Stormwater runoff drives viral community composition changes in inland freshwaters

PubMed Central

Williamson, Kurt E.; Harris, Jamie V.; Green, Jasmin C.; Rahman, Faraz; Chambers, Randolph M.

2014-01-01

Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities. Field data gathered from an agricultural watershed indicated that primary runoff can contain viral densities approximating those of receiving waters. Furthermore, viruses attached to suspended colloids made up a large fraction of the total load, particularly in early stages of the storm. At a second field site (stormwater retention pond), RAPD-PCR profiling showed that the viral community of the pond changed dramatically over the course of two intense storms while relatively little change was observed over similar time scales in the absence of disturbance. Comparisons of planktonic and particle-associated viral communities revealed two completely distinct communities, suggesting that particle-associated viruses represent a potentially large and overlooked portion of aquatic viral abundance and diversity. Our findings show that stormwater runoff can quickly change the composition of freshwater microbial communities. Based on these findings, increased storms in the coastal mid-Atlantic region predicted by most climate change models will likely have important impacts on the structure and function of local freshwater microbial communities. PMID:24672520

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Contrasting outcomes of species- and community-level analyses of the temporal consistency of functional composition.

PubMed

Katabuchi, Masatoshi; Wright, S Joseph; Swenson, Nathan G; Feeley, Kenneth J; Condit, Richard; Hubbell, Stephen P; Davies, Stuart J

2017-09-01

Multiple anthropogenic drivers affect every natural community, and there is broad interest in using functional traits to understand and predict the consequences for future biodiversity. There is, however, no consensus regarding the choice of analytical methods. We contrast species- and community-level analyses of change in the functional composition for four traits related to drought tolerance using three decades of repeat censuses of trees in the 50-ha Forest Dynamics Plot on Barro Colorado Island, Panama. Community trait distributions shifted significantly through time, which may indicate a shift toward more drought tolerant species. However, at the species level, changes in abundance were unrelated to trait values. To reconcile these seemingly contrasting results, we evaluated species-specific contributions to the directional shifts observed at the community level. Abundance changes of just one to six of 312 species were responsible for the community-level shifts observed for each trait. Our results demonstrate that directional changes in community-level functional composition can result from idiosyncratic change in a few species rather than widespread community-wide changes associated with functional traits. Future analyses of directional change in natural communities should combine community-, species-, and possibly individual-level analyses to uncover relationships with function that can improve understanding and enable prediction. © 2017 by the Ecological Society of America.

Mesoscale and sub-mesoscale variability in phytoplankton community composition in the Sargasso Sea

NASA Astrophysics Data System (ADS)

Cotti-Rausch, Bridget E.; Lomas, Michael W.; Lachenmyer, Eric M.; Goldman, Emily A.; Bell, Douglas W.; Goldberg, Stacey R.; Richardson, Tammi L.

2016-04-01

The Sargasso Sea is a dynamic physical environment in which strong seasonal variability combines with forcing by mesoscale (~100 km) eddies. These drivers determine nutrient, light, and temperature regimes and, ultimately, the composition and productivity of the phytoplankton community. On four cruises (2011 and 2012; one eddy per cruise), we investigated links between water column structure and phytoplankton community composition in the Sargasso at a range of time and space scales. On all cruises, cyanobacteria (Prochlorococcus and Synechococcus) dominated the phytoplankton numerically, while haptophytes were the dominant eukaryotes (up to 60% of total chl-a). There were substantial effects of mesoscale and sub-mesoscale forcing on phytoplankton community composition in both spring and summer. Downwelling (in anticyclones) resulted in Prochlorococcus abundances that were 22-66% higher than at 'outside' stations. Upwelling (in cyclones) was associated with significantly higher abundances and POC biomass of nanoeukaryotes. In general, however, each eddy had its own unique characteristics. The center of anticyclone AC1 (spring 2011) had the lowest phytoplankton biomass (chl-a) of any eddy we studied and had lower nitrate+nitrite (N+N <5 mmol m-2) and eukaryote chl-a biomass as compared to its edge and to the Bermuda Atlantic Time-Series station (BATS). At the center of cyclone C1 (summer 2011), we observed uplift of the 26.5 kg m-3 isopycnal and high nutrient inventories (N+N=74±46 mmol m-2). We also observed significantly higher haptophyte chl-a (non-coccolithophores) and lower cyanobacterial chl-a at the center and edge of C1 as compared to outside the eddy at BATS. Cyclone C2 (spring 2012) exhibited a deep mixed layer, yet had relatively low nutrient concentrations. We observed a shift in the taxonomic composition of haptophytes between a coccolithophore-dominated community in C2 (98% of total haptophyte chl-a) and a non-coccolithophore community at BATS. In

Patterns of vegetation and grasshopper community composition.

PubMed

Kemp, W P; Harvey, S J; O'Neill, K M

1990-06-01

A study was conducted to evaluate differences in rangeland grasshopper communities over environmental gradients in Gallatin Valley, Montana, USA. The concept of habitat type (Daubenmire 1966) was used as a basis for discriminating between groupings of patches based on vegetation. A total of 39 patches were selected that represented five recognized grassland habitat types (Mueggler and Stewart 1980), as well as two disturbed types (replanting within a known habitat type). Repeated sampling in 1988 of both the insect and plant communities yielded a total of 40 grasshopper (19 664 individuals) and 97 plant species. Detrended Correspondence Analysis (DCA) indicated that patch classifications based on presence and percent cover of plants were appropriate and showed good between-group (habitat type) separation for patches along gradients of precipitation/elevation and plant community complexity. Results from undisturbed habitats showed that plant and grasshopper species composition changed over observed environmental gradients and suggested that habitat type influenced not only species presence, but also relative abundance. Discussion is presented that relates results with patch-use and core and satellite species paradigms.

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

PubMed Central

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

PubMed

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Biodiversity increases functional and compositional resistance, but decreases resilience in phytoplankton communities.

PubMed

Baert, Jan M; De Laender, Frederik; Sabbe, Koen; Janssen, Colin R

2016-12-01

There is now ample evidence that biodiversity stabilizes aggregated ecosystem functions, such as primary production, in changing environments. In primary producer systems, this stabilizing effect is found to be driven by higher functional resistance (i.e., reduced changes in functions by environmental changes) rather than through higher functional resilience (i.e., rapid recovery following environmental changes) in more diverse systems. The stability of aggregated ecosystem functions directly depends on changes in species composition and by consequence their functional contributions to ecosystem functions. Still, it remains only theoretically explored how biodiversity can stabilize ecosystem functions by affecting compositional stability. Here, we demonstrate how biodiversity effects on compositional stability drive biodiversity effects on functional stability in diatom communities. In a microcosm experiment, we exposed 39 communities of five different levels of species richness (1, 2, 4, 6, and 8 species) to three concentrations of a chemical stressor (0, 25, and 250 μg/L atrazine) for four weeks, after which all communities were transferred to atrazine-free medium for three more weeks. Biodiversity simultaneously increased, increasing functional and compositional resistance, but decreased functional and compositional resilience. These results confirm the theoretically proposed link between biodiversity effects on functional and compositional stability in primary producer systems, and provide a mechanistic underpinning for observed biodiversity-stability relationships. Finally, we discuss how higher compositional stability can be expected to become increasingly important in stabilizing ecosystem functions under field conditions when multiple environmental stressors fluctuate simultaneously. © 2016 by the Ecological Society of America.

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PubMed

Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

2017-01-01

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  < 0.01), Streptococcus ( p  < 0.01), and Rothia ( p  < 0.01). Staphylococcus ( p  < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella ( p  < 0.01), Granulicatella ( p  < 0.01), Prevotella ( p  < 0.01), and Gemella ( p  = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra.

PubMed

Semenova, Tatiana A; Morgado, Luis N; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József

2015-01-01

Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic richness of soil ascomycetes in dry and moist tundra types. Using deep Ion Torrent sequencing, we quantified how OTU assemblage and richness of different orders of Ascomycota changed in response to summer warming. Experimental warming significantly altered ascomycete communities with stronger responses observed in the moist tundra compared with dry tundra. The proportion of several lichenized and moss-associated fungi decreased with warming, while the proportion of several plant and insect pathogens and saprotrophic species was higher in the warming treatment. The observed alterations in both taxonomic and ecological groups of ascomycetes are discussed in relation to previously reported warming-induced shifts in arctic plant communities, including decline in lichens and bryophytes and increase in coverage and biomass of shrubs. © 2014 John Wiley & Sons Ltd.

Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

PubMed

Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

2017-11-01

The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

Dynamics of phytoplankton community composition in the western Gulf of Maine

NASA Astrophysics Data System (ADS)

Moore, Timothy S.

This dissertation is founded on the importance of phytoplankton community composition to marine biogeochemistry and ecosystem processes and motivated by the need to understand their distributions on regional to global scales. The ultimate goal was to predict surface phytoplankton communities using satellite remote sensing by relating marine habitats--defined through a statistical description of environmental properties--to different phytoplankton communities. While phytoplankton community composition is governed by the interplay of abiotic and biotic interactions, the strategy adopted here was to focus on the physical abiotic factors. This allowed for the detection of habitats from ocean satellites based on abiotic factors that were linked to associated phytoplankton communities. The research entailed three studies that addressed different aspects of the main goal using a dataset collected in the western Gulf of Maine over a 3-year period. The first study evaluated a chemotaxonomic method that quantified phytoplankton composition from pigment data. This enabled the characterization of three phytoplankton communities, which were defined by the relative abundance of diatoms and flagellates. The second study examined the cycles of these communities along with environmental variables, and the results revealed that the three phytoplankton communities exhibited an affinity to different hydrographic regimes. The third study focused on the implementation of a classifier that predicted phytoplankton communities from environmental variables. Its ability to differentiate communities dominated by diatoms versus flagellates was shown to be high. However, the increase in data imprecision when using satellite data led to lowered performance and favored an approach that incorporated fuzzy logic. The fuzzy method is well suited to characterize the uncertainties in phytoplankton community prediction, and provides a measure of confidence on predicted communities. The final product of

Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

PubMed

Kumar, Arvind; Rai, Lal Chand

2017-07-01

Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients.

PubMed

Radujkovic, Dajana; Verbruggen, Erik; Sigurdsson, Bjarni D; Leblans, Niki I W; Janssens, Ivan A; Vicca, Sara; Weedon, James T

2018-02-01

Global change is expected to affect soil microbial communities through their responsiveness to temperature. It has been proposed that prolonged exposure to elevated temperatures may lead to progressively larger effects on soil microbial community composition. However, due to the relatively short-term nature of most warming experiments, this idea has been challenging to evaluate. The present study took the advantage of natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies the effect of warming on microbial community composition compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed only starting from the warming intensity of +9°C in the long term and +7°C/+3°C in the short term, for bacteria and fungi, respectively. Our results suggest that microbial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years (+2.2°C to +8.3°C). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

USGS Publications Warehouse

Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

2015-01-01

Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

PubMed Central

Yooseph, Shibu; Ininbergs, Karolina; Goll, Johannes; Asplund-Samuelsson, Johannes; McCrow, John P.; Celepli, Narin; Allen, Lisa Zeigler; Ekman, Martin; Lucas, Andrew J.; Hagström, Åke; Thiagarajan, Mathangi; Brindefalk, Björn; Richter, Alexander R.; Andersson, Anders F.; Tenney, Aaron; Lundin, Daniel; Tovchigrechko, Andrey; Nylander, Johan A. A.; Brami, Daniel; Badger, Jonathan H.; Allen, Andrew E.; Rusch, Douglas B.; Hoffman, Jeff; Norrby, Erling; Friedman, Robert; Pinhassi, Jarone; Venter, J. Craig; Bergman, Birgitta

2014-01-01

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. PMID:24586863

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

PubMed

Dupont, Chris L; Larsson, John; Yooseph, Shibu; Ininbergs, Karolina; Goll, Johannes; Asplund-Samuelsson, Johannes; McCrow, John P; Celepli, Narin; Allen, Lisa Zeigler; Ekman, Martin; Lucas, Andrew J; Hagström, Åke; Thiagarajan, Mathangi; Brindefalk, Björn; Richter, Alexander R; Andersson, Anders F; Tenney, Aaron; Lundin, Daniel; Tovchigrechko, Andrey; Nylander, Johan A A; Brami, Daniel; Badger, Jonathan H; Allen, Andrew E; Rusch, Douglas B; Hoffman, Jeff; Norrby, Erling; Friedman, Robert; Pinhassi, Jarone; Venter, J Craig; Bergman, Birgitta

2014-01-01

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization.

PubMed

Enwall, Karin; Philippot, Laurent; Hallin, Sara

2005-12-01

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

Modeling the effects of free-living marine bacterial community composition on heterotrophic remineralization rates and biogeochemical carbon cycling

NASA Astrophysics Data System (ADS)

Teel, E.; Liu, X.; Cram, J. A.; Sachdeva, R.; Fuhrman, J. A.; Levine, N. M.

2016-12-01

Global oceanic ecosystem models either disregard fluctuations in heterotrophic bacterial remineralization or vary remineralization as a simple function of temperature, available carbon, and nutrient limitation. Most of these models were developed before molecular techniques allowed for the description of microbial community composition and functional diversity. Here we investigate the impact of a dynamic heterotrophic community and variable remineralization rates on biogeochemical cycling. Specifically, we integrated variable microbial remineralization into an ecosystem model by utilizing molecular community composition data, association network analysis, and biogeochemical rate data from the San Pedro Ocean Time-series (SPOT) station. Fluctuations in free-living bacterial community function and composition were examined using monthly environmental and biological data collected at SPOT between 2000 and 2011. On average, the bacterial community showed predictable seasonal changes in community composition and peaked in abundance in the spring with a one-month lag from peak chlorophyll concentrations. Bacterial growth efficiency (BGE), estimated from bacterial production, was found to vary widely at the site (5% to 40%). In a multivariate analysis, 47.6% of BGE variability was predicted using primary production, bacterial community composition, and temperature. A classic Nutrient-Phytoplankton-Zooplankton-Detritus model was expanded to include a heterotroph module that captured the observed relationships at the SPOT site. Results show that the inclusion of dynamic bacterial remineralization into larger oceanic ecosystem models can significantly impact microzooplankton grazing, the duration of surface phytoplankton blooms, and picophytoplankton primary production rates.

Bacterial Community Composition and Extracellular Enzyme Activity in Temperate Streambed Sediment during Drying and Rewetting

PubMed Central

Pohlon, Elisabeth; Ochoa Fandino, Adriana; Marxsen, Jürgen

2013-01-01

Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after

Interactive effects between plant functional types and soil factors on tundra species diversity and community composition.

PubMed

Iturrate-Garcia, Maitane; O'Brien, Michael J; Khitun, Olga; Abiven, Samuel; Niklaus, Pascal A; Schaepman-Strub, Gabriela

2016-11-01

Plant communities are coupled with abiotic factors, as species diversity and community composition both respond to and influence climate and soil characteristics. Interactions between vegetation and abiotic factors depend on plant functional types (PFT) as different growth forms will have differential responses to and effects on site characteristics. However, despite the importance of different PFT for community assembly and ecosystem functioning, research has mainly focused on vascular plants. Here, we established a set of observational plots in two contrasting habitats in northeastern Siberia in order to assess the relationship between species diversity and community composition with soil variables, as well as the relationship between vegetation cover and species diversity for two PFT (nonvascular and vascular). We found that nonvascular species diversity decreased with soil acidity and moisture and, to a lesser extent, with soil temperature and active layer thickness. In contrast, no such correlation was found for vascular species diversity. Differences in community composition were found mainly along soil acidity and moisture gradients. However, the proportion of variation in composition explained by the measured soil variables was much lower for nonvascular than for vascular species when considering the PFT separately. We also found different relationships between vegetation cover and species diversity according the PFT and habitat. In support of niche differentiation theory, species diversity and community composition were related to edaphic factors. The distinct relationships found for nonvascular and vascular species suggest the importance of considering multiple PFT when assessing species diversity and composition and their interaction with edaphic factors. Synthesis : Identifying vegetation responses to edaphic factors is a first step toward a better understanding of vegetation-soil feedbacks under climate change. Our results suggest that incorporating

Receding Water Line and Interspecific Competition Determines Plant Community Composition and Diversity in Wetlands in Beijing

PubMed Central

Wang, Zhengjun; Gong, Huili; Zhang, Jing

2015-01-01

Climate and human-induced wetland degradation has accelerated in recent years, not only resulting in reduced ecosystem services but also greatly affecting the composition and diversity of wetland plant communities. To date, the knowledge of the differences in community parameters and their successional trends in degraded wetlands remains scarce. Here based on remote sensing images, geographic information system technology, and statistical methods, we produced a successional gradient map of the Yeyahu Wetland Nature Reserve in Beijing, which has experienced a steady decline in water level in recent decades. In addition, we analyzed community composition and diversity along with each identified gradient. The results showed that community diversity decreases while dominance increases with the progress of succession, with the highest diversity occurring during the early stage of succession. Moreover, the community demonstrates greater similarity among subareas during later successional stages, and the similarity coefficients calculated from the important value (IV) of each species are more accurate. Correlation analysis showed that the impact of soil factors on diversity was not significant at a subarea scale, although these nutrients showed an increasing trend with the community succession. Furthermore, the IVs of the dominant species had a particularly significant impact on diversity, showing a significantly negative correlation with diversity indices and a significantly positive correlation with dominance indices. Further analysis showed that the retreat of water level resulted from sustained drought and local human activities was a major extrinsic driving force resulting in observed differences in the community successional stages, which resulted in differences in community composition and diversity. On the other hand, interspecific competition was the main intrinsic mechanism, which significantly influenced the IVs of the dominant species and community diversity

Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

PubMed

Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

2016-05-01

Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observing Community Residences.

