time. This means that radical oxygen and oxygen molecules are clearly generated in the plasma, and this is one index to confirm that radical reaction has definitely occurred between the gas and the PEN film surface with a low-pressure high-frequency plasma.

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area.

PubMed

Han, Xue-Mei; Liu, Yu-Rong; Zheng, Yuan-Ming; Zhang, Xiao-Xia; He, Ji-Zheng

2014-01-01

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

Molecular Structures and Sorption Mechanisms of Biochars as Heterogeneous Carbon Materials

NASA Astrophysics Data System (ADS)

Chen, Baoliang; Chen, Zaiming; Xiao, Xin; Fang, Qile

2015-04-01

Surface functional groups such as carboxyl play a vital role in the environmental applications of biochar as a soil amendment. However, the quantification of oxygen-containing groups on a biochar surface still lacks systematical investigation. An integrated method combining chemical and spectroscopic techniques was established to quantitatively identify the chemical states, dissociation constants (pKa), and contents of oxygen-containing groups on dairy manure-derived biochars prepared at 100-700 °C. The dissociation pH of carboxyl groups on the biochar surface covered a wide range of pH values (pH 2-11), due to the varied structural micro-environments and chemical states. For low temperature biochars (≤350 °C), carboxyl existed not only as hydrogen-bonded carboxyl and unbonded carboxyl groups but also formed esters at the surface of biochars. The esters consumed OH‒ via saponification in the alkaline pH region and enhanced the dissolution of organic matter from biochars. For high temperature biochars (≥500 °C), esters came from carboxyl were almost eliminated via carbonization (ester pyrolysis), while lactones were developed. The surface density of carboxyl groups on biochars decreased sharply with the increase of the biochar-producing temperature, but the total contents of the surface carboxyls for different biochars were comparable (with a difference < 3-fold) as a result of the expanded surface area at high pyrolytic temperatures. Understanding the wide pKa ranges and the abundant contents of carboxyl groups on biochars is a prerequisite to recognition of the multi-functional applications and biogeochemical cycling of biochars. A schematic diagram for the dissociation of acid/base groups on biochar surfaces and their related functions was depicted. The protonated biochars favor inorganic anion adsorption and ionizable organic chemical sorption, while the deprotonated biochars favor cationic nutrient retention, heavy metal immobilization, and the release of dissolved materials. For low temperature biochars (i.e., DM100, DM250 and DM350), the acid/base group dissociation directly controls the pH buffering properties of biochars. The resulting surface charges regulate biochars in nutrient retention, sorption/immobilization of hazardous pollutants and biochar particle dispersing properties. Meanwhile, dissociation of acid/base groups affects carbon and silica biogeochemical cycling by regulating the release of organic matter from the cleavage of esters and dissolution of the Si-containing minerals. For high temperature biochars (i.e., DM500 and DM700), the effect of acid/base dissociation on organic matter dissolution is eliminated, but other functions are similar. CGs are the major acid/base groups on biochar surfaces. In field applications, such abundant CGs are worthy of concern in terms of multiple functions of biochars, such as soil pH adjustment, soil nutrient retention, and toxic metals immobilization.

Contribution of different functional groups to the diet of major predatory fishes at a seagrass meadow in northeastern Japan

NASA Astrophysics Data System (ADS)

Yamada, Katsumasa; Hori, Masakazu; Tanaka, Yoshiyuki; Hasegawa, Natsuki; Nakaoka, Masahiro

2010-01-01

We examined the variation in habitat use and diet of three dominant fish species ( Myoxocephalus brandti, Pholidapus dybowskii, and Pholis crassispina) in a seagrass meadow in the Akkeshi-ko estuary in northeastern Japan, where broad and dense Zostera marina beds exist, using a semi-quantitative census of the fishes and analyses of their stomach contents. Differences among the three fish species in the temporal variation in abundance of each age class (mainly 1- and 2-year age classes) indicated that the temporal pattern of utilization of the seagrass meadow were different among them. In the semi-quantitative dietary analysis, two prey categories, i.e., taxonomic group (order and suborder) and functional group, were used to explain the variation in prey composition with size-dependent changes. The six prey functional groups were classified based on the ecological traits of the prey, i.e., trophic level, size, and life type (habitat and behavior). Ontogenetic shifts in prey of the three fish species could be fully explained by a combination of the two prey categories, and not by the use of only one category (taxonomic or functional group). The pattern of ontogenetic shifts in prey differed among the fish species and size (age) classes. These results indicate that segregation of habitat (seagrass meadow) and prey group (taxonomic and functional group) is performed among the three species, which may contribute to their coexistence in this estuary.

WRKY transcription factor genes in wild rice Oryza nivara

PubMed Central

Xu, Hengjian; Watanabe, Kenneth A.; Zhang, Liyuan; Shen, Qingxi J.

2016-01-01

The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara. PMID:27345721

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; González, Angélica L; Doebeli, Michael; Farjalla, Vinicius F

2017-08-01

Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Extrapolating non-target risk of Bt crops from laboratory to field.

PubMed

Duan, Jian J; Lundgren, Jonathan G; Naranjo, Steve; Marvier, Michelle

2010-02-23

The tiered approach to assessing ecological risk of insect-resistant transgenic crops assumes that lower tier laboratory studies, which expose surrogate non-target organisms to high doses of insecticidal proteins, can detect harmful effects that might be manifested in the field. To test this assumption, we performed meta-analyses comparing results for non-target invertebrates exposed to Bacillus thuringiensis (Bt) Cry proteins in laboratory studies with results derived from independent field studies examining effects on the abundance of non-target invertebrates. For Lepidopteran-active Cry proteins, laboratory studies correctly predicted the reduced field abundance of non-target Lepidoptera. However, laboratory studies incorporating tri-trophic interactions of Bt plants, herbivores and parasitoids were better correlated with the decreased field abundance of parasitoids than were direct-exposure assays. For predators, laboratory tri-trophic studies predicted reduced abundances that were not realized in field studies and thus overestimated ecological risk. Exposure to Coleopteran-active Cry proteins did not significantly reduce the laboratory survival or field abundance of any functional group examined. Our findings support the assumption that laboratory studies of transgenic insecticidal crops show effects that are either consistent with, or more conservative than, those found in field studies, with the important caveat that laboratory studies should explore all ecologically relevant routes of exposure.

Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

PubMed Central

Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

2016-01-01

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

NASA Astrophysics Data System (ADS)

Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

2013-12-01

Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

Effects of Transgenic Bt+CpTI cotton on the abundance and diversity of rhizosphere ammonia oxidizing bacteria and archaea.

PubMed

Dong, Lianhua; Meng, Ying; Wang, Jing; Sun, Guoqing

2016-09-01

Genetically modified crops (GMCs) hold great promise for improving agricultural output, but at the same time present challenges in terms of environmental safety assessment. Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and archaea (AOA), are very important functional microbial groups in nitrogen cycle. The abundance and diversity of AOA and AOB in the rhizosphere of genetically modified cotton (SGK321) and non-GM cotton (SY321) across growth stages were investigated using real time quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Results showed that cotton genotype had a significant effect on the change in abundance of AOA and AOB, as indicated by amoA copy number. Variations in AOB abundance in rhizosphere of SY321 differed from those in SGK321. The number of AOB in the rhizosphere of SY321 fluctuated considerably: It dramatically decreased from 1.2?106 copies g-1 dry soil to 3?105 copies g-1 dry soil during the flowering stage and then increased to 1.1?106 copies g-1 and 1.5?106 copies g-1 at the belling and boll opening stages, respectively. However, abundance of AOB in the rhizosphere of SGK321 was relatively stable during all the stages of growth. The effect of SGK321 and SY321 on AOA number was quite similar to that of AOB: AOA abundance in SGK321 increased smoothly from 1.0 ?105 copies g-1 dry soil to 1.4?106 copies g-1 dry soil during growth, but that in SY321 fluctuated. Correspondence analysis (CA), canonical CA (CCA), and partial CCA (pCCA) of T-RFLP profiles of AOA and AOB showed that AOB community changed across growth stages in both cotton genotypes, and cotton genotype was the most important factor affecting the AOA community. In conclusion, the current findings indicated no adverse effect of GM cotton on functional microorganisms.

Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

PubMed Central

Zhao, Jun; Wang, Baozhan

2015-01-01

Paddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaeal amoA gene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance of Nitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), and Nitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of 13C-labeled DNA further revealed that 13CO2 was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA and Nitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated with Nitrosospira sp. strain L115 and the Nitrosospira multiformis lineage and that the 13C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic “Candidatus Nitrososphaera gargensis,” uncultured fosmid 29i4, and acidophilic “Candidatus Nitrosotalea devanaterra” lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields. PMID:25724959

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens.

PubMed

De Cesare, Alessandra; Sirri, Federico; Manfreda, Gerardo; Moniaci, Paola; Giardini, Alberto; Zampiga, Marco; Meluzzi, Adele

2017-01-01

This study examines the effects of the dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) (LA) on productive performances, incidence of foot pad dermatitis and caecum microbioma in broiler chickens. A total of 1,100 one-day old male Ross 308 chicks were divided into 2 groups of 16 replicates with 25 birds each and reared from 1-41 d. One group was fed a basal diet (CON) and the other group the same diet supplemented with LA. Caecum contents were collected from 4 selected birds at day one and 5 selected birds at the end of the rearing period. Then, they were submitted to DNA extraction and whole DNA shotgun metagenomic sequencing. Overall, the LA supplementation produced a significant beneficial effect on body weight gain between 15-28 d and improved feed conversion rate in the overall period. On the contrary, litter moisture, pH and incidence of the foot pad lesions were not affected by LA. Birds treated with LA showed a lower occurrence of pasty vent at both 14 and 28 d. At the end of the rearing period, Lachanospiraceae were significantly higher in LA birds in comparison to CON (17.07 vs 14.39%; P = 0.036). Moreover, Ruminococcus obeum, Clostridium clostridioforme, Roseburia intestinalis, Lachnospiraceae bacterium 14-2T and Coprococcus eutactus were significantly higher in LA birds in comparison to CON. The relative abundance of Lactobacillus acidophilus was comparable between LA and CON groups. However, a positive effect was observed in relation to the metabolic functions in the treated group, with particular reference to the higher abundance of β-glucosidase. In conclusion, the LA supplementation improved broiler productive performances and metabolic functions promoting animal health.

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens

PubMed Central

De Cesare, Alessandra; Manfreda, Gerardo; Moniaci, Paola; Giardini, Alberto; Zampiga, Marco; Meluzzi, Adele

2017-01-01

This study examines the effects of the dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) (LA) on productive performances, incidence of foot pad dermatitis and caecum microbioma in broiler chickens. A total of 1,100 one-day old male Ross 308 chicks were divided into 2 groups of 16 replicates with 25 birds each and reared from 1–41 d. One group was fed a basal diet (CON) and the other group the same diet supplemented with LA. Caecum contents were collected from 4 selected birds at day one and 5 selected birds at the end of the rearing period. Then, they were submitted to DNA extraction and whole DNA shotgun metagenomic sequencing. Overall, the LA supplementation produced a significant beneficial effect on body weight gain between 15–28 d and improved feed conversion rate in the overall period. On the contrary, litter moisture, pH and incidence of the foot pad lesions were not affected by LA. Birds treated with LA showed a lower occurrence of pasty vent at both 14 and 28 d. At the end of the rearing period, Lachanospiraceae were significantly higher in LA birds in comparison to CON (17.07 vs 14.39%; P = 0.036). Moreover, Ruminococcus obeum, Clostridium clostridioforme, Roseburia intestinalis, Lachnospiraceae bacterium 14-2T and Coprococcus eutactus were significantly higher in LA birds in comparison to CON. The relative abundance of Lactobacillus acidophilus was comparable between LA and CON groups. However, a positive effect was observed in relation to the metabolic functions in the treated group, with particular reference to the higher abundance of β-glucosidase. In conclusion, the LA supplementation improved broiler productive performances and metabolic functions promoting animal health. PMID:28472118

Geographic variability in amoeboid protists and other microbial groups in the water column of the lower Hudson River Estuary (New York, USA)

NASA Astrophysics Data System (ADS)

Juhl, Andrew R.; Anderson, O. Roger

2014-12-01

In comparison to other groups of planktonic microorganisms, relatively little is known about the role of amoeboid protists (amebas) in planktonic ecosystems. This study describes the first geographic survey of the abundance and biomass of amebas in an estuarine water column. Samples collected in the lower Hudson River Estuary were used to investigate relationships between ameba abundance and biomass and hydrographic variables (temperature, salinity, and turbidity), water depth (surface and near bottom), distance from mid-channel to shore, phytoplankton biomass (chlorophyll fluorescence) and the occurrence of other heterotrophic microbial groups (heterotrophic bacteria, nanoflagellates, and ciliates) in the plankton. Although salinity increased significantly towards the mouth of the estuary, there were no significant differences in the abundance or biomass of any microbial group in surface samples collected at three stations separated by 44 km along the estuary's mid-channel. Peak biomass values for all microbial groups were found at the station closest to shore, however, cross-channel trends in microbial abundance and biomass were not statistically significant. Although ameba abundance and biomass in most samples were low compared to other microbial groups, clear patterns in ameba distribution were nevertheless found. Unlike other microbial groups examined, ameba numbers and biomass greatly increased in near bottom water compared to surface samples. Ameba abundance and biomass (in surface samples) were also strongly related to increasing turbidity. The different relationships of ameba abundance and biomass with turbidity suggest a rising contribution of large amebas in microbial communities of the Hudson estuary when turbidity increases. These results, emphasizing the importance of particle concentration as attachment and feeding surfaces for amebas, will help identify the environmental conditions when amebas are most likely to contribute significantly to estuarine bacterivory and C-flux.

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater

PubMed Central

Voudanta, Eleni; Monchy, Sebastién; Delegrange, Alice; Vincent, Dorothée; Genitsaris, Savvas; Christaki, Urania

2016-01-01

Mussel biofiltration is a widely used approach for the mitigation of aquaculture water. In this study, we investigated the effect of mussel biofiltration on the communities of particle-associated bacteria and unicellular eukaryotes in a sea bass aquaculture in southern North Sea. We assessed the planktonic community changes before and after biofiltration based on the diversity of the 16S and 18S rRNA genes by using next generation sequencing technologies. Although there was no overall reduction in the operational taxonomic units (OTU) numbers between the control (no mussels) and the test (with mussels) tanks, a clear reduction in the relative abundance of the top three most dominant OTUs in every sampling time was observed, ranging between 2–28% and 16–82% for Bacteria and Eukarya, respectively. The bacterial community was dominated by OTUs related to phytoplankton blooms and/or high concentrations of detritus. Among the eukaryotes, several fungal and parasitic groups were found. Their relative abundance in most cases was also reduced from the control to the test tanks; a similar decreasing pattern was also observed for both major higher taxa and functional (trophic) groups. Overall, this study showed the effectiveness of mussel biofiltration on the decrease of microbiota abundance and diversity in seawater fueling fish farms. PMID:27069786

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater.

PubMed

Voudanta, Eleni; Kormas, Konstantinos Ar; Monchy, Sebastién; Delegrange, Alice; Vincent, Dorothée; Genitsaris, Savvas; Christaki, Urania

2016-01-01

Mussel biofiltration is a widely used approach for the mitigation of aquaculture water. In this study, we investigated the effect of mussel biofiltration on the communities of particle-associated bacteria and unicellular eukaryotes in a sea bass aquaculture in southern North Sea. We assessed the planktonic community changes before and after biofiltration based on the diversity of the 16S and 18S rRNA genes by using next generation sequencing technologies. Although there was no overall reduction in the operational taxonomic units (OTU) numbers between the control (no mussels) and the test (with mussels) tanks, a clear reduction in the relative abundance of the top three most dominant OTUs in every sampling time was observed, ranging between 2-28% and 16-82% for Bacteria and Eukarya, respectively. The bacterial community was dominated by OTUs related to phytoplankton blooms and/or high concentrations of detritus. Among the eukaryotes, several fungal and parasitic groups were found. Their relative abundance in most cases was also reduced from the control to the test tanks; a similar decreasing pattern was also observed for both major higher taxa and functional (trophic) groups. Overall, this study showed the effectiveness of mussel biofiltration on the decrease of microbiota abundance and diversity in seawater fueling fish farms.

Expanding zooplankton standing stock estimation from meso- to metazooplankton: A case study in the N. Aegean Sea (Mediterranean Sea)

NASA Astrophysics Data System (ADS)

Frangoulis, Constantin; Grigoratou, Maria; Zoulias, Theodore; Hannides, Cecelia C. S.; Pantazi, Maria; Psarra, Stella; Siokou, Ioanna

2017-10-01

Although metazooplankton includes a wide size range of organisms, our knowledge is essentially based on mesozooplankton. A first estimation of the metazooplankton standing stock in a Mediterranean area, and of its size fractions and functional groups are provided by combining data out of three nets with different mesh sizes (45, 200 and 500 μm). Data were collected along a gradient of oligotrophy in the frontal area created, where the waters of Black Sea origin meet those of Levantine Sea origin (Northeast Aegean Sea, Eastern Mediterranean). Metazooplankton biomass was dominated by mesozooplankton (0.2-2 mm), while meso- and microzooplankton (<0.2 mm) shared dominance of abundance. Copepods dominated both in abundance and biomass and were followed by nauplii in abundance and gelatinous carnivores or decapod-euphausiid larvae in biomass. The spatiotemporal variability of metazoans stock, biomass-size spectra linearity, carnivorous group contribution and copepod diversity, supported that metazooplankton tends to recede from steady-state when approaching less oligotrophic dynamic areas (such as fronts) or dynamic periods (such as the spring bloom). The need and the difficulties of obtaining a larger picture from a wider size range of metazoans for understanding the role of zooplankton are stressed.

Underwater Application of Quantitative PCR on an Ocean Mooring

PubMed Central

Preston, Christina M.; Harris, Adeline; Ryan, John P.; Roman, Brent; Marin, Roman; Jensen, Scott; Everlove, Cheri; Birch, James; Dzenitis, John M.; Pargett, Douglas; Adachi, Masao; Turk, Kendra; Zehr, Jonathon P.; Scholin, Christopher A.

2011-01-01

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions. PMID:21829630

Dynamic alterations in the gut microbiota and metabolome during the development of methionine-choline-deficient diet-induced nonalcoholic steatohepatitis.

PubMed

Ye, Jian-Zhong; Li, Ya-Ting; Wu, Wen-Rui; Shi, Ding; Fang, Dai-Qiong; Yang, Li-Ya; Bian, Xiao-Yuan; Wu, Jing-Jing; Wang, Qing; Jiang, Xian-Wan; Peng, Cong-Gao; Ye, Wan-Chun; Xia, Peng-Cheng; Li, Lan-Juan

2018-06-21

To investigate changes in gut microbiota and metabolism during nonalcoholic steatohepatitis (NASH) development in mice fed a methionine-choline-deficient (MCD) diet. Twenty-four male C57BL/6J mice were equally divided into four groups and fed a methionine-choline-sufficient diet for 2 wk (Control 2w group, n = 6) or 4 wk (Control 4w group, n = 6) or the MCD diet for 2 wk (MCD 2w group, n = 6) or 4 wk (MCD 4w group, n = 6). Liver injury, fibrosis, and intestinal barrier function were evaluated after 2 and 4 wk of feeding. The fecal microbiome and metabolome were studied using 16s rRNA deep sequencing and gas chromatography-mass spectrometry. The mice fed the MCD diet presented with simple hepatic steatosis and slight intestinal barrier deterioration after 2 wk. After 4 wk of feeding with the MCD diet, however, the mice developed prominent NASH with liver fibrosis, and the intestinal barrier was more impaired. Compared with the control diet, the MCD diet induced gradual gut microbiota dysbiosis, as evidenced by a marked decrease in the abundance of Alistipes and the ( Eubacterium ) coprostanoligenes group ( P < 0.001 and P < 0.05, respectively) and a significant increase in Ruminococcaceae UCG 014 abundance ( P < 0.05) after 2 wk. At 4 wk, the MCD diet significantly reduced the promising probiotic Bifidobacterium levels and markedly promoted Bacteroides abundance ( P < 0.05, and P < 0.01, respectively). The fecal metabolomic profile was also substantially altered by the MCD diet: At 2 wk, arachidic acid, hexadecane, palmitic acid, and tetracosane were selected as potential biomarkers that were significantly different in the corresponding control group, and at 4 wk, cholic acid, cholesterol, arachidic acid, tetracosane, and stearic acid were selected. The MCD diet induced persistent alterations in the gut microbiota and metabolome.

Dynamic alterations in the gut microbiota and metabolome during the development of methionine-choline-deficient diet-induced nonalcoholic steatohepatitis

PubMed Central

Ye, Jian-Zhong; Li, Ya-Ting; Wu, Wen-Rui; Shi, Ding; Fang, Dai-Qiong; Yang, Li-Ya; Bian, Xiao-Yuan; Wu, Jing-Jing; Wang, Qing; Jiang, Xian-Wan; Peng, Cong-Gao; Ye, Wan-Chun; Xia, Peng-Cheng; Li, Lan-Juan

2018-01-01

AIM To investigate changes in gut microbiota and metabolism during nonalcoholic steatohepatitis (NASH) development in mice fed a methionine-choline-deficient (MCD) diet. METHODS Twenty-four male C57BL/6J mice were equally divided into four groups and fed a methionine-choline-sufficient diet for 2 wk (Control 2w group, n = 6) or 4 wk (Control 4w group, n = 6) or the MCD diet for 2 wk (MCD 2w group, n = 6) or 4 wk (MCD 4w group, n = 6). Liver injury, fibrosis, and intestinal barrier function were evaluated after 2 and 4 wk of feeding. The fecal microbiome and metabolome were studied using 16s rRNA deep sequencing and gas chromatography-mass spectrometry. RESULTS The mice fed the MCD diet presented with simple hepatic steatosis and slight intestinal barrier deterioration after 2 wk. After 4 wk of feeding with the MCD diet, however, the mice developed prominent NASH with liver fibrosis, and the intestinal barrier was more impaired. Compared with the control diet, the MCD diet induced gradual gut microbiota dysbiosis, as evidenced by a marked decrease in the abundance of Alistipes and the (Eubacterium) coprostanoligenes group (P < 0.001 and P < 0.05, respectively) and a significant increase in Ruminococcaceae UCG 014 abundance (P < 0.05) after 2 wk. At 4 wk, the MCD diet significantly reduced the promising probiotic Bifidobacterium levels and markedly promoted Bacteroides abundance (P < 0.05, and P < 0.01, respectively). The fecal metabolomic profile was also substantially altered by the MCD diet: At 2 wk, arachidic acid, hexadecane, palmitic acid, and tetracosane were selected as potential biomarkers that were significantly different in the corresponding control group, and at 4 wk, cholic acid, cholesterol, arachidic acid, tetracosane, and stearic acid were selected. CONCLUSION The MCD diet induced persistent alterations in the gut microbiota and metabolome. PMID:29930468

Functional Versatility of AGY Serine Codons in Immunoglobulin Variable Region Genes

PubMed Central

Detanico, Thiago; Phillips, Matthew; Wysocki, Lawrence J.

2016-01-01

In systemic autoimmunity, autoantibodies directed against nuclear antigens (Ags) often arise by somatic hypermutation (SHM) that converts AGT and AGC (AGY) Ser codons into Arg codons. This can occur by three different single-base changes. Curiously, AGY Ser codons are far more abundant in complementarity-determining regions (CDRs) of IgV-region genes than expected for random codon use or from species-specific codon frequency data. CDR AGY codons are also more abundant than TCN Ser codons. We show that these trends hold even in cartilaginous fishes. Because AGC is a preferred target for SHM by activation-induced cytidine deaminase, we asked whether the AGY abundance was solely due to a selection pressure to conserve high mutability in CDRs regardless of codon context but found that this was not the case. Instead, AGY triplets were selectively enriched in the Ser codon reading frame. Motivated by reports implicating a functional role for poly/autoreactive specificities in antiviral antibodies, we also analyzed mutations at AGY in antibodies directed against a number of different viruses and found that mutations producing Arg codons in antiviral antibodies were indeed frequent. Unexpectedly, however, we also found that AGY codons mutated often to encode nearly all of the amino acids that are reported to provide the most frequent contacts with Ag. In many cases, mutations producing codons for these alternative amino acids in antiviral antibodies were more frequent than those producing Arg codons. Mutations producing each of these key amino acids required only single-base changes in AGY. AGY is the only codon group in which two-thirds of random mutations generate codons for these key residues. Finally, by directly analyzing X-ray structures of immune complexes from the RCSB protein database, we found that Ag-contact residues generated via SHM occurred more often at AGY than at any other codon group. Thus, preservation of AGY codons in antibody genes appears to have been driven by their exceptional functional versatility, despite potential autoreactive consequences. PMID:27920779

Assessing the trophic state of Linhos lake: a first step towards ecological rehabilitation.

PubMed

Pereira, R; Soares, A M V M; Ribeiro, R; Gonçalves, F

2002-03-01

Lack of recognition of the value of wetlands has led to the loss of considerable areas of these ecosystems in the past. Linhos lake (Figueira da Foz, Portugal) is a good example of one of these ecosystems, in which human intervention was responsible for its environmental degradation and led to its precocious terrestrialization. Physico-chemical conditions and zooplankton community structure were studied in Linhos lake, in order to evaluate ecosystem functioning and to acquire baseline information. The system is characterised by high oxygen depletion. Spatial heterogeneity was confirmed by the existence of significant differences in total densities for the three zooplanktonic groups. Rotifers were the most abundant group attaining their maximum density in April (2251 x 1 ind/l). Keratella quadrata, K. cochlearis, Polyarthra vulgaris, Filinia terminalis and Hexarthra mira were the main abundant species. Correspondence analysis suggested temperature as the main controlling factor in species seasonality. In order to prevent the precocious disappearance of the lake some restoration measures were proposed based on zooplankton community structure.

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

PubMed Central

Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A.

2016-01-01

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere. PMID:26935537

Shifting plant species composition in response to climate change stabilizes grassland primary production.

PubMed

Liu, Huiying; Mi, Zhaorong; Lin, Li; Wang, Yonghui; Zhang, Zhenhua; Zhang, Fawei; Wang, Hao; Liu, Lingli; Zhu, Biao; Cao, Guangmin; Zhao, Xinquan; Sanders, Nathan J; Classen, Aimée T; Reich, Peter B; He, Jin-Sheng

2018-04-17

The structure and function of alpine grassland ecosystems, including their extensive soil carbon stocks, are largely shaped by temperature. The Tibetan Plateau in particular has experienced significant warming over the past 50 y, and this warming trend is projected to intensify in the future. Such climate change will likely alter plant species composition and net primary production (NPP). Here we combined 32 y of observations and monitoring with a manipulative experiment of temperature and precipitation to explore the effects of changing climate on plant community structure and ecosystem function. First, long-term climate warming from 1983 to 2014, which occurred without systematic changes in precipitation, led to higher grass abundance and lower sedge abundance, but did not affect aboveground NPP. Second, an experimental warming experiment conducted over 4 y had no effects on any aspect of NPP, whereas drought manipulation (reducing precipitation by 50%), shifted NPP allocation belowground without affecting total NPP. Third, both experimental warming and drought treatments, supported by a meta-analysis at nine sites across the plateau, increased grass abundance at the expense of biomass of sedges and forbs. This shift in functional group composition led to deeper root systems, which may have enabled plant communities to acquire more water and thus stabilize ecosystem primary production even with a changing climate. Overall, our study demonstrates that shifting plant species composition in response to climate change may have stabilized primary production in this high-elevation ecosystem, but it also caused a shift from aboveground to belowground productivity.

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

PubMed Central

Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

2015-01-01

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems. PMID:25575307

The basics of thiols and cysteines in redox biology and chemistry.

PubMed

Poole, Leslie B

2015-03-01

Cysteine is one of the least abundant amino acids, yet it is frequently found as a highly conserved residue within functional (regulatory, catalytic, or binding) sites in proteins. It is the unique chemistry of the thiol or thiolate group of cysteine that imparts to functional sites their specialized properties (e.g., nucleophilicity, high-affinity metal binding, and/or ability to form disulfide bonds). Highlighted in this review are some of the basic biophysical and biochemical properties of cysteine groups and the equations that apply to them, particularly with respect to pKa and redox potential. Also summarized are the types of low-molecular-weight thiols present in high concentrations in most cells, as well as the ways in which modifications of cysteinyl residues can impart or regulate molecular functions important to cellular processes, including signal transduction. Copyright © 2014 Elsevier Inc. All rights reserved.

**1**5N-NMR INVESTIGATION OF HYDROXYLAMINE DERIVATIZED HUMIC SUBSTANCES.

USGS Publications Warehouse

Thorn, Kevin A.; Arterburn, Jeffrey B.; Mikita, Michael A.

1986-01-01

Humic substances are the most abundant naturally occurring refactory organic compounds in soils and water. They have a broad range of physical, chemical and physiological properties. In soils, humic substances contribute to the cation exchange capacity, help maintain the physical structure, and play a role in plant growth and nutrition. In aquatic systems, humic substances serve to regulate the levels of inorganic constituents, yield trihalomethanes upon chlorination, and transport or concentrate organic and inorganic pollutants. The oxygen containing functional groups of humic and fulvic acids are believed to play a key role in the chemical properties of humic substances. This study was undertaken to gain additional information on the specific types of oxygen functionalities in humic substances. Since the analysis of hydroxyl moieties had been earlier established, we focused our attention on the analysis of ketone and aldehyde functional groups in humic substances.

Sequence and Expression Analyses of Ethylene Response Factors Highly Expressed in Latex Cells from Hevea brasiliensis

PubMed Central

Piyatrakul, Piyanuch; Yang, Meng; Putranto, Riza-Arief; Pirrello, Julien; Dessailly, Florence; Hu, Songnian; Summo, Marilyne; Theeravatanasuk, Kannikar; Leclercq, Julie; Kuswanhadi; Montoro, Pascal

2014-01-01

The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors. PMID:24971876

Fish community-based measures of estuarine ecological quality and pressure-impact relationships

NASA Astrophysics Data System (ADS)

Fonseca, Vanessa F.; Vasconcelos, Rita P.; Gamito, Rita; Pasquaud, Stéphanie; Gonçalves, Catarina I.; Costa, José L.; Costa, Maria J.; Cabral, Henrique N.

2013-12-01

Community-based responses of fish fauna to anthropogenic pressures have been extensively used to assess the ecological quality of estuarine ecosystems. Several methodologies have been developed recently combining metrics reflecting community structure and function. A fish community facing significant environmental disturbances will be characterized by a simplified structure, with lower diversity and complexity. However, estuaries are naturally dynamic ecosystems exposed to numerous human pressures, making it difficult to distinguish between natural and anthropogenic-induced changes to the biological community. In the present work, the variability of several fish metrics was assessed in relation to different pressures in estuarine sites. The response of a multimetric index (Estuarine Fish Assessment Index) was also analysed. Overall, fish metrics and the multimetric index signalled anthropogenic stress, particularly environmental chemical pollution. The fish assemblage associated with this type of pressure was characterized by lower species diversity, lower number of functional guilds, lower abundance of marine migrants and of piscivorous individuals, and higher abundance of estuarine resident species. A decreased ecological quality status, based on the EFAI, was also determined for sites associated with this pressure group. Ultimately, the definition of each pressure groups favoured a stressor-specific analysis, evidencing pressure patterns and accounting for multiple factors in a highly dynamic environment.

Bottom-up control of macrobenthic communities in a guanotrophic coastal system.

PubMed

Signa, Geraldina; Mazzola, Antonio; Costa, Valentina; Vizzini, Salvatrice

2015-01-01

Soft bottom macrobenthic communities were studied seasonally in three coastal ponds (Marinello ponds, Italy) at increasing distances from a gull (Larus michahellis) colony to investigate the effect of seabird-induced eutrophication (i.e. guanotrophication) on macrobenthic fauna. We hypothesized that enhanced nutrient concentration and organic load caused by guano input significantly alter the trophic and sedimentological condition of ponds, affecting benthic fauna through a bottom-up control. The influence of a set of environmental features on macrobenthic assemblages was also tested. Overall, the lowest macrobenthic abundances and functional group diversity were found in deeper sites, especially in the pond characterised by severe guanotrophication, where the higher disturbance resulted in a decline in suspension feeders and carnivores in favour of deposit feeders. An increase in opportunistic/tolerant taxa (e.g. chironomid larvae and paraonids) and totally azoic sediments were also found as an effect of the harshest environmental conditions, resulting in a very poor ecological status. We conclude that macrobenthic assemblages of the Marinello coastal system display high spatial variability due to a synergistic effect of trophic status and the geomorphological features of the ponds. The macrobenthic response to guanotrophication, which was a clear decrease in abundance, diversity and trophic functional groups, was associated with the typical response to severe eutrophication, magnified by the geomorphological features.

Longitudinal Changes in Physical Habitat and Macroinvertebrate Assemblages Along a Neotropical Stream Continuum

NASA Astrophysics Data System (ADS)

Colon-Gaud, C.; Whiles, M. R.

2005-05-01

Information on the structure and function of upland Neotropical streams is lacking compared to many other regions. We examined habitat characteristics and macroinvertebrate assemblages along an 8-km stretch of a stream originating on the continental divide in central Panama in order to examine patterns along a stream continuum. Wetted width and discharge ranged from 1 m and 18 L/s, respectively in the uppermost headwaters to 12 m and 1,580 L/s, respectively at the lowest reach examined. Percent substrate composition showed a decrease in fine particle sizes from upper headwater reaches (38%) to the lowest reach (10%). A total of 61 macroinvertebrate taxa were identified along the continuum, with more taxa present in lower reaches (45) compared to headwaters (28), but responses of individual groups varied. Trichoptera, Ephemeroptera, and Diptera richness increased from headwaters to the lowest site, whereas Hemiptera and Coleoptera richness decreased along the gradient. Collector-gatherers and predators were the dominant functional groups (~70% of total abundance) and changed little across sites. Shredder abundance was highest in headwaters (15% of total), while scrapers (20%) and collector/filterers (11%) peaked in the lower reaches. These patterns suggest that upland streams in this region follow basic tenets of the River Continuum Concept.

Sequence and expression analyses of ethylene response factors highly expressed in latex cells from Hevea brasiliensis.

PubMed

Piyatrakul, Piyanuch; Yang, Meng; Putranto, Riza-Arief; Pirrello, Julien; Dessailly, Florence; Hu, Songnian; Summo, Marilyne; Theeravatanasuk, Kannikar; Leclercq, Julie; Kuswanhadi; Montoro, Pascal

2014-01-01

The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors.

Bottom-Up Control of Macrobenthic Communities in a Guanotrophic Coastal System

PubMed Central

Signa, Geraldina; Mazzola, Antonio; Costa, Valentina; Vizzini, Salvatrice

2015-01-01

Soft bottom macrobenthic communities were studied seasonally in three coastal ponds (Marinello ponds, Italy) at increasing distances from a gull (Larus michahellis) colony to investigate the effect of seabird-induced eutrophication (i.e. guanotrophication) on macrobenthic fauna. We hypothesized that enhanced nutrient concentration and organic load caused by guano input significantly alter the trophic and sedimentological condition of ponds, affecting benthic fauna through a bottom-up control. The influence of a set of environmental features on macrobenthic assemblages was also tested. Overall, the lowest macrobenthic abundances and functional group diversity were found in deeper sites, especially in the pond characterised by severe guanotrophication, where the higher disturbance resulted in a decline in suspension feeders and carnivores in favour of deposit feeders. An increase in opportunistic/tolerant taxa (e.g. chironomid larvae and paraonids) and totally azoic sediments were also found as an effect of the harshest environmental conditions, resulting in a very poor ecological status. We conclude that macrobenthic assemblages of the Marinello coastal system display high spatial variability due to a synergistic effect of trophic status and the geomorphological features of the ponds. The macrobenthic response to guanotrophication, which was a clear decrease in abundance, diversity and trophic functional groups, was associated with the typical response to severe eutrophication, magnified by the geomorphological features. PMID:25679400

Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

PubMed

Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

2014-12-01

Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments.

Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

PubMed

Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

2014-11-11

Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments.

Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests.

PubMed

Lamarre, Greg P A; Hérault, Bruno; Fine, Paul V A; Vedel, Vincent; Lupoli, Roland; Mesones, Italo; Baraloto, Christopher

2016-01-01

Arthropods represent most of global biodiversity, with the highest diversity found in tropical rain forests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass sampling of arthropod communities within three major habitat types of lowland Amazonian rain forest, including terra firme clay, white-sand and seasonally flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in the two regions. The overall arthropod community composition exhibited strong turnover among habitats and between regions. In particular, seasonally flooded forest habitats of both regions comprised unique assemblages. Overall, 17·7% (26 of 147) of arthropod families showed significant preferences for a particular habitat type. We present a first reproducible arthropod functional classification among the 147 taxa based on similarity among 21 functional traits describing feeding source, major mouthparts and microhabitats inhabited by each taxon. We identified seven distinct functional groups whose relative abundance contrasted strongly across the three habitats, with sap and leaf feeders showing higher abundances in terra firme clay forest. Our novel arthropod functional classification provides an important complement to link these contrasting patterns of composition to differences in forest functioning across geographical and environmental gradients. This study underlines that both environment and biogeographical processes are responsible for driving arthropod taxonomic composition while environmental filtering is the main driver of the variance in functional composition. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

DOE PAGES

Xiong, Weili; Brown, Christopher T.; Morowitz, Michael J.; ...

2017-07-10

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. But, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for eachmore » of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We also identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. By applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.« less

Intra-Amniotic Administration (Gallus gallus) of Cicer arietinum and Lens culinaris Prebiotics Extracts and Duck Egg White Peptides Affects Calcium Status and Intestinal Functionality

PubMed Central

Hou, Tao; Glahn, Raymond P.; Tako, Elad

2017-01-01

Calcium (Ca) is one of the most abundant inorganic elements in the human body and has many important physiological roles. Prebiotics and bioactive peptides are two important substances used to promote calcium uptake. However, the difference in mechanisms of the calcium uptake from these two supplements is not clear. By using the Gallus gallus model and the intra-amniotic administration procedure, the aim of this study was to investigate whether Ca status, intestinal functionality, and health-promoting bacterial populations were affected by prebiotics extracted from chickpea and lentil, and duck egg white peptides (DPs). Eleven groups (non-injected; 18 MΩ H2O; 4 mmol/L CaCl2; 50 mg/mL chickpea + 4 mmol/L CaCl2; 50 mg/mL lentil + 4 mmol/L CaCl2; 40 mg/mL DPs + 4 mmol/L CaCl2; 5 mg/mL Val-Ser-Glu-Glu (VSEE) + 4 mmol/L CaCl2; 50 mg/mL chickpea; 50 mg/mL lentil; 40 mg/mL DPs; 5 mg/mL VSEE) were utilized. Upon hatch, blood, cecum, small intestine, liver and bone were collected for assessment of serum bone alkaline phosphate level (BALP), the relative abundance of intestinal microflora, expression of Ca-related genes, brush border membrane (BBM) functional genes, and liver and bone mineral levels, respectively. The BALP level increased in the presence of lentil, DPs and VSEE (p < 0.05). The relative abundance of probiotics increased significantly (p < 0.05) by VSEE + Ca and chickpea. The expression of CalbindinD9k (Ca transporter) increased (p < 0.05) in Ca, chickpea + Ca and lentil + Ca groups. In addition, the brush border membrane functionality genes expressions increased (p < 0.05) by the chickpea or lentil extracts. Prebiotics and DPs beneficially affected the intestinal microflora and duodenal villus surface area. This research expands the understanding of the prebiotics’ properties of chickpea and lentil extracts, and peptides’ effects on calcium metabolism and gut health. PMID:28754012

Intra-Amniotic Administration (Gallus gallus) of Cicer arietinum and Lens culinaris Prebiotics Extracts and Duck Egg White Peptides Affects Calcium Status and Intestinal Functionality.

PubMed

Hou, Tao; Kolba, Nikolai; Glahn, Raymond P; Tako, Elad

2017-07-21

Calcium (Ca) is one of the most abundant inorganic elements in the human body and has many important physiological roles. Prebiotics and bioactive peptides are two important substances used to promote calcium uptake. However, the difference in mechanisms of the calcium uptake from these two supplements is not clear. By using the Gallus gallus model and the intra-amniotic administration procedure, the aim of this study was to investigate whether Ca status, intestinal functionality, and health-promoting bacterial populations were affected by prebiotics extracted from chickpea and lentil, and duck egg white peptides (DPs). Eleven groups (non-injected; 18 MΩ H₂O; 4 mmol/L CaCl₂; 50 mg/mL chickpea + 4 mmol/L CaCl₂; 50 mg/mL lentil + 4 mmol/L CaCl₂; 40 mg/mL DPs + 4 mmol/L CaCl₂; 5 mg/mL Val-Ser-Glu-Glu (VSEE) + 4 mmol/L CaCl₂; 50 mg/mL chickpea; 50 mg/mL lentil; 40 mg/mL DPs; 5 mg/mL VSEE) were utilized. Upon hatch, blood, cecum, small intestine, liver and bone were collected for assessment of serum bone alkaline phosphate level (BALP), the relative abundance of intestinal microflora, expression of Ca-related genes, brush border membrane (BBM) functional genes, and liver and bone mineral levels, respectively. The BALP level increased in the presence of lentil, DPs and VSEE ( p < 0.05). The relative abundance of probiotics increased significantly ( p < 0.05) by VSEE + Ca and chickpea. The expression of CalbindinD9k (Ca transporter) increased ( p < 0.05) in Ca, chickpea + Ca and lentil + Ca groups. In addition, the brush border membrane functionality genes expressions increased ( p < 0.05) by the chickpea or lentil extracts. Prebiotics and DPs beneficially affected the intestinal microflora and duodenal villus surface area. This research expands the understanding of the prebiotics' properties of chickpea and lentil extracts, and peptides' effects on calcium metabolism and gut health.

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Weili; Brown, Christopher T.; Morowitz, Michael J.

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. But, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for eachmore » of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We also identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. By applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.« less

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

PubMed

Xiong, Weili; Brown, Christopher T; Morowitz, Michael J; Banfield, Jillian F; Hettich, Robert L

2017-07-10

Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.

Local and Landscape Drivers of Parasitoid Abundance, Richness, and Composition in Urban Gardens.

PubMed

Burks, Julia M; Philpott, Stacy M

2017-04-01

Urbanization negatively affects biodiversity, yet some urban habitat features can support diversity. Parasitoid wasps, an abundant and highly diverse group of arthropods, can inhabit urban areas and do well in areas with higher host abundance, floral resources, or local or landscape complexity. Parasitoids provide biological control services in many agricultural habitats, yet few studies have examined diversity and abundance of parasitoids in urban agroecosystems to understand how to promote conservation and function. We examined the local habitat and landscape drivers of parasitoid abundance, superfamily and family richness, and parasitoid composition in urban gardens in the California central coast. Local factors included garden size, ground cover type, herbaceous plant species, and number of trees and shrubs. Landscape characteristics included land cover and landscape diversity around gardens. We found that garden size, mulch cover, and urban cover within 500 m of gardens predicted increases in parasitoid abundance within gardens. The height of herbaceous vegetation and tree and shrub richness predicted increases in superfamily and family richness whereas increases in urban cover resulted in declines in parasitoid richness. Abundance of individual superfamilies and families responded to a wide array of local and landscape factors, sometimes in opposite ways. Composition of parasitoid communities responded to changes in garden size, herbaceous plant cover, and number of flowers. Thus, both local scale management and landscape planning may impact the abundance, diversity, and community composition of parasitoids in urban gardens, and may result in differences in the effectiveness of parasitoids in biological control. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Impacts of invasive plants on resident animals across ecosystems, taxa, and feeding types: a global assessment.

PubMed

Schirmel, Jens; Bundschuh, Mirco; Entling, Martin H; Kowarik, Ingo; Buchholz, Sascha

2016-02-01

As drivers of global change, biological invasions have fundamental ecological consequences. However, it remains unclear how invasive plant effects on resident animals vary across ecosystems, animal classes, and functional groups. We performed a comprehensive meta-analysis covering 198 field and laboratory studies reporting a total of 3624 observations of invasive plant effects on animals. Invasive plants had reducing (56%) or neutral (44%) effects on animal abundance, diversity, fitness, and ecosystem function across different ecosystems, animal classes, and feeding types while we could not find any increasing effect. Most importantly, we found that invasive plants reduced overall animal abundance, diversity and fitness. However, this significant overall effect was contingent on ecosystems, taxa, and feeding types of animals. Decreasing effects of invasive plants were most evident in riparian ecosystems, possibly because frequent disturbance facilitates more intense plant invasions compared to other ecosystem types. In accordance with their immediate reliance on plants for food, invasive plant effects were strongest on herbivores. Regarding taxonomic groups, birds and insects were most strongly affected. In insects, this may be explained by their high frequency of herbivory, while birds demonstrate that invasive plant effects can also cascade up to secondary consumers. Since data on impacts of invasive plants are rather limited for many animal groups in most ecosystems, we argue for overcoming gaps in knowledge and for a more differentiated discussion on effects of invasive plant on native fauna. © 2015 John Wiley & Sons Ltd.

Chemical Abundances of Planetary Nebulae in the Bulge and Disk of M31

NASA Technical Reports Server (NTRS)

Jacoby, George H.; Ciardullo, Robin

1998-01-01

We derive abundances and central star parameters for 15 planetary nebulae (PNe) in M31: 12 in the bulge and 3 in a disk field 14 kpc from the nucleus. No single abundance value characterizes the bulge stars: although the median abundances of the sample are similar to those seen for PNe in the LMC, the distribution of abundances is several times broader, spanning over 1 decade. None of the PNe in our sample approach the super metal-rich ([Fe/H] approximately 0.25) expectations for the bulge of M31, although a few PNe in the sample of Stasinska, Richer, & Mc Call (1998) come close. This [O/H] vs [Fe/H] discrepancy is likely due to a combination of factors, including an inability of metal-rich stars to produce bright PNe, a luminosity selection effect, and an abundance gradient in the bulge of M31. We show that PNe that are near the bright limit of the [O III] lambda.5007 planetary nebula luminosity function (PNLF) span nearly a decade in oxygen abundance, and thus, support the use of the PNLF for deriving distances to galaxies (Jacoby 1996) with differing metallicities. We also identify a correlation between central star mass and PN dust formation that partially alleviates any dependence of the PNLF maximum magnitude on population age. Additionally, we identify a spatially compact group of 5 PNe having unusually high O/H; this subgroup may arise from a recent merger, but velocity information is needed to assess the true nature of the objects.

[Distribution and seasonal dynamics of meiofauna in intertidal zone of Qingdao sandy beaches, Shandong Province of East China].

PubMed

Li, Ha; Hua, Er; Zhang, Zhi-Nan

2012-12-01

An investigation was conducted on the abundance, group composition, and distribution of meiofauna at the Second Beach of Taiping Bay and the Shilaoren Beach in Qingdao in January, April, July, and October 2008, aimed to analyze the distribution and seasonal dynamics of meiofauna in the intertidal zone of Qingdao sandy beaches. The measurements of environmental factors, including sediment grain size, interstitial water salinity, interstitial water temperature, organic matter content (TOC), and chlorophyll a (Chl a) content, were made simultaneously. There existed obvious seasonal differences in the environment factors, which could be clustered into two groups, i. e. , spring-winter group (January and April) and summer-autumn group (July and October). At the Second Beach of Taiping Bay, the mean annual abundance of meiofauna was (1167.3 +/- 768.3) ind x 10 cm(-2), and the most dominant group was Nematoda, accounting for 91% of the total. The meiofaunal group composition and abundance at the Second Beach differed horizontally, with the abundance ranked as high tide zone < middle tide zone < low tide zone. The meiofaunal group composition and abundance also varied seasonally, with high values in spring/winter and low values in summer/autumn (spring > winter > autumn > summer). The vertical distribution of the meiofauna in the high and middle tide zones of the Second Beach varied seasonally too. The meiofauna migrated downward with increasing temperature, concentrated in surface layer in winter and migrated downward in summer. At the Shilaoren Beach, the mean annual abundance of meiofauna was (1130.2 +/- 1419.1) ind x 10 cm(-2), and Nematoda accounted for 85% of the total. There was a great similarity of the environmental factors in the middle tide zone of the Second Beach and Shilaoren Beach, which led to no differences in the meiofaunal group composition and abundance. However, the vertical distribution of the meiofauna differed between the two beaches. When the temperature decreased, the meiofauna at Shilaoren Beach migrated downward. The ANOVA and BIOENV analyses showed that the TOC and MD phi were most responsible for the distribution of meiofauna among the tidal zones, the interstitial water temperature, MD phi, and TOC were the main causes of the seasonal variation of meiofaunal group composition and abundance, whereas the sediment Chl a affected the vertical migration of meiofauna. Tourism-induced sediment variation was another factor affecting the meiofaunal abundance, group composition, and distribution.

Pattern Genes Suggest Functional Connectivity of Organs

NASA Astrophysics Data System (ADS)

Qin, Yangmei; Pan, Jianbo; Cai, Meichun; Yao, Lixia; Ji, Zhiliang

2016-05-01

Human organ, as the basic structural and functional unit in human body, is made of a large community of different cell types that organically bound together. Each organ usually exerts highly specified physiological function; while several related organs work smartly together to perform complicated body functions. In this study, we present a computational effort to understand the roles of genes in building functional connection between organs. More specifically, we mined multiple transcriptome datasets sampled from 36 human organs and tissues, and quantitatively identified 3,149 genes whose expressions showed consensus modularly patterns: specific to one organ/tissue, selectively expressed in several functionally related tissues and ubiquitously expressed. These pattern genes imply intrinsic connections between organs. According to the expression abundance of the 766 selective genes, we consistently cluster the 36 human organs/tissues into seven functional groups: adipose & gland, brain, muscle, immune, metabolism, mucoid and nerve conduction. The organs and tissues in each group either work together to form organ systems or coordinate to perform particular body functions. The particular roles of specific genes and selective genes suggest that they could not only be used to mechanistically explore organ functions, but also be designed for selective biomarkers and therapeutic targets.

Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages.

PubMed

Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

2016-01-01

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. Published by Oxford University Press on behalf of the Annals of Botany Company.

The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches

PubMed Central

Wemheuer, Bernd; Wemheuer, Franziska; Hollensteiner, Jacqueline; Meyer, Frauke-Dorothee; Voget, Sonja; Daniel, Rolf

2015-01-01

Phytoplankton blooms exhibit a severe impact on bacterioplankton communities as they change nutrient availabilities and other environmental factors. In the current study, the response of a bacterioplankton community to a Phaeocystis globosa spring bloom was investigated in the southern North Sea. For this purpose, water samples were taken inside and reference samples outside of an algal spring bloom. Structural changes of the bacterioplankton community were assessed by amplicon-based analysis of 16S rRNA genes and transcripts generated from environmental DNA and RNA, respectively. Several marine groups responded to bloom presence. The abundance of the Roseobacter RCA cluster and the SAR92 clade significantly increased in bloom presence in the total and active fraction of the bacterial community. Functional changes were investigated by direct sequencing of environmental DNA and mRNA. The corresponding datasets comprised more than 500 million sequences across all samples. Metatranscriptomic data sets were mapped on representative genomes of abundant marine groups present in the samples and on assembled metagenomic and metatranscriptomic datasets. Differences in gene expression profiles between non-bloom and bloom samples were recorded. The genome-wide gene expression level of Planktomarina temperata, an abundant member of the Roseobacter RCA cluster, was higher inside the bloom. Genes that were differently expressed included transposases, which showed increased expression levels inside the bloom. This might contribute to the adaptation of this organism toward environmental stresses through genome reorganization. In addition, several genes affiliated to the SAR92 clade were significantly upregulated inside the bloom including genes encoding for proteins involved in isoleucine and leucine incorporation. Obtained results provide novel insights into compositional and functional variations of marine bacterioplankton communities as response to a phytoplankton bloom. PMID:26322028

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

PubMed

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

Spatiotemporal diversity, structure and trophic guilds of insect assemblages in a semi-arid Sabkha ecosystem

PubMed Central

Menasria, Taha; Neffar, Souad; Chafaa, Smail; Bradai, Lyès; Chaibi, Rachid; Mekahlia, Mohamed Nacer; Bendjoudi, Djamel; Si Bachir, Abdelkrim

2015-01-01

The current study highlights some knowledge on the diversity and structure of insect communities and trophic groups living in Sabkha Djendli (semi-arid area of Northeastern Algeria). The entomofauna was monthly sampled from March to November 2006 using pitfall traps at eight sites located at the vicinity of the Sabkha. Structural and diversity parameters (species richness, Shannon index, evenness) were measured for both insect orders and trophic guilds. The canonical correspondence analysis (CCA) was applied to determine how vegetation parameters (species richness and cover) influence spatial and seasonal fluctuations of insect assemblages. The catches totalled 434 insect individuals classified into 75 species, 62 genera, 31 families and 7 orders, of which Coleoptera and Hymenoptera were the most abundant and constant over seasons and study stations. Spring and autumn presented the highest values of diversity parameters. Individual-based Chao-1 species richness estimator indicated 126 species for the total individuals captured in the Sabkha. Based on catch abundances, the structure of functional trophic groups was predators (37.3%), saprophages (26.7%), phytophages (20.5%), polyphages (10.8%), coprophages (4.6%); whereas in terms of numbers of species, they can be classified as phytophages (40%), predators (25.3%), polyphages (13.3%), saprophages (12%), coprophages (9.3%). The CCA demonstrated that phytophages and saprophages as well as Coleoptera and Orthoptera were positively correlated with the two parameters of vegetation, especially in spring and summer. While the abundance of coprophages was positively correlated with species richness of plants, polyphage density was positively associated with vegetation cover. The insect community showed high taxonomic and functional diversity that is closely related to diversity and vegetation cover in different stations of the wetland and seasons. PMID:25825682

Relationships Among Chondrite Groups as Inferred from Presolar-Grain Abundances

NASA Technical Reports Server (NTRS)

Huss, G. R.; Meshik, A. P.; Hohenberg, C. M.; Smith, J. B.

2002-01-01

Presolar-grain abundances show that C chondrites consist of two quite distinct groups, those containing primitive material, and those consisting of processed material. Ordinary chondrites are intermediate in many properties between these groups. Additional information is contained in the original extended abstract.

Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river.

PubMed

Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

2016-08-01

Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on bacterial group changes in polluted urban rivers.

Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil.

PubMed

Ahn, Jae-Hyung; Choi, Min-Young; Kim, Byung-Yong; Lee, Jong-Sik; Song, Jaekyeong; Kim, Gun-Yeob; Weon, Hang-Yeon

2014-08-01

The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.

Ecosystem size structure response to 21st century climate projection: large fish abundance decreases in the central North Pacific and increases in the California Current.

PubMed

Woodworth-Jefcoats, Phoebe A; Polovina, Jeffrey J; Dunne, John P; Blanchard, Julia L

2013-03-01

Output from an earth system model is paired with a size-based food web model to investigate the effects of climate change on the abundance of large fish over the 21st century. The earth system model, forced by the Intergovernmental Panel on Climate Change (IPCC) Special report on emission scenario A2, combines a coupled climate model with a biogeochemical model including major nutrients, three phytoplankton functional groups, and zooplankton grazing. The size-based food web model includes linkages between two size-structured pelagic communities: primary producers and consumers. Our investigation focuses on seven sites in the North Pacific, each highlighting a specific aspect of projected climate change, and includes top-down ecosystem depletion through fishing. We project declines in large fish abundance ranging from 0 to 75.8% in the central North Pacific and increases of up to 43.0% in the California Current (CC) region over the 21st century in response to change in phytoplankton size structure and direct physiological effects. We find that fish abundance is especially sensitive to projected changes in large phytoplankton density and our model projects changes in the abundance of large fish being of the same order of magnitude as changes in the abundance of large phytoplankton. Thus, studies that address only climate-induced impacts to primary production without including changes to phytoplankton size structure may not adequately project ecosystem responses. © 2012 Blackwell Publishing Ltd.

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

PubMed

Jiao, Shuo; Luo, Yantao; Lu, Mingmei; Xiao, Xiao; Lin, Yanbing; Chen, Weimin; Wei, Gehong

2017-06-01

Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl 2 ) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for β-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Balancing ecosystem function, services and disservices resulting from expanding goose populations.

PubMed

Buij, Ralph; Melman, Theodorus C P; Loonen, Maarten J J E; Fox, Anthony D

2017-03-01

As goose populations increase in abundance, their influence on ecological processes is increasing. We review the evidence for key ecological functions of wild goose populations in Eurasia and North America, including aquatic invertebrate and plant propagule transport, nutrient deposition in terrestrial and aquatic ecosystems, the influence of goose populations on vegetation biomass, carbon storage and methane emission, species diversity and disease transmission. To estimate the implications of their growing abundance for humans, we explore how these functions contribute to the provision of ecosystem services and disservices. We assess the weight, extent and trends among such impacts, as well as the balance of their value to society. We examine key unresolved issues to enable a more balanced assessment of the economic costs or benefits of migratory geese along their flyways, including the spatial and temporal variation in services and their contrasting value to different user groups. Many ecological functions of geese are concluded to provide neither services nor disservices and, ecosystem disservices currently appear to outweigh services, although this varies between regions. We consider an improved quantification of ecosystem services and disservices, and how these vary along population flyways with respect to variation in valuing certain cultural services, and under different management scenarios aimed at reducing their disservices, essential for a more balanced management of goose populations.

Dietary Selenium Deficiency or Excess Reduces Sperm Quality and Testicular mRNA Abundance of Nuclear Glutathione Peroxidase 4 in Rats.

PubMed

Zhou, Ji-Chang; Zheng, Shijie; Mo, Junluan; Liang, Xiongshun; Xu, Yuanfei; Zhang, Huimin; Gong, Chunmei; Liu, Xiao-Li; Lei, Xin Gen

2017-10-01

Background: Glutathione peroxidase (GPX) 4 and selenoprotein P (SELENOP) are abundant, and several variants are expressed in the testis. Objective: We determined the effects of dietary selenium deficiency or excess on sperm quality and expressions of GPX4 and SELENOP variants in rat testis and liver. Methods: After weaning, male Sprague-Dawley rats were fed a Se-deficient basal diet (BD) for 5 wk until they were 9 wk old [mean ± SEM body weight (BW) = 256 ± 5 g]. They were then fed the BD diet alone (deficient) or with 0.25 (adequate), 3 (excess), or 5 (excess) mg Se/kg for 4 wk. Testis, liver, blood, and semen were collected to assay for selenoprotein mRNA and protein abundances, selenium concentration, GPX activity, 8-hydroxy-deoxyguanosine concentration, and sperm quality. Results: Dietary selenium supplementations elevated ( P < 0.05) tissue selenium concentrations and GPX activities. Compared with those fed BD + 0.25 mg Se/kg, rats fed BD showed lower ( P < 0.05) BW gain (86%) and sperm density (57%) but higher ( P < 0.05) plasma 8-hydroxy-deoxyguanosine concentrations (189%), and nonprogressive sperm motility (4.4-fold). Likewise, rats fed BD + 5 mg Se/kg had ( P = 0.06) lower BW gain and higher (1.9-fold) sperm deformity rates than those in the selenium-adequate group. Compared with the selenium-adequate group, dietary selenium deficiency (BD) or excess (BD + 3 or 5 mg Se/kg) resulted in 45-77% lower ( P < 0.05) nuclear Gpx4 ( nGpx4 ) mRNA abundance in the testis. Rats fed BD had lower ( P < 0.05) mRNA levels of 2 Selenop variants in both testis and liver than those in the other groups. Testicular SELENOP was 155-170% higher ( P < 0.05) in rats fed BD + 5 mg Se/kg and hepatic c/mGPX4 was 13-15% lower ( P < 0.05) in rats fed BD than in the other groups. Conclusions: The mRNA abundance of rat testicular nGPX4 responded to dietary selenium concentrations in similar ways to sperm parameters and may be used as a sensitive marker to assess appropriate Se status for male function. © 2017 American Society for Nutrition.

The Abundances of the Fe Group Elements in Early B Stars in the Magellanic Clouds and Our Galaxy

NASA Astrophysics Data System (ADS)

Peters, Geraldine Joan; Adelman, Saul Joseph

2015-08-01

The abundances of the Fe-peak elements (Ti, V, Cr, Mn, Fe, Co, and Ni) are of interest as they are important for assessing opacities for stellar evolution calculations, confirming theoretical calculations of explosive nucleosynthesis, and inferring the past history of supernova activity in a galaxy. FUSE FUV spectra of early B stars in the LMC and SMC and HST/STIS FUV/NUV spectra of nearby B stars in our galaxy are analyzed with the Hubeny/Lanz programs TLUSTY/SYNSPEC to determine abundance for the Fe group elements and produce a map of these abundances in the Magellanic Clouds (MC) and Magellanic Bridge (MB). Except for four weak multiplets of Fe III there are no measurable lines from the Fe group in the optical region. The Fe group species found in the FUV spectra of early B stars are primarily in the second stage of ionization. The best set of lines in the FUSE spectral region are Fe III (UV1), V III 1150 Å, and Cr III 1137 Å. Analysis of the galactic B stars provides a good assessment of the reliability of the atomic parameters that are used for the MC calculations. Twenty-two early B stars in the MC and MB and five in our galaxy were analyzed. In general the Fe group abundances range from solar to slightly below solar in our region of the galaxy. But in the MCs the abundances of V, Cr, and Fe tend to be significantly lower than the mean metal abundances for the galaxy. Maps of the Fe group abundances and their variations in the LMC and SMC, tracers of recent enrichment of the ISM from supernova activity, are shown. Support from NASA grants NAG5-13212, NNX10AD66G, STScI HST-GO-13346.22, and USC’s Women in Science and Engineering (WiSE) program is greatly appreciated.

The Abundances of the Fe Group Elements in Early B Stars in the Magellanic Clouds and Bridge

NASA Astrophysics Data System (ADS)

Peters, Geraldine J.; Adelman, Saul J.

2016-01-01

The abundances of three Fe Group elements (V, Cr, and Fe) in 9 early main-sequence band B stars in the LMC, 7 in the SMC , and two in the Magellanic Bridge have been determined from archival FUSE observations and the Hubeny/Lanz NLTE programs TLUSTY/SYNSPEC. Lines from the Fe group elements, except for a few weak multiplets of Fe III, are not observable in the optical spectral region. The best set of lines in the FUSE spectral region are Fe III (UV1), V III 1150 Å, and Cr III 1137 Å. The abundances of these elements in early B stars are a marker for recent SNe Ia activity, as a single exploding white dwarf can deliver 0.5 solar masses of Ni-56 that decays into Fe to the ISM. The Fe group abundances in an older population of stars primarily reflect SNe II activity, in which a single explosion delivers only 0.07 solar masses of Ni-56 to the ISM (the rest remains trapped in the neutron star). The abundances of the Fe group elements in early B stars not only track SNe Ia activity but are also important for computing evolutionary tracks for massive stars. In general, the Fe abundance relative to the sun's value is comparable to the mean abundances for the lighter elements in the Clouds/Bridge but the values of [V,Cr/Fe]sun are smaller. This presentation will discuss the spatial distribution of the Fe Group elements in the Magellanic Clouds, and compare it with our galaxy in which the abundance of Fe declines with radial distance from the center. Support from NASA grants NAG5-13212, NNX10AD66G, STScI HST-GO-13346.22, and USC's Women in Science and Engineering (WiSE) program is greatly appreciated.

Environmental drivers of the distribution of nitrogen functional genes at a watershed scale.

PubMed

Tsiknia, Myrto; Paranychianakis, Nikolaos V; Varouchakis, Emmanouil A; Nikolaidis, Nikolaos P

2015-06-01

To date only few studies have dealt with the biogeography of microbial communities at large spatial scales, despite the importance of such information to understand and simulate ecosystem functioning. Herein, we describe the biogeographic patterns of microorganisms involved in nitrogen (N)-cycling (diazotrophs, ammonia oxidizers, denitrifiers) as well as the environmental factors shaping these patterns across the Koiliaris Critical Zone Observatory, a typical Mediterranean watershed. Our findings revealed that a proportion of variance ranging from 40 to 80% of functional genes abundance could be explained by the environmental variables monitored, with pH, soil texture, total organic carbon and potential nitrification rate being identified as the most important drivers. The spatial autocorrelation of N-functional genes ranged from 0.2 to 6.2 km and prediction maps, generated by cokriging, revealed distinct patterns of functional genes. The inclusion of functional genes in statistical modeling substantially improved the proportion of variance explained by the models, a result possibly due to the strong relationships that were identified among microbial groups. Significant relationships were set between functional groups, which were further mediated by land use (natural versus agricultural lands). These relationships, in combination with the environmental variables, allow us to provide insights regarding the ecological preferences of N-functional groups and among them the recently identified clade II of nitrous oxide reducers. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

PubMed Central

Graves, Christopher J.; Makrides, Elizabeth J.; Schmidt, Victor T.; Giblin, Anne E.; Cardon, Zoe G.

2016-01-01

ABSTRACT Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. IMPORTANCE In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. PMID:26944843

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.

PubMed

Graves, Christopher J; Makrides, Elizabeth J; Schmidt, Victor T; Giblin, Anne E; Cardon, Zoe G; Rand, David M

2016-05-01

Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. Copyright © 2016 Graves et al.

De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

PubMed Central

Li, De-Zhu; Guo, Zhen-Hua

2012-01-01

Background Transcriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species, and the advent of next-generation sequencing (NGS) technologies has greatly decreased the cost and time required for this process. Transcriptome data are especially desirable in bamboo species, as certain members constitute an economically and culturally important group of mostly semelparous plants with remarkable flowering features, yet little bamboo genomic research has been performed. Here we present, for the first time, extensive sequence and transcript abundance data for the floral transcriptome of a key bamboo species, Dendrocalamus latiflorus, obtained using the Illumina GAII sequencing platform. Our further goal was to identify patterns of gene expression during bamboo flower development. Results Approximately 96 million sequencing reads were generated and assembled de novo, yielding 146,395 high quality unigenes with an average length of 461 bp. Of these, 80,418 were identified as putative homologs of annotated sequences in the public protein databases, of which 290 were associated with the floral transition and 47 were related to flower development. Digital abundance analysis identified 26,529 transcripts differentially enriched between two developmental stages, young flower buds and older developing flowers. Unigenes found at each stage were categorized according to their putative functional categories. These sequence and putative function data comprise a resource for future investigation of the floral transition and flower development in bamboo species. Conclusions Our results present the first broad survey of a bamboo floral transcriptome. Although it will be necessary to validate the functions carried out by these genes, these results represent a starting point for future functional research on D. latiflorus and related species. PMID:22916120

Large woody debris input and its influence on channel structure in agricultural lands of Southeast Brazil.

PubMed

de Paula, Felipe Rossetti; Ferraz, Silvio Frosini de Barros; Gerhard, Pedro; Vettorazzi, Carlos Alberto; Ferreira, Anderson

2011-10-01

Riparian forests are important for the structure and functioning of stream ecosystems, providing structural components such as large woody debris (LWD). Changes in these forests will cause modifications in the LWD input to streams, affecting their structure. In order to assess the influence of riparian forests changes in LWD supply, 15 catchments (third and fourth order) with riparian forests at different conservation levels were selected for sampling. In each catchment we quantified the abundance, volume and diameter of LWD in stream channels; the number, area and volume of pools formed by LWD and basal area and tree diameter of riparian forest. We found that riparian forests were at a secondary successional stage with predominantly young trees (diameter at breast height <10 cm) in all studied streams. Results showed that basal area and diameter of riparian forest differed between the stream groups (forested and non-forested), but tree density did not differ between groups. Differences were also observed in LWD abundance, volume, frequency of LWD pools with subunits and area and volume of LWD pools. LWD diameter, LWD that form pools diameter and frequency of LWD pools without subunits did not differ between stream groups. Regression analyses showed that LWD abundance and volume, and frequency of LWD pools (with and without subunits) were positively related with the proportion of riparian forest. LWD diameter was not correlated to riparian tree diameter. The frequency of LWD pools was correlated to the abundance and volume of LWD, but characteristics of these pools (area and volume) were not correlated to the diameter of LWD that formed the pools. These results show that alterations in riparian forest cause modifications in the LWD abundance and volume in the stream channel, affecting mainly the structural complexity of these ecosystems (reduction in the number and structural characteristics of LWD pools). Our results also demonstrate that riparian forest conservation actions must consider not only its extension, but also successional stage to guarantee the quantity and quality of LWD necessary to enable the structuring of stream channels.

Visible Light Organic Photoredox-Catalyzed C-H Alkoxylation of Imidazopyridine with Alcohol.

PubMed

Kibriya, Golam; Samanta, Sadhanendu; Jana, Sourav; Mondal, Susmita; Hajra, Alakananda

2017-12-15

The visible light-mediated C-3 alkoxylation of imidazopyridines with alcohols has been achieved using rose bengal as an organic photoredox catalyst at room temperature. Widely abundant air acts as the terminal oxidant that avoids the use of a stoichiometric amount of peroxo compounds. A wide range of functional groups could be tolerated under the reaction conditions to produce C(sp 2 )-H alkoxylated products in high yields.

The Lithium Abundances of a Large Sample of Red Giants

NASA Astrophysics Data System (ADS)

Liu, Y. J.; Tan, K. F.; Wang, L.; Zhao, G.; Sato, Bun'ei; Takeda, Y.; Li, H. N.

2014-04-01

The lithium abundances for 378 G/K giants are derived with non-local thermodynamic equilibrium correction considered. Among these are 23 stars that host planetary systems. The lithium abundance is investigated, as a function of metallicity, effective temperature, and rotational velocity, as well as the impact of a giant planet on G/K giants. The results show that the lithium abundance is a function of metallicity and effective temperature. The lithium abundance has no correlation with rotational velocity at v sin i < 10 km s-1. Giants with planets present lower lithium abundance and slow rotational velocity (v sin i < 4 km s-1). Our sample includes three Li-rich G/K giants, 36 Li-normal stars, and 339 Li-depleted stars. The fraction of Li-rich stars in this sample agrees with the general rate of less than 1% in the literature, and the stars that show normal amounts of Li are supposed to possess the same abundance at the current interstellar medium. For the Li-depleted giants, Li-deficiency may have already taken place at the main sequence stage for many intermediate mass (1.5-5 M ⊙) G/K giants. Finally, we present the lithium abundance and kinematic parameters for an enlarged sample of 565 giants using a compilation of the literature, and confirm that the lithium abundance is a function of metallicity and effective temperature. With the enlarged sample, we investigate the differences between the lithium abundance in thin-/thick-disk giants, which indicate that the lithium abundance in thick-disk giants is more depleted than that in thin-disk giants.

Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition.

PubMed

Tonietto, Rebecca K; Ascher, John S; Larkin, Daniel J

2017-04-01

Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the midwestern United States, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to provide ancillary benefits to bees through increased foraging and nesting resources. We investigated community assembly of bees across a chronosequence of restored eastern tallgrass prairies and compared patterns to those in control and reference habitats (old fields and prairie remnants, respectively). We collected bees for 3 yr and measured diversity and abundance of in-bloom flowering plants, vegetation structure, ground cover, and surrounding land use as predictors of bee abundance and bee taxonomic and functional diversity. We found that site-level variables, but not site type or restoration age, were significant predictors of bee abundance (bloom diversity, P = 0.004; bare ground cover, P = 0.02) and bee diversity (bloom diversity, P = 0.01). There were significant correlations between overall composition of bee and blooming plant communities (Mantel test, P = 0.002), and both plant and bee assemblages in restorations were intermediate between those of old fields and remnant prairies. Restorations exhibited high bee beta diversity, i.e., restored sites' bee assemblages were taxonomically and functionally differentiated from each other. This pattern was strong in younger restorations (<20 yr old), but absent from older restorations (>20 yr), suggesting restored prairie bee communities become more similar to one another and more similar to remnant prairie bee communities over time with the arrival of more species and functional groups of bees. Our results indicate that old fields, restorations, and remnants provide habitat for diverse and abundant bee communities, but continued restoration of old fields will help support and conserve bee communities more similar to reference bee communities characteristic of remnant prairies. © 2016 by the Ecological Society of America.