ERIC Educational Resources Information Center

Taylor, Steven J.; Bogdan, Robert

The document offers guidelines effectively monitoring the quality of care provided in community residences serving people with disabilities. An initial section offers suggestions on observation and evaluation procedures. The remainder of the document lists possible questions to be asked in 19 areas: location, building and yard, relations with the…

Metals other than uranium affected microbial community composition in a historical uranium-mining site.

PubMed

Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

2015-12-01

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

The community ecology of pathogens: coinfection, coexistence and community composition.

PubMed

Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

2015-04-01

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology. © 2015 John Wiley & Sons Ltd/CNRS.

Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir.

PubMed

Boucher, Delphine; Jardillier, Ludwig; Debroas, Didier

2006-01-01

The succession in bacterial community composition was studied over two years in the epilimnion and hypolimnion of two freshwater systems: a natural lake (Pavin Lake) and a lake-reservoir (Sep Reservoir). The bacterial community composition was determined by cloning-sequencing of 16S rRNA and by terminal restriction fragment length polymorphism. Despite large hydrogeological differences, in the Sep Reservoir and Pavin Lake the dominant bacteria were from the same taxonomic divisions, particularly Actinobacteria and Betaproteobacteria. In both ecosystems, these major bacterial divisions showed temporal fluctuations that were much less marked than those occurring at a finer phylogenetic scale. Nutrient availability and mortality factors, the nature of which differed from one lake to another, covaried with the temporal variations in the bacterial community composition at all sampling depths, whereas factors related to seasonal forces (temperature and outflow for Sep Reservoir) seemed to account only for the variation of the hypolimnion bacterial community composition. No seasonal reproducibility in temporal evolution of bacterial community from one year to the next was observed.

Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

PubMed

Hubert, Nathaniel A; Gehring, Catherine A

2008-09-01

Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

Bacterial diversity and community composition from seasurface to subseafloor.

PubMed

Walsh, Emily A; Kirkpatrick, John B; Rutherford, Scott D; Smith, David C; Sogin, Mitchell; D'Hondt, Steven

2016-04-01

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

PubMed Central

Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

2015-01-01

Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

Effects of climate change on plant population growth rate and community composition change.

PubMed

Chang, Xiao-Yu; Chen, Bao-Ming; Liu, Gang; Zhou, Ting; Jia, Xiao-Rong; Peng, Shao-Lin

2015-01-01

The impacts of climate change on forest community composition are still not well known. Although directional trends in climate change and community composition change were reported in recent years, further quantitative analyses are urgently needed. Previous studies focused on measuring population growth rates in a single time period, neglecting the development of the populations. Here we aimed to compose a method for calculating the community composition change, and to testify the impacts of climate change on community composition change within a relatively short period (several decades) based on long-term monitoring data from two plots-Dinghushan Biosphere Reserve, China (DBR) and Barro Colorado Island, Panama (BCI)-that are located in tropical and subtropical regions. We proposed a relatively more concise index, Slnλ, which refers to an overall population growth rate based on the dominant species in a community. The results indicated that the population growth rate of a majority of populations has decreased over the past few decades. This decrease was mainly caused by population development. The increasing temperature had a positive effect on population growth rates and community change rates. Our results promote understanding and explaining variations in population growth rates and community composition rates, and are helpful to predict population dynamics and population responses to climate change.

Effects of simulated acid rain on soil fauna community composition and their ecological niches.

PubMed

Wei, Hui; Liu, Wen; Zhang, Jiaen; Qin, Zhong

2017-01-01

Acid rain is one of the severest environmental issues globally. Relative to other global changes (e.g., warming, elevated atmospheric [CO 2 ], and nitrogen deposition), however, acid rain has received less attention than its due. Soil fauna play important roles in multiple ecological processes, but how soil fauna community responds to acid rain remains less studied. This microcosm experiment was conducted using latosol with simulated acid rain (SAR) manipulations to observe potential changes in soil fauna community under acid rain stress. Four pH levels, i.e., pH 2.5, 3.5, 4.5, and 5.5, and a neutral control of pH 7.0 were set according to the current pH condition and acidification trend of precipitation in southern China. As expected, we observed that the SAR treatments induced changes in soil fauna community composition and their ecological niches in the tested soil; the treatment effects tended to increase as acidity increased. This could be attributable to the environmental stresses (such as acidity, porosity and oxygen supply) induced by the SAR treatments. In addition to direct acidity effect, we propose that potential changes in permeability and movability of water and oxygen in soils induced by acid rain could also give rise to the observed shifts in soil fauna community composition. These are most likely indirect pathways of acid rain to affect belowground community. Moreover, we found that nematodes, the dominating soil fauna group in this study, moved downwards to mitigate the stress of acid rain. This is probably detrimental to soil fauna in the long term, due to the relatively severer soil conditions in the deep than surface soil layer. Our results suggest that acid rain could change soil fauna community and the vertical distribution of soil fauna groups, consequently changing the underground ecosystem functions such as organic matter decomposition and greenhouse gas emissions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

PubMed

Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

2013-10-01

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor

PubMed Central

Zhang, Q; Shuwen, G; Zhang, J; Fane, AG; Kjelleberg, S; Rice, SA; McDougald, D

2015-01-01

Aims Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Methods and Results Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Conclusions Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. Significance and Impact of the Study This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. PMID:25604265

Testing the functional significance of microbial community composition.

Treesearch

Michael S. Strickland; Christian Lauber; Noah Fierer; Mark A. Bradford

2009-01-01

A critical assumption underlying terrestrial ecosystem models is that soil microbial communities, when placed in a common environment, will function in an identical manner regardless of the composition...

Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

PubMed

Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

2010-06-01

The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

PubMed

Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

2015-02-15

Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

Methane flux and carbon isotope composition correlate to shifting plant and microbial communities along a permafrost thaw gradient

NASA Astrophysics Data System (ADS)

McCalley, C. K.; Mondav, R.; Chanton, J.; Crill, P. M.; Hodgkins, S. B.; Kim, E.; Rich, V. I.; Wehr, R.; Woodcroft, B. J.; Tyson, G. W.; Saleska, S. R.

2012-12-01

Methane flux from high latitude wetlands is a critical component of the global carbon budget and is highly sensitive to climate change, with observed and predicted increases as permafrost thaws. Microorganisms mediate wetland methane cycling, but connections between ecosystem-scale flux and underlying microbial dynamics are poorly understood. To address this gap we used isotopic (laser absorption spectrometry) and molecular (16S rRNA gene amplicon sequencing) techniques in a high latitude (68° N) wetland to investigate the relationship between microbial community composition and methane emissions across a permafrost thaw gradient. The transition from permafrost dominated, well drained palsas, through intermediate thaw sites dominated by Sphagnum spp., to wet sites with no underlying permafrost dominated by Eriophorum angustifolium is associated with substantial increases in methane emission. Across this thaw progression the carbon isotopic composition of emitted methane increased from -79.5 ‰ in the intermediate-thawing site to -66.4 ‰ in the thawed site, indicating a relative shift from CO2-reductive towards acetoclastic methanogenesis. Increases in methane flux under thaw were correlated with increasing abundance of methane-producing archaeal clades and increases in methane isotopic composition were associated with shifts in the archaeal community. While CO2 reducing methanogens were found throughout thawing and thawed sites, methanogens of the Methanosarcina (the order of Archaea that contains all known acetoclastic methanogens) were most associated with the fully thawed site. These results directly link microbial community composition to ecosystem scale changes in the magnitude and isotopic composition of methane emissions under permafrost thaw. If isotopic shifts of this magnitude are characteristic of methane dynamics under permafrost loss they should also become detectable in global atmospheric methane observations, providing a global scale tracer of

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor.

PubMed

Zhang, Q; Shuwen, G; Zhang, J; Fane, A G; Kjelleberg, S; Rice, S A; McDougald, D

2015-04-01

Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. © 2015 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.

PubMed

Biswas, Kristi; Turner, Susan J

2012-02-01

Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

Land Cover and Rainfall Interact to Shape Waterbird Community Composition

PubMed Central

Studds, Colin E.; DeLuca, William V.; Baker, Matthew E.; King, Ryan S.; Marra, Peter P.

2012-01-01

Human land cover can degrade estuaries directly through habitat loss and fragmentation or indirectly through nutrient inputs that reduce water quality. Strong precipitation events are occurring more frequently, causing greater hydrological connectivity between watersheds and estuaries. Nutrient enrichment and dissolved oxygen depletion that occur following these events are known to limit populations of benthic macroinvertebrates and commercially harvested species, but the consequences for top consumers such as birds remain largely unknown. We used non-metric multidimensional scaling (MDS) and structural equation modeling (SEM) to understand how land cover and annual variation in rainfall interact to shape waterbird community composition in Chesapeake Bay, USA. The MDS ordination indicated that urban subestuaries shifted from a mixed generalist-specialist community in 2002, a year of severe drought, to generalist-dominated community in 2003, of year of high rainfall. The SEM revealed that this change was concurrent with a sixfold increase in nitrate-N concentration in subestuaries. In the drought year of 2002, waterbird community composition depended only on the direct effect of urban development in watersheds. In the wet year of 2003, community composition depended both on this direct effect and on indirect effects associated with high nitrate-N inputs to northern parts of the Bay, particularly in urban subestuaries. Our findings suggest that increased runoff during periods of high rainfall can depress water quality enough to alter the composition of estuarine waterbird communities, and that this effect is compounded in subestuaries dominated by urban development. Estuarine restoration programs often chart progress by monitoring stressors and indicators, but rarely assess multivariate relationships among them. Estuarine management planning could be improved by tracking the structure of relationships among land cover, water quality, and waterbirds. Unraveling these

Land cover and rainfall interact to shape waterbird community composition.

PubMed

Studds, Colin E; DeLuca, William V; Baker, Matthew E; King, Ryan S; Marra, Peter P

2012-01-01

Human land cover can degrade estuaries directly through habitat loss and fragmentation or indirectly through nutrient inputs that reduce water quality. Strong precipitation events are occurring more frequently, causing greater hydrological connectivity between watersheds and estuaries. Nutrient enrichment and dissolved oxygen depletion that occur following these events are known to limit populations of benthic macroinvertebrates and commercially harvested species, but the consequences for top consumers such as birds remain largely unknown. We used non-metric multidimensional scaling (MDS) and structural equation modeling (SEM) to understand how land cover and annual variation in rainfall interact to shape waterbird community composition in Chesapeake Bay, USA. The MDS ordination indicated that urban subestuaries shifted from a mixed generalist-specialist community in 2002, a year of severe drought, to generalist-dominated community in 2003, of year of high rainfall. The SEM revealed that this change was concurrent with a sixfold increase in nitrate-N concentration in subestuaries. In the drought year of 2002, waterbird community composition depended only on the direct effect of urban development in watersheds. In the wet year of 2003, community composition depended both on this direct effect and on indirect effects associated with high nitrate-N inputs to northern parts of the Bay, particularly in urban subestuaries. Our findings suggest that increased runoff during periods of high rainfall can depress water quality enough to alter the composition of estuarine waterbird communities, and that this effect is compounded in subestuaries dominated by urban development. Estuarine restoration programs often chart progress by monitoring stressors and indicators, but rarely assess multivariate relationships among them. Estuarine management planning could be improved by tracking the structure of relationships among land cover, water quality, and waterbirds. Unraveling these

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Experimental soil warming shifts the fungal community composition at the alpine treeline.

PubMed

Solly, Emily F; Lindahl, Björn D; Dawes, Melissa A; Peter, Martina; Souza, Rômulo C; Rixen, Christian; Hagedorn, Frank

2017-07-01

Increased CO 2 emissions and global warming may alter the composition of fungal communities through the removal of temperature limitation in the plant-soil system, faster nitrogen (N) cycling and changes in the carbon (C) allocation of host plants to the rhizosphere. At a Swiss treeline featuring Larix decidua and Pinus uncinata, the effects of multiple years of CO 2 enrichment and experimental soil warming on the fungal community composition in the organic horizons were analysed using 454-pyrosequencing of ITS2 amplicons. Sporocarp production and colonization of ectomycorrhizal root tips were investigated in parallel. Fungal community composition was significantly altered by soil warming, whereas CO 2 enrichment had little effect. Tree species influenced fungal community composition and the magnitude of the warming responses. The abundance of ectomycorrhizal fungal taxa was positively correlated with N availability, and ectomycorrhizal taxa specialized for conditions of high N availability proliferated with warming, corresponding to considerable increases in inorganic N in warmed soils. Traits related to N utilization are important in determining the responses of ectomycorrhizal fungi to warming in N-poor cold ecosystems. Shifts in the overall fungal community composition in response to higher temperatures may alter fungal-driven processes with potential feedbacks on ecosystem N cycling and C storage at the alpine treeline. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Composition and structure of arbuscular-mycorrhizal communities in El Palmar National Park, Argentina.

PubMed

Velázquez, María S; Cabello, Marta N; Barrera, Marcelo

2013-01-01

The arbuscular-mycorrhizal-fungal (AMF) communities from the El Palmar National Park of Entre Ríos Province, Argentina, were investigated and characterized. The species of AMF present in five distinct vegetation types-gallery forest, grassland, marsh, palm forest, and scrubland-were isolated, identified and quantified over 2 y. Forty-six AMF morphotaxa were found. The composition of the AMF communities differed between the seasons, soil and vegetation types. Seasonal variations were observed in members of the Acaulosporaceae, Archaeosporaceae, Claroideoglomeraceae, Gigasporaceae and Pacisporaceae. Depending on soil type, the AMF-spore communities were dominated by members of one of the two main orders of the Glomeromycota. AMF communities from grassland and palm forest, which occur on sandy soils, comprised primarily members of the Diversisporales, with a high percentage of species of Acaulospora and of Gigasporaceae. Communities from the gallery forest, marsh and scrubland, which occur on loam-clay soils, were composed of members of the Glomerales, with a high percentage of spores from species of Glomus. Thus, both AMF and plant communities would appear to be strongly and similarly influenced by edaphic conditions.

Biofouling community composition across a range of environmental conditions and geographical locations suitable for floating marine renewable energy generation.

PubMed

Macleod, Adrian K; Stanley, Michele S; Day, John G; Cook, Elizabeth J

2016-01-01

Knowledge of biofouling typical of marine structures is essential for engineers to define appropriate loading criteria in addition to informing other stakeholders about the ecological implications of creating novel artificial environments. There is a lack of information regarding biofouling community composition (including weight and density characteristics) on floating structures associated with future marine renewable energy generation technologies. A network of navigation buoys were identified across a range of geographical areas, environmental conditions (tidal flow speed, temperature and salinity), and deployment durations suitable for future developments. Despite the perceived importance of environmental and temporal factors, geographical location explained the greatest proportion of the observed variation in community composition, emphasising the importance of considering geography when assessing the impact of biofouling on device functioning and associated ecology. The principal taxa associated with variation in biofouling community composition were mussels (Mytilus edulis), which were also important when determining loading criteria.

Urban stormwater runoff drives denitrifying community composition through changes in sediment texture and carbon content.

PubMed

Perryman, Shane E; Rees, Gavin N; Walsh, Christopher J; Grace, Michael R

2011-05-01

The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

Night-time lighting alters the composition of marine epifaunal communities

PubMed Central

Davies, Thomas W.; Coleman, Matthew; Griffith, Katherine M.; Jenkins, Stuart R.

2015-01-01

Marine benthic communities face multiple anthropogenic pressures that compromise the future of some of the most biodiverse and functionally important ecosystems in the world. Yet one of the pressures these ecosystems face, night-time lighting, remains unstudied. Light is an important cue in guiding the settlement of invertebrate larvae, and altering natural regimes of nocturnal illumination could modify patterns of recruitment among sessile epifauna. We present the first evidence of night-time lighting changing the composition of temperate epifaunal marine invertebrate communities. Illuminating settlement surfaces with white light-emitting diode lighting at night, to levels experienced by these communities locally, both inhibited and encouraged the colonization of 39% of the taxa analysed, including three sessile and two mobile species. Our results indicate that ecological light pollution from coastal development, shipping and offshore infrastructure could be changing the composition of marine epifaunal communities. PMID:25926694

Rapid decay of tree-community composition in Amazonian forest fragments

PubMed Central

Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

2006-01-01

Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

Storm-scale dynamics of bacterial community composition in throughfall and stemflow

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

2017-12-01

Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

Urban greenness influences airborne bacterial community composition.