Mapping genomic features to functional traits through microbial whole genome sequences.

PubMed

Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

2014-01-01

Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

Pinenes: Abundant and Renewable Building Blocks for a Variety of Sustainable Polymers.

PubMed

Winnacker, Malte

2018-05-14

Pinenes - a group of monoterpenes containing a double bond - are very suitable renewable building blocks for a variety of sustainable polymers and materials. Their abundance from mainly non-edible parts of plants as well as the feasibility to isolate them render these compounds unique amongst the variety of biomass that is utilizable for novel materials. Accordingly, their use for the synthesis of biobased polymers has been investigated intensively, and strong progress has been made with this especially within the past 2-3 years. Direct cationic or radical polymerization via the double bonds as well as polymerization upon their further functionalization can afford a variety of sustainable polymers suitable for many applications, which is summarized in this article. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Does allopreening control avian ectoparasites?

PubMed

Villa, Scott M; Goodman, Graham B; Ruff, James S; Clayton, Dale H

2016-07-01

For birds, the first line of defence against ectoparasites is preening. The effectiveness of self-preening for ectoparasite control is well known. By contrast, the ectoparasite control function of allopreening-in which one birds preens another-has not been rigorously tested. We infested captive pigeons with identical numbers of parasitic lice, and then compared rates of allopreening to the abundance of lice on the birds over time. We documented a negative relationship between rates of allopreening and the number of lice on birds. Moreover, we found that allopreening was a better predictor of louse abundance than self-preening. Our data suggest that allopreening may be a more important means of ectoparasite defence than self-preening when birds live in groups. Our results have important implications for the evolution of social behaviour. © 2016 The Author(s).

Effects of an increase in population of sika deer on beetle communities in deciduous forests.

PubMed

Iida, Taichi; Soga, Masashi; Koike, Shinsuke

2016-01-01

The overabundance of large herbivores is now recognized as a serious ecological problem. However, the resulting ecological consequences remain poorly understood. The ecological effects of an increase in sika deer, Cervus nippon Temminck (Cervidae), on three insect groups of beetles was investigated: ground beetles (Carabidae), carrion beetles (Silphidae), and dung beetles (Scarabaeidae and Geotrupidae) on Nakanoshima Island, Hokkaido, northern Japan. We collected beetles on Nakanoshima Island (experimental site) and lakeshore areas (control site) and compared the species richness, abundance, diversity index, and community composition of beetles between the sites. Results showed that although both species diversity and abundance of carabid beetles were significantly higher at the lakeshore site, those of dung and carrion beetles were higher at the island site. It was additionally observed that abundance of larger carabid beetles was higher at the lakeshore site, whereas that of small-sized carabid beetles did not differ between the lakeshore and island sites. For dung beetles, abundance of smaller species was higher at the island site, whereas that of large species did not differ between the lakeshore and island sites. Abundance of two body sizes (small and large) of carrion beetles were both higher at the island site. Overall, the findings of this study demonstrated that an increase in deer population altered the insect assemblages at an island scale, suggesting further changes in ecosystem functions and services in this region.

High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers.

PubMed

Yu, Tiantian; Liang, Qianyong; Niu, Mingyang; Wang, Fengping

2017-08-01

The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ant diversity as a direct and indirect driver of pselaphine rove beetle (Coleoptera: Staphylinidae) functional diversity in tropical rainforests, Sabah, Malaysian Borneo.

PubMed

Psomas, Elizabeth; Holdsworth, Sholto; Eggleton, Paul

2018-04-20

Pselaphinae is a species-rich beetle subfamily found globally, with many exhibiting myrmecophily-a symbiotic association with ants. Pselaphine-ant associations vary from facultative to obligate, but direct behavioral observations still remain scarce. Pselaphines are speciose and ecologically abundant within tropical leaf litter invertebrate communities where ants dominate, implying a potentially important ecological role that may be affected by habitat disturbances that impact ants. In this study, we measured and analyzed putative functional traits of leaf litter pselaphines associated with myrmecophily through morphometric analysis. We calculated "myrmecophile functional diversity" of pselaphines at different sites and examined this measure's relationship with ant abundance, in both old growth and logged rainforest sites in Sabah, Borneo. We show that myrmecophile functional diversity of pselaphine beetles increases as ant abundance increases. Old growth rainforest sites support a high abundance of ants, which is associated with a high abundance of probable myrmecophilous pselaphines. These results suggest a potential link between adult morphological characters and the functional role these beetles play in rainforest litter as ecological interaction partners with ants. © 2018 Wiley Periodicals, Inc.

Impact of Grassland Reseeding, Herbicide Spraying and Ploughing on Diversity and Abundance of Soil Arthropods.

PubMed

Liu, Wei; Zhang, Junling; Norris, Stuart L; Murray, Philip J

2016-01-01

In order to determine the interactive effect of reseeding, herbicide spraying and ploughing on soil fauna communities, we conducted a grassland reseeding experiment combined with pre-reseed management to examine how with the whole reseeding process affects soil faunal composition. Sampling occasions and exact treatments were as follows: (1) before chemical herbicide spray; (2) after spray but before ploughing; (3) after ploughing but before reseeding; and (4) after 1 year of recovery. Our results demonstrate that, Acari and Collembola were the two soil fauna taxa with the highest abundance and accounted for around 96% of the relative total abundance among the various managements. Herbicide application tended to increase soil invertebrate abundance. Conversely, subsequent ploughing significantly reduced soil invertebrate abundance and had an obvious negative effect on soil primary and secondary decomposers, which were mainly due to the variations of Acari (especially Oribatida) and Coleoptera group abundance. Moreover, reseeding also reduced the individual number of the groups mentioned above, and favored those predators with a larger body size and individual weight. After 1 year recovery, Collembola abundance recovered to the pre-treatment levels, while with Arthropod and Acari groups were still fluctuating.

Impact of Grassland Reseeding, Herbicide Spraying and Ploughing on Diversity and Abundance of Soil Arthropods

PubMed Central

Liu, Wei; Zhang, Junling; Norris, Stuart L.; Murray, Philip J.

2016-01-01

In order to determine the interactive effect of reseeding, herbicide spraying and ploughing on soil fauna communities, we conducted a grassland reseeding experiment combined with pre-reseed management to examine how with the whole reseeding process affects soil faunal composition. Sampling occasions and exact treatments were as follows: (1) before chemical herbicide spray; (2) after spray but before ploughing; (3) after ploughing but before reseeding; and (4) after 1 year of recovery. Our results demonstrate that, Acari and Collembola were the two soil fauna taxa with the highest abundance and accounted for around 96% of the relative total abundance among the various managements. Herbicide application tended to increase soil invertebrate abundance. Conversely, subsequent ploughing significantly reduced soil invertebrate abundance and had an obvious negative effect on soil primary and secondary decomposers, which were mainly due to the variations of Acari (especially Oribatida) and Coleoptera group abundance. Moreover, reseeding also reduced the individual number of the groups mentioned above, and favored those predators with a larger body size and individual weight. After 1 year recovery, Collembola abundance recovered to the pre-treatment levels, while with Arthropod and Acari groups were still fluctuating. PMID:27555863

Soil Microbial Community Responses to Short-term Multiple Experimental Climate Change Drivers

NASA Astrophysics Data System (ADS)

Li, Guanlin; Lee, Jongyeol; Lee, Sohye; Roh, Yujin; Son, Yowhan

2016-04-01

It is agreed that soil microbial communities are responsible for the cycling of carbon and nutrients in ecosystems; however, the response of these microbial communities to climate change has not been clearly understood. In this study, we measured the direct and interactive effects of climate change drivers on soil bacterial and fungal communities (abundance and composition) in an open-field multifactor climate change experiment. The experimental treatment system was established with two-year-old Pinus densiflora seedlings at Korea University in April 2013, and consisted of six different treatments with three replicates: two levels of air temperature warming (control and +3° C) were crossed with three levels of precipitation manipulation (control, -30% and +30%). After 2.5 years of treatments, in August, 2015, soil samples were collected from the topsoil (0-15cm) of all plots (n=18). High-throughput sequencing technology was used to assess the abundance and composition of soil bacterial and fungal community. Analysis of variance for a blocked split-plot design was used to detect the effects of climate change drivers and their interaction on the abundance and composition of soil bacterial and fungal community. Our results showed that 1) only the significant effect of warming on fungal community abundance was observed (P <0.05); 2) on average, warming decreased both bacterial and fungal community abundance by 20.90% and 32.30%, 6.69% and 45.89%, 14.71% and 19.56% in control, decreased, and increased precipitation plots, respectively; 3) however, warming increased the relative bacterium/fungus ratio on average by 14.03%, 37.03% and 14.31% in control, decreased, and increased precipitation plots, respectively; 4) the phylogenetic distribution of bacterial and fungal groups and their relative abundance varied among treatments; 5) treatments altered the relative abundance of Ascomycota and Basidiomycota, where Ascomycota decreased with a concomitant increase in the Basidiomycota across all treatments; and 6) the shift induced by treatments in the dominant fungal group was larger than bacterial group. Since soil microorganisms differ in their susceptibility to stressors, the changes in the soil microbial communities may result from treatment-induced shifts in soil temperature and moisture. Our results indicate that climate change drivers and their interactions may cause changes in abundance and composition of soil microbial communities, especially for the fungal community. These results illustrate climate change drivers and their interactions may select for distinct soil microbial communities, and these community changes may shape the way ecosystems function in the future. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

WRKY transcription factor genes in wild rice Oryza nivara.

PubMed

Xu, Hengjian; Watanabe, Kenneth A; Zhang, Liyuan; Shen, Qingxi J

2016-08-01

The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Response of rocky invertebrate diversity, structure and function to the vertical layering of vegetation

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Gorostiaga, José María; Saiz-Salinas, José Ignacio

2014-06-01

Macroalgae comprise a prominent part of the rocky benthos where many invertebrates develop, and are believed to be undergoing severe declines worldwide. In order to investigate how the vegetation structure (crustose, basal and canopy layers) contributes to the diversity, structure and function of benthic invertebrates, a total of 31 subtidal transects were sampled along the northeast Atlantic coast of Spain. Significant positive relationships were found between the canopy layer and faunal abundance, taxonomic diversity and functional group diversity. Canopy forming algae were also related to epiphytic invertebrates, medium size forms, colonial strategy and suspensivores. By contrast, basal algae showed negative relationships with all variables tested except for detritivores. Multivariate multiple regression analyses (DISTLM) point to crustose as well as canopy layers as the best link between seaweeds and invertebrate assemblage structure. A close relationship was found between taxonomic and functional diversities. In general, low levels of taxonomic redundancy were detected for functional groups correlated with vegetation structure. A conceptual model based on the results is proposed, describing distinct stages of invertebrate assemblages in relation to the vertical structure of vegetation.

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

PubMed Central

2013-01-01

Background The diverse microbial populations that inhabit pristine aquifers are known to catalyze critical in situ biogeochemical reactions, yet little is known about how the structure and diversity of this subsurface community correlates with and impacts upon groundwater chemistry. Herein we examine 8,786 bacterial and 8,166 archaeal 16S rRNA gene sequences from an array of monitoring wells in the Mahomet aquifer of east-central Illinois. Using multivariate statistical analyses we provide a comparative analysis of the relationship between groundwater chemistry and the microbial communities attached to aquifer sediment along with those suspended in groundwater. Results Statistical analyses of 16S rRNA gene sequences showed a clear distinction between attached and suspended communities; with iron-reducing bacteria far more abundant in attached samples than suspended, while archaeal clones related to groups associated with anaerobic methane oxidation and deep subsurface gold mines (ANME-2D and SAGMEG-1, respectively) distinguished the suspended community from the attached. Within the attached bacterial community, cloned sequences most closely related to the sulfate-reducing Desulfobacter and Desulfobulbus genera represented 20% of the bacterial community in wells where the concentration of sulfate in groundwater was high (> 0.2 mM), compared to only 3% in wells with less sulfate. Sequences related to the genus Geobacter, a genus containing ferric-iron reducers, were of nearly equal abundance (15%) to the sulfate reducers under high sulfate conditions, however their relative abundance increased to 34% when sulfate concentrations were < 0.03 mM. Also, in areas where sulfate concentrations were <0.03 mM, archaeal 16S rRNA gene sequences similar to those found in methanogens such as Methanosarcina and Methanosaeta comprised 73–80% of the community, and dissolved CH4 ranged between 220 and 1240 μM in these groundwaters. In contrast, methanogens (and their product, CH4) were nearly absent in samples collected from groundwater samples with > 0.2 mM sulfate. In the suspended fraction of wells where the concentration of sulfate was between 0.03 and 0.2 mM, the archaeal community was dominated by sequences most closely related to the ANME-2D, a group of archaea known for anaerobically oxidizing methane. Based on available energy (∆GA) estimations, results varied little for both sulfate reduction and methanogenesis throughout all wells studied, but could favor anaerobic oxidation of methane (AOM) in wells containing minimal sulfate and dihydrogen, suggesting AOM coupled with H2-oxidizing organisms such as sulfate or iron reducers could be an important pathway occurring in the Mahomet aquifer. Conclusions Overall, the results show several distinct factors control the composition of microbial communities in the Mahomet aquifer. Bacteria that respire insoluble substrates such as iron oxides, i.e. Geobacter, comprise a greater abundance of the attached community than the suspended regardless of groundwater chemistry. Differences in community structure driven by the concentration of sulfate point to a clear link between the availability of substrate and the abundance of certain functional groups, particularly iron reducers, sulfate reducers, methanogens, and methanotrophs. Integrating both geochemical and microbiological observations suggest that the relationships between these functional groups could be driven in part by mutualism, especially between ferric-iron and sulfate reducers. PMID:23800252

Molecular simulation of CO2/CH4 adsorption in brown coal: Effect of oxygen-, nitrogen-, and sulfur-containing functional groups

NASA Astrophysics Data System (ADS)

Dang, Yong; Zhao, Lianming; Lu, Xiaoqing; Xu, Jing; Sang, Pengpeng; Guo, Sheng; Zhu, Houyu; Guo, Wenyue

2017-11-01

The CO2/CH4 adsorption behaviors in brown coal at the temperatures of 298, 313, and 373 K and in the pressure range of 0.005-10 MPa were investigated by molecular dynamics (MD), density functional theory (DFT), and grand canonical Monte Carlo (GCMC) simulations. The absolute adsorption isotherms of single-component CH4 and CO2 exhibit type-I Langmuir adsorption behavior showing a negative influence of temperature. For the binary CO2/CH4 mixture, brown coal shows super high selectivity of CO2 over CH4 at pressures below 0.2 MPa, which then decreases quickly and finally tends to be constant when the pressure increases. The high competitive adsorption of CO2 originates from the effects of (i) the large electrostatic contributions, (ii) the conducive micropore environment with pore sizes below 0.56 nm, and (iii) the stronger adsorption of CO2 with respect to CH4. These effects are strengthened by the high-density oxygen-containing, pyridine, and thiophene functional groups contained in brown coal, which provide abundant and strong adsorption sites for CO2, but show weaker affinity to CH4. Furthermore, the influence of various nitrogen- and sulfur-containing functional groups on the CO2 adsorption capacity was also investigated. The results indicate that the basicity of the oxygen- and nitrogen-containing groups has a large influence on the CO2 adsorption, while for the sulfur functional groups the determining factor is the polarity.

Gut microbiomes of Indian children of varying nutritional status.

PubMed

Ghosh, Tarini Shankar; Gupta, Sourav Sen; Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S; Nair, G Balakrish

2014-01-01

Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.

Gut Microbiomes of Indian Children of Varying Nutritional Status

PubMed Central

Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S.; Nair, G. Balakrish

2014-01-01

Background Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Methodology/Principal Findings Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. Conclusions The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition. PMID:24763225

Effects of invasive plants on arthropods.

PubMed

Litt, Andrea R; Cord, Erin E; Fulbright, Timothy E; Schuster, Greta L

2014-12-01

Non-native plants have invaded nearly all ecosystems and represent a major component of global ecological change. Plant invasions frequently change the composition and structure of vegetation communities, which can alter animal communities and ecosystem processes. We reviewed 87 articles published in the peer-reviewed literature to evaluate responses of arthropod communities and functional groups to non-native invasive plants. Total abundance of arthropods decreased in 62% of studies and increased in 15%. Taxonomic richness decreased in 48% of studies and increased in 13%. Herbivorous arthropods decreased in response to plant invasions in 48% of studies and increased in 17%, likely due to direct effects of decreased plant diversity. Predaceous arthropods decreased in response to invasive plants in 44% of studies, which may reflect indirect effects due to reductions in prey. Twenty-two percent of studies documented increases in predators, which may reflect changes in vegetation structure that improved mobility, survival, or web-building for these species. Detritivores increased in 67% of studies, likely in response to increased litter and decaying vegetation; no studies documented decreased abundance in this functional group. Although many researchers have examined effects of plant invasions on arthropods, sizeable information gaps remain, specifically regarding how invasive plants influence habitat and dietary requirements. Beyond this, the ability to predict changes in arthropod populations and communities associated with plant invasions could be improved by adopting a more functional and mechanistic approach. Understanding responses of arthropods to invasive plants will critically inform conservation of virtually all biodiversity and ecological processes because so many organisms depend on arthropods as prey or for their functional roles, including pollination, seed dispersal, and decomposition. Given their short generation times and ability to respond rapidly to ecological change, arthropods may be ideal targets for restoration and conservation activities. © 2014 Society for Conservation Biology.

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

PubMed

Meereis, Florian; Kaufmann, Michael

2004-10-15

The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

The deep biosphere in terrestrial sediments in the chesapeake bay area, virginia, USA.

PubMed

Breuker, Anja; Köweker, Gerrit; Blazejak, Anna; Schippers, Axel

2011-01-01

For the first time quantitative data on the abundance of Bacteria, Archaea, and Eukarya in deep terrestrial sediments are provided using multiple methods (total cell counting, quantitative real-time PCR, Q-PCR and catalyzed reporter deposition-fluorescence in situ hybridization, CARD-FISH). The oligotrophic (organic carbon content of ∼0.2%) deep terrestrial sediments in the Chesapeake Bay area at Eyreville, Virginia, USA, were drilled and sampled up to a depth of 140 m in 2006. The possibility of contamination during drilling was checked using fluorescent microspheres. Total cell counts decreased from 10(9) to 10(6) cells/g dry weight within the uppermost 20 m, and did not further decrease with depth below. Within the top 7 m, a significant proportion of the total cell counts could be detected with CARD-FISH. The CARD-FISH numbers for Bacteria were about an order of magnitude higher than those for Archaea. The dominance of Bacteria over Archaea was confirmed by Q-PCR. The down core quantitative distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes as well as functional genes involved in different biogeochemical processes was revealed by Q-PCR for the uppermost 10 m and for 80-140 m depth. Eukarya and the Fe(III)- and Mn(IV)-reducing bacterial group Geobacteriaceae were almost exclusively found in the uppermost meter (arable soil), where reactive iron was detected in higher amounts. The bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi, highly abundant in marine sediments, were found up to the maximum sampling depth in high copy numbers at this terrestrial site as well. A similar high abundance of the functional gene cbbL encoding for the large subunit of RubisCO suggests that autotrophic microorganisms could be relevant in addition to heterotrophs. The functional gene aprA of sulfate reducing bacteria was found within distinct layers up to ca. 100 m depth in low copy numbers. The gene mcrA of methanogens was not detectable. Cloning and sequencing data of 16S rRNA genes revealed sequences of typical soil Bacteria. The closest relatives of the archaeal sequences were Archaea recovered from terrestrial and marine environments. Phylogenetic analysis of the Crenarchaeota and Euryarchaeota revealed new members of the uncultured South African Gold Mine Group, Deep Sea Hydrothermal Vent Euryarchaeotal Group 6, and Miscellaneous Crenarcheotic Group clusters.

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

PubMed Central

Smith, Cindy J.; Dong, Liang F.; Wilson, John; Stott, Andrew; Osborn, A. Mark; Nedwell, David B.

2015-01-01

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Colne estuary over an annual cycle. Denitrification rates declined down the estuary, while DNRA rates were higher at the estuary head and middle than the EM. In four out of the six 2-monthly time-points, rates of DNRA were greater than denitrification at each site. Abundance of gene markers for nitrate-reduction (nitrate reductase narG and napA), denitrification (nitrite reductase nirS) and DNRA (DNRA nitrite reductase nrfA) declined along the estuary with significant relationships between denitrification and nirS abundance, and DNRA and nrfA abundance. Spatially, rates of denitrification, DNRA and corresponding functional gene abundances decreased along the estuary. However, temporal correlations between rate processes and functional gene and transcript abundances were not observed. PMID:26082763

Predicting Changes in Macrophyte Community Structure from Functional Traits in a Freshwater Lake: A Test of Maximum Entropy Model

PubMed Central

Fu, Hui; Zhong, Jiayou; Yuan, Guixiang; Guo, Chunjing; Lou, Qian; Zhang, Wei; Xu, Jun; Ni, Leyi; Xie, Ping; Cao, Te

2015-01-01

Trait-based approaches have been widely applied to investigate how community dynamics respond to environmental gradients. In this study, we applied a series of maximum entropy (maxent) models incorporating functional traits to unravel the processes governing macrophyte community structure along water depth gradient in a freshwater lake. We sampled 42 plots and 1513 individual plants, and measured 16 functional traits and abundance of 17 macrophyte species. Study results showed that maxent model can be highly robust (99.8%) in predicting the species relative abundance of macrophytes with observed community-weighted mean (CWM) traits as the constraints, while relative low (about 30%) with CWM traits fitted from water depth gradient as the constraints. The measured traits showed notably distinct importance in predicting species abundances, with lowest for perennial growth form and highest for leaf dry mass content. For tuber and leaf nitrogen content, there were significant shifts in their effects on species relative abundance from positive in shallow water to negative in deep water. This result suggests that macrophyte species with tuber organ and greater leaf nitrogen content would become more abundant in shallow water, but would become less abundant in deep water. Our study highlights how functional traits distributed across gradients provide a robust path towards predictive community ecology. PMID:26167856

Activity and the Li abundances in the FGK dwarfs⋆

NASA Astrophysics Data System (ADS)

Mishenina, T. V.; Soubiran, C.; Kovtyukh, V. V.; Katsova, M. M.; Livshits, M. A.

2012-11-01

Aims: The aim of the present study is to determine the Li abundances for a large set of the FGK dwarfs and to analyse the connections between the Li content, stellar parameters, and activity. Methods: The atmospheric parameters, rotational velocities and the Li abundances were determined from a homogeneous collection of the echelle spectra with high resolution and a high signal-to-noise ratio. The rotational velocities vsini were determined by calibrating the cross-correlation function. The effective temperatures Teff were estimated by the line-depth ratio method. The surface gravities log g were computed by two methods: the iron ionization balance and the parallax. The LTE Li abundances were computed using synthetic spectra method. The behaviour of the Li abundance was examined in correlation with Teff, [Fe/H] , as well as with vsini and the level of activity in three stellar groups of the different temperature range. Results: The stellar parameters and the Li abundances are presented for 150 slow rotating stars of the lower part of the main sequence. The studied stars show a decline in the Li abundance with decreasing temperature Teff and a significant spread, which should be due to the difference of age of stars. The correlations between the Li abundances, rotational velocities vsini, and the level of the chromospheric activity were discovered for the stars with 6000 > Teff > 5700 K, and it is tighter for the stars with 5700 > Teff > 5200 K. The target stars with Teff < 5200 K do not show any correlation between log A(Li) and vsini. The relationship between the chromospheric and coronal fluxes in active with detected Li as well as in less active stars gives a hint that there exist different conditions in the action of the dynamo mechanism in those stars. Conclusions: We found that the Li-activity correlation is evident only in a restricted temperature range and the Li abundance spread seems to be present in a group of low chromospheric activity stars that also show a broad spread in the chromospheric vs. coronal activity. Based on the spectra collected with the ELODIE spectrograph using the 1.93-m telescope at the Observatoire de Haute Provence (CNRS, France).Full Table 3 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/547/A106

Accounting for Subgroup Structure in Line-Transect Abundance Estimates of False Killer Whales (Pseudorca crassidens) in Hawaiian Waters

PubMed Central

Bradford, Amanda L.; Forney, Karin A.; Oleson, Erin M.; Barlow, Jay

2014-01-01

For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai’i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479–5,030) and 552 (CV = 1.09; 95% CI = 97–3,123) individuals, respectively. Subgroup structure is an important factor to consider in line-transect analyses of false killer whales and other species with complex grouping patterns. PMID:24587372

Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

PubMed

Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

2014-01-01

For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97-3,123) individuals, respectively. Subgroup structure is an important factor to consider in line-transect analyses of false killer whales and other species with complex grouping patterns.

Comparing Amino Acid Abundances and Distributions Across Carbonaceous Chondrite Groups

NASA Technical Reports Server (NTRS)

Burton, Aaron S.; Callahan, Michael P.; Glavin, Daniel P.; Elsila, Jamie E.; Dworkin, Jason P.

2012-01-01

Meteorites are grouped according to bulk properties such as chemical composition and mineralogy. These parameters can vary significantly among the different carbonaceous chondrite groups (CI, CM, CO, CR, CH, CB, CV and CK). We have determined the amino acid abundances of more than 30 primary amino acids in meteorites from each of the eight groups, revealing several interesting trends. There are noticeable differences in the structural diversity and overall abundances of amino acids between meteorites from the different chondrite groups. Because meteorites may have been an important source of amino acids to the prebiotic Earth and these organic compounds are essential for life as we know it, the observed variations of these molecules may have been important for the origins of life.

Shifting plant species composition in response to climate change stabilizes grassland primary production

PubMed Central

Liu, Huiying; Mi, Zhaorong; Lin, Li; Wang, Yonghui; Zhang, Zhenhua; Zhang, Fawei; Wang, Hao; Liu, Lingli; Zhu, Biao; Cao, Guangmin; Zhao, Xinquan; Sanders, Nathan J.; Reich, Peter B.

2018-01-01

The structure and function of alpine grassland ecosystems, including their extensive soil carbon stocks, are largely shaped by temperature. The Tibetan Plateau in particular has experienced significant warming over the past 50 y, and this warming trend is projected to intensify in the future. Such climate change will likely alter plant species composition and net primary production (NPP). Here we combined 32 y of observations and monitoring with a manipulative experiment of temperature and precipitation to explore the effects of changing climate on plant community structure and ecosystem function. First, long-term climate warming from 1983 to 2014, which occurred without systematic changes in precipitation, led to higher grass abundance and lower sedge abundance, but did not affect aboveground NPP. Second, an experimental warming experiment conducted over 4 y had no effects on any aspect of NPP, whereas drought manipulation (reducing precipitation by 50%), shifted NPP allocation belowground without affecting total NPP. Third, both experimental warming and drought treatments, supported by a meta-analysis at nine sites across the plateau, increased grass abundance at the expense of biomass of sedges and forbs. This shift in functional group composition led to deeper root systems, which may have enabled plant communities to acquire more water and thus stabilize ecosystem primary production even with a changing climate. Overall, our study demonstrates that shifting plant species composition in response to climate change may have stabilized primary production in this high-elevation ecosystem, but it also caused a shift from aboveground to belowground productivity. PMID:29666319

Microbial Community Composition and Functional Capacity in a Terrestrial Ferruginous, Sulfate-Depleted Mud Volcano

PubMed Central

Tu, Tzu-Hsuan; Wu, Li-Wei; Lin, Yu-Shih; Imachi, Hiroyuki; Lin, Li-Hung; Wang, Pei-Ling

2017-01-01

Terrestrial mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-depleted MV of eastern Taiwan. Geochemical profiles combined with 16S rRNA gene abundances indicated that anaerobic oxidation of methane (AOM) mediated by ANME-2a group coincided with iron/manganese reduction by Desulfuromonadales at shallow depths deprived of sulfate. The activity of AOM was stimulated either by methane alone or by methane and a range of electron acceptors, such as sulfate, ferrihydrite, and artificial humic acid. Metagenomic analyses revealed that functional genes for AOM and metal reduction were more abundant at shallow intervals. In particular, genes encoding pili expression and electron transport through multi-heme cytochromes were prevalent, suggesting potential intercellular interactions for electron transport involved in AOM. For comparison, genes responsible for methanogenesis and degradation of chitin and plant-derived molecules were more abundant at depth. The gene distribution combined with the enhanced proportions of 16S rRNA genes related to methanogens and heterotrophs, and geochemical characteristics suggest that particulate organic matter was degraded into various organic entities that could further fuel in situ methanogenesis. Finally, genes responsible for aerobic methane oxidation were more abundant in the bubbling pool and near-surface sediments. These methane oxidizers account for the ultimate attenuation of methane discharge into the atmosphere. Overall, our results demonstrated that various community members were compartmentalized into stratified niches along geochemical gradients. These community members form a metabolic network that cascades the carbon transformation from the upstream degradation of recalcitrant organic carbon with fermentative production of labile organic entities and methane to downstream methane oxidation and metal reduction near the surface. Such a metabolic architecture enables effective methane removal under ferruginous, sulfate-depleted conditions in terrestrial MVs. PMID:29163423

Microbial Community Composition and Functional Capacity in a Terrestrial Ferruginous, Sulfate-Depleted Mud Volcano.

PubMed

Tu, Tzu-Hsuan; Wu, Li-Wei; Lin, Yu-Shih; Imachi, Hiroyuki; Lin, Li-Hung; Wang, Pei-Ling

2017-01-01

Terrestrial mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-depleted MV of eastern Taiwan. Geochemical profiles combined with 16S rRNA gene abundances indicated that anaerobic oxidation of methane (AOM) mediated by ANME-2a group coincided with iron/manganese reduction by Desulfuromonadales at shallow depths deprived of sulfate. The activity of AOM was stimulated either by methane alone or by methane and a range of electron acceptors, such as sulfate, ferrihydrite, and artificial humic acid. Metagenomic analyses revealed that functional genes for AOM and metal reduction were more abundant at shallow intervals. In particular, genes encoding pili expression and electron transport through multi-heme cytochromes were prevalent, suggesting potential intercellular interactions for electron transport involved in AOM. For comparison, genes responsible for methanogenesis and degradation of chitin and plant-derived molecules were more abundant at depth. The gene distribution combined with the enhanced proportions of 16S rRNA genes related to methanogens and heterotrophs, and geochemical characteristics suggest that particulate organic matter was degraded into various organic entities that could further fuel in situ methanogenesis. Finally, genes responsible for aerobic methane oxidation were more abundant in the bubbling pool and near-surface sediments. These methane oxidizers account for the ultimate attenuation of methane discharge into the atmosphere. Overall, our results demonstrated that various community members were compartmentalized into stratified niches along geochemical gradients. These community members form a metabolic network that cascades the carbon transformation from the upstream degradation of recalcitrant organic carbon with fermentative production of labile organic entities and methane to downstream methane oxidation and metal reduction near the surface. Such a metabolic architecture enables effective methane removal under ferruginous, sulfate-depleted conditions in terrestrial MVs.

Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance.

PubMed

Johnson, Kenneth L; Mason, Christopher J; Muddiman, David C; Eckel, Jeanette E

2004-09-01

This study quantifies the experimental uncertainty for LC retention time, mass measurement precision, and ion abundance obtained from replicate nLC-dual ESI-FT-ICR analyses of the low molecular weight fraction of serum. We used ultrafiltration to enrich the < 10-kDa fraction of components from the high-abundance proteins in a pooled serum sample derived from ovarian cancer patients. The THRASH algorithm for isotope cluster detection was applied to five replicate nLC-dual ESI-FT-ICR chromatograms. A simple two-level grouping algorithm was applied to the more than 7000 isotope clusters found in each replicate and identified 497 molecular species that appeared in at least four of the replicates. In addition, a representative set of 231 isotope clusters, corresponding to 188 unique molecular species, were manually interpreted to verify the automated algorithm and to set its tolerances. For nLC retention time reproducibility, 95% of the 497 species had a 95% confidence interval of the mean of +/- 0.9 min or less without the use of chromatographic alignment procedures. Furthermore, 95% of the 497 species had a mass measurement precision of < or = 3.2 and < or = 6.3 ppm for internally and externally calibrated spectra, respectively. Moreover, 95% of replicate ion abundance measurements, covering an ion abundance range of approximately 3 orders of magnitude, had a coefficient of variation of less than 62% without using any normalization functions. The variability of ion abundance was independent of LC retention time, mass, and ion abundance quartile. These measures of analytical reproducibility establish a statistical rationale for differentiating healthy and disease patient populations for the elucidation of biomarkers in the low molecular fraction of serum. Copyright 2004 American Chemical Society

Rumen microbial abundance and fermentation profile during severe subacute ruminal acidosis and its modulation by plant derived alkaloids in vitro.

PubMed

Mickdam, Elsayed; Khiaosa-Ard, Ratchaneewan; Metzler-Zebeli, Barbara U; Klevenhusen, Fenja; Chizzola, Remigius; Zebeli, Qendrim

2016-06-01

Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and fermentation profiles using a severe subacute ruminal acidosis (SARA) in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA), containing quaternary benzophenanthridine and protopine alkaloids, of which sanguinarine and chelerythrine were the major bioactive compounds. Induction of severe SARA strongly affected the rumen microbial composition and fermentation variables without suppressing the abundance of total bacteria. Protozoa and fungi were more sensitive to the low ruminal pH condition than bacteria. Induction of severe SARA clearly depressed degradation of fiber (P < 0.001), which came along with a decreased relative abundance of fibrolytic Ruminococcus albus and Fibrobacter succinogenes (P < 0.001). Under severe SARA conditions, the genus Prevotella, Lactobacillus group, Megasphaera elsdenii, and Entodinium spp. (P < 0.001) were more abundant, whereas Ruminobacter amylophilus was less abundant. SARA largely suppressed methane formation (-70%, P < 0.001), although total methanogenic 16S rRNA gene abundance was not affected. According to principal component analysis, Methanobrevibacter spp. correlated to methane concentration. Addition of PDA modulated ruminal fermentation under normal conditions such as enhanced (P < 0.05) concentration of total SCFA, propionate and valerate, and increased (P < 0.05) degradation of crude protein compared with the unsupplemented control diet. Our results indicate strong shifts in the microbial community during severe SARA compared to normal conditions. Supplementation of PDA positively modulates ruminal fermentation under normal ruminal pH conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Plant Functional Group Composition Modifies the Effects of Precipitation Change on Grassland Ecosystem Function

PubMed Central

Fry, Ellen L.; Manning, Pete; Allen, David G. P.; Hurst, Alex; Everwand, Georg; Rimmler, Martin; Power, Sally A.

2013-01-01

Temperate grassland ecosystems face a future of precipitation change, which can alter community composition and ecosystem functions through reduced soil moisture and waterlogging. There is evidence that functionally diverse plant communities contain a wider range of water use and resource capture strategies, resulting in greater resistance of ecosystem function to precipitation change. To investigate this interaction between composition and precipitation change we performed a field experiment for three years in successional grassland in southern England. This consisted of two treatments. The first, precipitation change, simulated end of century predictions, and consisted of a summer drought phase alongside winter rainfall addition. The second, functional group identity, divided the plant community into three groups based on their functional traits- broadly described as perennials, caespitose grasses and annuals- and removed these groups in a factorial design. Ecosystem functions related to C, N and water cycling were measured regularly. Effects of functional groupidentity were apparent, with the dominant trend being that process rates were higher under control conditions where a range of perennial species were present. E.g. litter decomposition rates were significantly higher in plots containing several perennial species, the group with the highest average leaf N content. Process rates were also very strongly affected by the precipitation change treatmentwhen perennial plant species were dominant, but not where the community contained a high abundance of annual species and caespitose grasses. This contrasting response could be attributable to differing rooting patterns (shallower structures under annual plants, and deeper roots under perennials) and faster nutrient uptake in annuals compared to perennials. Our results indicate that precipitation change will have a smaller effect on key process rates in grasslandscontaining a range of perennial and annual species, and that maintaining the presence of key functional groups should be a crucial consideration in future grassland management. PMID:23437300

Global patterns and predictions of seafloor biomass using random forests.