PubMed

Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

2016-11-15

Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

PubMed

Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

2016-10-01

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

Fire severity mediates climate-driven shifts in understorey community composition of black spruce stands of interior Alaska

Treesearch

Emily L. Bernhardt; Teresa N. Hollingsworth; F. Stuart Chapin

2011-01-01

Question: How do pre-fire conditions (community composition and environmental characteristics) and climate-driven disturbance characteristics (fire severity) affect post-fire community composition in black spruce stands? Location: Northern boreal forest, interior Alaska. Methods: We compared plant community composition and environmental stand characteristics in 14...

Composition of breeding bird communities in Gulf Coast Chenier Plain marshes: Effects of winter burning

USGS Publications Warehouse

Gabrey, S.W.; Afton, A.D.

2004-01-01

Marsh managers along the Gulf Coast Chenier Plain frequently use winter burns to alter marsh vegetation and improve habitat quality for wintering waterfowl. However, effects of these burns on marsh avifauna are not well documented. We recorded abundances of breeding bird species and vegetation structure in burned and unburned control marshes during one breeding season before (1996) and two breeding seasons after (1997, 1998) experimental winter burns. We used non-metric multidimensional scaling analysis to assess the extent and direction of changes in bird community compositions of burned and unburned control marshes and to investigate the influence of vegetation structure on bird community composition. Overall, we found that Seaside Sparrows (Emberizidae: Ammodramus maritimus [Wilson]) and Red-winged Blackbirds and Boat-tailed Grackles (Icteridae: Agelaius phoeniceus [L.] and Quiscalus major Vieillot, respectively) comprised > 85% of observed birds. In burned marshes during the first breeding season following experimental burns (1997), icterid abundance increased while Seaside Sparrow abundance decreased relative to pre-burn (1996) conditions. This pattern was reversed during the second breeding season post-burn. No obvious patterns of change in avian abundance were detected in unburned control marshes over the 3-year period. Qualitative changes in breeding bird community composition were related to effects of winter burning on percent cover of dead vegetation and Spartina patens (Aiton) Muhl.

Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

NASA Astrophysics Data System (ADS)

Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

2015-04-01

In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

Prevalence of Antibiotic Resistance Genes and Bacterial Community Composition in a River Influenced by a Wastewater Treatment Plant

PubMed Central

Marti, Elisabet; Jofre, Juan; Balcazar, Jose Luis

2013-01-01

Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs), their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP) effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla TEM, bla CTX-M, bla SHV, erm(B), sul(I), sul(II), tet(O) and tet(W) were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river. PMID:24205347

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared

Responses of plant community composition and biomass production to warming and nitrogen deposition in a temperate meadow ecosystem.

PubMed

Zhang, Tao; Guo, Rui; Gao, Song; Guo, Jixun; Sun, Wei

2015-01-01

Climate change has profound influences on plant community composition and ecosystem functions. However, its effects on plant community composition and biomass production are not well understood. A four-year field experiment was conducted to examine the effects of warming, nitrogen (N) addition, and their interactions on plant community composition and biomass production in a temperate meadow ecosystem in northeast China. Experimental warming had no significant effect on plant species richness, evenness, and diversity, while N addition highly reduced the species richness and diversity. Warming tended to reduce the importance value of graminoid species but increased the value of forbs, while N addition had the opposite effect. Warming tended to increase the belowground biomass, but had an opposite tendency to decrease the aboveground biomass. The influences of warming on aboveground production were dependent upon precipitation. Experimental warming had little effect on aboveground biomass in the years with higher precipitation, but significantly suppressed aboveground biomass in dry years. Our results suggest that warming had indirect effects on plant production via its effect on the water availability. Nitrogen addition significantly increased above- and below-ground production, suggesting that N is one of the most important limiting factors determining plant productivity in the studied meadow steppe. Significant interactive effects of warming plus N addition on belowground biomass were also detected. Our observations revealed that environmental changes (warming and N deposition) play significant roles in regulating plant community composition and biomass production in temperate meadow steppe ecosystem in northeast China.

Responses of Plant Community Composition and Biomass Production to Warming and Nitrogen Deposition in a Temperate Meadow Ecosystem

PubMed Central

Gao, Song; Guo, Jixun; Sun, Wei

2015-01-01

Climate change has profound influences on plant community composition and ecosystem functions. However, its effects on plant community composition and biomass production are not well understood. A four-year field experiment was conducted to examine the effects of warming, nitrogen (N) addition, and their interactions on plant community composition and biomass production in a temperate meadow ecosystem in northeast China. Experimental warming had no significant effect on plant species richness, evenness, and diversity, while N addition highly reduced the species richness and diversity. Warming tended to reduce the importance value of graminoid species but increased the value of forbs, while N addition had the opposite effect. Warming tended to increase the belowground biomass, but had an opposite tendency to decrease the aboveground biomass. The influences of warming on aboveground production were dependent upon precipitation. Experimental warming had little effect on aboveground biomass in the years with higher precipitation, but significantly suppressed aboveground biomass in dry years. Our results suggest that warming had indirect effects on plant production via its effect on the water availability. Nitrogen addition significantly increased above- and below-ground production, suggesting that N is one of the most important limiting factors determining plant productivity in the studied meadow steppe. Significant interactive effects of warming plus N addition on belowground biomass were also detected. Our observations revealed that environmental changes (warming and N deposition) play significant roles in regulating plant community composition and biomass production in temperate meadow steppe ecosystem in northeast China. PMID:25874975

Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition.

PubMed

Striebel, Maren; Schabhüttl, Stefanie; Hodapp, Dorothee; Hingsamer, Peter; Hillebrand, Helmut

2016-11-01

Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering?

PubMed

Moreno-Pino, Mario; De la Iglesia, Rodrigo; Valdivia, Nelson; Henríquez-Castilo, Carlos; Galán, Alexander; Díez, Beatriz; Trefault, Nicole

2016-07-01

Spatial environmental heterogeneity influences diversity of organisms at different scales. Environmental filtering suggests that local environmental conditions provide habitat-specific scenarios for niche requirements, ultimately determining the composition of local communities. In this work, we analyze the spatial variation of microbial communities across environmental gradients of sea surface temperature, salinity and photosynthetically active radiation and spatial distance in Fildes Bay, King George Island, Antarctica. We hypothesize that environmental filters are the main control of the spatial variation of these communities. Thus, strong relationships between community composition and environmental variation and weak relationships between community composition and spatial distance are expected. Combining physical characterization of the water column, cell counts by flow cytometry, small ribosomal subunit genes fingerprinting and next generation sequencing, we contrast the abundance and composition of photosynthetic eukaryotes and heterotrophic bacterial local communities at a submesoscale. Our results indicate that the strength of the environmental controls differed markedly between eukaryotes and bacterial communities. Whereas eukaryotic photosynthetic assemblages responded weakly to environmental variability, bacteria respond promptly to fine-scale environmental changes in this polar marine system. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Drivers of cyanobacterial diversity and community composition in mangrove soils in south-east Brazil.

PubMed

Rigonato, Janaina; Kent, Angela D; Alvarenga, Danillo O; Andreote, Fernando D; Beirigo, Raphael M; Vidal-Torrado, Pablo; Fiore, Marli F

2013-04-01

Cyanobacteria act as primary producers of carbon and nitrogen in nutrient-poor ecosystems such as mangroves. This important group of microorganisms plays a critical role in sustaining the productivity of mangrove ecosystems, but the structure and function of cyanobacteria assemblages can be perturbed by anthropogenic influences. The aim of this work was to assess the community structure and ecological drivers that influence the cyanobacterial community harboured in two Brazilian mangrove soils, and examine the long-term effects of oil contamination on these keystone species. Community fingerprinting results showed that, although cyanobacterial communities are distinct between the two mangroves, the structure and diversity of the assemblages exhibit similar responses to environmental gradients. In each ecosystem, cyanobacteria occupying near-shore areas were similar in composition, indicating importance of marine influences for structuring the community. Analysis of 16S rRNA sequences revealed the presence of diverse cyanobacterial communities in mangrove sediments, with clear differences among mangrove habitats along a transect from shore to forest. While near-shore sites in both mangroves were mainly occupied by Prochlorococcus and Synechococcus genera, sequences retrieved from other mangrove niches were mainly affiliated with uncultured cyanobacterial 16S rRNA. The most intriguing finding was the large number of potentially novel cyanobacteria 16S rRNA sequences obtained from a previously oil-contaminated site. The abundance of cyanobacterial 16S rRNA sequences observed in sites with a history of oil contamination was significantly lower than in the unimpacted areas. This study emphasized the role of environmental drivers in determining the structure of cyanobacterial communities in mangrove soils, and suggests that anthropogenic impacts may also act as ecological filters that select cyanobacterial taxa. These results are an important contribution to our

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China

PubMed Central

Zhang, Haihan; Wang, Yue; Chen, Shengnan; Zhao, Zhenfang; Feng, Ji; Zhang, Zhonghui; Lu, Kuanyu; Jia, Jingyu

2018-01-01

Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi’an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (CODMn) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively (p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., CODMn and total nitrogen, TN). Several microbes (Legionella sp. and Streptococcus sp

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi'an, China.

PubMed

Zhang, Haihan; Wang, Yue; Chen, Shengnan; Zhao, Zhenfang; Feng, Ji; Zhang, Zhonghui; Lu, Kuanyu; Jia, Jingyu

2018-03-07

Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi'an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (COD Mn ) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively ( p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., COD Mn and total nitrogen, TN). Several microbes ( Legionella sp. and Streptococcus sp

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

PubMed

Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

2015-03-01

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Effects of landscape anthropization on mosquito community composition and abundance

NASA Astrophysics Data System (ADS)

Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

2016-07-01

Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

Effects of landscape anthropization on mosquito community composition and abundance

PubMed Central

Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

2016-01-01

Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

Ecological observations on an East African bat community

USGS Publications Warehouse

O'Shea, Thomas J.; Vaughan, Terry A.

1980-01-01

The structure and ecology of bat faunas is a subject of interest to mammalogists (Findley, 1976; Wilson, 1973). Syntopic African bat communities, however, have received little study in comparison with neotropical faunas (cf. Fleming et al., 1972; LaVal and Fitch, 1977; McNab, 1971). Verschuren (1957) presented natural history information and species accounts for a localized central African bat fauna. Foraging related characteristics of a Rhodesian community have also been analyzed (Fenton, 1975; Fenton et al., 1977), but not on a seasonal basis. Other reports on African bat faunas are restricted to regional summaries (cf. Koopman, 1975 or Rosevear, 1965) and do not consider ecological aspects of a single localized community. The purpose of our study was to follow species composition, reproduction, and foraging related characteristics of an East African bat fauna over a full annual cycle.

Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)

PubMed Central

Delport, Tiffany C.; Power, Michelle L.; Harcourt, Robert G.; Webster, Koa N.

2016-01-01

ABSTRACT Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of

Shifts in microbial community composition following surface application of dredged river sediments.

PubMed

Baniulyte, Dovile; Favila, Emmanuel; Kelly, John J

2009-01-01

Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In order to determine the effects of this drastic habitat change on sediment microbial communities, we examined sediment physical, chemical, and microbial characteristics at the time of sediment application to the soil surface as well as 1 and 2 years after application. Microbial community biomass was determined by measurement of lipid phosphate. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, and clone library sequencing of 16S rRNA genes. Results indicated that the moisture content, organic carbon, and total nitrogen content of the sediment all decreased over time. Total microbial biomass did not change over the course of the study, but there were significant changes in the composition of the microbial communities. PLFA analysis revealed relative increases in fungi, actinomycetes, and Gram positive bacteria. T-RFLP analysis indicated a significant shift in bacterial community composition within 1 year of application, and clone library analysis revealed relative increases in Proteobacteria, Gemmatimonadetes, and Bacteriodetes and relative decreases in Acidobacteria, Spirochaetes, and Planctomycetes. These results provide insight into microbial community shifts following land application of dredged sediment.

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest

PubMed Central

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting. PMID:26317523

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest.

PubMed

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting.

Do temperate tree species diversity and identity influence soil microbial community function and composition?

PubMed

Khlifa, Rim; Paquette, Alain; Messier, Christian; Reich, Peter B; Munson, Alison D

2017-10-01

Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM), and tree identity. The site was a 4-year-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroResp ™ system, respectively. The relationship between tree species richness and glucose-induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO 2 ) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR]), with higher biomass (glucose-induced respiration [GIR]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity-leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Applications of Satellite Observations of Tropospheric Composition

NASA Astrophysics Data System (ADS)

Monks, Paul S.; Beirle, Steffen

A striking feature of the field of tropospheric composition is the sheer number of chemical species that have been detected and measured with satellite instruments. The measurements have found application both in atmospheric chemistry itself, providing evidence, for example, of unexpected cryochemistry in the Arctic regions, and also in environmental monitoring with, for example, the observed growth in NO2 emissions over eastern Asia. Chapter 8 gives an overview of the utility of satellite observations for measuring tropospheric composition, dealing with each of the many compounds seen in detail. A comprehensive compound by compound table of the many studies performed is a most useful feature.

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function

PubMed Central

Traving, Sachia J.; Rowe, Owen; Jakobsen, Nina M.; Sørensen, Helle; Dinasquet, Julie; Stedmon, Colin A.; Andersson, Agneta; Riemann, Lasse

2017-01-01

Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of elevated DOM on a coastal pelagic food web from the coastal northern Baltic Sea, in a 32-day mesocosm experiment. In particular, the study addresses the response of bacterioplankton to differences in character and composition of supplied DOM. The supplied DOM differed in stoichiometry and quality and had pronounced effects on the recipient bacterioplankton, driving compositional changes in response to DOM type. The shifts in bacterioplankton community composition were especially driven by the proliferation of Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Alpha- and Betaproteobacteria populations. The DOM additions stimulated protease activity and a release of inorganic nutrients, suggesting that DOM was actively processed. However, no difference between DOM types was detected in these functions despite different community compositions. Extensive release of re-mineralized carbon, nitrogen and phosphorus was associated with the bacterial processing, corresponding to 25–85% of the supplied DOM. The DOM additions had a negative effect on phytoplankton with decreased Chl a and biomass, particularly during the first half of the experiment. However, the accumulating nutrients likely stimulated phytoplankton biomass which was observed to increase towards the end of the experiment. This suggests that the nutrient access partially outweighed the negative effect of increased light attenuation by accumulating DOM. Taken together, our experimental data suggest that parts of the future elevated riverine DOM supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and

The assembly of ecological communities inferred from taxonomic and functional composition

Treesearch

Eric R. Sokol; E.F. Benfield; Lisa K. Belden; H. Maurice. Valett

2011-01-01

Among-site variation in metacommunities (beta diversity) is typically correlated with the distance separating the sites (spatial lag). This distance decay in similarity pattern has been linked to both niche-based and dispersal-based community assembly hypotheses. Here we show that beta diversity patterns in community composition, when supplemented with functional-trait...

Compositional stability and diversity of vascular plant communities following logging disturbance in Appalachian forests.

PubMed

Belote, R Travis; Jones, Robert H; Wieboldt, Thomas F

2012-03-01

Human-caused changes in disturbance regimes and introductions of nonnative species have the potential to result in widespread, directional changes in forest community structure. The degree that plant community composition persists or changes following disturbances depends on the balance between local extirpation and colonization by new species, including nonnatives. In this study, we examined species losses and gains, and entry of native vs. exotic species to determine how oak forests in the Appalachian Mountains might shift in species composition following a gradient of pulse disturbances (timber harvesting). We asked (1) how compositional stability of the plant community (resistance and resilience) was influenced by disturbance intensity, (2) whether community responses were driven by extirpation or colonization of species, and (3) how disturbance intensity influenced total and functional group diversity, including the nonnative proportion of the flora through time. We collected data at three spatial scales and three times, including just before, one year post-disturbance, and 10 years post-disturbance. Resistance was estimated using community distance measures between pre- and one year post-disturbance, and resilience using community distance between pre- and 10-year post-disturbance conditions. The number of colonizing and extirpated species between sampling times was analyzed for all species combined and for six functional groups. Resistance and resilience decreased with increasing timber-harvesting disturbance; compositional stability was lower in the most disturbed plots, which was driven by colonization, but not extirpation, of species. Colonization of species also led to increases in diversity after disturbance that was typically maintained after 10 years following disturbance. Most of the community-level responses were driven by post-disturbance colonization of native forbs and graminoids. The nonnative proportion of plant species tended to increase

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents.

PubMed

Ochoa-Hueso, Raúl; Collins, Scott L; Delgado-Baquerizo, Manuel; Hamonts, Kelly; Pockman, William T; Sinsabaugh, Robert L; Smith, Melinda D; Knapp, Alan K; Power, Sally A

2018-03-05

The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

PubMed

Lindh, Markus V; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

2015-01-01

Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

PubMed Central

Lindh, Markus V.; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

2015-01-01

Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates. PMID

Phytoplankton community composition in nearshore coastal waters of Louisiana

EPA Science Inventory

Phytoplankton community compositions within near-shore coastal and estuarine waters of Louisiana were characterized by relative abundance, biovolume, and taxonomic identification to genus and species when possible. The range of total nitrogen was 0.5 to 1.3 mg L-1 and total phos...

Associations between retail food store exterior advertisements and community demographic and socioeconomic composition.

PubMed

Isgor, Zeynep; Powell, Lisa; Rimkus, Leah; Chaloupka, Frank

2016-05-01

This paper examines the association between the prevalence of various types of outdoor food and beverage advertising found on the building exteriors and properties of retail food outlets and community racial/ethnic and socioeconomic composition in a nationwide sample of food outlets in the U.S. Our major finding from multivariable analysis is that food stores in low-income communities have higher prevalence of all food and beverage ads, including those for unhealthy products such as regular soda, controlling for community racial/ethnic composition and other covariates. This adds to growing research pointing to socioeconomic disparities in food and beverage marketing exposure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of long-term drainage on microbial community composition vary between peatland types

NASA Astrophysics Data System (ADS)

Urbanová, Zuzana; Barta, Jiri

2016-04-01

Peatlands represent an important reservoir of carbon, but their functioning can be threatened by water level drawdown caused by climate or land use change. Knowledge of how microbial communities respond to long-term drainage in different peatland types could help improve predictions of the effect of climate change on these ecosystems. We investigated the effect of long-term drainage on microbial community composition in bog, fen and spruce swamp forests (SSF) in the Sumava Mountains (Czech Republic), using high-throughput barcoded sequencing, in relation to peat biochemical properties. Longterm drainage had substantial effects, which depended strongly on peatland type, on peat biochemical properties and microbial community composition. The effect of drainage was most apparent on fen, followed by SSF, and lowest on bog. Long-term drainage led to lower pH, reduced peat decomposability and increased bulk density, which was reflected by reduced microbial activity. Bacterial diversity decreased and Acidobacteria became the dominant phylum on drained sites, reflecting a convergence in bacterial community composition across peatlands after long-term drainage. The archaeal communities changed very strongly and became similar across drained peatlands. Overall, the characteristic differences between distinct peatland types under natural conditions were diminished by long-term drainage. Bog represented a relatively resilient system while fen seemed to be very sensitive to environmental changes.

Evaluation of CESM1 (WACCM) with Observations of Stratospheric Composition

NASA Astrophysics Data System (ADS)

Kinnison, Doug; Froidevaux, Lucien; Garcia, Rolando; Fuller, Ryan

2017-04-01

The Community Earth System Model version 1 (CESM1) Whole Atmosphere Community Climate Model (WACCM) is used in this study. CESM1 (WACCM) includes a detailed representation of tropospheric through lower thermospheric chemistry and physical processes. Simulations for this work were based on scenarios defined by the Chemistry Climate Model Initiative (CCMI). These scenarios included both free-running (FR) and specified-dynamics versions (SD) of CESM1 (WACCM). Comparisons were made with global monthly zonal mean stratospheric data records from satellite-based remote measurements created by the Global Ozone Chemistry and Related Trace gas Data Records for the Stratosphere (GOZCARDS) project. These data records were drawn from high quality measurements of stratospheric composition starting in 1979 for ozone and in the early 1990s for other species. We discuss stratospheric variability and trends through analyses of observed time series of ozone (O3), hydrogen chloride (HCl), nitrous oxide (N2O), nitric acid (HNO3), and water vapor (H2O), and we contrast the fits from the FR and SD model versions. Conclusions from this work have aided in the development of a new version of CESM (WACCM) that will be used in the next Intergovernmental Panel on Climate Change (IPCC) Coupled Model Intercomparison Project Phase 6 (CMIP6) assessment.

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

USGS Publications Warehouse

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

PubMed

Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir; Qian, Pei-Yuan

2014-11-04

Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper treatment on

The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

PubMed Central

Hawlena, Hadas; Rynkiewicz, Evelyn; Toh, Evelyn; Alfred, Andrew; Durden, Lance A; Hastriter, Michael W; Nelson, David E; Rong, Ruichen; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith

2013-01-01

Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment. PMID:22739493

Observing and modelling phytoplankton community structure in the North Sea

NASA Astrophysics Data System (ADS)

Ford, David A.; van der Molen, Johan; Hyder, Kieran; Bacon, John; Barciela, Rosa; Creach, Veronique; McEwan, Robert; Ruardij, Piet; Forster, Rodney

2017-03-01

Phytoplankton form the base of the marine food chain, and knowledge of phytoplankton community structure is fundamental when assessing marine biodiversity. Policy makers and other users require information on marine biodiversity and other aspects of the marine environment for the North Sea, a highly productive European shelf sea. This information must come from a combination of observations and models, but currently the coastal ocean is greatly under-sampled for phytoplankton data, and outputs of phytoplankton community structure from models are therefore not yet frequently validated. This study presents a novel set of in situ observations of phytoplankton community structure for the North Sea using accessory pigment analysis. The observations allow a good understanding of the patterns of surface phytoplankton biomass and community structure in the North Sea for the observed months of August 2010 and 2011. Two physical-biogeochemical ocean models, the biogeochemical components of which are different variants of the widely used European Regional Seas Ecosystem Model (ERSEM), were then validated against these and other observations. Both models were a good match for sea surface temperature observations, and a reasonable match for remotely sensed ocean colour observations. However, the two models displayed very different phytoplankton community structures, with one better matching the in situ observations than the other. Nonetheless, both models shared some similarities with the observations in terms of spatial features and inter-annual variability. An initial comparison of the formulations and parameterizations of the two models suggests that diversity between the parameter settings of model phytoplankton functional types, along with formulations which promote a greater sensitivity to changes in light and nutrients, is key to capturing the observed phytoplankton community structure. These findings will help inform future model development, which should be coupled

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

PubMed Central

Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C. B.; Jacobsen, Carsten S.

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha-1 to alkaline at 167 t ha-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha-1 followed by significant decrease at 167 t ha-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition.

PubMed

Bang-Andreasen, Toke; Nielsen, Jeppe T; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C B; Jacobsen, Carsten S

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha -1 . We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha -1 to alkaline at 167 t ha -1 . Bacterial numbers significantly increased up to a wood ash dose of 22 t ha -1 followed by significant decrease at 167 t ha -1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha -1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha -1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha -1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna.

PubMed

Busse, Annika; Antiqueira, Pablo A P; Neutzling, Alexandre S; Wolf, Anna M; Romero, Gustavo Q; Petermann, Jana S

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems.

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna

PubMed Central

Antiqueira, Pablo A. P.; Neutzling, Alexandre S.; Wolf, Anna M.; Romero, Gustavo Q.; Petermann, Jana S.

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems. PMID:29401522

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions

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

He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhousemore » gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions

DOE PAGES

He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.; ...

2015-05-19

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhousemore » gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

PubMed

He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

2015-05-19

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef, Australia

PubMed Central

Graham, Nicholas A. J.; Chong-Seng, Karen M.; Huchery, Cindy; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.

2014-01-01

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into

Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil

PubMed Central

Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

2016-01-01

The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC–MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on

Soil Microbe Active Community Composition and Capability of Responding to Litter Addition after 12 Years of No Inputs

PubMed Central

Brewer, Elizabeth; Yarwood, Rockie; Lajtha, Kate; Myrold, David

2013-01-01

One explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ∼110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance. PMID:23263952

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

PubMed Central

Eldridge, David J; Woodhouse, Jason N; Curlevski, Nathalie J A; Hayward, Matthew; Brown, Mark V; Neilan, Brett A

2015-01-01

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance. PMID:25932616

Effects of biochar blends on microbial community composition in two coastal plain soils

EPA Science Inventory

The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

PubMed

Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

2014-12-01

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Temporal changes in community composition of heterotrophic bacteria during in situ iron enrichment in the western subarctic Pacific (SEEDS-II)

NASA Astrophysics Data System (ADS)

Kataoka, Takafumi; Suzuki, Koji; Hayakawa, Maki; Kudo, Isao; Higashi, Seigo; Tsuda, Atsushi

2009-12-01

Little is known about the effects of iron enrichment in high-nitrate low-chlorophyll (HNLC) waters on the community composition of heterotrophic bacteria, which are crucial to nutrient recycling and microbial food webs. Using denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments, we investigated the heterotrophic eubacterial community composition in surface waters during an in situ iron-enrichment experiment (SEEDS-II) in the western subarctic Pacific in the summer of 2004. DGGE fingerprints representing the community composition of eubacteria differed inside and outside the iron-enriched patch. Sequencing of DGGE bands revealed that at least five phylotypes of α-proteobacteria including Roseobacter, Cytophaga-Flavobacteria- Bacteroides (CFB), γ-proteobacteria, and Actinobacteria occurred in almost all samples from the iron-enriched patch. Diatoms did not bloom during SEEDS-II, but the eubacterial composition in the iron-enriched patch was similar to that in diatom blooms observed previously. Although dissolved organic carbon (DOC) accumulation was not detected in surface waters during SEEDS-II, growth of the Roseobacter clade might have been particularly stimulated after iron additions. Two identified phylotypes of CFB were closely related to the genus Saprospira, whose algicidal activity might degrade the phytoplankton assemblages increased by iron enrichment. These results suggest that the responses of heterotrophic bacteria to iron enrichment could differ among phylotypes during SEEDS-II.

Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo.

PubMed

Geml, József; Morgado, Luis N; Semenova-Nelsen, Tatiana A; Schilthuizen, Menno

2017-07-01

The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)▿

PubMed Central

Evans, Paul N.; Hinds, Lyn A.; Sly, Lindsay I.; McSweeney, Christopher S.; Morrison, Mark; Wright, André-Denis G.

2009-01-01

The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight. PMID:19218421

Seasonal composition and activity of sulfate-reducing prokaryotic communities in seagrass bed sediments

EPA Science Inventory

Sulfate-reducing prokaryotes (SRP) play a key role in the carbon and nutrient cycles of coastal marine, vegetated ecosystems, but the interactions of SRP communities with aquatic plants remain little studied. The abundance, activity, and community composition of SRP was studied i...

FORAGE FISH AND ZOOPLANKTON COMMUNITY COMPOSITION IN WESTERN LAKE SUPERIOR

EPA Science Inventory

We assessed the abundance, size, and species composition of the fish and zooplankton communities of western Lake Superior during 1996 and 1997. Data were analyzed for 3 ecoregions (Duluth-Superior (1), Apostle Islands (2), Minnesota coast (3) differing in lake bathymetry, phsiodo...

Satellite Observations for Detecting and Tracking Changes in Atmospheric Composition

NASA Technical Reports Server (NTRS)

Neil, Doreen O.; Kondragunbta, Shobha; Osterman, Gregory; Pickering, Kenneth; Pinder, Robert W.; Prados, Ana I.; Szykman, James

2009-01-01

The satellite observations provide constraints on detailed atmospheric modeling, including emissions inventories, indications of transport, harmonized data over vast areas suitable for trends analysis, and a link between spatial scales ranging from local to global, and temporal scales from diurnal to interannual. 1 The National Oceanic and Atmospheric Administration's (NOAA) long-term commitments help provide these observations in cooperation with international meteorological organizations. NASA s long-term commitments will advance scientifically important observations as part of its Earth Science Program, and will assist the transition of the science measurements to applied analyses through the Applied Science Program. Both NASA and NOAA have begun to provide near realtime data and tools to visualize and analyze satellite data,2 while maintaining data quality, validation, and standards. Consequently, decision-makers can expect satellite data services to support air quality decision making now and in the future. The international scientific community's Integrated Global Atmosphere Chemistry Observation System Report3 outlined a plan for ground-based, airborne and satellite measurements and models to integrate the observations into a four-dimensional representation of the atmosphere (space and time) to support assessment and policy information needs. This plan is being carried out under the Global Earth Observation System of Systems (GEOSS). Demonstrations of such an integrated capability4 provide new understanding of the changing atmosphere and link policy decisions to benefits for society. In this article, we highlight the use of satellite data to constrain biomass burning emissions, to assess oxides of nitrogen (NO(x)) emission reductions, and to contribute to state implementation plans, as examples of the use of satellite observations for detecting and tracking changes in atmospheric composition.

Telescope Array UHECR composition measurement via stereoscopic fluorescence observation

NASA Astrophysics Data System (ADS)

Stroman, Thomas; Bergman, Douglas; Telescope Array Collaboration

2016-03-01

When entering Earth's atmosphere at ultra-high energies, cosmic rays (UHECRs) produce extensive air showers whose longitudinal development is influenced by the incident primary particle's mass. Each longitudinal shower profile reaches its maximum particle count at an atmospheric slant depth Xmax, and the distributions of observed Xmax values can be compared to those predicted by detailed simulations of the air-shower physics and the detector; accurately simulated compositions that most closely resemble that found in nature will produce the best agreement between predicted and observed Xmax distributions. This is the basis of composition measurement at the Telescope Array experiment, the largest and most sensitive UHECR detector in the northern hemisphere. At the perimeter of a large surface-detector array are three fluorescence telescope stations, whose overlapping apertures enable high-precision reconstruction of Xmax from stereoscopic observation of air-shower longitudinal profiles. We present the distribution of Xmax observed during eight years of operation, and from comparisons with several simulated combinations of composition and high-energy hadronic physics, we show that a low primary mass is favored at E >10 18 . 2 eV.

Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

NASA Astrophysics Data System (ADS)

Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

2013-12-01

The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

PubMed

Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

2018-07-01

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

Impact of biological soil crusts and desert plants on soil microfaunal community composition

USGS Publications Warehouse

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

2010-01-01

Carbon and nitrogen are supplied by a variety of sources in the desert food web; both vascular and non-vascular plants and cyanobacteria supply carbon, and cyanobacteria and plant-associated rhizosphere bacteria are sources of biological nitrogen fixation. The objective of this study was to compare the relative influence of vascular plants and biological soil crusts on desert soil nematode and protozoan abundance and community composition. In the first experiment, biological soil crusts were removed by physical trampling. Treatments with crust removed had fewer nematodes and a greater relative ratio of bacterivores to microphytophages than treatments with intact crust. However, protozoa composition was similar with or without the presence of crusts. In a second experiment, nematode community composition was characterized along a spatial gradient away from stems of grasses or shrubs. Although nematodes generally occurred in increasing abundance nearer to plant stems, some genera (such as the enrichment-type Panagrolaimus) increased disproportionately more than others (such as the stress-tolerant Acromoldavicus). We propose that the impact of biological soil crusts and desert plants on soil microfauna, as reflected in the community composition of microbivorous nematodes, is a combination of carbon input, microclimate amelioration, and altered soil hydrology. ?? Springer Science + Business Media B.V. 2009.

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

USGS Publications Warehouse

Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

2013-01-01

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Plant community composition and vegetation height, Barrow, Alaska, Ver. 1

DOE Data Explorer

Siegrist, Julia; Norby, Richard; Sloan, Victoria; Iversen, Colleen; Brooks, Jonathan; Liebig, Jennifer; Wood, Sarah

2014-04-25

This dataset contains i) the results of field surveys of plant community composition and vegetation height made between 17th and 29th July 2012 in 48, 1 x 1 m plots located in areas A-D of Intensive Site 1 at the Next-Generation Ecosystem Experiments (NGEE) Arctic site near Barrow, Alaska and ii) results of a mapping exercise undertaken in August 2013 using two perpendicular transects across each polygon containing vegetation plots to determine the boundaries of vegetation communities described in 2012.

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

PubMed

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Predator community composition is linked to soil carbon retention across a human land use gradient.

PubMed

Schmitz, Oswald J; Buchkowski, Robert W; Smith, Jeffrey R; Telthorst, Mark; Rosenblatt, Adam E

2017-05-01

Soil carbon (C) storage is a major component of the carbon cycle. Consensus holds that soil C uptake and storage is regulated by plant-microbe-soil interactions. However, the contribution of animals in aboveground food webs to this process has been overlooked. Using insights from prior long-term experimentation in an old-field ecosystem and mathematical modeling, we predicted that the amount of soil C retention within a field should increase with the proportion of active hunting predators comprising the aboveground community of active hunting and sit-and-wait predators. This comes about because predators with different hunting modes have different cascading effects on plants. Our test of the prediction revealed that the composition of the arthropod predator community and associated cascading effects on the plant community explained 41% of variation in soil C retention among 15 old fields across a human land use gradient. We also evaluated the potential for several other candidate factors to explain variation in soil C retention among fields, independent of among-field variation in the predator community. These included live plant biomass, insect herbivore community composition, soil arthropod decomposer community composition, degree of land use development around the fields, field age, and soil texture. None of these candidate variables significantly explained soil C retention among the fields. The study offers a generalizable understanding of the pathways through which arthropod predator community composition can contribute to old-field ecosystem carbon storage. This insight helps support ongoing efforts to understand and manage the effects of anthropogenic land use change on soil C storage. © 2017 by the Ecological Society of America.