PubMed

Wei, Chih-Lin; Rowe, Gilbert T; Escobar-Briones, Elva; Boetius, Antje; Soltwedel, Thomas; Caley, M Julian; Soliman, Yousria; Huettmann, Falk; Qu, Fangyuan; Yu, Zishan; Pitcher, C Roland; Haedrich, Richard L; Wicksten, Mary K; Rex, Michael A; Baguley, Jeffrey G; Sharma, Jyotsna; Danovaro, Roberto; MacDonald, Ian R; Nunnally, Clifton C; Deming, Jody W; Montagna, Paul; Lévesque, Mélanie; Weslawski, Jan Marcin; Wlodarska-Kowalczuk, Maria; Ingole, Baban S; Bett, Brian J; Billett, David S M; Yool, Andrew; Bluhm, Bodil A; Iken, Katrin; Narayanaswamy, Bhavani E

2010-12-30

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.

Global Patterns and Predictions of Seafloor Biomass Using Random Forests

PubMed Central

Wei, Chih-Lin; Rowe, Gilbert T.; Escobar-Briones, Elva; Boetius, Antje; Soltwedel, Thomas; Caley, M. Julian; Soliman, Yousria; Huettmann, Falk; Qu, Fangyuan; Yu, Zishan; Pitcher, C. Roland; Haedrich, Richard L.; Wicksten, Mary K.; Rex, Michael A.; Baguley, Jeffrey G.; Sharma, Jyotsna; Danovaro, Roberto; MacDonald, Ian R.; Nunnally, Clifton C.; Deming, Jody W.; Montagna, Paul; Lévesque, Mélanie; Weslawski, Jan Marcin; Wlodarska-Kowalczuk, Maria; Ingole, Baban S.; Bett, Brian J.; Billett, David S. M.; Yool, Andrew; Bluhm, Bodil A.; Iken, Katrin; Narayanaswamy, Bhavani E.

2010-01-01

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management. PMID:21209928

Low-temperature anaerobic digestion is associated with differential methanogenic protein expression.

PubMed

Gunnigle, Eoin; Siggins, Alma; Botting, Catherine H; Fuszard, Matthew; O'Flaherty, Vincent; Abram, Florence

2015-05-01

Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

PubMed Central

Dias, Armando Cavalcante Franco; Pereira e Silva, Michele de Cassia; Cotta, Simone Raposo; Dini-Andreote, Francisco; Soares, Fábio Lino; Salles, Joana Falcão; Azevedo, João Lúcio; van Elsas, Jan Dirk

2012-01-01

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies. PMID:22941088

Abundance and genetic diversity of nifH gene sequences in anthropogenically affected Brazilian mangrove sediments.

PubMed

Dias, Armando Cavalcante Franco; Pereira e Silva, Michele de Cassia; Cotta, Simone Raposo; Dini-Andreote, Francisco; Soares, Fábio Lino; Salles, Joana Falcão; Azevedo, João Lúcio; van Elsas, Jan Dirk; Andreote, Fernando Dini

2012-11-01

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

The lithium abundances of a large sample of red giants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Y. J.; Tan, K. F.; Wang, L.

2014-04-20

The lithium abundances for 378 G/K giants are derived with non-local thermodynamic equilibrium correction considered. Among these are 23 stars that host planetary systems. The lithium abundance is investigated, as a function of metallicity, effective temperature, and rotational velocity, as well as the impact of a giant planet on G/K giants. The results show that the lithium abundance is a function of metallicity and effective temperature. The lithium abundance has no correlation with rotational velocity at v sin i < 10 km s{sup –1}. Giants with planets present lower lithium abundance and slow rotational velocity (v sin i < 4more » km s{sup –1}). Our sample includes three Li-rich G/K giants, 36 Li-normal stars, and 339 Li-depleted stars. The fraction of Li-rich stars in this sample agrees with the general rate of less than 1% in the literature, and the stars that show normal amounts of Li are supposed to possess the same abundance at the current interstellar medium. For the Li-depleted giants, Li-deficiency may have already taken place at the main sequence stage for many intermediate mass (1.5-5 M {sub ☉}) G/K giants. Finally, we present the lithium abundance and kinematic parameters for an enlarged sample of 565 giants using a compilation of the literature, and confirm that the lithium abundance is a function of metallicity and effective temperature. With the enlarged sample, we investigate the differences between the lithium abundance in thin-/thick-disk giants, which indicate that the lithium abundance in thick-disk giants is more depleted than that in thin-disk giants.« less

Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.

PubMed

Magwanga, Richard Odongo; Lu, Pu; Kirungu, Joy Nyangasi; Lu, Hejun; Wang, Xingxing; Cai, Xiaoyan; Zhou, Zhongli; Zhang, Zhenmei; Salih, Haron; Wang, Kunbo; Liu, Fang

2018-01-15

Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars. The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress.

Variable responses of human microbiomes to dietary supplementation with resistant starch.

PubMed

Venkataraman, A; Sieber, J R; Schmidt, A W; Waldron, C; Theis, K R; Schmidt, T M

2016-06-29

The fermentation of dietary fiber to various organic acids is a beneficial function provided by the microbiota in the human large intestine. In particular, butyric acid contributes to host health by facilitating maintenance of epithelial integrity, regulating inflammation, and influencing gene expression in colonocytes. We sought to increase the concentration of butyrate in 20 healthy young adults through dietary supplementation with resistant starch (unmodified potato starch-resistant starch (RS) type 2). Fecal samples were collected from individuals to characterize butyrate concentration via liquid chromatography and composition of the microbiota via surveys of 16S rRNA-encoding gene sequences from the Illumina MiSeq platform. Random Forest and LEfSe analyses were used to associate responses in butyrate production to features of the microbiota. RS supplementation increased fecal butyrate concentrations in this cohort from 8 to 12 mmol/kg wet feces, but responses varied widely between individuals. Individuals could be categorized into three groups based upon butyrate concentrations before and during RS: enhanced, high, and low (n = 11, 3, and 6, respectively). Fecal butyrate increased by 67 % in the enhanced group (from 9 to 15 mmol/kg), while it remained ≥11 mmol/kg in the high group and ≤8 mmol/kg in the low group. Microbiota analyses revealed that the relative abundance of RS-degrading organisms-Bifidobacterium adolescentis or Ruminococcus bromii-increased from ~2 to 9 % in the enhanced and high groups, but remained at ~1.5 % in the low group. The lack of increase in RS-degrading bacteria in the low group may explain why there was no increase in fecal butyrate in response to RS. The microbiota of individuals in the high group were characterized by an elevated abundance of the butyrogenic microbe Eubacterium rectale (~6 % in high vs. 3 % in enhanced and low groups) throughout the study. We document the heterogeneous responses in butyrate concentrations upon RS supplementation and identify characteristic of the microbiota that appear to underlie this variation. This study complements and extends other studies that call for personalized approaches to manage beneficial functions provided by gut microbiomes.

Elemental abundance differences between nuclei acclerated in CIR shocks and solar flares

NASA Technical Reports Server (NTRS)

Dietrich, W. F.; Simpson, J. A.

1985-01-01

Measurement of the ratios of nuclear abundances H/He, CNO/Fe-group and the Fe-group/HE for 51 passages of Corotating Interaction Regions (CIRs) at 1 AU, and measurement of these ratios from 620 solar flares in the energy range 0.6 to 4 MeV per nucleon, show that CIR shock acceleration alone does not change significantly these ratios from the values they have for solar system abundances or the solar wind. The solar flare ratios continue to reflect strong biases in the abundances, consistent with requirements for multistage acceleration rpocesses at the Sun.

Renewable Chemicals: Dehydroxylation of Glycerol and Polyols

PubMed Central

ten Dam, Jeroen; Hanefeld, Ulf

2011-01-01

The production of renewable chemicals is gaining attention over the past few years. The natural resources from which they can be derived in a sustainable way are most abundant in sugars, cellulose and hemicellulose. These highly functionalized molecules need to be de-functionalized in order to be feedstocks for the chemical industry. A fundamentally different approach to chemistry thus becomes necessary, since the traditionally employed oil-based chemicals normally lack functionality. This new chemical toolbox needs to be designed to guarantee the demands of future generations at a reasonable price. The surplus of functionality in sugars and glycerol consists of alcohol groups. To yield suitable renewable chemicals these natural products need to be defunctionalized by means of dehydroxylation. Here we review the possible approaches and evaluate them from a fundamental chemical aspect. PMID:21887771

Lipid profiles of follicular fluid from cows submitted to ovarian superstimulation.

PubMed

Santos, P H; Fontes, P K; Franchi, F F; Nogueira, M F G; Belaz, K R A; Tata, A; Eberlin, M N; Sudano, M J; Barros, C M; Castilho, A C S

2017-05-01

Ovarian superstimulation with exogenous gonadotropins has been extensively used to produce in vivo-derived embryos for embryo transfer in cattle. This process modifies the antral follicle microenvironment and affects oocyte and embryo quality as well the differentiation of granulosa cells. Lipids play significant roles in the cell, such as energy storage, cell structure, and fine-tuning of the physical properties and functions of biological membranes. The phospholipid (PL) contents as well as the effects of superstimulatory treatments on the PL profile of follicular fluid from cows, however, remain unknown. Therefore, to gain insight into the effects of superstimulation with follicle-stimulating hormone (FSH; P-36 protocol) or FSH combined with equine chorionic gonadotropin (eCG; P-36/eCG protocol) on the profile and abundance of PL from cows submitted or not submitted to superstimulatory protocols, were treated with these two superstimulatory protocols. As a control, non-superstimulated cows were only submitted to estrous synchronization. The follicular fluid was aspirated, the remaining cells removed and the follicular fluid stored at -80 °C until extraction. The lipid screening was performed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and this technique allowed the identification of sphingomyelins (SM) and phosphatidylcholines (PC) and phosphoethanolamines (PE). The relative abundance of the ions observed in the three experimental groups was analyzed by multivariate and univariate statistical models. The phospholipid SM (16:0) and PC (36:4) and/or PC (34:1) were less (P < 0.05) abundant in the P-36 group compared to the control or P-36/eCG groups. However, the PC (34:2) was more (P < 0.05) abundant in both group of superstimulated cows compared to the control. In summary, ovarian superstimulation seems to modulate the PL content of bovine follicular fluid with a significant increase in PC (34:2), which jointly with others PC and SM, seems to offer a suitable biomarker involved with reproductive processes successful as ovary superstimulation response and embryo development. Copyright © 2017. Published by Elsevier Inc.

Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

PubMed

Ricotta, Carlo

2003-01-01

Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

New multidimensional functional diversity indices for a multifaceted framework in functional ecology.

PubMed

Villéger, Sébastien; Mason, Norman W H; Mouillot, David

2008-08-01

Functional diversity is increasingly identified as an important driver of ecosystem functioning. Various indices have been proposed to measure the functional diversity of a community, but there is still no consensus on which are most suitable. Indeed, none of the existing indices meets all the criteria required for general use. The main criteria are that they must be designed to deal with several traits, take into account abundances, and measure all the facets of functional diversity. Here we propose three indices to quantify each facet of functional diversity for a community with species distributed in a multidimensional functional space: functional richness (volume of the functional space occupied by the community), functional evenness (regularity of the distribution of abundance in this volume), and functional divergence (divergence in the distribution of abundance in this volume). Functional richness is estimated using the existing convex hull volume index. The new functional evenness index is based on the minimum spanning tree which links all the species in the multidimensional functional space. Then this new index quantifies the regularity with which species abundances are distributed along the spanning tree. Functional divergence is measured using a novel index which quantifies how species diverge in their distances (weighted by their abundance) from the center of gravity in the functional space. We show that none of the indices meets all the criteria required for a functional diversity index, but instead we show that the set of three complementary indices meets these criteria. Through simulations of artificial data sets, we demonstrate that functional divergence and functional evenness are independent of species richness and that the three functional diversity indices are independent of each other. Overall, our study suggests that decomposition of functional diversity into its three primary components provides a meaningful framework for its quantification and for the classification of existing functional diversity indices. This decomposition has the potential to shed light on the role of biodiversity on ecosystem functioning and on the influence of biotic and abiotic filters on the structure of species communities. Finally, we propose a general framework for applying these three functional diversity indices.

ETHOS - an effective theory of structure formation: predictions for the high-redshift Universe - abundance of galaxies and reionization

NASA Astrophysics Data System (ADS)

Lovell, Mark R.; Zavala, Jesús; Vogelsberger, Mark; Shen, Xuejian; Cyr-Racine, Francis-Yan; Pfrommer, Christoph; Sigurdson, Kris; Boylan-Kolchin, Michael; Pillepich, Annalisa

2018-07-01

We contrast predictions for the high-redshift galaxy population and reionization history between cold dark matter (CDM) and an alternative self-interacting dark matter model based on the recently developed ETHOS framework that alleviates the small-scale CDM challenges within the Local Group. We perform the highest resolution hydrodynamical cosmological simulations (a 36 Mpc3 volume with gas cell mass of ˜ 105 M_{⊙} and minimum gas softening of ˜180 pc) within ETHOS to date - plus a CDM counterpart - to quantify the abundance of galaxies at high redshift and their impact on reionization. We find that ETHOS predicts galaxies with higher ultraviolet (UV) luminosities than their CDM counterparts and a faster build-up of the faint end of the UV luminosity function. These effects, however, make the optical depth to reionization less sensitive to the power spectrum cut-off: the ETHOS model differs from the CDM τ value by only 10 per cent and is consistent with Planck limits if the effective escape fraction of UV photons is 0.1-0.5. We conclude that current observations of high-redshift luminosity functions cannot differentiate between ETHOS and CDM models, but deep James Webb Space Telescope surveys of strongly lensed, inherently faint galaxies have the potential to test non-CDM models that offer attractive solutions to CDM's Local Group problems.

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease

PubMed Central

Jiang, Weiwei; Wu, Na; Wang, Xuemei; Chi, Yujing; Zhang, Yuanyuan; Qiu, Xinyun; Hu, Ying; Li, Jing; Liu, Yulan

2015-01-01

Non-alcoholic fatty liver disease (NAFLD) has recently been considered to be under the influence of the gut microbiota, which might exert toxic effects on the human host after intestinal absorption and delivery to the liver via the portal vein. In this study, the composition of the gut microbiota in NAFLD patients and healthy subjects was determined via 16S ribosomal RNA Illumina next-generation sequencing. Among those taxa displaying greater than 0.1% average abundance in all samples, five genera, including Alistipes and Prevotella, were significantly more abundant in the gut microbiota of healthy subjects compared to NAFLD patients. Alternatively, Escherichia, Anaerobacter, Lactobacillus and Streptococcus were increased in the gut microbiota of NAFLD patients compared to healthy subjects. In addition, decreased numbers of CD4+ and CD8+ T lymphocytes and increased levels of TNF-α, IL-6 and IFN-γ were detected in the NAFLD group compared to the healthy group. Furthermore, irregularly arranged microvilli and widened tight junctions were observed in the gut mucosa of the NAFLD patients via transmission electron microscopy. We postulate that aside from dysbiosis of the gut microbiota, gut microbiota-mediated inflammation of the intestinal mucosa and the related impairment in mucosal immune function play an important role in the pathogenesis of NAFLD. PMID:25644696

Accounting for imperfect detection of groups and individuals when estimating abundance.

PubMed

Clement, Matthew J; Converse, Sarah J; Royle, J Andrew

2017-09-01

If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities <1. Common estimators include double-observer models, distance sampling models and combined double-observer and distance sampling models (known as mark-recapture-distance-sampling models; MRDS). When animals reside in groups, however, the assumption of independent detection is violated. In this case, the standard approach is to account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under-counted, but not over-counted. The estimator combines an MRDS model with an N-mixture model to account for imperfect detection of individuals. The new MRDS-Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS-Nmix model to an MRDS model. Abundance estimates generated by the MRDS-Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re-allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size.

Accounting for imperfect detection of groups and individuals when estimating abundance

USGS Publications Warehouse

Clement, Matthew J.; Converse, Sarah J.; Royle, J. Andrew

2017-01-01

If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities <1. Common estimators include double-observer models, distance sampling models and combined double-observer and distance sampling models (known as mark-recapture-distance-sampling models; MRDS). When animals reside in groups, however, the assumption of independent detection is violated. In this case, the standard approach is to account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under-counted, but not over-counted. The estimator combines an MRDS model with an N-mixture model to account for imperfect detection of individuals. The new MRDS-Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS-Nmix model to an MRDS model. Abundance estimates generated by the MRDS-Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re-allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size.

Dimethyl fumarate reduces the risk of mycotoxins via improving intestinal barrier and microbiota

PubMed Central

Ma, Ning; Wu, Yi; Xie, Fei; Du, Kexin; Wang, Yuan; Shi, Linxin; Ji, Linbao; Liu, Tianyi; Ma, Xi

2017-01-01

The effects of dimethyl fumarate (DMF) on mycotoxins and animal growth performance are well documented. However, its mechanism of anti-mildew effects is still unknown. The current study investigated how DMF detoxified the mycotoxin and improved the growth performance using BALB/c mice model, especially its effects on intestinal barrier function and gut micro-ecology. Our study also compared with the ultraviolet radiation (UR) treatment, a traditional anti-mildew control (TC). The results indicated that the DMF treatment had a lower contents of mycotoxin, better growth performance and improved mucosal morphology (P < 0.05), accompanied with the decreased intestinal permeability and the tighter gut barrier. Moreover, the efficiency of DMF was better than TC (P < 0.05). 16S rRNA gene sequence analysis revealed that the richness and diversity of bacteria was increased in DMF treatment. The most abundant OTUs belonged to Firmicutes and Bacteroidetes, and their changes in DMF were more moderate than the TC group, suggesting a more stable micro-ecology and the positive impact of DMF on the biodiversity of intestine. Specifically, the increased abundance of bacteria producing short-chain fatty acids (SCFAs), such as Gemella, Roseburia, Bacillus and Bacteroides in DMF group and prebiotics such as Lactobacillus in TC group, suggested a more healthier microbial composition and distribution. These findings supported that DMF had significant effects on animal's growth performance and intestinal barrier function by modulating the pathway of nutrient absorption and increasing the diversity and balance of gut microbes, which also illuminate that DMF is more efficient than traditional anti-mildew method. PMID:28574825

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

PubMed Central

Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; Haber, Markus; Blom, Jochen; Marshall, Christopher W.; Gilbert, Jack A.; Hentschel, Ute

2015-01-01

ABSTRACT The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack. PMID:26037118

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

DOE PAGES

Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; ...

2015-06-02

The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all fourmore » symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.« less

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.

The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all fourmore » symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.« less

Structures of Chlorophyll Catabolites in Bananas (Musa acuminata) Reveal a Split Path of Chlorophyll Breakdown in a Ripening Fruit

PubMed Central

Moser, Simone; Müller, Thomas; Holzinger, Andreas; Lütz, Cornelius; Kräutler, Bernhard

2012-01-01

Abstract The disappearance of chlorophyll is a visual sign of fruit ripening. Yet, chlorophyll breakdown in fruit has hardly been explored; its non-green degradation products are largely unknown. Here we report the analysis and structure elucidation of colorless tetrapyrrolic chlorophyll breakdown products in commercially available, ripening bananas (Musa acuminata, Cavendish cultivar). In banana peels, chlorophyll catabolites were found in an unprecedented structural richness: a variety of new fluorescent chlorophyll catabolites (FCCs) and nonfluorescent chlorophyll catabolites (NCCs) were detected. As a rule, FCCs exist only "fleetingly" and are hard to observe. However, in bananas several of the FCCs (named Mc-FCCs) were persistent and carried an ester function at the propionate side-chain. NCCs were less abundant, and exhibited a free propionic acid group, but functional modifications elsewhere. The modifications of NCCs in banana peels were similar to those found in NCCs from senescent leaves. They are presumed to be introduced by enzymatic transformations at the stage of the mostly unobserved, direct FCC-precursors. The observed divergent functional group characteristics of the Mc-FCCs versus those of the Mc-NCCs indicated two major "late" processing lines of chlorophyll breakdown in ripening bananas. The "last common precursor" at the branching point to either the persistent FCCs, or towards the NCCs, was identified as a temporarily abundant "secondary" FCC. The existence of two "downstream" branches of chlorophyll breakdown in banana peels, and the striking accumulation of persistent Mc-FCCs call for attention as to the still-elusive biological roles of the resulting colorless linear tetrapyrroles. PMID:22807397

Cascading top-down effects of changing oceanic predator abundances.

PubMed

Baum, Julia K; Worm, Boris

2009-07-01

1. Top-down control can be an important determinant of ecosystem structure and function, but in oceanic ecosystems, where cascading effects of predator depletions, recoveries, and invasions could be significant, such effects had rarely been demonstrated until recently. 2. Here we synthesize the evidence for oceanic top-down control that has emerged over the last decade, focusing on large, high trophic-level predators inhabiting continental shelves, seas, and the open ocean. 3. In these ecosystems, where controlled manipulations are largely infeasible, 'pseudo-experimental' analyses of predator-prey interactions that treat independent predator populations as 'replicates', and temporal or spatial contrasts in predator populations and climate as 'treatments', are increasingly employed to help disentangle predator effects from environmental variation and noise. 4. Substantial reductions in marine mammals, sharks, and piscivorous fishes have led to mesopredator and invertebrate predator increases. Conversely, abundant oceanic predators have suppressed prey abundances. Predation has also inhibited recovery of depleted species, sometimes through predator-prey role reversals. Trophic cascades have been initiated by oceanic predators linking to neritic food webs, but seem inconsistent in the pelagic realm with effects often attenuating at plankton. 5. Top-down control is not uniformly strong in the ocean, and appears contingent on the intensity and nature of perturbations to predator abundances. Predator diversity may dampen cascading effects except where nonselective fisheries deplete entire predator functional groups. In other cases, simultaneous exploitation of predator and prey can inhibit prey responses. Explicit consideration of anthropogenic modifications to oceanic foodwebs should help inform predictions about trophic control. 6. Synthesis and applications. Oceanic top-down control can have important socio-economic, conservation, and management implications as mesopredators and invertebrates assume dominance, and recovery of overexploited predators is impaired. Continued research aimed at integrating across trophic levels is needed to understand and forecast the ecosystem effects of changing oceanic predator abundances, the relative strength of top-down and bottom-up control, and interactions with intensifying anthropogenic stressors such as climate change.

Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China

PubMed Central

Wang, Shaojun; Chen, Han Y. H.; Tan, Yan; Fan, Huan; Ruan, Honghua

2016-01-01

Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon’s and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability. PMID:26857390

Coupling suitable prey field to in situ fish larval condition and abundance in a subtropical estuary

NASA Astrophysics Data System (ADS)

Machado, Irene; Calliari, Danilo; Denicola, Ana; Rodríguez-Graña, Laura

2017-03-01

Survival of fish larvae is influenced by the suitability of the prey field and its variability in time and space. Relationships among food quality, quantity and recruitment have been explored in temperate ecosystems where spawning and secondary production are strongly seasonal, but for subtropical estuaries the mechanisms responsible for larval survival remain poorly identified. This study evaluated the nutritional condition (feeding incidence and AARS activity) and abundance of a multi-specific assemblage of fish larvae from a subtropical estuary in South America (Solís Grande, Uruguay) during the fish reproductive season; and related both variables to prey abundance, composition, size and fatty acids content. The larval assemblage was composed of 13 species belonging to different functional groups and composition varied seasonally. Contrary to expectations larval condition did not match an increase in prey quality. Food availability was high throughout the study period, although significant changes existed in the size and taxonomic structure of the prey assemblage. The temporal succession of complementary factors - temperature, prey composition, abundance and quality - promoted a wide window of opportunity for larvae, where quality seemed to have compensated quantity. Such combination of factors could allow an extended larval survival along the spawning season. These findings underline the importance of a better understanding of subtropical estuaries as nursery areas.

Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China.

PubMed

Wang, Shaojun; Chen, Han Y H; Tan, Yan; Fan, Huan; Ruan, Honghua

2016-02-09

Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon's and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability.

Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

PubMed

Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

2015-07-01

Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature. © 2015 John Wiley & Sons Ltd/CNRS.

Infections with the Sexually Transmitted Pathogen Nosema apis Trigger an Immune Response in the Seminal Fluid of Honey Bees (Apis mellifera).

PubMed

Grassl, Julia; Peng, Yan; Baer-Imhoof, Barbara; Welch, Mat; Millar, A Harvey; Baer, Boris

2017-01-06

Honey bee (Apis mellifera) males are highly susceptible to infections with the sexually transmitted fungal pathogen Nosema apis. However, they are able to suppress this parasite in the ejaculate using immune molecules in the seminal fluid. We predicted that males respond to infections by altering the seminal fluid proteome to minimize the risk to sexually transmit the parasite to the queen and her colony. We used iTRAQ isotopic labeling to compare seminal fluid proteins from infected and noninfected males and found that N. apis infections resulted in significant abundance changes in 111 of the 260 seminal fluid proteins quantitated. The largest group of proteins with significantly changed abundances consisted of 15 proteins with well-known immune-related functions, which included two significantly more abundant chitinases in the seminal fluid of infected males. Chitinases were previously hypothesized to be involved in honey bee antifungal activity against N. apis. Here we show that infection with N. apis triggers a highly specific immune response in the seminal fluid of honey bee males.

Ethanol Dimer: Observation of Three New Conformers by Broadband Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Loru, Donatella; Peña, Isabel; Sanz, M. Eugenia

2017-06-01

The conformational behaviour of the hydrogen-bonded cluster ethanol dimer has been reinvestigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency region. Three new conformers ({tt}, {tg}+, and {g}-{g}+) have been identified together with the three ({g}+{g}+, {g}-{t}, and {g}+{t}) previously observed by Hearn et al. (J. Chem. Phys. 123, 134324, 2005) and their rotational and centrifugal distortion constants have been determined. By using different carrier gases in the supersonic expansion, the relative abundances of the observed conformers have been estimated. The monosubstituted ^{13}C species and some of the ^{18}O species of the most abundant conformers {g}+{g}+, {g}-{t}, and {tt} have been observed in their natural abundance, which led to the partial determination of their r_{s} structures, and the r_{0} structure for the {tt} conformer. The six observed conformers are stabilized by the delicate interplay of primary O-H...O and secondary C-H...O hydrogen bonds, and dispersion interactions between the methyl groups. Density functional and ab initio methods with different basis sets are benchmarked against the experimental data.

A plague epizootic in the black-tailed prairie dog (Cynomys ludovicianus).

PubMed

Pauli, Jonathan N; Buskirk, Steven W; Williams, Elizabeth S; Edwards, William H

2006-01-01

Plague is the primary cause for the rangewide decline in prairie dog (Cynomys spp.) distribution and abundance, yet our knowledge of plague dynamics in prairie dog populations is limited. Our understanding of the effects of plague on the most widespread species, the black-tailed prairie dog (C. ludovicianus), is particularly weak. During a study on the population biology of black-tailed prairie dogs in Wyoming, USA, plague was detected in a colony under intensive monitoring, providing a unique opportunity to quantify various consequences of plague. The epizootic reduced juvenile abundance by 96% and adult abundance by 95%. Of the survivors, eight of nine adults and one of eight juveniles developed antibodies to Yersinia pestis. Demographic groups appeared equally susceptible to infection, and age structure was unaffected. Survivors occupied three small coteries and exhibited improved body condition, but increased flea infestation compared to a neighboring, uninfected colony. Black-tailed prairie dogs are capable of surviving a plague epizootic and reorganizing into apparently functional coteries. Surviving prairie dogs may be critical in the repopulation of plague-decimated colonies and, ultimately, the evolution of plague resistance.

Consumption of guar gum and retrograded high-amylose corn resistant starch increases IL-10 abundance without affecting pro-inflammatory cytokines in the colon of pigs fed a high-fat diet.

PubMed

Fan, M Z; Archbold, T; Lackeyram, D; Liu, Q; Mine, Y; Paliyath, G

2012-12-01

Increases in dietary intake of viscous and nonviscous soluble fiber are reported to improve bowel health. However, related biological mechanisms are not very clear. This study was conducted to examine if colonic inflammation would occur in a typical Western diet model and determine if consumption of soluble fiber components would attenuate potential detrimental effects by differentially affecting colonic abundances of anti-inflammatory cytokine IL-10 and 2 pro-inflammatory cytokines tumor necrosis factor-alpha (TNF-α) and IL-6 in pigs fed a high-fat basal diet supplemented, respectively, with 15% viscous soluble fiber guar gum (GG) and 15% nonviscous soluble fiber, that is, retrograded high-amylose corn (Zea mays) resistant starch (RS). A total of 24 Yorkshire growing barrows were assigned into a standard corn and soybean (Glycine max) meal (SBM)-based grower diet as a positive control (PC), an animal protein-based high-fat basal diet as the negative control (NC), and 2 NC basal diets supplemented with 15% GG and 15% RS, respectively, according to a completely randomized block design for 4 wk. Abundance of these cytokines in homogenized and extracted colonic tissue supernatant samples was measured by ELISA. Although colonic IL-10 abundance was lower (P < 0.05) in the corn and SBM-based PC group than that in the high-fat basal NC group, there were no differences (P > 0.05) in colonic abundances of TNF-α and IL-6 between NC and PC groups and among all of the treatment groups. Compared with the NC group, consumption of GG and RS at 15% increased (P < 0.05) colonic IL-10 abundance. Moreover, there was no difference (P > 0.05) in colonic IL-10 abundance between the 15% GG and the 15% RS groups. Thus, consumption of a typical high-fat Western diet did not induce colonic inflammation. Diets supplemented with 15% GG or 15% RS may protect the colon from developing inflammation by enhancing IL-10 abundance.

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

PubMed Central

Jin, Jinpu; Zhang, He; Kong, Lei; Gao, Ge; Luo, Jingchu

2014-01-01

With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences. PMID:24174544

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

PubMed Central

Jiao, Jinzhen; Huang, Jinyu; Zhou, Chuanshe

2015-01-01

Understanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative real-time PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P < 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed that Proteobacteria, Firmicutes, and Bacteroidetes were detected as the dominant phyla regardless of the age group, and the abundance of Proteobacteria declined quadratically with age (P < 0.001), while the abundances of Bacteroidetes (P = 0.088) and Firmicutes (P = 0.009) increased with age. At the genus level, Escherichia (80.79%) dominated at day zero, while Prevotella, Butyrivibrio, and Campylobacter surged (linearly; P < 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P = 0.013) with age. In addition, the abundances of the genera Butyrivibrio, Campylobacter, and Desulfobulbus were positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen. PMID:25769827

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center.

PubMed

Anantharaman, Karthik; Breier, John A; Dick, Gregory J

2016-01-01

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

PubMed Central

de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

2012-01-01

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems. PMID:22787457

Transcriptional response of skeletal muscle to a low-protein gestation diet in porcine offspring accumulates in growth- and cell cycle-regulating pathways.

PubMed

Oster, Michael; Murani, Eduard; Metges, Cornelia C; Ponsuksili, Siriluck; Wimmers, Klaus

2012-08-17

Inadequate maternal protein supply during gestation represents an environmental factor that affects physiological signaling pathways with long-term consequences for growth, function, and structure of various tissues. Hypothesizing that the offspring's transcriptome is persistently altered by maternal diets, we used a porcine model to monitor the longitudinal expression changes in muscle to identify pathways relevant to fetal initiation of postnatal growth and development. German Landrace gilts were fed isoenergetic gestational diets containing 6.5% (LP) or 12.1% protein. The longissimus dorsi samples were collected from offspring at 94 days postconception (dpc) and 1, 28, and 188 days postnatum (dpn) for expression profiling. At 94 dpc, 1 dpn, and 28 dpn relatively few transcripts (<130) showed an altered abundance between the dietary groups. In fact, at 94 dpc genes of G2/M checkpoint regulation and mitotic roles of Polo-like kinases showed lowered transcript abundance in LP. At 188 dpn 677 transcripts were altered including those related to oxidative phosphorylation, citrate cycle, fatty acid metabolism (higher abundance in LP) and cell cycle regulation (lower abundance in LP). Correspondingly, transcriptional alterations during pre and postnatal development differed considerably among dietary groups, particularly for genes related to cell cycle regulation (G1/S and G2/M checkpoint regulation; cyclines), growth factor signaling (GH, IGF1, mTOR, RAN, VEGF, INSR), lipid metabolism, energy metabolism, and nucleic acid metabolism. In skeletal muscle, fetal programming related to maternal LP diets disturbed gene expression in growth-related pathways into adulthood. Diet-dependent gene expression may hamper proper development, thereby affecting signaling pathways related to energy utilization.

Aryl hydrocarbon receptor promotes RORγt⁺ group 3 ILCs and controls intestinal immunity and inflammation.

PubMed

Qiu, Ju; Zhou, Liang

2013-11-01

Unlike adaptive immune cells that require antigen recognition and functional maturation during infection, innate lymphoid cells (ILCs) usually respond to pathogens promptly and serve as the first line of defense in infectious diseases. RAR-related orphan receptor (RORγt)⁺ group 3 ILCs are one of the innate cell populations that have recently been intensively studied. During the fetal stage of development, RORγt⁺ group 3 ILCs (e.g., lymphoid tissue inducer cells) are required for lymphoid organogenesis. In adult mice, RORγt⁺ group 3 ILCs are abundantly present in the gut to exert immune defensive functions. Under certain circumstances, however, RORγt⁺ group 3 ILCs can be pathogenic and contribute to intestinal inflammation. Aryl hydrocarbon receptor (Ahr), a ligand-dependent transcriptional factor, is widely expressed by various immune and non-immune cells. In the gut, the ligand for Ahr can be derived/generated from diet, microflora, and/or host cells. Ahr has been shown to regulate different cell populations in the immune system including RORγt⁺ group 3 ILCs, T helper (Th)17/22 cells, γδT cells, regulatory T cells (Tregs), Tr1 cells, and antigen presenting cells. In this review, we will focus on the development and function of RORγt⁺ group 3 ILCs, and discuss the role of Ahr in intestinal immunity and inflammation in mice and in humans. A better understanding of the function of Ahr in the gut is important for developing new therapeutic means to target Ahr in future treatment of infectious and autoimmune diseases.

Interactions of the Hindgut Mucosa-Associated Microbiome with Its Host Regulate Shedding of Escherichia coli O157:H7 by Cattle.