Changes in fungal community composition in response to experimental soil warming at the alpine treeline

NASA Astrophysics Data System (ADS)

Solly, Emily; Lindahl, Bjorn; Dawes, Melissa; Peter, Martina; Souza, Romulo; Rixen, Christian; Hagedorn, Frank

2017-04-01

Increased CO2 emissions and global warming may alter the composition of fungal communities through the reduction of low temperature limitation in the plant-soil system, faster nitrogen cycling and changes in the carbon allocation of host plants to the rhizosphere. Shifts in fungal community composition due to global changes are likely to affect the routes of carbon and nitrogen flows in the plant-soil system and alter the rates at which organic matter is decomposed. The main aim of our study was to estimate the effects of multiple years of free air CO2 enrichment (ambient concentration +200 ppm) and soil warming (+ 4°C) on the fungal community structure and composition. At an alpine treeline in Switzerland featuring two key high-elevation tree species, Larix decidua and Pinus uncinata, fungal communities within different organic horizons were analysed by high-throughput 454-pyrosequencing of ITS2 amplicons. In addition, we assessed the ectomycorrhizal community composition on root tips and monitored changes in sporocarp productivity of fungal species during the course of the experiment. Three years of experimental warming at the alpine treeline altered the composition of the fungal community in the organic horizons, whereas nine years of CO2 enrichment had only weak effects. Tree species influenced the composition of the fungal community and the magnitude of the responses of fungal functional groups to soil warming differed between plots with Larix and those with Pinus. The abundance of ectomycorrhizal fungi was positively correlated with nitrogen availability, and ectomycorrhizal taxa specialized for conditions of high nitrogen availability proliferated with warming, corresponding to considerable increases in extractable inorganic nitrogen in warmed soils. Changes in productivity of specific fungal fruiting bodies in response to soil warming (e.g. more Lactarius rufus sporocarps and less Hygrophorus speciousus sporocarps) were consistent with the 454-sequencing

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community.

PubMed

Sjöstedt, Johanna; Langenheder, Silke; Kritzberg, Emma; Karlsson, Christofer M G; Lindström, Eva S

2018-05-07

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences

Temporal dynamics of bird community composition: an analysis of baseline conditions from long-term data.

PubMed

Kampichler, Christian; Angeler, David G; Holmes, Richard T; Leito, Aivar; Svensson, Sören; van der Jeugd, Henk P; Wesołowski, Tomasz

2014-08-01

Numerous anthropogenic activities threaten the biodiversity found on earth. Because all ecological communities constantly experience temporal turnover due to natural processes, it is important to distinguish between change due to anthropogenic impact and the underlying natural rate of change. In this study, we used data sets on breeding bird communities that covered at least 20 consecutive years, from a variety of terrestrial ecosystems, to address two main questions. (1) How fast does the composition of bird communities change over time, and can we identify a baseline of natural change that distinguishes primeval systems from systems experiencing varying degrees of human impact? (2) How do patterns of temporal variation in composition vary among bird communities in ecosystems with different anthropogenic impacts? Time lag analysis (TLA) showed a pattern of increasing rate of temporal compositional change from large-scale primeval systems to disturbed and protected systems to distinctly successional systems. TLA slopes of <0.04 were typical for breeding bird communities with natural turnover, while communities subjected to anthropogenic impact were characterised by TLA slopes of >0.04. Most of the temporal variability of breeding bird communities was explained by slow changes occurring over decades, regardless of the intensity of human impact. In most of the time series, medium- and short-wave periodicity was not detected, with the exception of breeding bird communities subjected to periodic pulses (e.g. caterpillar outbreaks causing food resource peaks).

Using MLT Composition Observations to Evaluate Transport in a Comprehensive High Top Model

NASA Astrophysics Data System (ADS)

Smith, A. K.

2016-12-01

Gravity waves play an outsized role in the MLT: driving the mean meridional circulation, exerting a large degree of control over the mean winds and seasonal variations in temperature, and leading to diffusive vertical transport of heat and trace species. These waves are represented using a parameterization in the NCAR Whole Atmosphere Community Climate Model (WACCM), as in many other GCMs. To evaluate their impact, we need to consider not just the mean temperature and wind but the distributions of trace species that are affected by advection due to resolved winds and waves and diffusion associated with gravity wave dissipation. The responses of chemical species to changes in the gravity wave forcing are complex and sometimes unexpected. Transport and diffusion simultaneously affect all species and the heat and momentum budgets; subsequent interactions, and the strong dependence of reaction rates on temperature, affect the net impact of transport on the composition. In evaluating the model, we evaluate the simulations using a range of available observations of composition, including O, O3, CO, CO2, NO, NO2, OH, and H2O.

Community Engagement in Observational Human Exposure Studies

EPA Science Inventory

Although observational human exposure studies do not deliberately expose participants to chemicals or environmental conditions, merely involving people as research participants and conducting research inside homes raises ethical issues. Community engagement offers a promising st...

Species composition, community and population dynamics of two gallery forests from the Brazilian Cerrado domain

PubMed Central

Almado, Roosevelt P; Miazaki, Angela S; Diniz, Écio S; Moreira, Luis C B; Meira-Neto, João A.A.

2016-01-01

Abstract Background To understand the impacts of global changes on future community compositions, knowledge of community dynamics is of crucial importance. To improve our knowledge of community composition, biomass stock and maintenance of gallery forests in the Brazilian Cerrado, we provide two datasets from the 0.5 ha Corrego Fazendinha Gallery Forest Dynamics Plot and the Corrego Fundo Gallery Forest Dynamics Plot situated in the Bom Despacho region, Minas Gerais, Southeastern Brazil. New information We report diameter at breast height, basal area and height measurements of 3417 trees and treelets identified during three censuses in both areas. PMID:27660529

Using face validity to recognize empirical community observations.

PubMed

Gaber, John; Gaber, Sharon L

2010-05-01

There is a growing interest among international planning scholars to explore community participation in the plan making process from a qualitative research approach. In this paper the research assessment tool "face validity" is discussed as one way to help planners decipher when the community is sharing empirically grounded observations that can advance the applicability of the plan making process. Face validity provides a common sense assessment of research conclusions. It allows the assessor to look at an entire research project and ask: "on the face of things, does this research make sense?" With planners listening to citizen comments with an ear for face validity observations, holds open the opportunity for government to empirically learn from the community to see if they "got it right." And if not, to chart out a course on how they can get it right. Copyright 2009 Elsevier Ltd. All rights reserved.

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

PubMed Central

Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir

2014-01-01

ABSTRACT Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25370493

Are cattle surrogate wildlife? Savanna plant community composition explained by total herbivory more than herbivore type.

PubMed

Veblen, Kari E; Porensky, Lauren M; Riginos, Corinna; Young, Truman P

2016-09-01

The widespread replacement of wild ungulate herbivores by domestic livestock in African savannas is composed of two interrelated phenomena: (1) loss or reduction in numbers of individual wildlife species or guilds and (2) addition of livestock to the system. Each can have important implications for plant community dynamics. Yet very few studies have experimentally addressed the individual, combined, and potentially interactive effects of wild vs. domestic herbivore species on herbaceous plant communities within a single system. Additionally, there is little information about whether, and in which contexts, livestock might functionally replace native herbivore wildlife or, alternatively, have fundamentally different effects on plant species composition. The Kenya Long-term Exclosure Experiment, which has been running since 1995, is composed of six treatment combinations of mega-herbivores, meso-herbivore ungulate wildlife, and cattle. We sampled herbaceous vegetation 25 times between 1999 and 2013. We used partial redundancy analysis and linear mixed models to assess effects of herbivore treatments on overall plant community composition and key plant species. Plant communities in the six different herbivore treatments shifted directionally over time and diverged from each other substantially by 2013. Plant community composition was strongly related (R 2  = 0.92) to residual plant biomass, a measure of herbivore utilization. Addition of any single herbivore type (cattle, wildlife, or mega-herbivores) caused a shift in plant community composition that was proportional to its removal of plant biomass. These results suggest that overall herbivory pressure, rather than herbivore type or complex interactions among different herbivore types, was the main driver of changes in plant community composition. Individual plant species, however, did respond most strongly to either wild ungulates or cattle. Although these results suggest considerable functional similarity between

Diptera community composition and succession following habitat disturbance by wildfire

Treesearch

Michael A. Patten; Jutta C. Burger; Thomas R. Prentice; John T. Rotenberry; Richard A. Redak

2005-01-01

Both biogeographic (for example, latitude) and local (for example, soil) processes determine composition and succession of biotic communities. Postfire succession of vegetation has been studied intensively in chaparral and coastal sage scrub. Fewer studies have examined postfire succession of animals, even though fires can drastically alter their abundance and...

Land-use history alters contemporary insect herbivore community composition and decouples plant-herbivore relationships

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

Hahn, Philip G.; Orrock, John L.

1. Past land use can create altered soil conditions and plant communities that persist for decades, although the effects of these altered conditions on consumers are rarely investigated. 2. Using a large-scale field study at 36 sites in longleaf pine (Pinus palustris) woodlands, we examined whether historic agricultural land use leads to differences in the abundance and community composition of insect herbivores (grasshoppers, families Acrididae and Tettigoniidae). 3. We measured the cover of six plant functional groups and several environmental variables to determine whether historic agricultural land use affects the relationships between plant cover or environmental conditions and grasshopper assemblages.more » 4. Land-use history had taxa-specific effects and interacted with herbaceous plant cover to alter grasshopper abundances, leading to significant changes in community composition. Abundance of most grasshopper taxa increased with herbaceous cover in woodlands with no history of agriculture, but there was no relationship in post-agricultural woodlands. We also found that grasshopper abundance was negatively correlated with leaf litter cover. Soil hardness was greater in post-agricultural sites (i.e. more compacted) and was associated with grasshopper community composition. Both herbaceous cover and leaf litter cover are influenced by fire frequency, suggesting a potential indirect role of fire on grasshopper assemblages. 5. Our results demonstrate that historic land use may create persistent differences in the composition of grasshopper assemblages, while contemporary disturbances (e.g. prescribed fire) may be important for determining the abundance of grasshoppers, largely through the effect of fire on plants and leaf litter. Therefore, our results suggest that changes in the contemporary management regimes (e.g. increasing prescribed fire) may not be sufficient to shift the structure of grasshopper communities in post-agricultural sites towards

Land-use history alters contemporary insect herbivore community composition and decouples plant-herbivore relationships

DOE PAGES

Hahn, Philip G.; Orrock, John L.

2014-11-23

1. Past land use can create altered soil conditions and plant communities that persist for decades, although the effects of these altered conditions on consumers are rarely investigated. 2. Using a large-scale field study at 36 sites in longleaf pine (Pinus palustris) woodlands, we examined whether historic agricultural land use leads to differences in the abundance and community composition of insect herbivores (grasshoppers, families Acrididae and Tettigoniidae). 3. We measured the cover of six plant functional groups and several environmental variables to determine whether historic agricultural land use affects the relationships between plant cover or environmental conditions and grasshopper assemblages.more » 4. Land-use history had taxa-specific effects and interacted with herbaceous plant cover to alter grasshopper abundances, leading to significant changes in community composition. Abundance of most grasshopper taxa increased with herbaceous cover in woodlands with no history of agriculture, but there was no relationship in post-agricultural woodlands. We also found that grasshopper abundance was negatively correlated with leaf litter cover. Soil hardness was greater in post-agricultural sites (i.e. more compacted) and was associated with grasshopper community composition. Both herbaceous cover and leaf litter cover are influenced by fire frequency, suggesting a potential indirect role of fire on grasshopper assemblages. 5. Our results demonstrate that historic land use may create persistent differences in the composition of grasshopper assemblages, while contemporary disturbances (e.g. prescribed fire) may be important for determining the abundance of grasshoppers, largely through the effect of fire on plants and leaf litter. Therefore, our results suggest that changes in the contemporary management regimes (e.g. increasing prescribed fire) may not be sufficient to shift the structure of grasshopper communities in post-agricultural sites towards

Composition and diversity of weed communities in Al-Jouf province, northern Saudi Arabia

PubMed Central

Gomaa, Nasr H.

2012-01-01

The aim of this study was to identify the main weed communities in Al-Jouf province in northern Saudi Arabia. Moreover, the composition and diversity of these communities were studied in relation to soil variables and crop type. Some 54 stands representing olive orchards, date palm orchards, wheat crop and watermelon crop were studied, using ten quadrats (1 × 1 m) per stand. A total of 71 species belonging to 22 families and 61 genera were observed. The classification of vegetation using the Two Way Indicator Species Analysis (TWINSPAN) resulted in the recognition of four vegetation groups representing wheat crop, orchards in winter season, orchards in summer season and watermelon crop. These results suggested the importance of both crop and season for the formation of weed community. Detrended Correspondence Analysis (DCA) showed that these groups are clearly distinguished by the first two DCA axes. The species richness was higher in both olive and date palm orchards than in wheat and watermelon crops. This pattern of species richness could be related to farm management practices and habitat micro-heterogeneity. Soil electrical conductivity, organic carbon and soil texture showed significant correlations with species richness and the cover values of some dominant species, suggesting the significant role of soil characteristics in weed community structure and diversity. PMID:23961198

Effects of plant diversity, community composition and environmental parameters on productivity in montane European grasslands.

PubMed

Kahmen, Ansgar; Perner, Jörg; Audorff, Volker; Weisser, Wolfgang; Buchmann, Nina

2005-02-01

In the past years, a number of studies have used experimental plant communities to test if biodiversity influences ecosystem functioning such as productivity. It has been argued, however, that the results achieved in experimental studies may have little predictive value for species loss in natural ecosystems. Studies in natural ecosystems have been equivocal, mainly because in natural ecosystems differences in diversity are often confounded with differences in land use history or abiotic parameters. In this study, we investigated the effect of plant diversity on ecosystem functioning in semi-natural grasslands. In an area of 10x20 km, we selected 78 sites and tested the effects of various measures of diversity and plant community composition on productivity. We separated the effects of plant diversity on ecosystem functioning from potentially confounding effects of community composition, management or environmental parameters, using multivariate statistical analyses. In the investigated grasslands, simple measures of biodiversity were insignificant predictors of productivity. However, plant community composition explained productivity very well (R2=0.31) and was a better predictor than environmental variables (soil and site characteristics) or management regime. Thus, complex measures such as community composition and structure are important drivers for ecosystem functions in semi-natural grasslands. Furthermore, our data show that it is difficult to extrapolate results from experimental studies to semi-natural ecosystems, although there is a need to investigate natural ecosystems to fully understand the relationship of biodiversity and ecosystem functioning.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing's built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

NASA Astrophysics Data System (ADS)

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-01

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities.

PubMed

Rea, Maria Angelica; Standish, Christopher D; Shuster, Jeremiah; Bissett, Andrew; Reith, Frank

2018-05-03

Biofilms on placer gold (Au)-particle surfaces drive Au solubilization and re-concentration thereby progressively transforming the particles. Gold solubilization induces Au-toxicity; however, Au-detoxifying community members ameliorates Au-toxicity by precipitating soluble Au to metallic Au. We hypothesize that Au-dissolution and re-concentration (precipitation) places selective pressures on associated microbial communities, leading to compositional changes and subsequent Au-particle transformation. We analyzed Au-particles from eight United Kingdom sites using next generation sequencing, electron microscopy and micro-analyses. Gold particles contained biofilms composed of prokaryotic cells and extracellular polymeric substances intermixed with (bio)minerals. Across all sites communities were dominated by Proteobacteria (689, 97% Operational Taxonomic Units, 59.3% of total reads), with β-Proteobacteria being the most abundant. A wide range of Au-morphotypes including nanoparticles, micro-crystals, sheet-like Au and secondary rims, indicated that dissolution and re-precipitation occurred, and from this transformation indices were calculated. Multivariate statistical analyses showed a significant relationship between the extent of Au-particle transformation and biofilm community composition, with putative metal-resistant Au-cycling taxa linked to progressive Au transformation. These included the genera Pseudomonas, Leptothrix and Acinetobacter. Additionally, putative exoelectrogenic genera Rhodoferax and Geobacter were highly abundant. In conclusion, biogeochemical Au-cycling and Au-particle transformation occurred at all sites and exerted a strong influence on biofilm community composition.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

PubMed

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

PubMed Central

Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

PubMed

Stanish, Lee F; Hull, Natalie M; Robertson, Charles E; Harris, J Kirk; Stevens, Mark J; Spear, John R; Pace, Norman R

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

PubMed

Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

2010-10-01

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon

Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

PubMed Central

Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B.; Gaju, Nuria; Cazorla, Francisco M.

2015-01-01

One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

Effects of transgenic cry1Ie maize on non-lepidopteran pest abundance, diversity and community composition.