PubMed

Wang, Ou; McAllister, Tim A; Plastow, Graham; Stanford, Kim; Selinger, Brent; Guan, Le Luo

2018-01-01

Cattle are the primary carrier of Escherichia coli O157:H7, a foodborne human pathogen, and those shedding >10 4 CFU/gram of feces of E. coli O157:H7 are defined as supershedders (SS). This study investigated the rectoanal junction (RAJ) mucosa-associated microbiota and its relationship with host gene expression in SS and in cattle from which E. coli O157:H7 was not detected (nonshedders [NS]), aiming to elucidate the mechanisms involved in supershedding. In total, 14 phyla, 66 families, and 101 genera of RAJ mucosa-associated bacteria were identified and Firmicutes (61.5 ± 7.5%), Bacteroidetes (27.9 ± 6.4%), and Proteobacteria (5.5 ± 2.1%) were the predominant phyla. Differential abundance analysis of operational taxonomic units (OTUs) identified 2 OTUs unique to SS which were members of Bacteroides and Clostridium and 7 OTUs unique to NS which were members of Coprococcus , Prevotella , Clostridium , and Paludibacter Differential abundance analysis of predicted microbial functions (using PICRUSt [phylogenetic investigation of communities by reconstruction of unobserved states]) revealed that 3 pathways had higher abundance (log 2 fold change, 0.10 to 0.23) whereas 12 pathways had lower abundance (log 2 fold change, -0.36 to -0.20) in SS. In addition, we identified significant correlations between expression of 19 differentially expressed genes and the relative abundance of predicted microbial functions, including nucleic acid polymerization and carbohydrate and amino acid metabolism. Our findings suggest that differences in RAJ microbiota at both the compositional and functional levels may be associated with E. coli O157:H7 supershedding and that certain microbial groups and microbial functions may influence RAJ physiology of SS by affecting host gene expression. IMPORTANCE Cattle with fecal E. coli O157:H7 at >10 4 CFU per gram of feces have been defined as the supershedders, and they are responsible for the most of the E. coli O157:H7 spread into farm environment. Currently, no method is available for beef producers to eliminate shedding of E. coli O157:H7 in cattle, and the lack of information about the mechanisms of supershedding greatly impedes the development of effective methods. This study investigated the role of the rectoanal junction (RAJ) mucosa-associated microbiome in E. coli O157:H7 shedding, and our results indicated that the compositions and functions of RAJ microbiota differed between supershedders and nonshedders. The identified relationship between the differentially abundant microbes and 19 previously identified differentially expressed genes suggests the role of host-microbial interactions involved in E. coli O157:H7 supershedding. Our findings provide a fundamental understanding of the supershedding phenomenon which is essential for the development of strategies, such as the use of directly fed microbials, to reduce E. coli O157:H7 shedding in cattle. Copyright © 2017 American Society for Microbiology.

The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete

PubMed Central

Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis

2014-01-01

A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

PubMed

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Urinary Liver Type Fatty Acid Binding Protein Is Negatively Associated With Estimated Glomerular Filtration Rate in Renal Transplant Recipients With Graft Loss.

PubMed

Huang, Y-C; Chang, Y-S; Chen, C-C; Tsai, S-F; Yu, T-M; Wu, M-J; Chen, C-H

2018-05-01

Liver type fatty acid binding protein (L-FABP) is abundant not only in the liver but also in the kidney and is excreted in urine. Its primary function is to facilitate intracellular long chain fatty acid transport and it might also act as an endogenous antioxidant molecular. The purpose of this study was to investigate whether plasma or urinary L-FABP levels were associated with graft function in renal transplant recipients. Sixty-seven renal transplant recipients with a mean age of 48.8 years were recruited. The mean duration of renal transplantation was 4131 days. Recipients were divided into 2 groups based on their estimated glomerular filtration rate (eGFR) values: moderate graft function (eGFR ≥60 mL/min/1.73 m 2 ) and low graft function (eGFR <60 mL/min/1.73 m 2 ). Fasting plasma and urinary L-FABP levels were measured. There was no significant difference in plasma L-FABP level between the 2 groups, although recipients in the low graft function group had significantly lower urinary L-FABP level when compared with recipients in the moderate graft function group. Plasma and urinary L-FABP levels were not associated with eGFR in the 67 recipients; however, urinary L-FABP level (β = -1.24, P = .037) and level adjusted by urinary creatinine (β = -0.75, P = .046) were significantly negatively associated with eGFR in recipients with low graft function after adjusting for potential confounders. Increased urinary L-FABP level seems to be a significant indicator of decreased graft function in renal transplant recipients with loss of graft function. Copyright © 2018 Elsevier Inc. All rights reserved.

Metagenomic insights into the effect of oxytetracycline on microbial structures, functions and functional genes in sediment denitrification.

PubMed

Zou, Yong; Lin, Manxia; Xiong, Wenguang; Wang, Mei; Zhang, Jiaxuan; Wang, Mianzhi; Sun, Yongxue

2018-06-02

Denitrification is an indispensable pathway of nitrogen removal in aquatic ecosystems, and plays an important role in decreasing eutrophication induced by excessive reactive nitrogen pollution. Aquatic environments also suffer from antibiotic pollution due to runoff from farms and sewage systems. The aim of this study was to investigate the effect of oxytetracycline stress on denitrifying functional genes, the microbial community and metabolic pathways in sediments using high-throughput sequencing and metagenomic analysis. The oxytetracycline was observed to significantly inhibit the abundance of nirK and nosZ genes (P < 0.001). KEGG pathway annotation indicated that oxytetracycline treatment decreased the abundance of nitrate reductase, nitrite reductase and N 2 O reductase. Functional annotations revealed that oxytetracycline exposure decreased the abundance of the protein metabolism subsystem in the bacterial community. Metagenomic sequencing demonstrated that the abundance of Proteobacteria and Firmicutes increased with oxytetracycline exposure while the Actinobacteria decreased. In sediments, Pseudomonas and Bradyrhizobium were major contributors to denitrification and oxytetracycline exposure resulted in a decreased abundance of Bradyrhizobium. These results indicated that oxytetracycline residues influences the denitrifier community and may heighten occurrence of reactive nitrogen in aquatic ecosystems. Copyright © 2018. Published by Elsevier Inc.

Sorption mechanism of enrofloxacin on humic acids extracted from Brazilian soils.

PubMed

Martínez-Mejía, Mónica J; Sato, Isabela; Rath, Susanne

2017-07-01

Veterinary antimicrobials are emerging environmental contaminants of concern. In this study, the sorption of enrofloxacin (ENR) onto humic acids (HAs) extracted from three Brazilian soils was evaluated. HAs were characterized by elemental analysis and solid 13 C nuclear magnetic resonance spectroscopy. The sorption of ENR onto HAs was at least 20-fold higher than onto the soils from which they were separated. Ionic and cation bridging are the primary interactions involved. The interactions driven by cation exchange are predominant on HAs, which appear to have abundant carboxylic groups and a relatively high proportion of H-bond donor moieties with carbohydrate-like structures. Interactions explained by cation bridging and/or surface complexation on HAs are facilitated by moieties containing conjugated ligands, significant content of oxygen-containing functional groups, such as phenolic-OH or lignin-like structures. HAs containing electron-donating phenolic moieties and carboxylic acid ligand groups exhibit a sorption mechanism that is primarily driven by strong metal binding, favoring the formation of ternary complexes between functional groups of the organic matter and drugs.

Biodiversity of man-made open habitats in an underused country: a class of multispecies abundance models for count data

USGS Publications Warehouse

Yamaura, Yuichi; Royle, J. Andrew; Shimada, Naoaki; Asanuma, Seigo; Sato, Tamotsu; Taki, Hisatomo; Makino, Shun'ichi

2012-01-01

Since the 1960s, Japan has become highly dependent on foreign countries for natural resources, and the amount of managed lands (e.g. coppice, grassland, and agricultural field) has declined. Due to infrequent natural and human disturbance, early-successional species are now declining in Japan. Here we surveyed bees, birds, and plants in four human-disturbed open habitats (pasture, meadow, young planted forest, and abandoned clear-cut) and two forest habitats (mature planted forest and natural old-growth). We extended a recently developed multispecies abundance model to accommodate count data, and used the resulting models to estimate species-, functional group-, and community-level state variables (abundance and species richness) at each site, and compared them among the six habitats. Estimated individual-level detection probability was quite low for bee species (mean across species = 0.003; 0.16 for birds). Thirty-two (95% credible interval: 13-64) and one (0-4) bee and bird species, respectively, were suggested to be undetected by the field survey. Although habitats in which community-level abundance and species richness was highest differed among taxa, species richness and abundance of early-successional species were similar in the four disturbed open habitats across taxa except for plants in the pasture habitat which was a good habitat only for several exotic species. Our results suggest that human disturbance, especially the revival of plantation forestry, may contribute to the restoration of early-successional species in Japan

Differences in coprophilous beetle communities structure in Sierra de Minas (Uruguay): a mosaic landscape.

PubMed

González-Vainer, Patricia; Morelli, E; Defeo, O

2012-10-01

Coprophilous beetles represent an abundant and rich group with critical importance in the functioning of terrestrial ecosystems. Most coprophagous beetles have a stenotopic distribution in relation to vegetation types. Because of this, they are usually very sensitive to environmental changes and are considered well suited as bioindicator organisms. The aim of this study was to analyze variations in coprophilous beetle assemblages in natural and anthropogenic habitats. Coprophilous beetle communities were sampled monthly for 1 year using pitfall traps baited with cow dung, in native xeric upland forests, 15-years-old plantations of Pinus elliottii and pastures in Sierra de Minas, Lavalleja, Uruguay. A total of 7,436 beetles were caught and identified to species or morphospecies level. The most abundant families were Aphodiidae, Scarabaeidae, and Staphylinidae. Differences in species richness, abundance, Shannon index, evenness, and dominance were detected between habitats. Abundances of most frequent families were significantly higher in both kinds of forests. Species richness and diversity of Aphodiidae and Staphylinidae were higher in forests, while Scarabaeidae showed the highest richness and diversity in pine plantations. Species composition significantly differed between habitats. Uroxys terminalis Waterhouse and Ataenius perforatus Harold typified the assemblages in native forests and pine plantations and also discriminated both communities because of their differential pattern of abundance between habitats. Typifying species in pastures were Onthophagus hirculus, Ateuchus robustus (Harold), and Ataenius platensis Blanchard. Habitat type had a strong effect on the coprophilous beetle community structure and composition.

Gut microbial functional maturation and succession during human early life.

PubMed

Cerdó, Tomás; Ruiz, Alicia; Acuña, Inmaculada; Jáuregui, Ruy; Jehmlich, Nico; Haange, Sven-Bastian; von Bergen, Martin; Suárez, Antonio; Campoy, Cristina

2018-04-24

The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Study on the dominant species of Pteropoda in East China Sea

NASA Astrophysics Data System (ADS)

Xu, Zhaoli; Li, Chunju

2006-06-01

Based on the data of four seasonal marine surveys in the East China Sea (23°30' 33°N, 118°30' 128°E)during 1997 2000, the author studied the ecological characters of dominant Pteropoda species in the area. Results showed that there were five dominant Pteropoda species, more in summer, less in autumn and even in other seasons. These species, though belonging warm water species, can be categorized into two different groups in habitability. The first group was adapted in summer and autumn, including Creseis acicula, Desmopterus papilio and Creseis virgule, while the second group in winter and spring, represented by Limacina trochiformis and Agadina syimpsoni. The first group was more abundant than the second one. Besides, the first group contributed more to the Pteropoda abundance having higher occurrence frequency and aggregation intensity than the second. In horizontal distribution, the first group species reside in nearshore, and they could migrate to shallow place near estuary and aggregated in high density, while the second one was different: lower abundance, less occurred and aggregated because they were halophilic warm water species, and they were usually abundant in offshore area.

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

PubMed Central

Wafula, Denis; White, John R.; Canion, Andy; Jagoe, Charles; Pathak, Ashish

2015-01-01

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem. PMID:26253672

EXPLORING ANTICORRELATIONS AND LIGHT ELEMENT VARIATIONS IN NORTHERN GLOBULAR CLUSTERS OBSERVED BY THE APOGEE SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mészáros, Szabolcs; Martell, Sarah L.; Shetrone, Matthew

We investigate the light-element behavior of red giant stars in northern globular clusters (GCs) observed by the SDSS-III Apache Point Observatory Galactic Evolution Experiment. We derive abundances of 9 elements (Fe, C, N, O, Mg, Al, Si, Ca, and Ti) for 428 red giant stars in 10 GCs. The intrinsic abundance range relative to measurement errors is examined, and the well-known C–N and Mg–Al anticorrelations are explored using an extreme-deconvolution code for the first time in a consistent way. We find that Mg and Al drive the population membership in most clusters, except in M107 and M71, the two mostmore » metal-rich clusters in our study, where the grouping is most sensitive to N. We also find a diversity in the abundance distributions, with some clusters exhibiting clear abundance bimodalities (for example M3 and M53) while others show extended distributions. The spread of Al abundances increases significantly as cluster average metallicity decreases as previously found by other works, which we take as evidence that low metallicity, intermediate mass AGB polluters were more common in the more metal-poor clusters. The statistically significant correlation of [Al/Fe] with [Si/Fe] in M15 suggests that {sup 28}Si leakage has occurred in this cluster. We also present C, N, and O abundances for stars cooler than 4500 K and examine the behavior of A(C+N+O) in each cluster as a function of temperature and [Al/Fe]. The scatter of A(C+N+O) is close to its estimated uncertainty in all clusters and independent of stellar temperature. A(C+N+O) exhibits small correlations and anticorrelations with [Al/Fe] in M3 and M13, but we cannot be certain about these relations given the size of our abundance uncertainties. Star-to-star variations of α-element (Si, Ca, Ti) abundances are comparable to our estimated errors in all clusters.« less

Exploring Anticorrelations and Light Element Variations in Northern Globular Clusters Observed by the APOGEE Survey

NASA Astrophysics Data System (ADS)

Mészáros, Szabolcs; Martell, Sarah L.; Shetrone, Matthew; Lucatello, Sara; Troup, Nicholas W.; Bovy, Jo; Cunha, Katia; García-Hernández, Domingo A.; Overbeek, Jamie C.; Allende Prieto, Carlos; Beers, Timothy C.; Frinchaboy, Peter M.; García Pérez, Ana E.; Hearty, Fred R.; Holtzman, Jon; Majewski, Steven R.; Nidever, David L.; Schiavon, Ricardo P.; Schneider, Donald P.; Sobeck, Jennifer S.; Smith, Verne V.; Zamora, Olga; Zasowski, Gail

2015-05-01

We investigate the light-element behavior of red giant stars in northern globular clusters (GCs) observed by the SDSS-III Apache Point Observatory Galactic Evolution Experiment. We derive abundances of 9 elements (Fe, C, N, O, Mg, Al, Si, Ca, and Ti) for 428 red giant stars in 10 GCs. The intrinsic abundance range relative to measurement errors is examined, and the well-known C-N and Mg-Al anticorrelations are explored using an extreme-deconvolution code for the first time in a consistent way. We find that Mg and Al drive the population membership in most clusters, except in M107 and M71, the two most metal-rich clusters in our study, where the grouping is most sensitive to N. We also find a diversity in the abundance distributions, with some clusters exhibiting clear abundance bimodalities (for example M3 and M53) while others show extended distributions. The spread of Al abundances increases significantly as cluster average metallicity decreases as previously found by other works, which we take as evidence that low metallicity, intermediate mass AGB polluters were more common in the more metal-poor clusters. The statistically significant correlation of [Al/Fe] with [Si/Fe] in M15 suggests that 28Si leakage has occurred in this cluster. We also present C, N, and O abundances for stars cooler than 4500 K and examine the behavior of A(C+N+O) in each cluster as a function of temperature and [Al/Fe]. The scatter of A(C+N+O) is close to its estimated uncertainty in all clusters and independent of stellar temperature. A(C+N+O) exhibits small correlations and anticorrelations with [Al/Fe] in M3 and M13, but we cannot be certain about these relations given the size of our abundance uncertainties. Star-to-star variations of α-element (Si, Ca, Ti) abundances are comparable to our estimated errors in all clusters.

Conformation of a Group 2 Late Embryogenesis Abundant Protein from Soybean. Evidence of Poly (l-Proline)-type II Structure1

PubMed Central

Soulages, Jose L.; Kim, Kangmin; Arrese, Estela L.; Walters, Christina; Cushman, John C.

2003-01-01

Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (l-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (l-proline)-type II-like helical conformation at 12°C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80°C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt α-helical structure and to interact with phospholipid bilayers through amphipathic α-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic stress-related damage to macromolecular structures. PMID:12644649

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors.

PubMed

Gao, Minghong; Liu, Jiwen; Qiao, Yanlu; Zhao, Meixun; Zhang, Xiao-Hua

2017-04-01

Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.

Hyperdominance in Amazonian forest carbon cycling

PubMed Central

Fauset, Sophie; Johnson, Michelle O.; Gloor, Manuel; Baker, Timothy R.; Monteagudo M., Abel; Brienen, Roel J.W.; Feldpausch, Ted R.; Lopez-Gonzalez, Gabriela; Malhi, Yadvinder; ter Steege, Hans; Pitman, Nigel C.A.; Baraloto, Christopher; Engel, Julien; Pétronelli, Pascal; Andrade, Ana; Camargo, José Luís C.; Laurance, Susan G.W.; Laurance, William F.; Chave, Jerôme; Allie, Elodie; Vargas, Percy Núñez; Terborgh, John W.; Ruokolainen, Kalle; Silveira, Marcos; Aymard C., Gerardo A.; Arroyo, Luzmila; Bonal, Damien; Ramirez-Angulo, Hirma; Araujo-Murakami, Alejandro; Neill, David; Hérault, Bruno; Dourdain, Aurélie; Torres-Lezama, Armando; Marimon, Beatriz S.; Salomão, Rafael P.; Comiskey, James A.; Réjou-Méchain, Maxime; Toledo, Marisol; Licona, Juan Carlos; Alarcón, Alfredo; Prieto, Adriana; Rudas, Agustín; van der Meer, Peter J.; Killeen, Timothy J.; Marimon Junior, Ben-Hur; Poorter, Lourens; Boot, Rene G.A.; Stergios, Basil; Torre, Emilio Vilanova; Costa, Flávia R.C.; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Groot, Nikée; Arets, Eric; Moscoso, Victor Chama; Castro, Wendeson; Coronado, Euridice N. Honorio; Peña-Claros, Marielos; Stahl, Clement; Barroso, Jorcely; Talbot, Joey; Vieira, Ima Célia Guimarães; van der Heijden, Geertje; Thomas, Raquel; Vos, Vincent A.; Almeida, Everton C.; Davila, Esteban Álvarez; Aragão, Luiz E.O.C.; Erwin, Terry L.; Morandi, Paulo S.; de Oliveira, Edmar Almeida; Valadão, Marco B.X.; Zagt, Roderick J.; van der Hout, Peter; Loayza, Patricia Alvarez; Pipoly, John J.; Wang, Ophelia; Alexiades, Miguel; Cerón, Carlos E.; Huamantupa-Chuquimaco, Isau; Di Fiore, Anthony; Peacock, Julie; Camacho, Nadir C. Pallqui; Umetsu, Ricardo K.; de Camargo, Plínio Barbosa; Burnham, Robyn J.; Herrera, Rafael; Quesada, Carlos A.; Stropp, Juliana; Vieira, Simone A.; Steininger, Marc; Rodríguez, Carlos Reynel; Restrepo, Zorayda; Muelbert, Adriane Esquivel; Lewis, Simon L.; Pickavance, Georgia C.; Phillips, Oliver L.

2015-01-01

While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few ‘hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region. PMID:25919449

Hyperdominance in Amazonian forest carbon cycling.

PubMed

Fauset, Sophie; Johnson, Michelle O; Gloor, Manuel; Baker, Timothy R; Monteagudo M, Abel; Brienen, Roel J W; Feldpausch, Ted R; Lopez-Gonzalez, Gabriela; Malhi, Yadvinder; ter Steege, Hans; Pitman, Nigel C A; Baraloto, Christopher; Engel, Julien; Pétronelli, Pascal; Andrade, Ana; Camargo, José Luís C; Laurance, Susan G W; Laurance, William F; Chave, Jerôme; Allie, Elodie; Vargas, Percy Núñez; Terborgh, John W; Ruokolainen, Kalle; Silveira, Marcos; Aymard C, Gerardo A; Arroyo, Luzmila; Bonal, Damien; Ramirez-Angulo, Hirma; Araujo-Murakami, Alejandro; Neill, David; Hérault, Bruno; Dourdain, Aurélie; Torres-Lezama, Armando; Marimon, Beatriz S; Salomão, Rafael P; Comiskey, James A; Réjou-Méchain, Maxime; Toledo, Marisol; Licona, Juan Carlos; Alarcón, Alfredo; Prieto, Adriana; Rudas, Agustín; van der Meer, Peter J; Killeen, Timothy J; Marimon Junior, Ben-Hur; Poorter, Lourens; Boot, Rene G A; Stergios, Basil; Torre, Emilio Vilanova; Costa, Flávia R C; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Groot, Nikée; Arets, Eric; Moscoso, Victor Chama; Castro, Wendeson; Coronado, Euridice N Honorio; Peña-Claros, Marielos; Stahl, Clement; Barroso, Jorcely; Talbot, Joey; Vieira, Ima Célia Guimarães; van der Heijden, Geertje; Thomas, Raquel; Vos, Vincent A; Almeida, Everton C; Davila, Esteban Álvarez; Aragão, Luiz E O C; Erwin, Terry L; Morandi, Paulo S; de Oliveira, Edmar Almeida; Valadão, Marco B X; Zagt, Roderick J; van der Hout, Peter; Loayza, Patricia Alvarez; Pipoly, John J; Wang, Ophelia; Alexiades, Miguel; Cerón, Carlos E; Huamantupa-Chuquimaco, Isau; Di Fiore, Anthony; Peacock, Julie; Camacho, Nadir C Pallqui; Umetsu, Ricardo K; de Camargo, Plínio Barbosa; Burnham, Robyn J; Herrera, Rafael; Quesada, Carlos A; Stropp, Juliana; Vieira, Simone A; Steininger, Marc; Rodríguez, Carlos Reynel; Restrepo, Zorayda; Muelbert, Adriane Esquivel; Lewis, Simon L; Pickavance, Georgia C; Phillips, Oliver L

2015-04-28

While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.

Quantitative chemical tagging, stellar ages and the chemo-dynamical evolution of the Galactic disc

NASA Astrophysics Data System (ADS)

Mitschang, A. W.; De Silva, G.; Zucker, D. B.; Anguiano, B.; Bensby, T.; Feltzing, S.

2014-03-01

The early science results from the new generation of high-resolution stellar spectroscopic surveys, such as Galactic Archaeology with HERMES (GALAH) and the Gaia European Southern Observatory survey (Gaia-ESO), will represent major milestones in the quest to chemically tag the Galaxy. Yet this technique to reconstruct dispersed coeval stellar groups has remained largely untested until recently. We build on previous work that developed an empirical chemical tagging probability function, which describes the likelihood that two field stars are conatal, that is, they were formed in the same cluster environment. In this work, we perform the first ever blind chemical tagging experiment, i.e. tagging stars with no known or otherwise discernible associations, on a sample of 714 disc field stars with a number of high-quality high-resolution homogeneous metal abundance measurements. We present evidence that chemical tagging of field stars does identify coeval groups of stars, yet these groups may not represent distinct formation sites, e.g. as in dissolved open clusters, as previously thought. Our results point to several important conclusions, among them that group finding will be limited strictly to chemical abundance space, e.g. stellar ages, kinematics, colours, temperature and surface gravity do not enhance the detectability of groups. We also demonstrate that in addition to its role in probing the chemical enrichment and kinematic history of the Galactic disc, chemical tagging represents a powerful new stellar age determination technique.

Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy

PubMed Central

Younge, Noelle; Yang, Qing; Seed, Patrick C.

2016-01-01

Objective To determine the effect of enteral fish oil and safflower oil supplementation on the intestinal microbiome in premature infants with an enterostomy. Study design Premature infants with an enterostomy were randomized to receive early enteral supplementation with a high fat-polyunsaturated fatty acid (HF-PUFA) blend of fish oil and safflower oil versus standard nutritional therapy. We used 16S rRNA gene sequencing for longitudinal profiling of the microbiome from the time of study entry until bowel reanastomosis. We used weighted gene co-expression network analysis to identify microbial community modules that differed between study groups over time. We performed imputed metagenomic analysis to determine metabolic pathways associated with the microbial genes. Results Sixteen infants were randomized to receive enteral HF-PUFA supplementation and 16 infants received standard care. The intestinal microbiota of infants in the treatment group differed from those in the control group, with greater bacterial diversity and lower abundance of Streptococcus, Clostridium, and many pathogenic genera within the Enterobacteriaceae family. We identified four microbial community modules with significant differences between groups over time. Imputed metagenomic analysis of the microbial genes revealed metabolic pathways that differed between groups, including metabolism of amino acids, carbohydrates, fatty acids, and secondary bile acid synthesis. Conclusion Enteral HF-PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota. Trial registration ClinicalTrials.gov: NCT01306838 PMID:27856001

Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy.

PubMed

Younge, Noelle; Yang, Qing; Seed, Patrick C

2017-02-01

To determine the effect of enteral fish oil and safflower oil supplementation on the intestinal microbiome in infants with an enterostomy born premature. Infants with an enterostomy born premature were randomized to receive early enteral supplementation with a high-fat polyunsaturated fatty acid (HF-PUFA) blend of fish oil and safflower oil vs standard nutritional therapy. We used 16S rRNA gene sequencing for longitudinal profiling of the microbiome from the time of study entry until bowel reanastomosis. We used weighted gene coexpression network analysis to identify microbial community modules that differed between study groups over time. We performed imputed metagenomic analysis to determine metabolic pathways associated with the microbial genes. Sixteen infants were randomized to receive enteral HF-PUFA supplementation, and 16 infants received standard care. The intestinal microbiota of infants in the treatment group differed from those in the control group, with greater bacterial diversity and lower abundance of Streptococcus, Clostridium, and many pathogenic genera within the Enterobacteriaceae family. We identified 4 microbial community modules with significant differences between groups over time. Imputed metagenomic analysis of the microbial genes revealed metabolic pathways that differed between groups, including metabolism of amino acids, carbohydrates, fatty acids, and secondary bile acid synthesis. Enteral HF-PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota. ClinicalTrials.gov:NCT01306838. Copyright © 2016 Elsevier Inc. All rights reserved.

Normalization and microbial differential abundance strategies depend upon data characteristics.

PubMed

Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob

2017-03-03

Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets (<20 samples per group) but tends towards a higher false discovery rate with more samples, very uneven (~10×) library sizes, and/or compositional effects. For drawing inferences regarding taxon abundance in the ecosystem, analysis of composition of microbiomes (ANCOM) is not only very sensitive (for >20 samples per group) but also critically the only method tested that has a good control of false discovery rate. These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.

Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea.

PubMed

Pizzetti, Ilaria; Fuchs, Bernhard M; Gerdts, Gunnar; Wichels, Antje; Wiltshire, Karen H; Amann, Rudolf

2011-07-01

Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ~90% of the Planctomycetes reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.

Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs.

PubMed

Qu, Huan; Huang, Yanjie; Shi, Yinghao; Liu, Ying; Wu, Shenglong; Bao, Wenbin

2018-05-18

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing-finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing-finishing pigs were randomly allocated to five diet groups: 0%,0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. Addition of 1.5% bamboo vinegar powder had the most similar effect on the intestinal microflora to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicute/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

Wood thrush nest success and post-fledging survival across a temporal pulse of small mammal abundance in an oak forest.

PubMed

Schmidt, Kenneth A; Rush, Scott A; Ostfeld, Richard S

2008-07-01

1. Synchronized mass production of seed crops, such as acorns, produces a resource pulse that may have far-reaching consequences for songbird populations through its effects on avian predators. Seed production in these forests represents only the first of several pulsed events. Secondary pulses emerge as mast-consuming rodents numerically respond to seed production and tertiary pulses emerge as generalist predators, such as raptors, numerically respond to rodents. In turn, these two groups reduce nest productivity and juvenile survivorship 1 and 2 years, respectively, after the initial pulse in seed production. 2. At our study site in south-eastern New York, USA, autumn acorn abundance (primary pulse) largely determines rodent abundance (secondary pulse) the following spring. We tested the hypotheses that the population dynamics of a shrub-nesting passerine (wood thrush Hylocichla mustelina), is influenced by rodents through the: (a) direct effect of predation by rodents; (b) indirect effect of rodents on the abundance of raptors (tertiary pulse); and (c) indirect effect of rodent abundance on raptor diet. The latter specifically hypothesizes that a crash in the rodent population in the wake of region-wide failure of acorn production leads to an extreme diet shift in raptors that increases post-fledging mortality in birds. 3. We conducted a 3-year study to examine variation in wood thrush nest success and fledgling survival, using radio telemetry, across a pulse of rodent abundance (i.e. low, medium and high). We also updated and reanalysed regional wood thrush population growth rates as a function of the annual variation in rodent abundance. 4. Fledgling survivorship, but not nest success, varied in relation to annual rodent abundance. Raptors and eastern chipmunks Tamias striatus were the most commonly identified predators on fledglings. Fledgling survivorship was greatest at intermediate rodent abundance consistent with a shift in raptor diet. Regional rate of wood thrush population growth showed a unimodal relationship with rodent abundance, peaking during years with intermediate rodent abundance. This unimodal pattern was due to wood thrush population growth rates near or below zero during rodent population crashes. 5. The telemetry study, pattern of regional abundance and synchronized population dynamics of coexisting thrushes suggest a common mechanism of behavioural changes in raptors in response to declines in rodent prey, which in turn affects thrush population dynamics.

Metal distributions out to 0.5 r {sub 180} in the intracluster medium of four galaxy groups observed with Suzaku

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sasaki, Toru; Matsushita, Kyoko; Sato, Kosuke, E-mail: j1213703@ed.tus.ac.jp, E-mail: matusita@rs.kagu.tus.ac.jp

2014-01-20

We studied the distributions of metal abundances and metal-mass-to-light ratios in the intracluster medium (ICM) of four galaxy groups, MKW 4, HCG 62, the NGC 1550 group, and the NGC 5044 group, out to ∼0.5 r {sub 180} observed with Suzaku. The iron abundance decreases with radius and is about 0.2-0.4 solar beyond 0.1 r {sub 180}. At a given radius in units of r {sub 180}, the iron abundance in the ICM of the four galaxy groups was consistent with or smaller than those of clusters of galaxies. The Mg/Fe and Si/Fe ratios in the ICM are nearly constantmore » at the solar ratio out to 0.5 r {sub 180}. We also studied systematic uncertainties in the derived metal abundances, comparing the results from two versions of atomic data for astrophysicists (ATOMDB) and single- and two-temperature model fits. Since the metals have been synthesized in galaxies, we collected K-band luminosities of galaxies from the Two Micron All Sky Survey catalog and calculated the integrated iron-mass-to-light-ratios (IMLR), or the ratios of the iron mass in the ICM to light from stars in galaxies. The groups with smaller gas-mass-to-light ratios have smaller IMLR values and the IMLR is inversely correlated with the entropy excess. Based on these abundance features, we discussed the past history of metal enrichment processes in groups of galaxies.« less

Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific.

PubMed

Belmar, Lucy; Molina, Verónica; Ulloa, Osvaldo

2011-11-01

We assessed the abundance and molecular phylogeny of archaeoplankton in the oxygen minimum zone (OMZ) of the eastern tropical South Pacific, using specific-probe hybridization and phylogenetic analysis of the SSU-rRNA gene. Euryarchaea from Marine Group-II (MG-II) were most abundant in the surface oxic layer, representing 4.0±2.0% of the total picoplankton, while crenarchaea from Group I.1a (G-I.1a) peaked at the oxyclines, with a relative abundance of 8.1±4.3% (upper oxycline). In most of the stations, the abundance of both the groups decreased at the core of the OMZ, where a secondary maximum in cell density is commonly observed. The majority of the phylotypes affiliated with one of three groups: MG-II, euryarchaeal Marine Group-III (MG-III) and G-I.1a (75.9%, 12.8% and 10.3%, respectively). While MG-II phylotypes were found throughout the water column and G-I.1a ones were predominantly found within the oxyclines, MG-III phylotypes came almost exclusively from the OMZ core. Higher archaeal richness was found within the OMZ, with some of the exclusive lineages grouping with sequences from the deep ocean and hydrothermal vents. Moreover, G-I.1a sequences from the OMZ grouped into a different subcluster from the aerobic ammonium-oxidizer Nitrosopumilus maritimus. Thus, the community structure of archaeoplankton in OMZs is rich and distinct, with G-I.1a members particularly prominent at the oxyclines. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

CHEERS: The chemical evolution RGS sample

NASA Astrophysics Data System (ADS)

de Plaa, J.; Kaastra, J. S.; Werner, N.; Pinto, C.; Kosec, P.; Zhang, Y.-Y.; Mernier, F.; Lovisari, L.; Akamatsu, H.; Schellenberger, G.; Hofmann, F.; Reiprich, T. H.; Finoguenov, A.; Ahoranta, J.; Sanders, J. S.; Fabian, A. C.; Pols, O.; Simionescu, A.; Vink, J.; Böhringer, H.

2017-11-01

Context. The chemical yields of supernovae and the metal enrichment of the intra-cluster medium (ICM) are not well understood. The hot gas in clusters of galaxies has been enriched with metals originating from billions of supernovae and provides a fair sample of large-scale metal enrichment in the Universe. High-resolution X-ray spectra of clusters of galaxies provide a unique way of measuring abundances in the hot intracluster medium (ICM). The abundance measurements can provide constraints on the supernova explosion mechanism and the initial-mass function of the stellar population. This paper introduces the CHEmical Enrichment RGS Sample (CHEERS), which is a sample of 44 bright local giant ellipticals, groups, and clusters of galaxies observed with XMM-Newton. Aims: The CHEERS project aims to provide the most accurate set of cluster abundances measured in X-rays using this sample. This paper focuses specifically on the abundance measurements of O and Fe using the reflection grating spectrometer (RGS) on board XMM-Newton. We aim to thoroughly discuss the cluster to cluster abundance variations and the robustness of the measurements. Methods: We have selected the CHEERS sample such that the oxygen abundance in each cluster is detected at a level of at least 5σ in the RGS. The dispersive nature of the RGS limits the sample to clusters with sharp surface brightness peaks. The deep exposures and the size of the sample allow us to quantify the intrinsic scatter and the systematic uncertainties in the abundances using spectral modeling techniques. Results: We report the oxygen and iron abundances as measured with RGS in the core regions of all 44 clusters in the sample. We do not find a significant trend of O/Fe as a function of cluster temperature, but we do find an intrinsic scatter in the O and Fe abundances from cluster to cluster. The level of systematic uncertainties in the O/Fe ratio is estimated to be around 20-30%, while the systematic uncertainties in the absolute O and Fe abundances can be as high as 50% in extreme cases. Thanks to the high statistics of the observations, we were able to identify and correct a systematic bias in the oxygen abundance determination that was due to an inaccuracy in the spectral model. Conclusions: The lack of dependence of O/Fe on temperature suggests that the enrichment of the ICM does not depend on cluster mass and that most of the enrichment likely took place before the ICM was formed. We find that the observed scatter in the O/Fe ratio is due to a combination of intrinsic scatter in the source and systematic uncertainties in the spectral fitting, which we are unable to separate. The astrophysical source of intrinsic scatter could be due to differences in active galactic nucleus activity and ongoing star formation in the brightest cluster galaxy. The systematic scatter is due to uncertainties in the spatial line broadening, absorption column, multi-temperature structure, and the thermal plasma models.

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

PubMed Central

Schneider, Thomas; Keiblinger, Katharina M; Schmid, Emanuel; Sterflinger-Gleixner, Katja; Ellersdorfer, Günther; Roschitzki, Bernd; Richter, Andreas; Eberl, Leo; Zechmeister-Boltenstern, Sophie; Riedel, Kathrin

2012-01-01

Leaf-litter decomposition is a central process in carbon cycling; however, our knowledge about the microbial regulation of this process is still scarce. Metaproteomics allows us to link the abundance and activity of enzymes during nutrient cycling to their phylogenetic origin based on proteins, the ‘active building blocks' in the system. Moreover, we employed metaproteomics to investigate the influence of environmental factors and nutrients on the decomposer structure and function during beech litter decomposition. Litter was collected at forest sites in Austria with different litter nutrient content. Proteins were analyzed by 1-D-SDS-PAGE followed by liquid-chromatography and tandem mass-spectrometry. Mass spectra were assigned to phylogenetic and functional groups by a newly developed bioinformatics workflow, assignments being validated by complementary approaches. We provide evidence that the litter nutrient content and the stoichiometry of C:N:P affect the decomposer community structure and activity. Fungi were found to be the main producers of extracellular hydrolytic enzymes, with no bacterial hydrolases being detected by our metaproteomics approach. Detailed investigation of microbial succession suggests that it is influenced by litter nutrient content. Microbial activity was stimulated at higher litter nutrient contents via a higher abundance and activity of extracellular enzymes. PMID:22402400

Energetic-particle abundances in impulsive solar flares

NASA Technical Reports Server (NTRS)

Reames, D. V.; Cane, H. V.; Von Rosenvinge, T. T.

1990-01-01

The abundances of elements and of He-3 in 90 solar electron events have been examined. It is found that the events fall into two distinct groups based upon their F/C ratio. Events in the F-rich group frequently have high He-3/He-4 ratios and are associated with type III and type V radio bursts in the parent flare. The F-poor events are associated with type IV bursts. These results on individual events support the conclusions of earlier work done with daily-averaged abundances.

Simple algorithms for remote determination of mineral abundances and particle sizes from reflectance spectra

NASA Technical Reports Server (NTRS)

Johnson, Paul E.; Smith, Milton O.; Adams, John B.

1992-01-01

Algorithms were developed, based on Hapke's (1981) equations, for remote determinations of mineral abundances and particle sizes from reflectance spectra. In this method, spectra are modeled as a function of end-member abundances and illumination/viewing geometry. The method was tested on a laboratory data set. It is emphasized that, although there exist more sophisticated models, the present algorithms are particularly suited for remotely sensed data, where little opportunity exists to independently measure reflectance versus article size and phase function.

Marginal bone loss around non-submerged implants is associated with salivary microbiome during bone healing.

PubMed

Duan, Xiao-Bo; Wu, Ting-Xi; Guo, Yu-Chen; Zhou, Xue-Dong; Lei, Yi-Ling; Xu, Xin; Mo, An-Chun; Wang, Yong-Yue; Yuan, Quan

2017-06-01

Marginal bone loss during bone healing exists around non-submerged dental implants. The aim of this study was to identify the relationship between different degrees of marginal bone loss during bone healing and the salivary microbiome. One hundred patients were recruited, and marginal bone loss around their implants was measured using cone beam computed tomography during a 3-month healing period. The patients were divided into three groups according to the severity of marginal bone loss. Saliva samples were collected from all subjected and were analysed using 16S MiSeq sequencing. Although the overall structure of the microbial community was not dramatically altered, the relative abundance of several taxonomic groups noticeably changed. The abundance of species in the phyla Spirochaeta and Synergistetes increased significantly as the bone loss became more severe. Species within the genus Treponema also exhibited increased abundance, whereas Veillonella, Haemophilus and Leptotrichia exhibited reduced abundances, in groups with more bone loss. Porphyromonasgingivalis, Treponemadenticola and Streptococcus intermedius were significantly more abundant in the moderate group and/or severe group. The severity of marginal bone loss around the non-submerged implant was associated with dissimilar taxonomic compositions. An increased severity of marginal bone loss was related to increased proportions of periodontal pathogenic species. These data suggest a potential role of microbes in the progression of marginal bone loss during bone healing.

Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups.

PubMed

Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong

2016-01-01

Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs.

The evolution of the lithium abundances of solar-type stars. II - The Ursa Major Group

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Pilachowski, Catherine A.; Fedele, Stephen B.; Jones, Burton F.

1993-01-01

We draw upon a recent study of the membership of the Ursa Major Group (UMaG) to examine lithium among 0.3 Gyr old solar-type stars. For most G and K dwarfs, Li confirms the conclusions about membership in UMaG reached on the basis of kinematics and chromospheric activity. G and K dwarfs in UMaG have less Li than comparable stars in the Pleiades. This indicates that G and K dwarfs undergo Li depletion while they are on the main sequence, in addition to any pre-main-sequence depletion they may have experienced. Moreover, the Li abundances of the Pleiades K dwarfs cannot be attributed to main-sequence depletion alone, demonstrating that pre-main-sequence depletion of Li also takes place. The sun's Li abundance implies that the main-sequence mechanism becomes less effective with age. The hottest stars in UMaG have Li abundances like those of hot stars in the Pleiades and Hyades and in T Tauris, and the two genuine UMaG members with temperatures near Boesgaard's Li chasm have Li abundances consistent with that chasm developing fully by 0.3 Gyr for stars with UMaG's metallicity. We see differences in the abundance of Li between UMaG members of the same spectral types, indicating that a real spread in the lithium abundance exists within this group.

A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

USGS Publications Warehouse

Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

2015-01-01

While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

Short-range forecast of Shershnevskoie (South Ural) water-storage algal blooms: preliminary results of predictors' choosing and membership functions' construction

NASA Astrophysics Data System (ADS)

Gayazova, Anna; Abdullaev, Sanjar

2014-05-01

Short-range forecasting of algal blooms in drinking water reservoirs and other waterbodies is an actual element of water treatment system. Particularly, Shershnevskoie reservoir - the source of drinking water for Chelyabinsk city (South Ural region of Russia) - is exposed to interannual, seasonal and short-range fluctuations of blue-green alga Aphanizomenon flos-aquae and other dominant species abundance, which lead to technological problems and economic costs and adversely affect the water treatment quality. Whereas the composition, intensity and the period of blooms affected not only by meteorological seasonal conditions but also by ecological specificity of waterbody, that's important to develop object-oriented forecasting, particularly, search for an optimal number of predictors for such forecasting. Thereby, firstly fuzzy logic and fuzzy artificial neural network patterns for blue-green alga Microcystis aeruginosa (M. aeruginosa) blooms prediction in nearby undrained Smolino lake were developed. These results subsequently served as the base to derive membership functions for Shernevskoie reservoir forecasting patterns. Time series with the total lenght about 138-159 days of dominant species seasonal abundance, water temperature, cloud cover, wind speed, mineralization, phosphate and nitrate concentrations were obtained through field observations held at Lake Smolino (Chelyabinsk) in the warm season of 2009 and 2011 with time resolution of 2-7 days. The cross-correlation analysis of the data revealed the potential predictors of M. aeruginosa abundance quasi-periodic oscillations: green alga Pediastrum duplex (P. duplex) abundance and mineralization for 2009, P. duplex abundance, water temperature and concentration of nitrates for 2011. According to the results of cross-correlation analysis one membership function "P. duplex abundance" and one rule linking M. aeruginosa and P. duplex abundances were set up for database of 2009. Analogically, for database of 2011 three rules, linking membership functions of temperature, P. duplex abundance, nitrate concentration and M. aeruginosa abundance were set up. Developed fuzzy logic rules were good to predict M. aeruginosa intense outbreaks. For ANN method of forecasting specially written program was used to train the fuzzy artificial neural network on number of input selected predictors' values and output predicted factor's values to set up the predictive rules and membership functions automatically. As a result, two models based on mineralization and P. duplex abundance were developed for 2009. For 2011 four patterns were developed, the best result was obtained for model based on temperature and P. duplex abundance. Developed methods of forecasting were applied to predict outbreaks of Aphanizomenon flos-aquae and M. aeruginosa abundance in Shershnevskoie reservoir. For this purpose long-term data of chemical parameters, measured once in a month, data of dominant species abundance, measured fifth in a week and data of turbidity, water color, alkalinity, pH, obtained each day, were analyzed. Based on these empirical data significant factors were determined, membership functions were set up and preliminary models for Shershnevskoie reservoir were developed. As expected, these models differ significantly from developed for Smolino lake ones and should be tested on new data sets.

Intestinal microbiota and oral administration of Enterococcus faecium associated with the growth performance of new-born piglets.

PubMed

Wang, Y B; Du, W; Fu, A K; Zhang, X P; Huang, Y; Lee, K H; Yu, K; Li, W F; Li, Y L

2016-09-01

The oral administration of Enterococcus faecium EF1 to new-born suckling and weaning piglets along with their growth performances and intestinal microbiota was investigated in this study. Twenty-four new-born piglets were initially divided into 2 groups. The probiotics group received 2 ml of 10% sterilised skimmed milk by oral gavage supplemented with 6×10(8) cfu/ml viable E. faecium EF1 at the first, the third and the fifth day after birth, while the control group received 2 ml of 10% sterilised skimmed milk without probiotics at the same time. Results showed that oral administration of E. faecium EF1 was associated with a remarkable increase on the body weight of piglets for both suckling and weaning periods, by 30.73% (P<0.01) and 320.84% (P<0.01), and also decreased the diarrhoea rate, by 43.21% (P<0.05) and 71.42% (P<0.05), respectively. In addition, 454-pyrosequencing analysis revealed that there was no significant difference in the intestinal microbial diversity of the suckling piglets between the two groups; nevertheless, when compared to the control group, the relative abundance of Firmicutes in the probiotics group was substantially augmented, while the relative abundance of Proteobacteria, Bacteroidetes and Fusobacteria diminished. However, results indicated that oral administration of E. faecium EF1 did not have any influence on the relative abundance of Firmicutes in weaning piglets rather than increasing the relative abundance of Bacteroidetes and decreasing the relative abundance of Proteobacteria. Furthermore, at the level of the Firmicutes phylum, the relative abundance of Lactobacillales in the probiotic group increased significantly. These findings suggest that oral administration of E. faecium EF1 to new-born piglets could improve the growth performance and intestinal microbiota of piglets for both suckling and weaning periods.

Predator-induced demographic shifts in coral reef fish assemblages

USGS Publications Warehouse

Ruttenberg, B.I.; Hamilton, S.L.; Walsh, S.M.; Donovan, M.K.; Friedlander, A.; DeMartini, E.; Sala, E.; Sandin, S.A.

2011-01-01

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ~10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management. ?? 2011 Ruttenberg et al.

Predator-Induced Demographic Shifts in Coral Reef Fish Assemblages

PubMed Central

Ruttenberg, Benjamin I.; Hamilton, Scott L.; Walsh, Sheila M.; Donovan, Mary K.; Friedlander, Alan; DeMartini, Edward; Sala, Enric; Sandin, Stuart A.

2011-01-01

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ∼10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management. PMID:21698165

Small Marine Protected Areas in Fiji Provide Refuge for Reef Fish Assemblages, Feeding Groups, and Corals.

PubMed

Bonaldo, Roberta M; Pires, Mathias M; Guimarães, Paulo Roberto; Hoey, Andrew S; Hay, Mark E

2017-01-01

The establishment of no-take marine protected areas (MPAs) on coral reefs is a common management strategy for conserving the diversity, abundance, and biomass of reef organisms. Generally, well-managed and enforced MPAs can increase or maintain the diversity and function of the enclosed coral reef, with some of the benefits extending to adjacent non-protected reefs. A fundamental question in coral reef conservation is whether these benefits arise within small MPAs (<1 km2), because larval input of reef organisms is largely decoupled from local adult reproduction. We examined the structure of fish assemblages, composition of fish feeding groups, benthic cover, and key ecosystem processes (grazing, macroalgal browsing, and coral replenishment) in three small (0.5-0.8 km2) no-take MPAs and adjacent areas where fisheries are allowed (non-MPAs) on coral reefs in Fiji. The MPAs exhibited greater species richness, density, and biomass of fishes than non-MPAs. Furthermore, MPAs contained a greater abundance and biomass of grazing herbivores and piscivores as well as a greater abundance of cleaners than fished areas. We also found differences in fish associations when foraging, with feeding groups being generally more diverse and having greater biomass within MPAs than adjacent non-MPAs. Grazing by parrotfishes was 3-6 times greater, and macroalgal browsing was 3-5 times greater in MPAs than in non-MPAs. On average, MPAs had 260-280% as much coral cover and only 5-25% as much macroalgal cover as their paired non-MPA sites. Finally, two of the three MPAs had three-fold more coral recruits than adjacent non-MPAs. The results of this study indicate that small MPAs benefit not only populations of reef fishes, but also enhance ecosystem processes that are critical to reef resilience within the MPAs.

Niche partitioning of marine group I Crenarchaeota in the euphotic and upper mesopelagic zones of the East China Sea.

PubMed

Hu, Anyi; Jiao, Nianzhi; Zhang, Rui; Yang, Zao

2011-11-01

Marine group I Crenarchaeota (MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase gene amoA, and the biotin carboxylase gene accA. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaeal amoA gene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaeal accA to amoA or to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaeal amoA and accA genes showed both "shallow" and "deep" groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.

High frequency of functional extinctions in ecological networks.

PubMed

Säterberg, Torbjörn; Sellman, Stefan; Ebenman, Bo

2013-07-25

Intensified exploitation of natural populations and habitats has led to increased mortality rates and decreased abundances of many species. There is a growing concern that this might cause critical abundance thresholds of species to be crossed, with extinction cascades and state shifts in ecosystems as a consequence. When increased mortality rate and decreased abundance of a given species lead to extinction of other species, this species can be characterized as functionally extinct even though it still exists. Although such functional extinctions have been observed in some ecosystems, their frequency is largely unknown. Here we use a new modelling approach to explore the frequency and pattern of functional extinctions in ecological networks. Specifically, we analytically derive critical abundance thresholds of species by increasing their mortality rates until an extinction occurs in the network. Applying this approach on natural and theoretical food webs, we show that the species most likely to go extinct first is not the one whose mortality rate is increased but instead another species. Indeed, up to 80% of all first extinctions are of another species, suggesting that a species' ecological functionality is often lost before its own existence is threatened. Furthermore, we find that large-bodied species at the top of the food chains can only be exposed to small increases in mortality rate and small decreases in abundance before going functionally extinct compared to small-bodied species lower in the food chains. These results illustrate the potential importance of functional extinctions in ecological networks and lend strong support to arguments advocating a more community-oriented approach in conservation biology, with target levels for populations based on ecological functionality rather than on mere persistence.

Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

PubMed Central

2012-01-01

Background Ethylene production and signalling play an important role in somatic embryogenesis, especially for species that are recalcitrant in in vitro culture. The AP2/ERF superfamily has been identified and classified in Hevea brasiliensis. This superfamily includes the ERFs involved in response to ethylene. The relative transcript abundance of ethylene biosynthesis genes and of AP2/ERF genes was analysed during somatic embryogenesis for callus lines with different regeneration potential, in order to identify genes regulated during that process. Results The analysis of relative transcript abundance was carried out by real-time RT-PCR for 142 genes. The transcripts of ERFs from group I, VII and VIII were abundant at all stages of the somatic embryogenesis process. Forty genetic expression markers for callus regeneration capacity were identified. Fourteen markers were found for proliferating calli and 35 markers for calli at the end of the embryogenesis induction phase. Sixteen markers discriminated between normal and abnormal embryos and, lastly, there were 36 markers of conversion into plantlets. A phylogenetic analysis comparing the sequences of the AP2 domains of Hevea and Arabidopsis genes enabled us to predict the function of 13 expression marker genes. Conclusions This first characterization of the AP2/ERF superfamily in Hevea revealed dramatic regulation of the expression of AP2/ERF genes during the somatic embryogenesis process. The gene expression markers of proliferating callus capacity to regenerate plants by somatic embryogenesis should make it possible to predict callus lines suitable to be used for multiplication. Further functional characterization of these markers opens up prospects for discovering specific AP2/ERF functions in the Hevea species for which somatic embryogenesis is difficult. PMID:23268714

OPC-28326, a selective peripheral vasodilator with angiogenic activity, mitigates postinfarction cardiac remodeling.

PubMed

Ogino, Atsushi; Takemura, Genzou; Hashimoto, Ayako; Kanamori, Hiromitsu; Okada, Hideshi; Nakagawa, Munehiro; Tsujimoto, Akiko; Goto, Kazuko; Kawasaki, Masanori; Nagashima, Kenshi; Miyakoda, Goro; Fujiwara, Takako; Yabuuchi, Youichi; Fujiwara, Hisayoshi; Minatoguchi, Shinya

2015-07-01

Although OPC-28326, 4-(N-methyl-2-phenylethylamino)-1-(3,5-dimethyl-4-propionyl-aminobenzoyl) piperidine hydrochloride monohydrate, was developed as a selective peripheral vasodilator with α2-adrenergic antagonist properties, it also reportedly exhibits angiogenic activity in an ischemic leg model. The purpose of this study was to examine the effect of OPC-28326 on the architectural dynamics and function of the infarcted left ventricle during the chronic stage of myocardial infarction. Myocardial infarction was induced in male C3H/He mice, after which the mice were randomly assigned into two groups: a control group receiving a normal diet and an OPC group whose diet contained 0.05% OPC-28326. The survival rate among the mice (n = 18 in each group) 4 wk postinfarction was significantly greater in the OPC than control group (83 vs. 44%; P < 0.05), and left ventricular remodeling and dysfunction were significantly mitigated. Histologically, infarct wall thickness was significantly greater in the OPC group, due in part to an abundance of nonmyocyte components, including blood vessels and myofibroblasts. Five days postinfarction, Ki-67-positive proliferating cells were more abundant in the granulation tissue in the OPC group, and there were fewer apoptotic cells. These effects were accompanied by activation of myocardial Akt and endothelial nitric oxide synthase. Hypoxia within the infarct issue, assessed using pimonidazole staining, was markedly attenuated in the OPC group. In summary, OPC-28326 increased the nonmyocyte population in infarct tissue by increasing proliferation and reducing apoptosis, thereby altering the tissue dynamics such that wall stress was reduced, which might have contributed to a mitigation of postinfarction cardiac remodeling and dysfunction. Copyright © 2015 the American Physiological Society.

Regulation of Innate Lymphoid Cells by Aryl Hydrocarbon Receptor

PubMed Central

Li, Shiyang; Bostick, John W.; Zhou, Liang

2018-01-01

With striking similarity to their adaptive T helper cell counterparts, innate lymphoid cells (ILCs) represent an emerging family of cell types that express signature transcription factors, including T-bet+ Eomes+ natural killer cells, T-bet+ Eomes− group 1 ILCs, GATA3+ group 2 ILCs, RORγt+ group 3 ILCs, and newly identified Id3+ regulatory ILC. ILCs are abundantly present in barrier tissues of the host (e.g., the lung, gut, and skin) at the interface of host–environment interactions. Active research has been conducted to elucidate molecular mechanisms underlying the development and function of ILCs. The aryl hydrocarbon receptor (Ahr) is a ligand-dependent transcription factor, best known to mediate the effects of xenobiotic environmental toxins and endogenous microbial and dietary metabolites. Here, we review recent progresses regarding Ahr function in ILCs. We focus on the Ahr-mediated cross talk between ILCs and other immune/non-immune cells in host tissues especially in the gut. We discuss the molecular mechanisms of the action of Ahr expression and activity in regulation of ILCs in immunity and inflammation, and the interaction between Ahr and other pathways/transcription factors in ILC development and function with their implication in disease. PMID:29354125

Chemical Abundance Analysis of Moving Group W11450 (Latham 1)

NASA Astrophysics Data System (ADS)

O'Connell, Julia E.; Martens, Kylee; Frinchaboy, Peter M.

2016-12-01

We present elemental abundances for all seven stars in Moving Group W11450 (Latham 1) to determine if they may be chemically related. These stars appear to be both spatially and kinematically related, but no spectroscopic abundance analysis exists in literature. Abundances for eight elements were derived via equivalent width analyses of high-resolution (R ˜ 60,000), high-signal-to-noise ratio (< {{S}}/{{N}}> ˜ 100) spectra obtained with the Otto Struve 2.1 m telescope and the Sandiford Echelle Spectrograph at McDonald Observatory. The large star-to-star scatter in metallicity, -0.55 ≤ [Fe/H] ≤slant 0.06 dex (σ = 0.25), implies these stars were not produced from the same chemically homogeneous molecular cloud, and are therefore not part of a remnant or open cluster as previously proposed. Prior to this analysis, it was suggested that two stars in the group, W11449 and W11450, are possible wide binaries. The candidate wide binary pair show similar chemical abundance patterns with not only iron but with other elements analyzed in this study, suggesting the proposed connection between these two stars may be real.

An Artificial Functional Family Filter in Homolog Searching in Next-generation Sequencing Metagenomics

PubMed Central

Du, Ruofei; Mercante, Donald; Fang, Zhide

2013-01-01

In functional metagenomics, BLAST homology search is a common method to classify metagenomic reads into protein/domain sequence families such as Clusters of Orthologous Groups of proteins (COGs) in order to quantify the abundance of each COG in the community. The resulting functional profile of the community is then used in downstream analysis to correlate the change in abundance to environmental perturbation, clinical variation, and so on. However, the short read length coupled with next-generation sequencing technologies poses a barrier in this approach, essentially because similarity significance cannot be discerned by searching with short reads. Consequently, artificial functional families are produced, in which those with a large number of reads assigned decreases the accuracy of functional profile dramatically. There is no method available to address this problem. We intended to fill this gap in this paper. We revealed that BLAST similarity scores of homologues for short reads from COG protein members coding sequences are distributed differently from the scores of those derived elsewhere. We showed that, by choosing an appropriate score cut-off, we are able to filter out most artificial families and simultaneously to preserve sufficient information in order to build the functional profile. We also showed that, by incorporated application of BLAST and RPS-BLAST, some artificial families with large read counts can be further identified after the score cutoff filtration. Evaluated on three experimental metagenomic datasets with different coverages, we found that the proposed method is robust against read coverage and consistently outperforms the other E-value cutoff methods currently used in literatures. PMID:23516532

Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

PubMed

Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

2014-01-01

The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

Lichen physiological traits and growth forms affect communities of associated invertebrates.

PubMed

Bokhorst, Stef; Asplund, Johan; Kardol, Paul; Wardle, David A

2015-09-01

While there has been much interest in the relationships between traits of primary producers and composition of associated invertebrate consumer communities, our knowledge is largely based on studies from vascular plants, while other types of functionally important producers, such as lichens, have rarely been considered. To address how physiological traits of lichens drive community composition of invertebrates, we collected thalli from 27 lichen species from southern Norway and quantified the communities of associated springtails, mites, and nematodes. For each lichen species, we measured key physiological thallus traits and determined whether invertebrate communities were correlated with these traits. We also explored whether invertebrate communities differed among lichen groups, categorized according to nitrogen-fixing ability, growth form, and substratum. Lichen traits explained up to 39% of the variation in abundances of major invertebrate groups. For many invertebrate groups, abundance was positively correlated with lichen N and P concentrations, N:P ratio, and the percentage of water content on saturation (WC), but had few relationships with concentrations of carbon-based secondary compounds. Diversity and taxonomic richness of invertebrate groups were sometimes also correlated with lichen N and N:P ratios. Nitrogen-fixing lichens showed higher abundance and diversity of some invertebrate groups than did non-N-fixing lichens. However, this emerged in part because most N-fixing lichens have a foliose growth form that benefits invertebrates, through, improving the microclimate, independently of N concentration. Furthermore, invertebrate communities associated with terricolous lichens were determined more by their close proximity to the soil invertebrate pool than by lichen traits. Overall, our results reveal that differences between lichen species have a large impact on the invertebrate communities that live among the thalli. Different invertebrate groups show contrasting responses to traits that are indicative of thallus quality (nutrient concentrations), and thallus growth form is often an important determinant of the invertebrate community. Given the large diversity of lichen traits and growth forms that occur in many ecosystems, lichen-invertebrate communities may be an important contributor to overall community diversity in boreal forests.

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies.

PubMed

Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Boulougouris, Georgios C; Melissas, Vasilios S; Troganis, Anastassios N

2017-05-31

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via 1 H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

Altered Gut Microbiota Composition Associated with Eczema in Infants.

PubMed

Zheng, Huajun; Liang, Hong; Wang, Yuezhu; Miao, Maohua; Shi, Tao; Yang, Fen; Liu, Enuo; Yuan, Wei; Ji, Zai-Si; Li, De-Kun

2016-01-01

Eczema is frequently the first manifestation of an atopic diathesis and alteration in the diversity of gut microbiota has been reported in infants with eczema. To identify specific bacterial communities associated with eczema, we conducted a case-control study of 50 infants with eczema (cases) and 51 healthy infants (controls). We performed high-throughput sequencing for V3-V4 hypervariable regions of the 16S rRNA genes from the gut fecal material. A total of 12,386 OTUs (operational taxonomic units) at a 97% similarity level were obtained from the two groups, and we observed a difference in taxa abundance, but not the taxonomic composition, of gut microbiota between the two groups. We identified four genera enriched in healthy infants: Bifidobacterium, Megasphaera, Haemophilus and Streptococcus; and five genera enriched in infants with eczema: Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis and Clostridium XlVa. Several species, such as Faecalibacterium prausnitzii and Ruminococcus gnavus, that are known to be associated with atopy or inflammation, were found to be significantly enriched in infants with eczema. Higher abundance of Akkermansia muciniphila in eczematous infants might reduce the integrity of intestinal barrier function and therefore increase the risk of developing eczema. On the other hand, Bacteroides fragilis and Streptococcus salivarius, which are known for their anti-inflammatory properties, were less abundant in infants with eczema. The observed differences in genera and species between cases and controls in this study may provide insight into the link between the microbiome and eczema risk.

Altered Gut Microbiota Composition Associated with Eczema in Infants

PubMed Central

Miao, Maohua; Shi, Tao; Yang, Fen; Liu, Enuo; Yuan, Wei; Ji, Zai-Si; Li, De-Kun

2016-01-01

Eczema is frequently the first manifestation of an atopic diathesis and alteration in the diversity of gut microbiota has been reported in infants with eczema. To identify specific bacterial communities associated with eczema, we conducted a case-control study of 50 infants with eczema (cases) and 51 healthy infants (controls). We performed high-throughput sequencing for V3–V4 hypervariable regions of the 16S rRNA genes from the gut fecal material. A total of 12,386 OTUs (operational taxonomic units) at a 97% similarity level were obtained from the two groups, and we observed a difference in taxa abundance, but not the taxonomic composition, of gut microbiota between the two groups. We identified four genera enriched in healthy infants: Bifidobacterium, Megasphaera, Haemophilus and Streptococcus; and five genera enriched in infants with eczema: Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis and Clostridium XlVa. Several species, such as Faecalibacterium prausnitzii and Ruminococcus gnavus, that are known to be associated with atopy or inflammation, were found to be significantly enriched in infants with eczema. Higher abundance of Akkermansia muciniphila in eczematous infants might reduce the integrity of intestinal barrier function and therefore increase the risk of developing eczema. On the other hand, Bacteroides fragilis and Streptococcus salivarius, which are known for their anti-inflammatory properties, were less abundant in infants with eczema. The observed differences in genera and species between cases and controls in this study may provide insight into the link between the microbiome and eczema risk. PMID:27812181

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.

PubMed

Rivero-Hinojosa, Samuel; Lau, Ling San; Stampar, Mojca; Staal, Jerome; Zhang, Huizhen; Gordish-Dressman, Heather; Northcott, Paul A; Pfister, Stefan M; Taylor, Michael D; Brown, Kristy J; Rood, Brian R

2018-06-07

Genomic characterization has begun to redefine diagnostic classifications of cancers. However, it remains a challenge to infer disease phenotypes from genomic alterations alone. To help realize the promise of genomics, we have performed a quantitative proteomics investigation using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and 41 tissue samples spanning the 4 genomically based subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying subgroup specific protein isoforms. Integrating our proteomic measurements with genomic data, we calculate a poor correlation between mRNA and protein abundance. Using EPIC 850 k methylation array data on the same tissues, we also investigate the influence of copy number alterations and DNA methylation on the proteome in an attempt to characterize the impact of these genetic features on the proteome. Reciprocally, we are able to use the proteome to identify which genomic alterations result in altered protein abundance and thus are most likely to impact biology. Finally, we are able to assemble protein-based pathways yielding potential avenues for clinical intervention. From these, we validate the EIF4F cap-dependent translation pathway as a novel druggable pathway in medulloblastoma. Thus, quantitative proteomics complements genomic platforms to yield a more complete understanding of functional tumor biology and identify novel therapeutic targets for medulloblastoma.

The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra).

PubMed

Amato, Katherine R; Leigh, Steven R; Kent, Angela; Mackie, Roderick I; Yeoman, Carl J; Stumpf, Rebecca M; Wilson, Brenda A; Nelson, Karen E; White, Bryan A; Garber, Paul A

2015-02-01

For most mammals, including nonhuman primates, diet composition varies temporally in response to differences in food availability. Because diet influences gut microbiota composition, it is likely that the gut microbiota of wild mammals varies in response to seasonal changes in feeding patterns. Such variation may affect host digestive efficiency and, ultimately, host nutrition. In this study, we investigate the temporal variation in diet and gut microbiota composition and function in two groups (N = 13 individuals) of wild Mexican black howler monkeys (Alouatta pigra) over a 10-month period in Palenque National Park, Mexico. Temporal changes in the relative abundances of individual bacterial taxa were strongly correlated with changes in host diet. For example, the relative abundance of Ruminococcaceae was highest during periods when energy intake was lowest, and the relative abundance of Butyricicoccus was highest when young leaves and unripe fruit accounted for 68 % of the diet. Additionally, the howlers exhibited increased microbial production of energy during periods of reduced energy intake from food sources. Because we observed few changes in howler activity and ranging patterns during the course of our study, we propose that shifts in the composition and activity of the gut microbiota provided additional energy and nutrients to compensate for changes in diet. Energy and nutrient production by the gut microbiota appears to provide an effective buffer against seasonal fluctuations in energy and nutrient intake for these primates and is likely to have a similar function in other mammal species.

Benthic Marine Cyanobacterial Mat Ecosystems: Biogeochemistry and Biomarkers

NASA Technical Reports Server (NTRS)

DesMarais, David J.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Cyanobacterial mats are complete ecosystems that can include processes of primary production, diagenesis and lithification. Light sustains oxygenic photosynthesis, which in turn provides energy, organic matter and oxygen to the community. Due to both absorption and scattering phenomena, incident light is transformed with depth in the mat, both in intensity and spectral composition. Mobile photo synthesizers optimize their position with respect to this light gradient. When photosynthesis ceases at night, the upper layers of the mat become reduced and sulfidic. Counteracting gradients of oxygen and sulfide combine to provide daily-contrasting environments separated on a scale of a few mm. The functional complexity of mats, coupled with the highly proximal and ordered spatial arrangement of biota, offers the potential for a staggering number of interactions. At a minimum, the products of each functional group of microorganisms affect the other groups both positively and negatively. For example, cyanobacteria generate organic matter (potential substrates) but also oxygen (a toxin for many anaerobes). Anaerobic activity recycles nutrients to the photosynthesizers but also generates potentially toxic sulfide. The combination of benefits and hazards of light, oxygen and sulfide promotes the allocation of the various essential mat processes between light and dark periods, and to various depths in the mat. Observations of mats have produced numerous surprises. For example, obligately anaerobic processes can occur in the presence of abundant oxygen, highly reduced gases are produced in the presence of abundant sulfate, meiofauna thrive at high sulfide concentrations, and the mats' constituent populations respond to environmental changes in complex ways. While photosynthetic bacteria dominate the biomass and productivity of the mat, nonphotosynthetic, anaerobic processes constitute the ultimate biological filter on the ecosystem's emergent biosignatures, including those sedimentary textures, organic compounds, and minerals that enter the fossil record. The ability of cyanobacterial mats to channel abundant solar energy into the creation and maintenance of complex structures and processes has created a multitude of consequences, both for sedimentation and for the early evolution of our biosphere.

Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

PubMed Central

Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

2014-01-01

European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide sufficiently large areas for butterflies. These findings have important implications for EU agricultural and conservation policy. Most importantly, conservation management needs to consider entire landscapes, and implement appropriate measures at multiple spatial scales. PMID:25058307

Lead and uranium group abundances in cosmic rays

NASA Technical Reports Server (NTRS)

Yadav, J. S.; Perelygin, V. P.

1985-01-01

The importance of Lead and Uranium group abundances in cosmic rays is discussed in understanding their evolution and propagation. The electronic detectors can provide good charge resolution but poor data statistics. The plastic detectors can provide somewhat better statistics but charge resolution deteriorates. The extraterrestrial crystals can provide good statistics but with poor charge resolution. Recent studies of extraterrestrial crystals regarding their calibration to accelerated uranium ion beam and track etch kinetics are discussed. It is hoped that a charge resolution of two charge units can be achieved provided an additional parameter is taken into account. The prospects to study abundances of Lead group, Uranium group and superheavy element in extraterrestrial crystals are discussed, and usefulness of these studies in the light of studies with electronic and plastic detectors is assessed.

Factors affecting the abundance of selected fishes near oil and gas platforms in the northern Gulf of Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stanley, D.R.; Wilson, C.A.

1991-01-01

A logbook program was initiated to determine the relative abundance of selected fish species around oil and gas platforms off the Louisiana coast. Logbooks were maintained by 55 anglers and 10 charterboat operators from March 1987 to March 1988. A total of 36,839 fish were caught representing over 46 different species. Principal component analysis (PCA) grouped the seventeen most abundant species into reef fish, pelagic fish, bluefish-red drum, Atlantic croaker-silver/sand seatrout, and cobia-shark-blue runner associations. Multiple regression analyses were used to compare PCA groupings to physical platform, temporal, geological, and angler characteristic variables and their interactions. Reef fish, Atlantic croaker,more » and silver/sand seatrout abundances were highest near large, structurally complex platforms in relatively deep water. High spotted seatrout abundances were correlated with small, unmanned oil and gas platforms in shallow water. Pelagic fish, bluefish, red drum, cobia, and shark abundances were not related to the physical parameters of the platforms.« less

Activities for leptin in bovine trophoblast cells.

PubMed

Hughes, C K; Xie, M M; McCoski, S R; Ealy, A D

2017-01-01

Leptin is involved in various reproductive processes in humans and rodents, including placental development and function. The specific ways that leptin influences placental development and function in cattle are poorly understood. This work was completed to explore how leptin regulates hormone, cytokine and metalloprotease transcript abundance, and cell proliferation in cultured bovine trophoblast cells. In the first set of studies, cells were cultured in the presence of graded recombinant bovine leptin concentrations (0, 10, 50, 250 ng/mL) for 6 or 24 h. Transcript profiles were examined from extracted RNA. Leptin supplementation did not affect abundance of the maternal recognition of pregnancy factor, interferon-tau (IFNT), but leptin increased (P < 0.05) abundance of chorionic somatomammotropin hormone 2 (CSH2; ie, placental lactogen) at both 6 and 24 h at each concentration tested. At 24 h, the greatest CSH2 abundance (P < 0.05) was detected in cells supplemented with 50 ng/mL leptin. Transcript abundance of the remodeling factor, metalloprotease 2 (MMP2), was greater (P < 0.05) in leptin-treated cells at 24 h but not at 6 h. The 24 h MMP2 response was greatest (P < 0.05) at 250 ng/mL. Transcript abundance for MMP9 was not altered by leptin treatment. In a separate set of studies, cell proliferation assays were completed. Leptin supplementation did not affect bovine trophoblast cell line proliferation at any dose tested. In conclusion, leptin supplementation did not affect bovine trophoblast cell proliferation or IFNT expression, but leptin increases CSH2 and MMP2 transcript abundance. Both of these factors are involved with peri-implantation and postimplantation placental development and function, and this implicates leptin as a potential mediator of early placental development and function in cattle. Copyright © 2016 Elsevier Inc. All rights reserved.

The Mean Life Squared Relationship for Abundances of Extinct Radioactivities

NASA Technical Reports Server (NTRS)

Lodders, K.; Cameron, A. G. W.

2004-01-01

We discovered that the abundances of now extinct radioactivities (relative to stable reference isotopes) in meteorites vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons but to calcium-aluminum inclusions (CAIs). Certain meteorites contain excesses in isotopic abundances from the decay of radioactive isotopes with half-lives much less than the age of the solar system. These short-lived radioactivities are now extinct, but they were alive when meteorites assembled in the early solar system. The origin of these radioactivities and the processes which control their abundances in the solar nebula are still not well understood. Some clues may come from our finding that the meteoritic abundances of now extinct radioactivities (relative to stable reference isotopes) vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons, but not to CAIs. This points to at least two different processes establishing the abundances of short-lived isotopes found in the meteoritic record.

Sulfur compounds in coal

NASA Technical Reports Server (NTRS)

Attar, A.; Corcoran, W. H.