PubMed

Guo, Jingfei; He, Kanglai; Bai, Shuxiong; Zhang, Tiantao; Liu, Yunjun; Wang, Fuxin; Wang, Zhenying

2016-12-01

Non-lepidopteran pests are exposed to, and may be influenced by, Bt toxins when feeding on Bt maize that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt). In order to assess the potential effects of transgenic cry1Ie maize on non-lepidopteran pest species and ecological communities, a 2-year field study was conducted to compare the non-lepidopteran pest abundance, diversity and community composition between transgenic cry1Ie maize (Event IE09S034, Bt maize) and its near isoline (Zong 31, non-Bt maize) by whole plant inspections. Results showed that Bt maize had no effects on non-lepidopteran pest abundance and diversity (Shannon-Wiener diversity index, Simpson's diversity index, species richness, and Pielou's index). There was a significant effect of year and sampling time on those indices analyzed. Redundancy analysis indicated maize type, sampling time and year totally explained 20.43 % of the variance in the non-lepidopteran pest community composition, but no association was presented between maize type (Bt maize and non-Bt maize) and the variance. Nonmetric multidimensional scaling analysis showed that sampling time and year, rather than maize type had close relationship with the non-lepidopteran pest community composition. These results corroborated the hypothesis that, at least in the short-term, the transgenic cry1Ie maize had negligible effects on the non-lepidopteran pest abundance, diversity and community composition.

Microbial community composition along a 50 000-year lacustrine sediment sequence

PubMed Central

Ariztegui, Daniel; Horn, Fabian; Kallmeyer, Jens; Orsi, William D

2018-01-01

Abstract For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth. PMID:29471361

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

PubMed Central

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-01-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition. PMID:27256545

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition.

PubMed

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-03

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

NASA Astrophysics Data System (ADS)

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

PubMed

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil

PubMed Central

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil.

PubMed

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [ Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of

A hierarchical examination of methane uptake: field patterns, lab physiology, community composition and biogeography

NASA Astrophysics Data System (ADS)

von Fischer, J. C.; Koyama, A.; Johnson, N. G.; Webb, C. T.

2015-12-01

Scaling problems abound in biogeochemistry. At the finest scale, soil microbes experience habitats and environmental changes that affect the chemical transformations of interest. We collect the DNA of these organisms from sites across landscapes and note differences in who is there, and we seek to evaluate why group membership changes in space (biogeography) and why activity rates change over time (physiology). The goal of efforts at finer scales is often to better predict patterns at larger scales. We conducted such a hierarchical examination of methane uptake in the Great Plains grasslands of North America, gathering data from 22 plots at 8 field locations, scattered from South Dakota to New Mexico and Colorado to Kansas. Our work provides insight into methanotroph biogeochemistry at all of these scales. For example, we found that methane uptake rates vary mostly due to the methanotroph activity, and less so due to diffusivity. A combination of field and lab observations reveal that methanotroph communities differ in their sensitivity to soil moisture and to ammonium (an inhibitor of methanotrophy). Examination of methanotroph community composition reveals tantalizing patterns in composition, dominance and richness across sites, that appears to be structured by patterns of precipitation and soil texture. We anticipate that greater synthesis of these hierarchical findings will paint a richer picture of methanotroph life and enable improved prediction of methane uptake at regional scales.

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil.

PubMed

Štursová, Martina; Bárta, Jiří; Šantrůčková, Hana; Baldrian, Petr

2016-12-01

Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m 2 ) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

PubMed Central

van Agtmaal, Maaike; van Os, Gera J.; Hol, W.H. Gera; Hundscheid, Maria P.J.; Runia, Willemien T.; Hordijk, Cornelis A.; de Boer, Wietse

2015-01-01

There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the

A close link between bacterial community composition and environmental heterogeneity in maritime Antarctic lakes.

PubMed

Villaescusa, Juan A; Casamayor, Emilio O; Rochera, Carlos; Velázquez, David; Chicote, Alvaro; Quesada, Antonio; Camacho, Antonio

2010-06-01

Seven maritime Antarctic lakes located on Byers Peninsula (Livingston Island, South Shetland Islands) were surveyed to determine the relationship between planktonic bacterial community composition and environmental features. Specifically, the extent to which factors other than low temperature determine the composition of bacterioplankton assemblages of maritime Antarctic lakes was evaluated. Both deep and shallow lakes in the central plateau of the Peninsula, as well as a coastal lake, were studied in order to fully account for the environmental heterogeneity of the Peninsula's lakes. The results showed that shallow coastal lakes display eutrophic conditions, mainly due to the influence of marine animals, whereas plateau lakes are generally deeper and most are oligotrophic, with very limited inputs of nutrients and organic matter. Meso-eutrophic shallow lakes are also present on the Peninsula; they contain microbial mats and a higher trophic status because of the biologically mediated active nutrient release from the sediments. Diversity studies of the lakes' planktonic bacterial communities using molecular techniques showed that bacterial diversity is lower in eutrophic than in oligotrophic lakes. The former also differed in community composition with respect to dominant taxa. Multivariate statistical analyses of environmental data yielded the same clustering of lakes as obtained based on the DGGE band pattern after DNA extraction and amplification of 16S rRNA gene fragments. Thus, even in extremely cold lakes, the bacterial community composition parallels other environmental factors, such as those related to trophic status. This correspondence is not only mediated by the influence of marine fauna but also by processes including sediment and ice melting dynamics. The bacterial community can therefore be considered to be equally representative as environmental abiotic variables in demonstrating the environmental heterogeneity among maritime Antarctic lakes.

Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence.

PubMed

Albornoz, Felipe E; Teste, François P; Lambers, Hans; Bunce, Michael; Murray, Dáithí C; White, Nicole E; Laliberté, Etienne

2016-10-01

Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis-driven shifts in edaphic properties, particularly pH and resin-exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long-term ecosystem development, even within the same hosts. However, these changes could not be attributed to short-term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer-term ecosystem-level feedback between soil, vegetation and ECM fungi during pedogenesis. © 2016 John Wiley & Sons Ltd.

Predicting ecosystem stability from community composition and biodiversity

USGS Publications Warehouse

Mazancourt, Claire de; Isbell, Forest; Larocque, Allen; Berendse, Frank; De Luca, Enrica; Grace, James B.; Haegeman, Bart; Polley, H. Wayne; Roscher, Christiane; Schmid, Bernhard; Tilman, David; van Ruijven, Jasper; Weigelt, Alexandra; Wilsey, Brian J.; Loreau, Michel

2013-01-01

As biodiversity is declining at an unprecedented rate, an important current scientific challenge is to understand and predict the consequences of biodiversity loss. Here, we develop a theory that predicts the temporal variability of community biomass from the properties of individual component species in monoculture. Our theory shows that biodiversity stabilises ecosystems through three main mechanisms: (1) asynchrony in species’ responses to environmental fluctuations, (2) reduced demographic stochasticity due to overyielding in species mixtures and (3) reduced observation error (including spatial and sampling variability). Parameterised with empirical data from four long-term grassland biodiversity experiments, our prediction explained 22–75% of the observed variability, and captured much of the effect of species richness. Richness stabilised communities mainly by increasing community biomass and reducing the strength of demographic stochasticity. Our approach calls for a re-evaluation of the mechanisms explaining the effects of biodiversity on ecosystem stability.

Ecosystem composition changes over the past millennium: model simulations and comparison with paleoecological observations

NASA Astrophysics Data System (ADS)

Liu, Y.; Rollinson, C.; Dietze, M.; McLachlan, J. S.; Poulter, B.; Quaife, T. L.; Raiho, A.; Ricciuto, D. M.; Schaefer, K. M.; Steinkamp, J.; Moore, D. J.

2015-12-01

Over multi-decadal to multi-centennial timescales, ecosystem function and carbon storage is largely influenced by vegetation composition. The predictability of ecosystem responses to climate change thus depends on the understanding of long-term community dynamics. Our study aims to quantify the influence of the most relevant ecological factors that control plant distribution and abundance, in contemporary terrestrial biosphere models and in paleo-records, and constrain the model processes and parameters with paleoecological data. We simulated vegetation changes at 6 sites in the northeastern United States over the past 1160 years using 7 terrestrial biosphere models and variations (CLM4.5-CN, ED2, ED2-LU, JULES-TRIFFID, LINKAGES, LPJ-GUESS, LPJ-wsl) driven by common paleoclimatic drivers. We examined plant growth, recruitment, and mortality (including other carbon turnover) of the plant functional types (PFTs) in the models, attributed the responses to three major factors (climate, competition, and disturbance), and estimated the relative effect of each factor. We assessed the model responses against plant-community theories (bioclimatic limits, niche difference, temporal variation and storage effect, and disturbance). We found that vegetation composition were sensitive to realized niche differences (e.g. differential growth response) among PFTs. Because many models assume unlimited dispersal and sometimes recruitment, the "storage effect" constantly affects community composition. Fire was important in determining the ecosystem composition, yet the vegetation to fire feedback was weak in the models. We also found that vegetation-composition changes in the simulations were driven to a much greater degree by growth as opposed to by turnover/mortality, when compared with those in paleoecological records. Our work suggest that 1) for forecasting slow changes in vegetation composition, we can use paleo-data to better quantify the realized niches of PFTs and associated

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities

PubMed Central

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities.

PubMed

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community

Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor

NASA Astrophysics Data System (ADS)

Gryta, Agata; Oszust, Karolina; Brzezińska, Małgorzata; Ziemiński, Krzysztof; Bilińska-Wielgus, Nina; Frąc, Magdalena

2017-07-01

The aim of the study was to elucidate the substantial relationship between the compositions of methanogen community that assembles in the anaerobic digester mass and link it to methane production activity. The results of the metagenomic studies were used to evaluate how the methanogen structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 days). Phylogenetically coherent populations of methanogens were assessed by 16S rRNA gene next-generation sequencing and terminal restriction fragment length polymorphism fingerprinting of a specific molecular marker, the mcrA gene. The results indicated multiple phylogenetically diverse methanogen populations associated with the various steps of anaerobic digestion. The stages of the anaerobic digestion process and waste retention times determine the microbial composition. The most dominant and acclimated microbial communities in all samples belonged to the genera Methanosaeta and Methanobacterium. The methane yield was consistent with the results of the microbial community structure, which indicated that acetotrophic Methanosaeta was the most active and most important during the methanogenic stage.

The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows

PubMed Central

Vaidya, Jueeli D.; van den Bogert, Bartholomeus; Edwards, Joan E.; Boekhorst, Jos; van Gastelen, Sanne; Saccenti, Edoardo; Plugge, Caroline M.; Smidt, Hauke

2018-01-01

DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method (p < 0.001) and fraction (p < 0.001). The 260/280 ratio was not affected by extraction (p = 0.08) but was affected by fraction (p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method (p < 0.001) but not affected by fraction (p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction (p = 0.012), and that PBB (p = 0.012) and FDSS (p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both. In

The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows.

PubMed

Vaidya, Jueeli D; van den Bogert, Bartholomeus; Edwards, Joan E; Boekhorst, Jos; van Gastelen, Sanne; Saccenti, Edoardo; Plugge, Caroline M; Smidt, Hauke

2018-01-01

DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method ( p < 0.001) and fraction ( p < 0.001). The 260/280 ratio was not affected by extraction ( p = 0.08) but was affected by fraction ( p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method ( p < 0.001) but not affected by fraction ( p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction ( p = 0.012), and that PBB ( p = 0.012) and FDSS ( p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

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

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE PAGES

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; ...

2017-03-13

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Reservoirs for Comets: Compositional Differences Based on Infrared Observations

NASA Astrophysics Data System (ADS)

Disanti, Michael A.; Mumma, Michael J.

Tracing measured compositions of comets to their origins continues to be of keen interest to cometary scientists and to dynamical modelers of Solar System formation and evolution. This requires building a taxonomy of comets from both present-day dynamical reservoirs: the Kuiper Belt (hereafter KB), sampled through observation of ecliptic comets (primarily Jupiter Family comets, or JFCs), and the Oort cloud (OC), represented observationally by the long-period comets and by Halley Family comets (HFCs). Because of their short orbital periods, JFCs are subjected to more frequent exposure to solar radiation compared with OC comets. The recent apparitions of the JFCs 9P/Tempel 1 and 73P/Schwassmann-Wachmann 3 permitted detailed observations of material issuing from below their surfaces—these comets added significantly to the compositional database on this dynamical class, which is under-represented in studies of cometary parent volatiles. This chapter reviews the latest techniques developed for analysis of high-resolution spectral observations from ˜2-5 μm, and compares measured abundances of native ices among comets. While no clear compositional delineation can be drawn along dynamical lines, interesting comparisons can be made. The sub-surface composition of comet 9P, as revealed by the Deep Impact ejecta, was similar to the majority of OC comets studied. Meanwhile, 73P was depleted in all native ices except HCN, similar to the disintegrated OC comet C/1999 S4 (LINEAR). These results suggest that 73P may have formed in the inner giant planets' region while 9P formed farther out or, alternatively, that both JFCs formed farther from the Sun but with 73P forming later in time.

Reservoirs for Comets: Compositional Differences Based on Infrared Observations

NASA Astrophysics Data System (ADS)

Disanti, Michael A.; Mumma, Michael J.

2008-07-01

Tracing measured compositions of comets to their origins continues to be of keen interest to cometary scientists and to dynamical modelers of Solar System formation and evolution. This requires building a taxonomy of comets from both present-day dynamical reservoirs: the Kuiper Belt (hereafter KB), sampled through observation of ecliptic comets (primarily Jupiter Family comets, or JFCs), and the Oort cloud (OC), represented observationally by the long-period comets and by Halley Family comets (HFCs). Because of their short orbital periods, JFCs are subjected to more frequent exposure to solar radiation compared with OC comets. The recent apparitions of the JFCs 9P/Tempel 1 and 73P/Schwassmann-Wachmann 3 permitted detailed observations of material issuing from below their surfaces—these comets added significantly to the compositional database on this dynamical class, which is under-represented in studies of cometary parent volatiles. This chapter reviews the latest techniques developed for analysis of high-resolution spectral observations from ˜2 5 μm, and compares measured abundances of native ices among comets. While no clear compositional delineation can be drawn along dynamical lines, interesting comparisons can be made. The sub-surface composition of comet 9P, as revealed by the Deep Impact ejecta, was similar to the majority of OC comets studied. Meanwhile, 73P was depleted in all native ices except HCN, similar to the disintegrated OC comet C/1999 S4 (LINEAR). These results suggest that 73P may have formed in the inner giant planets’ region while 9P formed farther out or, alternatively, that both JFCs formed farther from the Sun but with 73P forming later in time.

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P. A.; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescomposition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

Inference methods for spatial variation in species richness and community composition when not all species are detected

USGS Publications Warehouse

Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

1998-01-01

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (an associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larer number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on the methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species

Composition Instructors' Interactions with Classroom Discourse Communities: A Qualitative Study

ERIC Educational Resources Information Center

Winterberg, Sarah Griffith

2017-01-01

This study offered insight on the intermingling of discourse communities in the learning environment by examining experiences of composition instructors from a regional Southern university and their reflections of teaching students who struggled to navigate from home discourse to academic discourse. Merriam's basic qualitative research design…

Predicting ecosystem stability from community composition and biodiversity.

PubMed

de Mazancourt, Claire; Isbell, Forest; Larocque, Allen; Berendse, Frank; De Luca, Enrica; Grace, James B; Haegeman, Bart; Wayne Polley, H; Roscher, Christiane; Schmid, Bernhard; Tilman, David; van Ruijven, Jasper; Weigelt, Alexandra; Wilsey, Brian J; Loreau, Michel

2013-05-01

As biodiversity is declining at an unprecedented rate, an important current scientific challenge is to understand and predict the consequences of biodiversity loss. Here, we develop a theory that predicts the temporal variability of community biomass from the properties of individual component species in monoculture. Our theory shows that biodiversity stabilises ecosystems through three main mechanisms: (1) asynchrony in species' responses to environmental fluctuations, (2) reduced demographic stochasticity due to overyielding in species mixtures and (3) reduced observation error (including spatial and sampling variability). Parameterised with empirical data from four long-term grassland biodiversity experiments, our prediction explained 22-75% of the observed variability, and captured much of the effect of species richness. Richness stabilised communities mainly by increasing community biomass and reducing the strength of demographic stochasticity. Our approach calls for a re-evaluation of the mechanisms explaining the effects of biodiversity on ecosystem stability. © 2013 Blackwell Publishing Ltd/CNRS.

pCO2 effects on species composition and growth of an estuarine phytoplankton community

NASA Astrophysics Data System (ADS)

Grear, Jason S.; Rynearson, Tatiana A.; Montalbano, Amanda L.; Govenar, Breea; Menden-Deuer, Susanne

2017-05-01

The effects of ongoing changes in ocean carbonate chemistry on plankton ecology have important implications for food webs and biogeochemical cycling. However, conflicting results have emerged regarding species-specific responses to pCO2 enrichment and thus community responses have been difficult to predict. To assess community level effects (e.g., production) of altered carbonate chemistry, studies are needed that capitalize on the benefits of controlled experiments but also retain features of intact ecosystems that may exacerbate or ameliorate the effects observed in single-species or single cohort experiments. We performed incubations of natural plankton communities from Narragansett Bay, RI, USA in winter at ambient bay temperatures (5-13 °C), light and nutrient concentrations. Three levels of controlled and constant CO2 concentrations were imposed, simulating past, present and future conditions at mean pCO2 levels of 224, 361, and 724 μatm respectively. Samples for carbonate analysis, chlorophyll a, plankton size-abundance, and plankton species composition were collected daily and phytoplankton growth rates in three different size fractions (<5, 5-20, and >20 μm) were measured at the end of the 7-day incubation period. Community composition changed during the incubation period with major increases in relative diatom abundance, which were similar across pCO2 treatments. At the end of the experiment, 24-hr growth responses to pCO2 levels varied as a function of cell size. The smallest size fraction (<5 μm) grew faster at the elevated pCO2 level. In contrast, the 5-20 μm size fraction grew fastest in the Present treatment and there were no significant differences in growth rate among treatments in the >20 μm size fraction. Cell size distribution shifted toward smaller cells in both the Past and Future treatments but remained unchanged in the Present treatment. Similarity in Past and Future treatments for cell size distribution and growth rate (5-20 μm size

Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities.

PubMed

Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B; Gaju, Nuria; Cazorla, Francisco M; de Vicente, Antonio

2015-05-15

One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Physicochemical control of bacterial and protist community composition and diversity in Antarctic sea ice.

PubMed

Torstensson, Anders; Dinasquet, Julie; Chierici, Melissa; Fransson, Agneta; Riemann, Lasse; Wulff, Angela

2015-10-01

Due to climate change, sea ice experiences changes in terms of extent and physical properties. In order to understand how sea ice microbial communities are affected by changes in physicochemical properties of the ice, we used 454-sequencing of 16S and 18S rRNA genes to examine environmental control of microbial diversity and composition in Antarctic sea ice. We observed a high diversity and richness of bacteria, which were strongly negatively correlated with temperature and positively with brine salinity. We suggest that bacterial diversity in sea ice is mainly controlled by physicochemical properties of the ice, such as temperature and salinity, and that sea ice bacterial communities are sensitive to seasonal and environmental changes. For the first time in Antarctic interior sea ice, we observed a strong eukaryotic dominance of the dinoflagellate phylotype SL163A10, comprising 63% of the total sequences. This phylotype is known to be kleptoplastic and could be a significant primary producer in sea ice. We conclude that mixotrophic flagellates may play a greater role in the sea ice microbial ecosystem than previously believed, and not only during the polar night but also during summer when potential food sources are abundant. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

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

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the responsemore » to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCEThe influence of river water-groundwater mixing on hyporheic zone microbial community

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor.

PubMed

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C; Arntzen, Evan; Kennedy, David W; Larget, Bret R; Roden, Eric E

2017-08-15

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities ( in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to "cross-feeding" with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure

Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

PubMed

Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat

2014-03-01

Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community. Copyright © 2013

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

PubMed

Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

2015-06-01

The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

Do honeybees shape the bacterial community composition in floral nectar?

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

Canada's Composite Learning Index: A path towards learning communities

NASA Astrophysics Data System (ADS)

Cappon, Paul; Laughlin, Jarrett

2013-09-01

In the development of learning cities/communities, benchmarking progress is a key element. Not only does it permit cities/communities to assess their current strengths and weaknesses, it also engenders a dialogue within and between cities/communities on the means of enhancing learning conditions. Benchmarking thereby is a potentially motivational tool, energising further progress. In Canada, the Canadian Council on Learning created the world's first Composite Learning Index (CLI), the purpose of which is to measure the conditions of learning nationally, regionally and locally. Cities/communities in Canada have utilised the CLI Simulator, an online tool provided by the Canadian Council on Learning, to gauge the change in overall learning conditions which may be expected depending on which particular indicator is emphasised. In this way, the CLI has proved to be both a dynamic and a locally relevant tool for improvement, moreover a strong motivational factor in the development of learning cities/communities. After presenting the main features of the CLI, the authors of this paper sum up the lessons learned during its first 5 years (2006-2010) of existence, also with a view to its transferability to other regions. Indeed, the CLI model was already adopted in Europe by the German Bertelsmann foundation in 2010 and has the potential to be useful in many other countries as well.

Modeling plant composition as community continua in a forest landscape with LiDAR and hyperspectral remote sensing.

PubMed

Hakkenberg, C R; Peet, R K; Urban, D L; Song, C

2018-01-01

In light of the need to operationalize the mapping of forest composition at landscape scales, this study uses multi-scale nested vegetation sampling in conjunction with LiDAR-hyperspectral remotely sensed data from the G-LiHT airborne sensor to map vascular plant compositional turnover in a compositionally and structurally complex North Carolina Piedmont forest. Reflecting a shift in emphasis from remotely sensing individual crowns to detecting aggregate optical-structural properties of forest stands, predictive maps reflect the composition of entire vascular plant communities, inclusive of those species smaller than the resolution of the remotely sensed imagery, intertwined with proximate taxa, or otherwise obscured from optical sensors by dense upper canopies. Stand-scale vascular plant composition is modeled as community continua: where discrete community-unit classes at different compositional resolutions provide interpretable context for continuous gradient maps that depict n-dimensional compositional complexity as a single, consistent RGB color combination. In total, derived remotely sensed predictors explain 71%, 54%, and 48% of the variation in the first three components of vascular plant composition, respectively. Among all remotely sensed environmental gradients, topography derived from LiDAR ground returns, forest structure estimated from LiDAR all returns, and morphological-biochemical traits determined from hyperspectral imagery each significantly correspond to the three primary axes of floristic composition in the study site. Results confirm the complementarity of LiDAR and hyperspectral sensors for modeling the environmental gradients constraining landscape turnover in vascular plant composition and hold promise for predictive mapping applications spanning local land management to global ecosystem modeling. © 2017 by the Ecological Society of America.

Riparian-associated gastropods in western Washington: community composition and the effects of forest management

Treesearch

Alex D. Foster; Joan Ziegltrum

2013-01-01

We evaluated the abundance of riparian gastropod communities along headwater streams and their response to logging in southwestern Washington State. Terrestrial mollusks near logged streams with ~15 m fixed-width buffers were compared to logged streams with no buffers and to unlogged controls. Mollusk communities varied among sites relative to vegetative composition,...

Avian community composition and habitat importance in the Rio Grande corridor of New Mexico

Treesearch

David A. Leal; Raymond A. Meyer; Bruce C. Thompson

1996-01-01

We investigated avian species richness and abundance within vegetation communities of the Rio Grande Corridor of New Mexico during spring, summer, and fall 1992 and 1993. A subset of 64 transects, for which all bird and vegetation variables were available, representing 16 composite vegetation community types were subjected to canonical correlation analysis to...

Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean

PubMed Central

Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

2013-01-01

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

PubMed

Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

2014-10-01

Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

Looking inside and out: the impact of employee and community demographic composition on organizational diversity climate.

PubMed

Pugh, S Douglas; Dietz, Joerg; Brief, Arthur P; Wiley, Jack W

2008-11-01

An organization's diversity climate refers to employees' shared perceptions of the policies and practices that communicate the extent to which fostering diversity and eliminating discrimination is a priority in the organization. The authors propose a salient element of the organizational context, the racial composition of the community where the organization is located, serves an important signaling function that shapes the formation of climate perceptions. In a study of 142 retail bank units in the United States, evidence is found for a relationship between the racial composition of an organization's workforce and diversity climate that is moderated by the racial composition of the community where the organization is located. The results suggest that when few racial minorities live in the community in which an organization is embedded, workforce diversity has an impact on employees' diversity climate perceptions. As racial minority popular share increases, workforce diversity tends to lose this signaling value.

Physical observations of comets: Their composition, origin and evolution

NASA Technical Reports Server (NTRS)

Cochran, Anita L.; Barker, Edwin S.; Cochran, William D.

1991-01-01

The composition, origins, and evolution of comets were studied. The composition was studied using spectroscopic observations of primarily brighter comets at moderate and high resolution for the distribution of certain gases in the coma. The origins was addressed through an imaging search for the Kuiper belt of comets. The evolution was addressed by searching for a link between comets and asteroids using an imaging approach to search for an OH coma.

Vertical distribution of chlorophyll a concentration and phytoplankton community composition from in situ fluorescence profiles: a first database for the global ocean

NASA Astrophysics Data System (ADS)

Sauzède, R.; Lavigne, H.; Claustre, H.; Uitz, J.; Schmechtig, C.; D'Ortenzio, F.; Guinet, C.; Pesant, S.

2015-04-01

In vivo chlorophyll a fluorescence is a proxy of chlorophyll a concentration, and is one of the most frequently measured biogeochemical properties in the ocean. Thousands of profiles are available from historical databases and the integration of fluorescence sensors to autonomous platforms led to a significant increase of chlorophyll fluorescence profile acquisition. To our knowledge, this important source of environmental data has not yet been included in global analyses. A total of 268 127 chlorophyll fluorescence profiles from several databases as well as published and unpublished individual sources were compiled. Following a robust quality control procedure detailed in the present paper, about 49 000 chlorophyll fluorescence profiles were converted in phytoplankton biomass (i.e. chlorophyll a concentration) and size-based community composition (i.e. microphytoplankton, nanophytoplankton and picophytoplankton), using a~method specifically developed to harmonize fluorescence profiles from diverse sources. The data span over five decades from 1958 to 2015, including observations from all major oceanic basins and all seasons, and depths ranging from surface to a median maximum sampling depth of around 700 m. Global maps of chlorophyll a concentration and phytoplankton community composition are presented here for the first time. Monthly climatologies were computed for three of Longhurst's ecological provinces in order to exemplify the potential use of the data product. Original data sets (raw fluorescence profiles) as well as calibrated profiles of phytoplankton biomass and community composition are available in open access at PANGAEA, Data Publisher for Earth and Environmental Science. Raw fluorescence profiles: http://doi.pangaea.de/10.1594/PANGAEA.844212 and Phytoplankton biomass and community composition: http://doi.pangaea.de/10.1594/PANGAEA.844485.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

PubMed

Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

2017-11-01

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

The Importance of Dispersal for Bacterial Community Composition and Functioning

PubMed Central

Lindström, Eva S.; Östman, Örjan

2011-01-01

We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into. PMID:21998714

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

PubMed

Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

2015-06-02

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor.

PubMed

Nomoto, Naoki; Hatamoto, Masashi; Hirakata, Yuga; Ali, Muntjeer; Jayaswal, Komal; Iguchi, Akinori; Okubo, Tsutomu; Takahashi, Masanobu; Kubota, Kengo; Tagawa, Tadashi; Uemura, Shigeki; Yamaguchi, Takashi; Harada, Hideki

2018-05-01

The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

Summer microbial community composition governed by upper-ocean stratification and nutrient availability in northern Marguerite Bay, Antarctica

NASA Astrophysics Data System (ADS)

Rozema, Patrick D.; Biggs, Tristan; Sprong, Pim A. A.; Buma, Anita G. J.; Venables, Hugh J.; Evans, Claire; Meredith, Michael P.; Bolhuis, Henk

2017-05-01

The Western Antarctic Peninsula warmed significantly during the second half of the twentieth century, with a concurrent retreat of the majority of its glaciers, and marked changes in the sea-ice field. These changes may affect summertime upper-ocean stratification, and thereby the seasonal dynamics of phytoplankton and bacteria. In the present study, we examined coastal Antarctic microbial community dynamics by pigment analysis and applying molecular tools, and analysed various environmental parameters to identify the most important environmental drivers. Sampling focussed on the austral summer of 2009-2010 at the Rothera oceanographic and biological Time Series (RaTS) site in northern Marguerite bay, Antarctica. The Antarctic summer was characterized by a salinity decrease (measured at 15 m depth) coinciding with increased meteoric water fraction. Maximum Chl-a values of 35 μg l-1 were observed during midsummer and mainly comprised of diatoms. Microbial community fingerprinting revealed four distinct periods in phytoplankton succession during the summer while bacteria showed a delayed response to the phytoplankton community. Non-metric multidimensional scaling analyses showed that phytoplankton community dynamics were mainly directed by temperature, mixed layer depth and wind speed. Both high and low N/P ratios might have influenced phytoplankton biomass accumulation. The bacterioplankton community composition was mainly governed by Chl-a, suggesting a link to phytoplankton community changes. High-throughput 16S and 18S rRNA amplicon sequencing revealed stable eukaryotic and bacterial communities with regards to observed species, yet varying temporal relative contributions. Eukaryotic sequences were dominated by pennate diatoms in December followed by polar centric diatoms in January and February. Our results imply that the reduction of mixed layer depth during summer, caused by meltwater-related surface stratification, promotes a succession in diatoms rather

Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition.

PubMed

Kohrs, F; Heyer, R; Bissinger, T; Kottler, R; Schallert, K; Püttker, S; Behne, A; Rapp, E; Benndorf, D; Reichl, U

2017-08-01

Complex microbial communities are the functional core of anaerobic digestion processes taking place in biogas plants (BGP). So far, however, a comprehensive characterization of the microbiomes involved in methane formation is technically challenging. As an alternative, enriched communities from laboratory-scale experiments can be investigated that have a reduced number of organisms and are easier to characterize by state of the art mass spectrometric-based (MS) metaproteomic workflows. Six parallel laboratory digesters were inoculated with sludge from a full-scale BGP to study the development of enriched microbial communities under defined conditions. During the first three month of cultivation, all reactors (R1-R6) were functionally comparable regarding biogas productions (375-625 NL L reactor volume -1 d -1 ), methane yields (50-60%), pH values (7.1-7.3), and volatile fatty acids (VFA, <5 mM). Nevertheless, a clear impact of the temperature (R3, R4) and ammonia (R5, R6) shifts was observed for the respective reactors. In both reactors operated under thermophilic regime, acetic and propionic acid (10-20 mM) began to accumulate. While R4 recovered quickly from acidification, the levels of VFA remained to be high in R3 resulting in low pH values of 6.5-6.9. The digesters R5 and R6 operated under the high ammonia regime (>1 gNH 3 L -1 ) showed an increase to pH 7.5-8.0, accumulation of acetate (>10 mM), and decreasing biogas production (<125 NL L reactor volume -1 d -1 ). Tandem MS (MS/MS)-based proteotyping allowed the identification of taxonomic abundances and biological processes. Although all reactors showed similar performances, proteotyping and terminal restriction fragment length polymorphisms (T-RFLP) fingerprinting revealed significant differences in the composition of individual microbial communities, indicating multiple steady-states. Furthermore, cellulolytic enzymes and cellulosomal proteins of Clostridium thermocellum were identified to be specific

Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

PubMed Central

Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

2013-01-01

The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

Effects of rodent community diversity and composition on prevalence of an endemic bacterial pathogen - Bartonella

USGS Publications Warehouse

Bai, Y.; Kosoy, M.Y.; Calisher, C.H.; Cully, J.F.; Collinge, S.K.

2009-01-01

By studying Bartonella prevalence in rodent communities from 23 geographic sites in the western United States and one site in northern Mexico, the present study focused on the effects of rodent community diversity (measured by richness and Shannon index) and composition on prevalence of Bartonella infections. The analysis showed negative correlations of Bartonella prevalence with rodent richness and Shannon index. Further, Bartonella prevalence varied among rodent genera/species. Three models were applied to explain the observations. (1) Within-species/genus transmission: Bartonella strains usually are host-specific and adding non-host species would decrease Bartonella prevalence in its principal host through reduction of host contact (encounter reduction); (2) Frequency-dependence: Adding hosts would decrease the proportion of all infected individuals in the community, resulting in a reduction in the number of contacts between susceptible and infected individuals that usually leads to transmission (transmission reduction); and (3) Dominant species effect: Dominant species, if not susceptible to Bartonellae, can constrain the abundance of susceptible hosts (susceptible host regulation). These mechanisms work in concert; and the level of Bartonella prevalence is an outcome of regulation of all of these mechanisms on the entire system.

Microplastics alter composition of fungal communities in aquatic ecosystems.