1977-01-01

The literature on the chemical structure of the organic sulfur compounds (or functional groups) in coal is reviewed. Four methods were applied in the literature to study the sulfur compounds in coal: direct spectrometric and chemical analysis, depolymerization in drastic conditions, depolymerization in mild conditions, and studies on simulated coal. The data suggest that most of the organic sulfur in coal is in the form of thiophenic structures and aromatic and aliphatic sulfides. The relative abundance of the sulfur groups in bituminous coal is estimated as 50:30:20%, respectively. The ratio changes during processing and during the chemical analysis. The main effects are the transformation during processing of sulfides to the more stable thiophenic compounds and the elimination of hydrogen sulfide.

Proteomic dataset of the sea urchin Paracentrotus lividus adhesive organs and secreted adhesive.

PubMed

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J R; Santos, Romana

2016-06-01

Sea urchins have specialized adhesive organs called tube feet, which mediate strong but reversible adhesion. Tube feet are composed by a disc, producing adhesive and de-adhesive secretions for substratum attachment, and a stem for movement. After detachment the secreted adhesive remains bound to the substratum as a footprint. Recently, a label-free quantitative proteomic approach coupled with the latest mass-spectrometry technology was used to analyze the differential proteome of Paracentrotus lividus adhesive organ, comparing protein expression levels in the tube feet adhesive part (the disc) versus the non-adhesive part (the stem), and also to profile the proteome of the secreted adhesive (glue). This data article contains complementary figures and results related to the research article "Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: a quantitative proteomics approach" (Lebesgue et al., 2016) [1]. Here we provide a dataset of 1384 non-redundant proteins, their fragmented peptides and expression levels, resultant from the analysis of the tube feet differential proteome. Of these, 163 highly over-expressed tube feet disc proteins (>3-fold), likely representing the most relevant proteins for sea urchin reversible adhesion, were further annotated in order to determine the potential functions. In addition, we provide a dataset of 611 non-redundant proteins identified in the secreted adhesive proteome, as well as their functional annotation and grouping in 5 major protein groups related with adhesive exocytosis, and microbial protection. This list was further analyzed to identify the most abundant protein groups and pinpoint putative adhesive proteins, such as Nectin, the most abundant adhesive protein in sea urchin glue. The obtained data uncover the key proteins involved in sea urchins reversible adhesion, representing a step forward to the development of new wet-effective bio-inspired adhesives.

Aquatic insect community structure under the influence of small dams in a stream of the Mogi-Guaçu river basin, state of São Paulo.

PubMed

Saulino, H H L; Corbi, J J; Trivinho-Strixino, S

2014-02-01

The fragmentation of lotic systems caused by construction of dams has modified many aquatic communities. The objective of this study was to analyse changes in the aquatic insect community structure by discontinuity of habitat created by dams along the Ribeirão das Anhumas, a sub-basin of the Mogi-Guaçu River (state of São Paulo, Brazil). Entomofauna collection was carried out in 10 segments upstream and downstream of five dams along the longitudinal profile of the stream, with a quick sampling method using a D net (mesh 250 mm) with 2 minutes of sampling effort. The insects were sorted and identified to the lowest possible taxonomic level and analysed by the Shannon diversity index, β diversity, richness estimated by rarefaction curves and relative participation of functional feeding groups. The results showed a slight reduction in diversity in the downstream segments, as well as along the longitudinal profile of the stream. However, there were no significant differences in abundance and richness between the upstream and downstream segments, indicating that the dams did not influence these variables. Differences were observed in the functional feeding groups along the longitudinal profile. Predator and gatherer insects were dominant in all segments analysed. The feeding group of shredders was more abundant in the segment DSIII with the participation of Marilia Müller (Odontoceridae - Trichoptera), although we observed a decrease of shredders and scrapers with the decrease of the canopy cover reducing values of β diversity in the continuum of Ribeirão das Anhumas. This result demonstrated the importance of the conservation of the riparian vegetation in order to maintain the integrity of the stream.

Proteomic dataset of the sea urchin Paracentrotus lividus adhesive organs and secreted adhesive

PubMed Central

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G.; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J.R.; Santos, Romana

2016-01-01

Sea urchins have specialized adhesive organs called tube feet, which mediate strong but reversible adhesion. Tube feet are composed by a disc, producing adhesive and de-adhesive secretions for substratum attachment, and a stem for movement. After detachment the secreted adhesive remains bound to the substratum as a footprint. Recently, a label-free quantitative proteomic approach coupled with the latest mass-spectrometry technology was used to analyze the differential proteome of Paracentrotus lividus adhesive organ, comparing protein expression levels in the tube feet adhesive part (the disc) versus the non-adhesive part (the stem), and also to profile the proteome of the secreted adhesive (glue). This data article contains complementary figures and results related to the research article “Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: a quantitative proteomics approach” (Lebesgue et al., 2016) [1]. Here we provide a dataset of 1384 non-redundant proteins, their fragmented peptides and expression levels, resultant from the analysis of the tube feet differential proteome. Of these, 163 highly over-expressed tube feet disc proteins (>3-fold), likely representing the most relevant proteins for sea urchin reversible adhesion, were further annotated in order to determine the potential functions. In addition, we provide a dataset of 611 non-redundant proteins identified in the secreted adhesive proteome, as well as their functional annotation and grouping in 5 major protein groups related with adhesive exocytosis, and microbial protection. This list was further analyzed to identify the most abundant protein groups and pinpoint putative adhesive proteins, such as Nectin, the most abundant adhesive protein in sea urchin glue. The obtained data uncover the key proteins involved in sea urchins reversible adhesion, representing a step forward to the development of new wet-effective bio-inspired adhesives. PMID:27182547

Structures of chlorophyll catabolites in bananas (Musa acuminata) reveal a split path of chlorophyll breakdown in a ripening fruit.

PubMed

Moser, Simone; Müller, Thomas; Holzinger, Andreas; Lütz, Cornelius; Kräutler, Bernhard

2012-08-27

The disappearance of chlorophyll is a visual sign of fruit ripening. Yet, chlorophyll breakdown in fruit has hardly been explored; its non-green degradation products are largely unknown. Here we report the analysis and structure elucidation of colorless tetrapyrrolic chlorophyll breakdown products in commercially available, ripening bananas (Musa acuminata, Cavendish cultivar). In banana peels, chlorophyll catabolites were found in an unprecedented structural richness: a variety of new fluorescent chlorophyll catabolites (FCCs) and nonfluorescent chlorophyll catabolites (NCCs) were detected. As a rule, FCCs exist only "fleetingly" and are hard to observe. However, in bananas several of the FCCs (named Mc-FCCs) were persistent and carried an ester function at the propionate side-chain. NCCs were less abundant, and exhibited a free propionic acid group, but functional modifications elsewhere. The modifications of NCCs in banana peels were similar to those found in NCCs from senescent leaves. They are presumed to be introduced by enzymatic transformations at the stage of the mostly unobserved, direct FCC-precursors. The observed divergent functional group characteristics of the Mc-FCCs versus those of the Mc-NCCs indicated two major "late" processing lines of chlorophyll breakdown in ripening bananas. The "last common precursor" at the branching point to either the persistent FCCs, or towards the NCCs, was identified as a temporarily abundant "secondary" FCC. The existence of two "downstream" branches of chlorophyll breakdown in banana peels, and the striking accumulation of persistent Mc-FCCs call for attention as to the still-elusive biological roles of the resulting colorless linear tetrapyrroles. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functionalizable and ultra stable nanoparticles coated with zwitterionic poly(carboxybetaine) in undiluted blood serum.

PubMed

Yang, Wei; Zhang, Lei; Wang, Shanlin; White, Andrew D; Jiang, Shaoyi

2009-10-01

A new surface chemistry presenting an abundance of functional groups for ligand immobilization in an ultra-low fouling background all in one material for nanoparticles was introduced. This surface platform, as demonstrated by zwitterionic poly(carboxybetaine acrylamide) (polyCBAA) coated nanoparticles, is not only ultra stable in undiluted human blood serum, but also can be conjugated to biomolecules conveniently and effectively. Thus, this surface chemistry is ideal to create multi-functional nanoparticles for targeted delivery and diagnostics. In addition, this work clearly shows that 10% blood serum commonly used to evaluate the stability of nanoparticles is insufficient and a new evaluation criterion with undiluted blood serum is recommended.

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.

PubMed

Yamazaki, Yohei; Meirelles, Pedro Milet; Mino, Sayaka; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Thompson, Fabiano L; Sakai, Yuichi; Sawabe, Toko; Sawabe, Tomoo

2016-02-24

Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

Growth of sedimentary Bathyarchaeota on lignin as an energy source.

PubMed

Yu, Tiantian; Wu, Weichao; Liang, Wenyue; Lever, Mark Alexander; Hinrichs, Kai-Uwe; Wang, Fengping

2018-06-05

Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated 13 C from 13 C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.

Persistence and stability of fish community structure in a southwest New York stream

USGS Publications Warehouse

Hansen, Michael J.; Ramm, Carl W.

1994-01-01

We used multivariate and nonparametric statistics to examine persistence and stability of fish species in the upper 43 km of French Creek, New York. Species occurred in upstream and downstream groups in 1937 that persisted in 1979. However, the downstream group expanded its range in the drainage from 1937 to 1979 at the expense of the upstream group. A dam prevented further upstream expansion of the downstream group. Ranks of species abundances were stable, as tests of group similarity were significant. The abundances and distributions of benthic species were stable across seven sampling dates in 1980 despite several floods and repeated removals by sampling that could have altered community structure. We conclude that the fish community in French Creek persisted and was stable over the 42-yr interval, 1937-1979, and that abundances of benthic species were stable in summer 1980.

MicroRNAs in Muscle: Characterizing the Powerlifter Phenotype

PubMed Central

D'Souza, Randall F.; Bjørnsen, Thomas; Zeng, Nina; Aasen, Kirsten M. M.; Raastad, Truls; Cameron-Smith, David; Mitchell, Cameron J.

2017-01-01

Powerlifters are the epitome of muscular adaptation and are able to generate extreme forces. The molecular mechanisms underpinning the significant capacity for force generation and hypertrophy are not fully elucidated. MicroRNAs (miRs) are short non-coding RNA sequences that control gene expression via promotion of transcript breakdown and/or translational inhibition. Differences in basal miR expression may partially account for phenotypic differences in muscle mass and function between powerlifters and untrained age-matched controls. Muscle biopsies were obtained from m. vastus lateralis of 15 national level powerlifters (25.1 ± 5.8 years) and 13 untrained controls (24.1 ± 2.0 years). The powerlifters were stronger than the controls (isokinetic knee extension at 60°/s: 307.8 ± 51.6 Nm vs. 211.9 ± 41.9 Nm, respectively P < 0.001), and also had larger muscle fibers (type I CSA 9,122 ± 1,238 vs. 4,511 ± 798 μm2 p < 0.001 and type II CSA 11,100 ± 1,656 vs. 5,468 ± 1,477 μm2 p < 0.001). Of the 17 miRs species analyzed, 12 were differently expressed (p < 0.05) between groups with 7 being more abundant in powerlifters and five having lower expression. Established transcriptionally regulated miR downstream gene targets involved in muscle mass regulation, including myostatin and MyoD, were also differentially expressed between groups. Correlation analysis demonstrates the abundance of eight miRs was correlated to phenotype including peak strength, fiber size, satellite cell abundance, and fiber type regardless of grouping. The unique miR expression profiles between groups allow for categorization of individuals as either powerlifter or healthy controls based on a five miR signature (miR-126, -23b, -16, -23a, -15a) with considerable accuracy (100%). Thus, this unique miR expression may be important to the characterization of the powerlifter phenotype. PMID:28638346

Birds in Anthropogenic Landscapes: The Responses of Ecological Groups to Forest Loss in the Brazilian Atlantic Forest.

PubMed

Morante-Filho, José Carlos; Faria, Deborah; Mariano-Neto, Eduardo; Rhodes, Jonathan

2015-01-01

Habitat loss is the dominant threat to biodiversity and ecosystem functioning in terrestrial environments. In this study, we used an a priori classification of bird species based on their dependence on native forest habitats (forest-specialist and habitat generalists) and specific food resources (frugivores and insectivores) to evaluate their responses to forest cover reduction in landscapes in the Brazilian Atlantic Forest. From the patch-landscapes approach, we delimited 40 forest sites, and quantified the percentage of native forest within a 2 km radius around the center of each site (from 6 - 85%). At each site, we sampled birds using the point-count method. We used a null model, a generalized linear model and a four-parameter logistic model to evaluate the relationship between richness and abundance of the bird groups and the native forest amount. A piecewise model was then used to determine the threshold value for bird groups that showed nonlinear responses. The richness and abundance of the bird community as a whole were not affected by changes in forest cover in this region. However, a decrease in forest cover had a negative effect on diversity of forest-specialist, frugivorous and insectivorous birds, and a positive effect on generalist birds. The species richness and abundance of all ecological groups were nonlinearly related to forest reduction and showed similar threshold values, i.e., there were abrupt changes in individuals and species numbers when forest amount was less than approximately 50%. Forest sites within landscapes with forest cover that was less than 50% contained a different bird species composition than more extensively forested sites and had fewer forest-specialist species and higher beta-diversity. Our study demonstrated the pervasive effect of forest reduction on bird communities in one of the most important hotspots for bird conservation and shows that many vulnerable species require extensive forest cover to persist.

Birds in Anthropogenic Landscapes: The Responses of Ecological Groups to Forest Loss in the Brazilian Atlantic Forest

PubMed Central

Morante-Filho, José Carlos; Rhodes, Jonathan

2015-01-01

Habitat loss is the dominant threat to biodiversity and ecosystem functioning in terrestrial environments. In this study, we used an a priori classification of bird species based on their dependence on native forest habitats (forest-specialist and habitat generalists) and specific food resources (frugivores and insectivores) to evaluate their responses to forest cover reduction in landscapes in the Brazilian Atlantic Forest. From the patch-landscapes approach, we delimited 40 forest sites, and quantified the percentage of native forest within a 2 km radius around the center of each site (from 6 - 85%). At each site, we sampled birds using the point-count method. We used a null model, a generalized linear model and a four-parameter logistic model to evaluate the relationship between richness and abundance of the bird groups and the native forest amount. A piecewise model was then used to determine the threshold value for bird groups that showed nonlinear responses. The richness and abundance of the bird community as a whole were not affected by changes in forest cover in this region. However, a decrease in forest cover had a negative effect on diversity of forest-specialist, frugivorous and insectivorous birds, and a positive effect on generalist birds. The species richness and abundance of all ecological groups were nonlinearly related to forest reduction and showed similar threshold values, i.e., there were abrupt changes in individuals and species numbers when forest amount was less than approximately 50%. Forest sites within landscapes with forest cover that was less than 50% contained a different bird species composition than more extensively forested sites and had fewer forest-specialist species and higher beta-diversity. Our study demonstrated the pervasive effect of forest reduction on bird communities in one of the most important hotspots for bird conservation and shows that many vulnerable species require extensive forest cover to persist. PMID:26083245

Nitrogen fixation is not the only trait that determines the success of tropical legumes during secondary succession

NASA Astrophysics Data System (ADS)

Gei, Maria G.; Powers, Jennifer S.

2017-04-01

Legumes trees are well represented throughout the entire precipitation gradient of tropical forests. Many of these species are able to fix atmospheric dinitrogen through symbiosis and offer a mechanism to overcome nitrogen limitation typical of initial stages of secondary forest succession. While it is often assumed the success of legumes is linked to their fixation ability, the variation of other functional traits within this large group has received considerably less attention. Here we assessed legume abundance in secondary forest plots in 42 Neotropical chronosequences (the 2ndFOR network) that span a broad gradient of precipitation regimes and identified those traits that are favored in distinct successional environments. Our main finding is that in young secondary dry forests (5-20 years), legumes that have the potential to fix nitrogen and have small leaflet size become exceptionally abundant (up to 17-99% relative basal area). We suggest that in those species, reduced leaf area could help regulate leaf temperature and minimize water loss, and the cost of reduced total leaf area may be compensated by high photosynthetic rates maximized with nitrogen obtained through fixation. Overall, our study underscores great functional heterogeneity within tropical legumes, which likely translates into diverse biogeochemical cycles. In addition, these results provide a useful framework for active restoration of degraded areas, as it identifies a group of species that accumulate carbon at fast rates under warm and dry environments, conditions that are expected to become more common in the tropics.

Assessing the suitability of benthic foraminiferal morpho-groups to reconstruct paleomonsoon from Bay of Bengal

NASA Astrophysics Data System (ADS)

Manasa, M.; Saraswat, Rajeev; Nigam, Rajiv

2016-04-01

Temporal changes in benthic foraminiferal morpho-groups were suggested as an effective proxy to reconstruct past monsoon intensity from the Arabian Sea. Here, in order to test the applicability of temporal variation in morpho-groups to reconstruct past monsoon intensity from the Bay of Bengal, we have documented recent benthic foraminiferal distribution from the continental shelf region of the northwestern Bay of Bengal. Based on the external morphology, benthic foraminifera were categorized into rounded symmetrical (RSBF) and angular asymmetrical benthic foraminifera (AABF). Additionally, a few other dominant groups were also identified based on test composition (agglutinated, calcareous) and abundance (Asterorotalids and Nonions). The relative abundance of each group was compared with the ambient physico-chemical conditions, including dissolved oxygen, organic matter, salinity and temperature. We report that the RSBF are abundant in comparatively warm and well oxygenated waters of low salinity, suggesting a preference for high energy environment, whereas AABF dominate relatively cold, hypersaline deeper waters with low dissolved oxygen, indicating a low energy environment. The agglutinated foraminifera, Asterorotalids and Nonions dominate shallow water, low salinity regions, whereas the calcareous benthic foraminiferal abundance increases away from the riverine influx regions. Food availability, as estimated from organic carbon abundance in sediments, has comparatively less influence on faunal distribution in the northwestern Bay of Bengal, as compared to dissolved oxygen, temperature and salinity. We conclude that the factors associated with freshwater influx affect the distribution of benthic foraminiferal morpho-groups in the northwestern Bay of Bengal and thus it can be used to reconstruct past monsoon intensity from the Bay of Bengal.

Ecology of Root Colonizing Massilia (Oxalobacteraceae)

PubMed Central

Ofek, Maya; Hadar, Yitzhak; Minz, Dror

2012-01-01

Background Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae), a major group of rhizosphere and root colonizing bacteria of many plant species. Methodology/Principal Findings The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter) and potential competitors. Massilia absolute abundance and relative abundance (dominance) were positively related, and peaked (up to 85%) at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession. Conclusions In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche. PMID:22808103

Ecology of root colonizing Massilia (Oxalobacteraceae).

PubMed

Ofek, Maya; Hadar, Yitzhak; Minz, Dror

2012-01-01

Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae), a major group of rhizosphere and root colonizing bacteria of many plant species. The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter) and potential competitors. Massilia absolute abundance and relative abundance (dominance) were positively related, and peaked (up to 85%) at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession. In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche.

A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards.

PubMed

Kito, Keiji; Okada, Mitsuhiro; Ishibashi, Yuko; Okada, Satoshi; Ito, Takashi

2016-05-01

The accurate and precise absolute abundance of proteins can be determined using mass spectrometry by spiking the sample with stable isotope-labeled standards. In this study, we developed a strategy of hierarchical use of peptide-concatenated standards (PCSs) to quantify more proteins over a wider dynamic range. Multiple primary PCSs were used for quantification of many target proteins. Unique "ID-tag peptides" were introduced into individual primary PCSs, allowing us to monitor the exact amounts of individual PCSs using a "secondary PCS" in which all "ID-tag peptides" were concatenated. Furthermore, we varied the copy number of the "ID-tag peptide" in each PCS according to a range of expression levels of target proteins. This strategy accomplished absolute quantification over a wider range than that of the measured ratios. The quantified abundance of budding yeast proteins showed a high reproducibility for replicate analyses and similar copy numbers per cell for ribosomal proteins, demonstrating the accuracy and precision of this strategy. A comparison with the absolute abundance of transcripts clearly indicated different post-transcriptional regulation of expression for specific functional groups. Thus, the approach presented here is a faithful method for the absolute quantification of proteomes and provides insights into biological mechanisms, including the regulation of expressed protein abundance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predator functional response and prey survival: Direct and indirect interactions affecting a marked prey population

USGS Publications Warehouse

Miller, David A.; Grand, J.B.; Fondell, T.F.; Anthony, M.

2006-01-01

1. Predation plays an integral role in many community interactions, with the number of predators and the rate at which they consume prey (i.e. their functional response) determining interaction strengths. Owing to the difficulty of directly observing predation events, attempts to determine the functional response of predators in natural systems are limited. Determining the forms that predator functional responses take in complex systems is important in advancing understanding of community interactions. 2. Prey survival has a direct relationship to the functional response of their predators. We employed this relationship to estimate the functional response for bald eagle Haliaeetus leucocepalus predation of Canada goose Branta canadensis nests. We compared models that incorporated eagle abundance, nest abundance and alternative prey presence to determine the form of the functional response that best predicted intra-annual variation in survival of goose nests. 3. Eagle abundance, nest abundance and the availability of alternative prey were all related to predation rates of goose nests by eagles. There was a sigmoidal relationship between predation rate and prey abundance and prey switching occurred when alternative prey was present. In addition, predation by individual eagles increased as eagle abundance increased. 4. A complex set of interactions among the three species examined in this study determined survival rates of goose nests. Results show that eagle predation had both prey- and predator-dependent components with no support for ratio dependence. In addition, indirect interactions resulting from the availability of alternative prey had an important role in mediating the rate at which eagles depredated nests. As a result, much of the within-season variation in nest survival was due to changing availability of alternative prey consumed by eagles. 5. Empirical relationships drawn from ecological theory can be directly integrated into the estimation process to determine the mechanisms responsible for variation in observed survival rates. The relationship between predator functional response and prey survival offers a flexible and robust method to advance our understanding of predator-prey interactions in many complex natural systems where prey populations are marked and regularly visited. ?? 2006 British Ecological Society.

On the abundance of extreme voids II: a survey of void mass functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chongchitnan, Siri; Hunt, Matthew, E-mail: s.chongchitnan@hull.ac.uk, E-mail: m.d.hunt@2012.hull.ac.uk

2017-03-01

The abundance of cosmic voids can be described by an analogue of halo mass functions for galaxy clusters. In this work, we explore a number of void mass functions: from those based on excursion-set theory to new mass functions obtained by modifying halo mass functions. We show how different void mass functions vary in their predictions for the largest void expected in an observational volume, and compare those predictions to observational data. Our extreme-value formalism is shown to be a new practical tool for testing void theories against simulation and observation.

Composition and abundance of zooplankton groups from a coral reef lagoon in Puerto Morelos, Quintana Roo, Mexico, during an annual cycle.

PubMed

Alvarez-Cadena, José N; Ordóñez-López, Uriel; Almaral-Mendivil, Alma Rosa; Uicab-Sabido, Amira

2009-09-01

Zooplankton sampling was carried out monthly from January to December 1990 at station A near the coastline, and station B near the reef barrier, in a tropical coral reef lagoon in the Mexican Caribbean Sea. Samplings were made at midnight, near surface, with a conical net (mouth 0.40 m, mesh 330 microm) for 10 min. Salinity varied from 35.1 to 36.3 psu and temperature from 26.3 to 30.2 degrees C. The Bray-Curtis test applied to these results has defined two seasons: the dry season from November to May, and the wet season from June to October. A total of 37 zooplankton groups were found. Copepods were the most abundant contributing 49.0% of the total capture with Acartia espinata, Calanopia americana and Farranula gracilis as the most numerous. In the total zooplankton, however, cirripeds captured in only 15 samples of 24 were second in abundance (20.9%). Decapods, present all year-round and more abundant during the wet season, were third and contributed 19.2%. The rest of the groups were scarce and only amphipods (2.4%) and larvaceans (2.0%) were relatively abundant. The abundance of captured organisms correlated with the abiotic factors measured, thus, in the dry season, abundance was lower (mean 7.3 orgs/m3), while in the wet season the mean catch was 36.8 orgs/m3.

Effects of climate and forest structure on palms, bromeliads and bamboos in Atlantic Forest fragments of Northeastern Brazil.

PubMed

Hilário, R R; Toledo, J J

2016-01-01

Palms, bromeliads and bamboos are key elements of tropical forests and understanding the effects of climate, anthropogenic pressure and forest structure on these groups is crucial to forecast structural changes in tropical forests. Therefore, we investigated the effects of these factors on the abundance of these groups in 22 Atlantic forest fragments of Northeastern Brazil. Abundance of bromeliads and bamboos were assessed through indexes. Palms were counted within a radius of 20 m. We also obtained measures of vegetation structure, fragment size, annual precipitation, precipitation seasonality and human population density. We tested the effects of these predictors on plant groups using path analysis. Palm abundance was higher in taller forests with larger trees, closed canopy and sparse understory, which may be a result of the presence of seed dispersers and specific attributes of local palm species. Bromeliads were negatively affected by both annual precipitation and precipitation seasonality, what may reflect adaptations of these plants to use water efficiently, but also the need to capture water in a regular basis. Bamboos were not related to any predictor variable. As climate and forest structure affected the abundance of bromeliads and palms, human-induced climatic changes and disturbances in forest structure may modify the abundance of these groups. In addition, soil properties and direct measurements of human disturbance should be used in future studies in order to improve the predictability of models about plant groups in Northeastern Atlantic Forest.

Spatial and Temporal Dynamics of Mixotrophic Protists Within a Protected Glacial Lake

NASA Astrophysics Data System (ADS)

DeVaul, S. B.; Sanders, R. W.

2016-02-01

Bacterivorous protists are vital components of the aquatic food web as prey for zooplankton and top-down regulators of bacteria. Many bacterivores utilize mixotrophic nutrition that combines photosynthesis with ingestion of particulate matter. Mixotrophic protists are capable of substantial rates of bacterivory - often greater than co-occurring heterotrophic flagellates. It has been argued that mixotrophs may gain a competitive advantage in natural systems due to their ability to utilize photosynthesis during periods of reduced particulate food or phagotrophy during periods of decreased irradiance. A central goal of ecological study has been to understand and ultimately predict the composition of communities in response to varying environmental conditions. The objectives of this study were to determine seasonal abundances and bacterial ingestion rates of heterotrophic, phototrophic and mixotrophic nanoflagellates (hereafter referred to as HNAN, PNAN and MNAN) and identify abiotic drivers that influence spatial and temporal dynamics of these functional groups. Water samples were collected approximately monthly over a 1.5 year period from Lake Lacawac, a 13,000 year old lake with a protected watershed. Trends in MNAN abundance were related to seasonal patterns of thermal stratification and varied with depth. Maximum abundance occurred in the summer epilimnion. Although HNAN abundance tended to be greater than that of MNAN, the latter generally had a greater grazer impact on bacterial biomass within the epilimnion. During the study period, MNAN removed a maximum of 75% of the bacterial biomass daily in the metalimnion. Mixotroph abundance and grazing impact tended to decrease in deeper waters, and was nearly absent in the anaerobic hypolimnion in late summer and early autumn.

Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers

PubMed Central

Chiu, Chun-Huo; Chao, Anne

2014-01-01

Hill numbers (or the “effective number of species”) are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify “the effective number of equally abundant and (functionally) equally distinct species” in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration. PMID:25000299

Distance-based functional diversity measures and their decomposition: a framework based on Hill numbers.

PubMed

Chiu, Chun-Huo; Chao, Anne

2014-01-01

Hill numbers (or the "effective number of species") are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify "the effective number of equally abundant and (functionally) equally distinct species" in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.

Precision Measurements of Solar Energetic Particle Elemental Composition

NASA Technical Reports Server (NTRS)

Breneman, H.; Stone, E. C.

1985-01-01

Data from the Cosmic Ray Subsystem (CRS) aboard the Voyager 1 and 2 spaceraft were used to determined, solar energetic particle abundances or upper limits for all elements with Z 30 from a combined set of 10 solar flares during the 1977 to 1982 time period. Statistically meaningful abundances were determined for several rare elements including P, C1, K, Ti and Mn, while the precision of the mean abundances for the more abundant elements was proved. When compared to solar photospheric spectroscopic abundances, these new SEP abundances more clearly exhibit the step-function dependence on first ionization potential previously reported.

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype.

PubMed

Leite, Jakson; Fischer, Doreen; Rouws, Luc F M; Fernandes-Júnior, Paulo I; Hofmann, Andreas; Kublik, Susanne; Schloter, Michael; Xavier, Gustavo R; Radl, Viviane

2016-01-01

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea ( Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium , and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Natural windbreaks sustain bird diversity in a tea-dominated landscape.

PubMed

Sreekar, Rachakonda; Mohan, Anand; Das, Sandeep; Agarwal, Prerna; Vivek, Ramachandran

2013-01-01

Windbreaks often form networks of forest habitats that improve connectivity and thus conserve biodiversity, but little is known of such effects in the tropics. We determined bird species richness and community composition in windbreaks composed of remnant native vegetation amongst tea plantations (natural windbreaks), and compared it with the surrounding primary forests. Fifty-one, ten-minute point counts were conducted in each habitat type over three days. Despite the limited sampling period, our bird inventories in both natural windbreaks and primary forests were nearly complete, as indicated by bootstrap true richness estimator. Bird species richness and abundance between primary forests and windbreaks were similar, however a difference in bird community composition was observed. Abundances of important functional groups such as frugivores and insectivores did not vary between habitat types but nectarivores were more abundant in windbreaks, potentially as a result of the use of windbreaks as traveling routes, foraging and nesting sites. This preliminary study suggests that natural windbreaks may be important habitats for the persistence of bird species in a production landscape. However, a better understanding of the required physical and compositional characteristics for windbreaks to sustain bird communities is needed for effective conservation management.

Reducing complexity when studying seed dispersal at community scales: a functional classification of vertebrate seed dispersers in tropical forests.

PubMed

Dennis, Andrew J; Westcott, David A

2006-10-01

The process of seed dispersal has a profound effect on vegetation structure and diversity in tropical forests. However, our understanding of the process and our ability to predict its outcomes at a community scale are limited by the frequently large number of interactions associated with it. Here, we outline an approach to dealing with this complexity that reduces the number of unique interactions considered by classifying the participants according to their functional similarity. We derived a classification of dispersers based on the nature of the dispersal service they provide to plants. We described the quantities of fruit handled, the quality of handling and the diversity of plants to which the service is provided. We used ten broad disperser traits to group 26 detailed measures for each disperser. We then applied this approach to vertebrate dispersers in Australia's tropical forests. Using this we also develop a classification that may be more generally applicable. For each disperser, data relating to each trait was obtained either from the field or published literature. First, we identified dispersers whose service outcomes were so distinct that statistical analysis was not required and assigned them to functional groups. The remaining dispersers were assigned to functional groups using cluster analysis. The combined processes created 15 functional groups from 65 vertebrate dispersers in Australian tropical forests. Our approach--grouping dispersers on the basis of the type of dispersal service provided and the fruit types it is provided to--represents a means of reducing the complexity encountered in tropical seed dispersal systems and could be effectively applied in community level studies. It also represents a useful tool for exploring changes in dispersal services when the distribution and abundance of animal populations change due to human impacts.

Mutation abundance affects the therapeutic efficacy of EGFR-TKI in patients with advanced lung adenocarcinoma: A retrospective analysis.

PubMed

Wang, Huijuan; Zhang, Mina; Tang, Wanyu; Ma, Jie; Wei, Bing; Niu, Yuanyuan; Zhang, Guowei; Li, Peng; Yan, Xiangtao; Ma, Zhiyong

2018-03-22

To investigate the influence of mutation abundance and sites of epidermal growth factor receptor (EGFR) on therapeutic efficacies of EGFR-tyrosine kinase inhibitor (EGFR-TKIs) treatments of patients with advanced non-small cell lung carcinoma (NSCLC). EGFR mutational sites and mutation abundance were analyzed by amplification refractory mutation system (ARMS) in paraffin-embedded tissue sections taken from primary or metastatic tumors of 194 NSCLC patients. The median progression-free survival (PFS) time of the enrolled patients was 9.3 months (95% CI, 8.2-10.8 months). The PFS was significantly different with EGFR gene mutation abundance after EGFR-TKI therapy (P = 0.014). The median PFS was significantly longer when the cut-off value of EGFR mutation abundance of exon 19 or exon 21, and solely exon 19 was > 26.7% and 61.8%, respectively. For patients who received EGFR-TKI as first-line treatment, the median PFS was significantly longer in the high mutation abundance group than in the low mutation abundance group (12.7 vs 8.7 months, P = 0.002). The PFS benefits were greater in patients with a higher abundance of exon 19 deletion mutations in the EGFR gene after EGFR-TKI treatment and first line EGFR-TKI treatment led to improved PFS in high mutation abundance patients.

Estimating Lion Abundance using N-mixture Models for Social Species

PubMed Central

Belant, Jerrold L.; Bled, Florent; Wilton, Clay M.; Fyumagwa, Robert; Mwampeta, Stanslaus B.; Beyer, Dean E.

2016-01-01

Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170–551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species. PMID:27786283

Estimating Lion Abundance using N-mixture Models for Social Species.

PubMed

Belant, Jerrold L; Bled, Florent; Wilton, Clay M; Fyumagwa, Robert; Mwampeta, Stanslaus B; Beyer, Dean E

2016-10-27

Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170-551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species.

Resource distribution and group size in the common langur Semnopithecus entellus in southern India.

PubMed

Vasudev, Divya; Kumar, Ajith; Sinha, Anindya

2008-07-01

We investigated the influence of resource abundance and distribution on the group size and composition of the common langur Semnopithecus entellus in the contiguous forests of Bandipur National Park, Mudumalai Wildlife Sanctuary and Nagarahole National Park in southern India. We also explored any additional effect of predator pressure and the risk of take-over on the same attributes. Data on group composition and vegetation were collected from January to May 2006. The size and composition of 94 bisexual groups were obtained. The group size varied from 7 to 40 and the groups included unimale and multimale groups. Thirty-five all-male groups were encountered. Vegetation was sampled from 17 grids of dimension 1 km x 1 km, each containing twelve 25 m x 25 m plots. The list of food species was compiled from previous studies and observations made during the study period. The mean basal area of all the food trees within each plot and its coefficient of variation at the level of the grid were used to represent resource abundance and distribution, respectively. The number of adult females and males within groups were analyzed separately to test for differential effects on age-sex categories. Group size increased as resources became spatially more heterogeneous. The abundance of resources had a negative effect on group size. This study did not find evidence supporting the direct effect of predator presence or of the risk of take-over. Contrary to what were expected, adult males reacted more strongly and predictably to resources than did adult females. The group attributes and their relationship with food resource abundance and distribution differed between two sites in the study area possibly owing to langur subspecies differences.

Abundance of introduced species at home predicts abundance away in herbaceous communities

USGS Publications Warehouse

Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

2011-01-01

Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean.

PubMed

Alexander, Harriet; Rouco, Mónica; Haley, Sheean T; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

2015-11-03

A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate.

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

PubMed Central

Alexander, Harriet; Rouco, Mónica; Haley, Sheean T.; Wilson, Samuel T.; Karl, David M.; Dyhrman, Sonya T.

2015-01-01

A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate. PMID:26460011

Fish community diversity in the middle continental shelf of the East China Sea

NASA Astrophysics Data System (ADS)

Shan, Xiujuan; Jin, Xianshi; Zhou, Zhipeng; Dai, Fangqun

2011-11-01

The status of fishery stocks in the coastal waters of China is far from ideal, mainly due to climate change and the impacts of human activities (e.g., pollution and overfishing). Thus, the restoration and protection of fishery resources have become critical and complex. The stability and balanced structure of the fish community is a basic foundation for the protection of fishery resources. Based on data collected from bottom trawls by the R/V Beidou in continental shelf of the East China Sea in November 2006 and February 2007, changes in the composition and diversity of fish species and functional groups were analyzed. The research area was divided into offshore waters and inshore waters by the two-way indicator species analysis (TWIA). The results showed that the dominant species were different between offshore waters and inshore waters and also varied with the survey time. The most abundant family was Sciaenidae and Teraponidae in November 2006, Sciaenidae, Engraulidae and Triglidae were most abundant in February 2007. The species belonged mainly to mobile piscivores (G6), benthivores/piscivores (G4), benthivores (G3) and planktivores (G1), and the dominant species in November 2006 were commercial species (e.g. Larimichthys polyactis and Trichiurus japonicus), but small-sized species were dominant in February 2007 (e.g., Harpadon nehereus, Benthosema pterotum, Champsodon capensis, and Acropoma japonicum). The species diversity showed a similar trend as the functional group diversity. Stations with higher diversity were mainly distributed in inshore waters in February 2007, whereas higher diversity was found in offshore waters in November 2006. The highest biomass and species number were found in G6 group, followed by the G4, G5 and G1 groups. The distribution of the number of individuals of each functional group showed the opposite trend as that of the biomass distribution. In addition, the size spectra were mainly concentrated around 3-29 cm, and the individual number of fish species gradually decreased with the increase in body size, but the relative biomass showed a moderate fluctuation in each size class. These changes showed that species with faster growth rate and earlier maturity age became dominant in continental shelf of the East China Sea. So the variations in biological characteristics of fish should be fully considered in maintaining sustainable utilization of fishery resource.

Effect of onion peel extract on endothelial function and endothelial progenitor cells in overweight and obese individuals.

PubMed

Choi, Eun-Yong; Lee, Hansongyi; Woo, Jong Shin; Jang, Hyun Hee; Hwang, Seung Joon; Kim, Hyun Soo; Kim, Woo-Sik; Kim, Young-Seol; Choue, Ryowon; Cha, Yong-Jun; Yim, Jung-Eun; Kim, Weon

2015-09-01

Acute or chronic intake of polyphenol-rich foods has been reported to improve endothelial function. Quercetin, found abundantly in onion, is a potent antioxidant flavonoid. The aim of this study was to investigate whether consumption of onion peel extract (OPE) improves endothelial function in healthy overweight and obese individuals. This was a randomized double-blind, placebo-controlled study. Seventy-two healthy overweight and obese participants were randomly assigned to receive a red, soft capsule of OPE (100 mg quercetin/d, 50 mg quercetin twice daily; n = 36 participants) or an identical placebo capsule (n = 36) for 12 wk. Endothelial function, defined by flow-mediated dilation (FMD), circulating endothelial progenitor cells (EPCs) by flow cytometry, and laboratory test were determined at baseline and after treatment. Baseline characteristics and laboratory findings did not significantly differ between the two groups. Compared with baseline values, the OPE group showed significantly improved FMD at 12 wk (from 12.5 ± 5.2 to 15.2 ± 6.1; P = 0.002), whereas the placebo group showed no difference. Nitroglycerin-mediated dilation did not change in either group. EPC counts (44.2 ± 25.6 versus 52.3 ± 18.6; P = 0.005) and the percentage of EPCs were significantly increased in the OPE group. When FMD was divided into quartiles, rate of patients with endothelial dysfunction defined as lowest quartile (cutoff value, 8.6%) of FMD improved from 26% to 9% by OPE. Medium-term administration of OPE an improvement in FMD and circulating EPCs. Copyright © 2015 Elsevier Inc. All rights reserved.

A soil microcosm to test the effects of pollutants on soil nematode and microarthropod communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parmelee, R.W.; Wentsel, R.S.; Checkai, R.T.

1995-12-31

Previous studies have demonstrated that microcosms with field collected soil nematode and microarthropod communities are suitable model systems to detect effects of toxins on soil food web structure and function. The authors investigated the toxicity of copper, cadmium, malathion, and Aroclor 1254 to nematodes (total, bacterivores, fungivores, herbivores, omnivore-predators, hatchlings) and microarthropods (Prostigmata, Mesostigmata, Oribatida, Collembola, other arthropods). Nematodes were sensitive indicators of copper application, and total numbers were reduced at 100 {micro}g g{sup {minus}1}. Fungivore, bacterivore and omnivore-predators were the most susceptible trophic groups. Cadmium had no effects on either nematode or microarthropod communities. Microarthropods were more sensitive tomore » malathion than nematodes, and total microarthropod abundance was lower than controls at 320 {micro}g g{sup {minus}1}. Prostigmatid mites and other arthropods were the most affected groups. Only the herbivore nematode trophic group was affected by malathion, and numbers did not decline until 1,280 {micro}g g{sup {minus}1}. Aroclor 1254 also had a greater negative impact on microarthropods than on nematodes. Total microarthropod abundance declined at 2,500 {micro}g g{sup {minus}1}, while there was no effect on nematodes. Prostigmatid and oribatid mites were the most susceptible groups to PCB application. Strong differential sensitivity between nematode and microarthropod communities indicates that both groups need to be examined to fully evaluate the impact of chemicals on soil systems. The authors conclude that microcosms with field-collected communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.« less

Fish-mediated changes in bacterioplankton community composition: an in situ mesocosm experiment

NASA Astrophysics Data System (ADS)

Luo, Congqiang; Yi, Chunlong; Ni, Leyi; Guo, Longgen

2017-06-01

We characterized variations in bacterioplankton community composition (BCC) in mesocosms subject to three different treatments. Two groups contained fish (group one: Cyprinus carpio; group two: Hypophthalmichthys molitrix); and group three, the untreated mesocosm, was the control. Samples were taken seven times over a 49-day period, and BCC was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR). Results revealed that introduction of C. carpio and H. molitrix had a remarkable impact on the composition of bacterioplankton communities, and the BCC was significantly different between each treatment. Sequencing of DGGE bands revealed that the bacterioplankton community in the different treatment groups was consistent at a taxonomic level, but differed in its abundance. H. molitrix promoted the richness of Alphaproteobacteria and Actinobacteria, while more bands affiliated to Cyanobacteria were detected inC. carpio mesocosms. The redundancy analysis (RDA) result demonstrated that the BCC was closely related to the bottom-up (total phosphorus, chlorophyll a, phytoplankton biomass) and top-down forces (biomass of copepods and cladocera) in C. carpio and control mesocosms, respectively. We found no evidence for top-down regulation of BCC by zooplankton in H. molitrix mesocosms, while grazing by protozoa (heterotrophic nanoflagellates, ciliates) became the major way to regulate BCC. Total bacterioplankton abundances were significantly higher in C. carpio mesocosms because of high nutrient concentration and suspended solids. Our study provided insights into the relationship between fish and bacterioplankton at species level, leading to a deep understanding of the function of the microbial loop and the aquatic ecosystem.

Fish-mediated changes in bacterioplankton community composition: an in situ mesocosm experiment

NASA Astrophysics Data System (ADS)

Luo, Congqiang; Yi, Chunlong; Ni, Leyi; Guo, Longgen

2018-03-01

We characterized variations in bacterioplankton community composition (BCC) in mesocosms subject to three different treatments. Two groups contained fish (group one: Cyprinus carpio; group two: Hypophthalmichthys molitrix); and group three, the untreated mesocosm, was the control. Samples were taken seven times over a 49-d period, and BCC was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR). Results revealed that introduction of C. carpio and H. molitrix had a remarkable impact on the composition of bacterioplankton communities, and the BCC was significantly different between each treatment. Sequencing of DGGE bands revealed that the bacterioplankton community in the different treatment groups was consistent at a taxonomic level, but differed in its abundance. H. molitrix promoted the richness of Alphaproteobacteria and Actinobacteria, while more bands affiliated to Cyanobacteria were detected in C. carpio mesocosms. The redundancy analysis (RDA) result demonstrated that the BCC was closely related to the bottom-up (total phosphorus, chlorophyll a, phytoplankton biomass) and top-down forces (biomass of copepods and cladocera) in C. carpio and control mesocosms, respectively. We found no evidence for top-down regulation of BCC by zooplankton in H. molitrix mesocosms, while grazing by protozoa (heterotrophic nanoflagellates, ciliates) became the major way to regulate BCC. Total bacterioplankton abundances were significantly higher in C. carpio mesocosms because of high nutrient concentration and suspended solids. Our study provided insights into the relationship between fish and bacterioplankton at species level, leading to a deep understanding of the function of the microbial loop and the aquatic ecosystem.

Abundance and characteristics of snags in western Montana forests

Treesearch

Richard B. Harris

1999-01-01

Plot data from the U.S. Forest Service's Forest Inventory and Analysis program was used to characterize the abundance and selected characteristics of snags from forests in western Montana. Plots were grouped by whether they had a history of timber harvest, and the U.S. Forest Service classifications of forest type, habitat type, and potential vegetation group were...

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

DOE PAGES

Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.; ...

2017-11-14

Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium,Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collectedin situover 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response ofCurtobacteriumto seasonal variability andmore » the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across sixCurtobacteriumlineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits withinCurtobacteriumare conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understandingCurtobacteriumabundance and distribution in the environment. IMPORTANCE. Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). Here, we focused on the most abundant bacterium,Curtobacterium, which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.« less

Alterations in microbial community composition with increasing fCO2: a mesocosm study in the eastern Baltic Sea

NASA Astrophysics Data System (ADS)

Crawfurd, Katharine J.; Alvarez-Fernandez, Santiago; Mojica, Kristina D. A.; Riebesell, Ulf; Brussaard, Corina P. D.

2017-08-01

Ocean acidification resulting from the uptake of anthropogenic carbon dioxide (CO2) by the ocean is considered a major threat to marine ecosystems. Here we examined the effects of ocean acidification on microbial community dynamics in the eastern Baltic Sea during the summer of 2012 when inorganic nitrogen and phosphorus were strongly depleted. Large-volume in situ mesocosms were employed to mimic present, future and far future CO2 scenarios. All six groups of phytoplankton enumerated by flow cytometry ( < 20 µm cell diameter) showed distinct trends in net growth and abundance with CO2 enrichment. The picoeukaryotic phytoplankton groups Pico-I and Pico-II displayed enhanced abundances, whilst Pico-III, Synechococcus and the nanoeukaryotic phytoplankton groups were negatively affected by elevated fugacity of CO2 (fCO2). Specifically, the numerically dominant eukaryote, Pico-I, demonstrated increases in gross growth rate with increasing fCO2 sufficient to double its abundance. The dynamics of the prokaryote community closely followed trends in total algal biomass despite differential effects of fCO2 on algal groups. Similarly, viral abundances corresponded to prokaryotic host population dynamics. Viral lysis and grazing were both important in controlling microbial abundances. Overall our results point to a shift, with increasing fCO2, towards a more regenerative system with production dominated by small picoeukaryotic phytoplankton.

Regulation of metabolic health and adipose tissue function by group 2 innate lymphoid cells.

PubMed

Cautivo, Kelly M; Molofsky, Ari B

2016-06-01

Adipose tissue (AT) is home to an abundance of immune cells. With chronic obesity, inflammatory immune cells accumulate and promote insulin resistance and the progression to type 2 diabetes mellitus. In contrast, recent studies have highlighted the regulation and function of immune cells in lean, healthy AT, including those associated with type 2 or "allergic" immunity. Although traditionally activated by infection with multicellular helminthes, AT type 2 immunity is active independently of infection, and promotes tissue homeostasis, AT "browning," and systemic insulin sensitivity, protecting against obesity-induced metabolic dysfunction and type 2 diabetes mellitus. In particular, group 2 innate lymphoid cells (ILC2s) are integral regulators of AT type 2 immunity, producing the cytokines interleukin-5 and IL-13, promoting eosinophils and alternatively activated macrophages, and cooperating with and promoting AT regulatory T (Treg) cells. In this review, we focus on the recent developments in our understanding of group 2 innate lymphoid cell cells and type 2 immunity in AT metabolism and homeostasis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geography, environment and organismal traits in the diversification of a major tropical herbaceous angiosperm radiation

PubMed Central

2018-01-01

Abstract The generation of plant diversity involves complex interactions between geography, environment and organismal traits. Many macroevolutionary processes and emergent patterns have been identified in different plant groups through the study of spatial data, but rarely in the context of a large radiation of tropical herbaceous angiosperms. A powerful system for testing interrelated biogeographical hypotheses is provided by the terrestrial bromeliads, a Neotropical group of extensive ecological diversity and importance. In this investigation, distributional data for 564 species of terrestrial bromeliads were used to estimate variation in the position and width of species-level hydrological habitat occupancy and test six core hypotheses linking geography, environment and organismal traits. Taxonomic groups and functional types differed in hydrological habitat occupancy, modulated by convergent and divergent trait evolution, and with contrasting interactions with precipitation abundance and seasonality. Plant traits in the Bromeliaceae are intimately associated with bioclimatic differentiation, which is in turn strongly associated with variation in geographical range size and species richness. These results emphasize the ecological relevance of structural-functional innovation in a major plant radiation. PMID:29479409

Association of common variants in the human eyes shut ortholog (EYS) with statin-induced myopathy: evidence for additional functions of EYS.

PubMed

Isackson, Paul J; Ochs-Balcom, Heather M; Ma, Changxing; Harley, John B; Peltier, Wendy; Tarnopolsky, Mark; Sripathi, Naganand; Wortmann, Robert L; Simmons, Zachary; Wilson, Jon D; Smith, Stephen A; Barboi, Alexandru; Fine, Edward; Baer, Alan; Baker, Steven; Kaufman, Kenneth; Cobb, Beth; Kilpatrick, Jeffrey R; Vladutiu, Georgirene D

2011-10-01

Of the nearly 38 million people in the USA who receive statin therapy, 0.1-0.5% experience severe or life-threatening myopathic side effects. We performed a genome-wide association study (GWAS) in a group of patients with severe statin myopathy versus a statin-tolerant group to identify genetic susceptibility loci. Replication studies in independent groups of severe statin myopathy (n = 190) and statin-tolerant controls (n = 130) resulted in the identification of three single-nucleotide polymorphisms (SNPs), rs9342288, rs1337512, and rs3857532, in the eyes shut homolog (EYS) on chromosome 6 suggestive of an association with risk for severe statin myopathy (P = 0.0003-0.0008). Analysis of EYS cDNA demonstrated that EYS gene products are complex and expressed with relative abundance in the spinal cord as well as in the retina. Structural similarities of these EYS gene products to members of the Notch signaling pathway and to agrin suggest a possible functional role in the maintenance and regeneration of the structural integrity of skeletal muscle. Copyright © 2011 Wiley Periodicals, Inc.

An empirical examination of consumer effects across twenty degrees of latitude.

PubMed

Lavender, James T; Dafforn, Katherine A; Bishop, Melanie J; Johnston, Emma L

2017-09-01

The strength and importance of consumer effects are predicted to increase toward low latitudes, but this hypothesis has rarely been tested using a spatially consistent methodology. In a consumer-exclusion experiment spanning twenty degrees of latitude along the east Australian coast, the magnitude of consumer effects on sub-tidal sessile assemblage composition was not greater at low than high latitudes. Across caged and control assemblages, Shannon's diversity, Pielou's evenness, and richness of functional groups decreased with increasing latitude, but the magnitude of consumer effects on these metrics did not display consistent latitudinal gradients. Instead, latitudinal gradients in consumer effects were apparent for individual functional groups. Solitary ascidians displayed the pattern consistent with predictions of greater direct effects of predators at low than high latitude. As consumers reduced the biomass of this and other competitive dominants, groups less prone to predation (e.g., hydroids, various groups of bryozoans) were able to take advantage of freed space in the presence of consumers and show increased abundances there. This large-scale empirical study demonstrates the complexity of species interactions, and the failure of assemblage-level metrics to adequately capture consumer effects over large spatial gradients. © 2017 by the Ecological Society of America.

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.

ABSTRACT Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium , which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. Themore » response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. IMPORTANCE Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). We focused on the most abundant bacterium, Curtobacterium , which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.« less

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

DOE PAGES

Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.; ...

2017-11-14

ABSTRACT Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium , which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. Themore » response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. IMPORTANCE Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). We focused on the most abundant bacterium, Curtobacterium , which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.« less

Nickel-Catalyzed Phosphine Free Direct N-Alkylation of Amides with Alcohols.

PubMed

Das, Jagadish; Banerjee, Debasis

2018-03-16

Herein, we developed an operational simple, practical, and selective Ni-catalyzed synthesis of secondary amides. Application of renewable alcohols, earth-abundant and nonprecious nickel catalyst facilitates the transformations, releasing water as byproduct. The catalytic system is tolerant to a variety of functional groups including nitrile, allylic ether, and alkene and could be extended to the synthesis of bis-amide, antiemetic drug Tigan, and dopamine D2 receptor antagonist Itopride. Preliminary mechanistic studies revealed the participation of a benzylic C-H bond in the rate-determining step.

High throughput 16SrRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis.

PubMed

Zhao, Meng-Meng; Du, Shan-Shan; Li, Qiu-Hong; Chen, Tao; Qiu, Hui; Wu, Qin; Chen, Shan-Shan; Zhou, Ying; Zhang, Yuan; Hu, Yang; Su, Yi-Liang; Shen, Li; Zhang, Fen; Weng, Dong; Li, Hui-Ping

2017-02-01

This study aims to use high throughput 16SrRNA gene sequencing to examine the bacterial profile of lymph node biopsy samples of patients with sarcoidosis and to further verify the association between Propionibacterium acnes (P. acnes) and sarcoidosis. A total of 36 mediastinal lymph node biopsy specimens were collected from 17 cases of sarcoidosis, 8 tuberculosis (TB group), and 11 non-infectious lung diseases (control group). The V4 region of the bacterial 16SrRNA gene in the specimens was amplified and sequenced using the high throughput sequencing platform MiSeq, and bacterial profile was established. The data analysis software QIIME and Metastats were used to compare bacterial relative abundance in the three patient groups. Overall, 545 genera were identified; 38 showed significantly lower and 29 had significantly higher relative abundance in the sarcoidosis group than in the TB and control groups (P < 0.01). P. acnes 16SrRNA was exclusively found in all the 17 samples of the sarcoidosis group, whereas was not detected in the TB and control groups. The relative abundance of P. acnes in the sarcoidosis group (0.16% ± 0. 11%) was significantly higher than that in the TB (Metastats analysis: P = 0.0010, q = 0.0044) and control groups (Metastats analysis: P = 0.0010, q = 0.0038). The relative abundance of P. granulosum was only 0.0022% ± 0. 0044% in the sarcoidosis group. P. granulosum 16SrRNA was not detected in the other two groups. High throughput 16SrRNA gene sequencing appears to be a useful tool to investigate the bacterial profile of sarcoidosis specimens. The results suggest that P. acnes may be involved in sarcoidosis development.

Calculation of primordial abundances of light nuclei including a heavy sterile neutrino

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosquera, M.E.; Civitarese, O., E-mail: mmosquera@fcaglp.unlp.edu.ar, E-mail: osvaldo.civitarese@fisica.unlp.edu.ar

2015-08-01

We include the coupling of a heavy sterile neutrino with active neutrinos in the calculation of primordial abundances of light-nuclei. We calculate neutrino distribution functions and primordial abundances, as functions depending on a renormalization of the sterile neutrino distribution function (a), the sterile neutrino mass (m{sub s}) and the mixing angle (φ). Using the observable data, we set constrains on these parameters, which have the values 0a < 0.4, sin{sup 2} φ ≈ 0.12−0.39 and 0m{sub s} < 7 keV at 1σ level, for a fixed value of the baryon to photon ratio. When the baryon to photon ratio is allowed to vary, its extracted value ismore » in agreement with the values constrained by Planck observations and by the Wilkinson Microwave Anisotropy Probe (WMAP). It is found that the anomaly in the abundance of {sup 7}Li persists, in spite of the inclusion of a heavy sterile neutrino.« less

Interleukin-10 is differentially expressed in the small intestine and the colon experiencing chronic inflammation and ulcerative colitis induced by dextran sodium sulfate in young pigs.

PubMed

Lackeyram, D; Young, D; Kim, C J; Yang, C; Archbold, T L; Mine, Y; Fan, M Z

2017-03-31

Intestinal inflammation induced with dextran sodium sulfate (DSS) is used to study acute or chronic ulcerative colitis in animal models. Decreased gut tissue anti-inflammatory cytokine IL-10 concentration and mRNA abundance are associated with the development of chronic bowel inflammation. Twelve piglets of 3 days old were fitted with an intragastric catheter and randomly allocated into control and DSS groups by administrating either sterile saline or 1.25 g of DSS/kg body weight (BW) in saline per day, respectively, for 10 days. Growth rate and food conversion efficiency were reduced (p<0.05) in the DSS piglets compared with the control group. Quantitative histopathological grading of inflammation in the jejunum and colon collectively showed that the DSS treatment resulted in 12 fold greater (p<0.05) inflammation severity scoring in the colon than in the jejunum, indicative of chronic ulcerative colitis in the colon. Upper gut permeability endpoint was 27.4 fold higher (p<0.05) in the DSS group compared with the control group. The DSS group had higher concentrations and mRNA abundances (p<0.05) of TNF-alpha and IL-6 in the jejunal and colonic tissues compared with the control group. Colonic concentration and mRNA abundance of IL-10 were reduced (p<0.05), however, jejunal IL-10 mRNA abundance was increased (p<0.05) in the DSS group compared with the control group. In conclusion, administration of DSS at 1.25 g/kg BW for 10 days respectively induced acute inflammation in the jejunum and chronic inflammation and ulcerative colitis in the colon with substantially decreased colonic concentration and mRNA abundance of IL-10 in the young pigs, mimicking the IL-10 expression pattern in humans Associated with chronic bowel inflammation.

Vertical distributions and diel migrations of Euthecosomata in the northwest Sargasso Sea

NASA Astrophysics Data System (ADS)

Wormuth, John H.

1981-12-01

Vertical distributions and seasonal variations in abundance of nine abundant or frequent pteropod species or subspecies in the northwest Sargasso Sea are described. Factor analyses yielded two groups, diel migrators and non-migrators. In terms of water column abundances, tows taken in August and November are similar, as are tows in December and April. Most species show significant within-species agreement in depth distribution over the year but high variability in abundance. Regression analyses using environmental parameters as independent variables show significant correlations of species abundances with temperature.

Can functional equivalency between seagrasses and other coastal habitats offset loss of ecosystem health with reduced seagrass abundance?

NASA Astrophysics Data System (ADS)

Cebrian, J.; Anton, A.; Christiaen, B.; Gamble, R.; Stutes, J.

2016-02-01

Seagrasses provide important ecosystem services, such as habitat for fisheries, shoreline stabilization, pollution filtration, and carbon sequestration. Thus, seagrass loss may seriously compromise coastal ecosystem services worldwide. However, functional equivalency (or redundancy) between seagrasses and other components of coastal ecosystems, such as algae and marshes, can offset the loss of services under declining seagrass abundance. That is, if seagrasses are redundant with algae and marshes in their functionality, then ecosystem services may be preserved in changing coasts with declining seagrass but pervading algal and marsh communities. Here we present several instances of functional redundancy between seagrasses and other coastal components in the Northern Gulf of Mexico. We first examine how net ecosystem production, which sets a limit to carbon accumulation and export to neighbouring communities, changes with eutrophication-induced seagrass decline and concomitant increase in algal abundance. Results from comparative and manipulative field studies are congruent and show no change in net ecosystem production despite drastic shifts from seagrass to algal dominance. We further provide evidence that fringing marshes can counteract the reduction in habitat provision for structure-dependent fisheries due to seagrass loss. Using a large-scale field comparison we show that, as long as fringing marshes are preserved, the abundance and diversity of structure-dependent fisheries are maintained despite large seagrass loss. Functional redundancy for habitat provision also occurs between seagrasses and well-oxygenated macroagal stands, since canopy-dwelling faunal abundance remains unaltered if seagrasses are replaced by normoxic algal stands. In concert the results demonstrate substantial functional equivalency between seagrasses and other coastal components, and indicate seagrass loss does not necessarily result in depressed coastal ecosystem health and services.

Ecological structure and function differs between habitats dominated by seagrasses and green seaweeds.

PubMed

Tuya, Fernando; Png-Gonzalez, Lydia; Riera, Rodrigo; Haroun, Ricardo; Espino, Fernando

2014-07-01

Marine vegetated habitats, e.g. seagrass meadows, deliver essential functions and services to coastal ecosystems and human welfare. Impacts induced by humans, however, have facilitated the replacement of seagrasses by alternative vegetation, e.g. green rhizophytic seaweeds. The implications of habitat shifts for ecosystem attributes and processes and the services they deliver remain poorly known. In this study, we compared ecosystem structure and function between Cymodocea nodosa seagrass meadows and bottoms dominated by Caulerpa prolifera, a green, native, rhizophytic seaweed, through 5 ecological proxies: (i) primary production (via community metabolism), (ii) composition and abundance of epifauna (a proxy for provision of habitat for epifauna), composition and abundance of (iii) small-sized (juvenile) and (iv) large-sized (adult) fishes (proxies for provision of habitat for fishes), and (v) sediment retention (a proxy for sediment stabilization). Four of these proxies were greater in C. nodosa seagrass meadows than in C. prolifera beds: gross primary productivity (∼1.4 times), the total abundance, species density and biomass of small-sized fishes (∼2.1, 1.3 and 1.3 times, respectively), the total abundance and species density of large-sized fishes (∼3.6 and 1.5 times, respectively), and sediment stabilization (∼1.4 times). In contrast, the total abundance and species density of epifauna was larger (∼3.1 and 1.7 times, respectively) in C. prolifera than in C. nodosa seagrass beds. These results suggest that ecosystem structure and function may differ if seagrasses are replaced by green rhizophytic seaweeds. Importantly, ecosystem functions may not be appropriate surrogates for one another. As a result, assessments of ecosystem services associated with ecosystem functions cannot be based on exclusively one service that is expected to benefit other services. Copyright © 2014 Elsevier Ltd. All rights reserved.

Insight into the molecular composition of laboratory organic residues produced from interstellar/pre-cometary ice analogues using very high resolution mass spectrometry

NASA Astrophysics Data System (ADS)

Danger, G.; Fresneau, A.; Abou Mrad, N.; de Marcellus, P.; Orthous-Daunay, F.-R.; Duvernay, F.; Vuitton, V.; Le Sergeant d'Hendecourt, L.; Thissen, R.; Chiavassa, T.

2016-09-01

Experimental simulations in the laboratory may provide important information about the chemical evolution occurring in various astrophysical objects such as extraterrestrial ices. Interstellar or (pre)cometary ice analogues made of H2O, CH3OH, and NH3 at 77 K, when subjected to an energetic process (VUV photons, electrons or ions) and then warmed-up to room temperature, lead, in the laboratory, to the formation of an organic residue. In this paper we expand our previous analysis of the residues in order to obtain a better insight into their molecular content. Data analyses show that three different chemical groups are present in the residue in the negative electrospray ionization (ESI) mode: CHN, CHO and CHNOsbnd whereas only two groups are detected in the positive ESI mode: CHN and CHNO. In both cases, the CHNO group is the most abundant. The application of specific data treatment shows that residue mainly contains aliphatic linear molecules or cyclic structures connected to unsaturated chemical functions such as esters, carboxylic acids, amides or aldehydes. In lower abundances, some molecules do present aromatic structures. The comparison of our residue with organic compounds detected in the Murchison meteorite gives an interesting match, which suggests that laboratory simulation of interstellar ice chemistry is relevant to understand astrophysical organic matter evolution.

Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function.

PubMed

Cheeke, Tanya E; Phillips, Richard P; Brzostek, Edward R; Rosling, Anna; Bever, James D; Fransson, Petra

2017-04-01

While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Carbon turnover in topsoil and subsoil: The microbial response to root litter additions and different environmental conditions in a reciprocal soil translocation experiment

NASA Astrophysics Data System (ADS)

Preusser, Sebastian; Poll, Christian; Marhan, Sven; Kandeler, Ellen

2017-04-01

At the global scale, soil organic carbon (SOC) represents the largest active terrestrial organic carbon (OC) pool. Carbon dynamics in subsoil, however, vary from those in topsoil with much lower C concentrations in subsoil than in topsoil horizons, although more than 50 % of SOC is stored in subsoils below 30 cm soil depth. In addition, microorganisms in subsoil are less abundant, more heterogeneously distributed and the microbial communities have a lower diversity than those in topsoil. Especially in deeper soil, the impact of changes in habitat conditions on microorganisms involved in carbon cycling are largely unexplored and consequently the understanding of microbial functioning is limited. A reciprocal translocation experiment allowed us to investigate the complex interaction effects of altered environmental and substrate conditions on microbial decomposer communities in both topsoil and subsoil habitats under in situ conditions. We conducted this experiment with topsoil (5 cm soil depth) and subsoil (110 cm) samples of an acid and sandy Dystric Cambisol from a European beech (Fagus sylvatica L.) forest in Lower Saxony, Germany. In total 144 samples were buried into three depths (5 cm, 45 cm and 110 cm) and 13C-labelled root litter was added to expose the samples to different environmental conditions and to increase the substrate availability, respectively. Samples were taken in three month intervals up to a maximum exposure time of one year to follow the temporal development over the experimental period. Analyses included 13Cmic and 13C PLFA measurements to investigate the response of microbial abundance, community structure and 13C-root decomposition activity under the different treatments. Environmental conditions in the respective soil depths such as soil temperature and water content were recorded throughout the experimental period. All microbial groups (gram+ and gram- bacteria, fungi) showed highest relative 13C incorporation in 110 cm depth and samples with root addition had generally higher microbial abundances than those with no root addition. Here, especially fungi benefited from the additional carbon source with highly increased abundances in all incorporation depths. Also the altered environmental conditions in the different incorporation depths significantly influenced the different microbial groups. The steepest decrease with depth was detected in fungal abundance, while bacteria were less affected and increased in relative abundance in soil samples incorporated into subsoil layers. The highest seasonal variability in microbial abundance, however, was determined in 5 cm incorporation depth demonstrating the higher amplitude in micro-climatic and micro-environmental conditions in this near-surface soil habitat. In summary, this experiment demonstrated that carbon quality and quantity are the main factors restricting fungal abundance in deeper soil layers, while bacterial decomposer communities are adapted to a wider range of habitat conditions.

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

Microbial Shifts in the Intestinal Microbiota of Salmonella Infected Chickens in Response to Enrofloxacin

PubMed Central

Li, Jun; Hao, Haihong; Cheng, Guyue; Liu, Chunbei; Ahmed, Saeed; Shabbir, Muhammad A. B.; Hussain, Hafiz I.; Dai, Menghong; Yuan, Zonghui

2017-01-01

Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method. The average values of diversity indices were higher in the control group than in the three medicated groups. Non-metric multidimensional scaling (NMDS) analysis results showed that the microbial community of high dosage group was clearly separated from the other three groups. In total, 25 genera were significantly enriched (including 6 abundant genera: Lactococcus, Bacillus, Burkholderia, Pseudomonas, Rhizobium, and Acinetobacter) and 23 genera were significantly reduced in the medicated groups than in the control group for the treatment period, but these bacterial taxa recovered to normal levels after therapy withdrawal. Additionally, 5 genera were significantly reduced in both treatment and withdrawal periods (e.g., Blautia and Anaerotruncus) and 23 genera (e.g., Enterobacter and Clostridium) were significantly decreased only in the withdrawal period, indicating that these genera might be the potential targets for the fluoroquinolones antimicrobial effects. Specially, Enterococcus was significantly reduced under high dosage of enrofloxacin treatment, while significantly enriched in the withdrawal period, which was presumably due to the resistance selection. Predicted microbial functions associated with genetic information processing were significantly decreased in the high dosage group. Overall, enrofloxacin at a dosage of 100 mg/kg b.w. significantly altered the microbial community membership and structure, and microbial functions in the chicken intestine during the medication. This study fully investigates the chicken intestinal microbiota in response to enrofloxacin treatment and identifies potential targets against which the fluoroquinolones may have potent antimicrobial effects. These results provide insights into the effects of the usage of enrofloxacin on chicken and will aid in the prudent and rational use of antibiotics in poultry industry. PMID:28943868

Microbial Shifts in the Intestinal Microbiota of Salmonella Infected Chickens in Response to Enrofloxacin.

PubMed

Li, Jun; Hao, Haihong; Cheng, Guyue; Liu, Chunbei; Ahmed, Saeed; Shabbir, Muhammad A B; Hussain, Hafiz I; Dai, Menghong; Yuan, Zonghui

2017-01-01

Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method. The average values of diversity indices were higher in the control group than in the three medicated groups. Non-metric multidimensional scaling (NMDS) analysis results showed that the microbial community of high dosage group was clearly separated from the other three groups. In total, 25 genera were significantly enriched (including 6 abundant genera: Lactococcus , Bacillus , Burkholderia , Pseudomonas , Rhizobium , and Acinetobacter ) and 23 genera were significantly reduced in the medicated groups than in the control group for the treatment period, but these bacterial taxa recovered to normal levels after therapy withdrawal. Additionally, 5 genera were significantly reduced in both treatment and withdrawal periods (e.g., Blautia and Anaerotruncus ) and 23 genera (e.g., Enterobacter and Clostridium ) were significantly decreased only in the withdrawal period, indicating that these genera might be the potential targets for the fluoroquinolones antimicrobial effects. Specially, Enterococcus was significantly reduced under high dosage of enrofloxacin treatment, while significantly enriched in the withdrawal period, which was presumably due to the resistance selection. Predicted microbial functions associated with genetic information processing were significantly decreased in the high dosage group. Overall, enrofloxacin at a dosage of 100 mg/kg b.w. significantly altered the microbial community membership and structure, and microbial functions in the chicken intestine during the medication. This study fully investigates the chicken intestinal microbiota in response to enrofloxacin treatment and identifies potential targets against which the fluoroquinolones may have potent antimicrobial effects. These results provide insights into the effects of the usage of enrofloxacin on chicken and will aid in the prudent and rational use of antibiotics in poultry industry.

Quantification of amine functional groups and their influence on OM/OC in the IMPROVE network

NASA Astrophysics Data System (ADS)

Kamruzzaman, Mohammed; Takahama, Satoshi; Dillner, Ann M.

2018-01-01

Recently, we developed a method using FT-IR spectroscopy coupled with partial least squares (PLS) regression to measure the four most abundant organic functional groups, aliphatic C-H, alcohol OH, carboxylic acid OH and carbonyl C=O, in atmospheric particulate matter. These functional groups are summed to estimate organic matter (OM) while the carbon from the functional groups is summed to estimate organic carbon (OC). With this method, OM and OM/OC can be estimated for each sample rather than relying on one assumed value to convert OC measurements to OM. This study continues the development of the FT-IR and PLS method for estimating OM and OM/OC by including the amine functional group. Amines are ubiquitous in the atmosphere and come from motor vehicle exhaust, animal husbandry, biomass burning, and vegetation among other sources. In this study, calibration standards for amines are produced by aerosolizing individual amine compounds and collecting them on PTFE filters using an IMPROVE sampler, thereby mimicking the filter media and collection geometry of ambient standards. The moles of amine functional group on each standard and a narrow range of amine-specific wavenumbers in the FT-IR spectra (wavenumber range 1 550-1 500 cm-1) are used to develop a PLS calibration model. The PLS model is validated using three methods: prediction of a set of laboratory standards not included in the model, a peak height analysis and a PLS model with a broader wavenumber range. The model is then applied to the ambient samples collected throughout 2013 from 16 IMPROVE sites in the USA. Urban sites have higher amine concentrations than most rural sites, but amine functional groups account for a lower fraction of OM at urban sites. Amine concentrations, contributions to OM and seasonality vary by site and sample. Amine has a small impact on the annual average OM/OC for urban sites, but for some rural sites including amine in the OM/OC calculations increased OM/OC by 0.1 or more.

The impact of transposable elements on mammalian development

PubMed Central

Garcia-Perez, Jose L.; Widmann, Thomas J.; Adams, Ian R.

2018-01-01

Summary Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that significantly impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and how the somatic activity of TEs can influence gene regulatory networks. PMID:27875251