PubMed

Kettner, Marie Therese; Rojas-Jimenez, Keilor; Oberbeckmann, Sonja; Labrenz, Matthias; Grossart, Hans-Peter

2017-11-01

Despite increasing concerns about microplastic (MP) pollution in aquatic ecosystems, there is insufficient knowledge on how MP affect fungal communities. In this study, we explored the diversity and community composition of fungi attached to polyethylene (PE) and polystyrene (PS) particles incubated in different aquatic systems in north-east Germany: the Baltic Sea, the River Warnow and a wastewater treatment plant. Based on next generation 18S rRNA gene sequencing, 347 different operational taxonomic units assigned to 81 fungal taxa were identified on PE and PS. The MP-associated communities were distinct from fungal communities in the surrounding water and on the natural substrate wood. They also differed significantly among sampling locations, pointing towards a substrate and location specific fungal colonization. Members of Chytridiomycota, Cryptomycota and Ascomycota dominated the fungal assemblages, suggesting that both parasitic and saprophytic fungi thrive in MP biofilms. Thus, considering the worldwide increasing accumulation of plastic particles as well as the substantial vector potential of MP, especially these fungal taxa might benefit from MP pollution in the aquatic environment with yet unknown impacts on their worldwide distribution, as well as biodiversity and food web dynamics at large. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

PubMed Central

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

Epiphytic Macrolichen Community Composition Database—epiphytic lichen synusiae in forested areas of the US

Treesearch

Sarah. Jovan

2012-01-01

The Forest Inventory and Analysis (FIA) Program's Lichen Communities Indicator is used for tracking epiphytic macrolichen diversity and is applied for monitoring air quality and climate change effects on forest health in the United States. Started in 1994, the Epiphytic Macrolichen Community Composition Database (GIVD ID NA-US-012) now has over 8,000 surveys of...

The bacterial community composition of the surface microlayer in a high mountain lake.

PubMed

Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

2010-09-01

The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

Effects of habitat management treatments on plant community composition and biomass in a Montane wetland

USGS Publications Warehouse

Austin, J.E.; Keough, J.R.; Pyle, W.H.

2007-01-01

Grazing and burning are commonly applied practices that can impact the diversity and biomass of wetland plant communities. We evaluated the vegetative response of wetlands and adjacent upland grasslands to four treatment regimes (continuous idle, fall prescribed burning followed by idle, annual fall cattle grazing, and rotation of summer grazing and idle) commonly used by the U.S. Fish and Wildlife Service. Our study area was Grays Lake, a large, montane wetland in southeastern Idaho that is bordered by extensive wet meadows. We identified seven plant cover types, representing the transition from dry meadow to deep wetland habitats: mixed deep marsh, spikerush slough, Baltic rush (Juncus balticus), moist meadow, alkali, mesic meadow, and dry meadow. We compared changes in community composition and total aboveground biomass of each plant cover type between 1998, when all units had been idled for three years, and 1999 (1 yr post-treatment) and 2000 (2 yr post-treatment). Analysis using non-metric multidimensional scaling indicated that compositional changes varied among cover types, treatments, and years following treatment. Treatment-related changes in community composition were greatest in mixed deep marsh, Baltic rush, and mesic meadow. In mixed deep marsh and Baltic rush, grazing and associated trampling contributed to changes in the plant community toward more open water and aquatic species and lower dominance of Baltic rush; grazing and trampling also seemed to contribute to increased cover in mesic meadow. Changing hydrological conditions, from multiple years of high water to increasing drought, was an important factor influencing community composition and may have interacted with management treatments. Biomass differed among treatments and between years within cover types. In the wettest cover types, fall burning and grazing rotation treatments had greater negative impact on biomass than the idle treatment, but in drier cover types, summer grazing stimulated

Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones.

PubMed

Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B

2013-01-01

Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.

Bacterial Community Composition Associated with Chironomid Egg Masses

PubMed Central

Senderovich, Yigal; Halpern, Malka

2012-01-01

Chironomids (Diptera: Chironomidae) are the most widely distributed and often the most abundant insect in freshwater. They undergo a complete metamorphosis of four life stages, of which the egg, larva, and pupae are aquatic and the adult is terrestrial. Chironomid egg masses were found to be natural reservoirs of Vibrio cholerae and Aeromonas species. To expand the knowledge of the endogenous bacterial community associated with chironomid egg masses, denaturing gradient gel electrophoresis and clone analysis of 16S rRNA gene libraries were used in this study. Bacterial community composition associated with chironomid egg masses was found to be stable among different sampling periods. Cloned libraries of egg masses revealed that about 40% of the clones were related to bacteria known to degrade various toxicants. These findings were further supported when bacterial species that showed resistance to different toxic metals were isolated from egg masses and larval samples. Chironomids are found under a wide range of water conditions and are able to survive pollutants. However, little is known about their protective mechanisms under these conditions. Chironomid egg masses are inhabited by a stable endogenous bacterial community, which may potentially play a role in protecting chironomids from toxicants in polluted environments. Further study is needed to support this hypothesis. PMID:23461272

[Impact of land-use type changes on soil nitrification and ammonia-oxidizing bacterial community composition].

PubMed

Yang, Li-Lin; Mao, Ren-Zhao; Liu, Jun-Jie; Liu, Xiao-Jing

2011-11-01

A comparative study was conducted to determine nitrification potentials and ammonia-oxidizing bacterial (AOB) community composition in 0-20 cm soil depth in adjacent native forest,natural grassland, and cropland soils on the Tibetan Plateau, by incubation experiment and by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, respectively. Cropland has the highest nitrification potential and nitrate concentration among the three land-use types (LUT), approximately 9 folds and more than 11 folds than that of the forests and grasslands, respectively. NO3(-) -N accounted for 70%-90% of inorganic N in cropland soil, while NH4(+) -N was the main form of inorganic N in forest and grassland soils. Nitrification potentials and nitrate concentrations showed no significant difference between native forest and grassland soils. The native forest showed the lowest nitrification potentials and the lowest AOB diversity and community composition among the three LUT. Conversions from natural grasslands to croplands remarkably decreased the AOB diversity and composition, but croplands remain high similarity in AOB community composition compared with grasslands. The minimal and the lowest diversity of AOB in native forests directly resulted to the lowest nitrification potentials compared to natural grasslands and croplands. From the fact of the highest nitrification potentials and nitrate concentrations in croplands indicated that there were the most substantial AOB with higher activity and priority. The results provide evidence that changes of land-use type can affect both soil nitrogen internal cycling process, the diversity, community and activity of AOB, which further affect soil environment quality and the long-term sustainability of ecosystems.

Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols.

PubMed

Ma, Mingchao; Zhou, Jing; Ongena, Marc; Liu, Wenzheng; Wei, Dan; Zhao, Baisuo; Guan, Dawei; Jiang, Xin; Li, Jun

2018-02-13

Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.

Different mixing techniques in experimental mesocosms—does mixing affect plankton biomass and community composition?

PubMed Central

Striebel, Maren; Kirchmaier, Leo; Hingsamer, Peter

2014-01-01

Over the past four decades, mesocosm studies have been successfully used for a wide range of applications and have provided a lot of information on trophic interactions and biogeochemical cycling of aquatic ecosystem. However, the setup of such mesocosms (e.g., dimensions and duration of experiments) needs to be adapted to the relevant biological processes being investigated. Mixing of the water column is an important factor to be considered in mesocosm experiments because enclosing water in an artificial chamber always alters the mixing regime. Various approaches have been applied to generate mixing in experimental ecosystems, including pure mechanical mixing (e.g., using a disc), airlifts, bubbling with compressed air, and pumping. In this study, we tested different mixing techniques for outdoor mesocosms and their impact on plankton biomass and community composition. We compared mesocosms mixed with a disc, an airlift-system, and bubbling, and used a nonactively mixed mesocosm as a control. We investigated phytoplankton, ciliate, and zooplankton communities during a 19-d mesocosm experiment. Based on our results, we concluded that mechanical mixing with a disc was the most effective technique due to the undertow produced by lowering and lifting the disc. While no mixing technique affected seston biomass, zooplankton biomass was highest in the treatments mixed with the disc. The airlift treatments had the lowest relative share of small flagellates. However, no further differences in phytoplankton community composition occurred and no differences in zooplankton community composition existed between all actively mixed treatments. PMID:25729335

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

USGS Publications Warehouse

Cordova-Kreylos, A. L.; Cao, Y.; Green, P.G.; Hwang, H.-M.; Kuivila, K.M.; LaMontagne, M.G.; Van De Werfhorst, L. C.; Holden, P.A.; Scow, K.M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. Copyright ?? 2006, American Society for

Diversity, Composition, and Geographical Distribution of Microbial Communities in California Salt Marsh Sediments

PubMed Central

Córdova-Kreylos, Ana Lucía; Cao, Yiping; Green, Peter G.; Hwang, Hyun-Min; Kuivila, Kathryn M.; LaMontagne, Michael G.; Van De Werfhorst, Laurie C.; Holden, Patricia A.; Scow, Kate M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. PMID:16672478

Satellite Observations for Detecting and Tracking Changes in Atmospheric Composition

EPA Science Inventory

The international scientific community's Integrated Global Atmosphere Chemistry Observation System report outlined a plan for ground-based, airborne and satellite Measurements, and models to integrate the observations into a 4-dimensional representation of the atmosphere (space a...

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate.

PubMed

Yan, Lijuan; Sinkko, Hanna; Penttinen, Petri; Lindström, Kristina

2016-01-15

The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. Copyright © 2015 Elsevier B.V. All rights reserved.

Fitness trade-offs modify community composition under contrasting disturbance regimes in Pseudomonas fluorescens microcosms.

PubMed

Engelmoer, Daniel J P; Rozen, Daniel E

2009-11-01

Disturbance is thought to be a major factor influencing patterns of biodiversity. In addition, disturbance can modify community composition if there are species specific trade-offs between fitness and disturbance tolerance. Here, we examine the role of disturbance on the evolution of coexisting biofilm-forming morphotypes of Pseudomonas fluorescens maintained in spatially structured laboratory microcosms. We identified four heritably stable ecotypes that varied significantly in their competitiveness under different disturbance treatments. Furthermore, we identified significant trade-offs in competitiveness across disturbance treatments for three of four of these ecotypes. These trade-offs modified dominance relationships between strains and thus altered community composition, with a peak of ecotype diversity occurring at intermediate disturbance frequencies.

Effect of ocean acidification on the structure and fatty acid composition of a natural plankton community in the Baltic Sea

NASA Astrophysics Data System (ADS)

Bermúdez, Rafael; Winder, Monika; Stuhr, Annegret; Almén, Anna-Karin; Engström-Öst, Jonna; Riebesell, Ulf

2016-12-01

Increasing atmospheric carbon dioxide (CO2) is changing seawater chemistry towards reduced pH, which affects various properties of marine organisms. Coastal and brackish water communities are expected to be less affected by ocean acidification (OA) as these communities are typically adapted to high fluctuations in CO2 and pH. Here we investigate the response of a coastal brackish water plankton community to increasing CO2 levels as projected for the coming decades and the end of this century in terms of community and biochemical fatty acid (FA) composition. A Baltic Sea plankton community was enclosed in a set of offshore mesocosms and subjected to a CO2 gradient ranging from natural concentrations ( ˜ 347 µatm fCO2) up to values projected for the year 2100 ( ˜ 1333 µatm fCO2). We show that the phytoplankton community composition was resilient to CO2 and did not diverge between the treatments. Seston FA composition was influenced by community composition, which in turn was driven by silicate and phosphate limitation in the mesocosms and showed no difference between the CO2 treatments. These results suggest that CO2 effects are dampened in coastal communities that already experience high natural fluctuations in pCO2. Although this coastal plankton community was tolerant of high pCO2 levels, hypoxia and CO2 uptake by the sea can aggravate acidification and may lead to pH changes outside the currently experienced range for coastal organisms.

Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean.

PubMed

Dinasquet, Julie; Richert, Inga; Logares, Ramiro; Yager, Patricia; Bertilsson, Stefan; Riemann, Lasse

2017-06-01

The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, N-acetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Exposing NASA's Earth Observations to the Applications Community and Public

NASA Astrophysics Data System (ADS)

Boller, R. A.; Baynes, K.; Pressley, N. N.; Thompson, C. K.; Schmaltz, J. E.; King, B. A.; Wong, M. M.; Rice, Z.; Gunnoe, T.; Roberts, J. T.; Rodriguez, J.; De Luca, A. P.; King, J.

2017-12-01

NASA's Earth Observing System (EOS) generates a wealth of data products which are generally intended for scientific research. In recent years, however, this data has also become more accessible to the applications community and public through the Worldview app and Global Imagery Browse Services (GIBS). These mapping interfaces provide historical and near real-time access to NASA's Earth observations for a wide range of uses. This presentation will focus on how the applications community, public, and media use these interfaces for decision-making, leisure, and anything in between.

Exposing NASA's Earth Observations to the Applications Community and Public

NASA Technical Reports Server (NTRS)

Boller, R.; Baynes, K.; Pressley, N.; Thompson, C.; Cechini, M.; Schmaltz, J.; Wong, M.; King, B.; Rice, Z.; Sprague, J.;

Richness, composition and trophic groups of an avian community in the Pernambuco Endemism Centre, Alagoas, Brazil.

PubMed

Toledo-Lima, Guilherme S; Macario, Phoeve; Lyra-Neves, Rachel M de; Teixeira, Bruno P; Lima, Luiz A F de; Sugliano, Gabriel O S; Telino-Júnior, Wallace R

2014-09-01

In northeastern Brazil, the reduction of the natural forest cover to a series of small, isolated fragments has had negative consequences for the local avian fauna, in particular, a loss of the more specialized species, while the populations of some generalists have tended to increase. The present study focuses on the composition and trophic groups of a bird community on a farm in the northeastern Brazilian state of Alagoas. Monthly surveys were conducted between November 2008 and October 2009, based on mist-netting and systematic observations. Overall, 112 species were recorded, of which 76 were associated with the two forest fragments surveyed, while all the others were observed exclusively in the surrounding matrix of pasture and orchards. The bird community presented a predominance of insectivorous species, followed by omnivores. However, specialized trunk-creeping and understory insectivores accounted for only around 15% of the species in this feeding category. The reduced diversity of other guilds and species with more specialized diets, and the complete absence of sensitive species such as large parrots and raptors, reflects the severe fragmentation and degradation of the local forests, which has greatly reduced the availability of dietary resources and breeding sites.

Dynamics in benthic community composition and influencing factors in an upwelling-exposed coral reef on the Pacific coast of Costa Rica

PubMed Central

Sánchez-Noguera, Celeste; Roth, Florian; Jiménez, Carlos; Rixen, Tim; Cortés, Jorge; Wild, Christian

2015-01-01

Seasonal upwelling at the northern Pacific coast of Costa Rica offers the opportunity to investigate the effects of pronounced changes in key water parameters on fine-scale dynamics of local coral reef communities. This study monitored benthic community composition at Matapalo reef (10.539°N, 85.766°W) by weekly observations of permanent benthic quadrats from April 2013 to April 2014. Monitoring was accompanied by surveys of herbivore abundance and biomass and measurements of water temperature and inorganic nutrient concentrations. Findings revealed that the reef-building corals Pocillopora spp. exhibited an exceptional rapid increase from 22 to 51% relative benthic cover. By contrast, turf algae cover decreased from 63 to 24%, resulting in a corresponding increase in crustose coralline algae cover. The macroalga Caulerpa sertularioides covered up to 15% of the reef in April 2013, disappeared after synchronized gamete release in May, and subsequently exhibited slow regrowth. Parallel monitoring of influencing factors suggest that C. sertularioides cover was mainly regulated by their reproductive cycle, while that of turf algae was likely controlled by high abundances of herbivores. Upwelling events in February and March 2014 decreased mean daily seawater temperatures by up to 7 °C and increased nutrient concentrations up to 5- (phosphate) and 16-fold (nitrate) compared to mean values during the rest of the year. Changes in benthic community composition did not appear to correspond to the strong environmental changes, but rather shifted from turf algae to hard coral dominance over the entire year of observation. The exceptional high dynamic over the annual observation period encourages further research on the adaptation potential of coral reefs to environmental variability. PMID:26623190

Crack healing in cross-ply composites observed by dynamic mechanical analysis

NASA Astrophysics Data System (ADS)

Nielsen, Christian; Nemat-Nasser, Sia

2015-03-01

Cross-ply composites with healable polymer matrices are characterized using dynamic mechanical analysis (DMA). The [90,0]s samples are prepared by embedding layers of unidirectional glass or carbon fibers in 2MEP4FS, a polymer with thermally reversible covalent cross-links, which has been shown to be capable of healing internal cracks and fully recovering fracture toughness when the crack surfaces are kept in contact. After fabrication, cracks in the composites' transverse plies are observed due to residual thermal stresses introduced during processing. Single cantilever bending DMA measurements show the samples exhibit periods of increasing storage moduli with increasing temperature. These results are accurately modeled as a one-dimensional composite, which captures the underlying physics of the phenomenon. The effect of cracks on the stiffness is accounted for by a shear-lag model. The predicted crack density of the glass fiber composite is shown to fall within a range observed from microscopy images. Crack healing occurs as a function of temperature, with chemistry and mechanics-based rationales given for the onset and conclusion of healing. The model captures the essential physics of the phenomenon and yields results in accord with experimental observations.

Changes in ground beetle diversity and community composition in age structured forests (Coleoptera, Carabidae).

PubMed

Riley, Kathryn N; Browne, Robert A

2011-01-01

We examined diversity, community composition, and wing-state of Carabidae as a function of forest age in Piedmont North Carolina. Carabidae were collected monthly from 396 pitfall traps (12×33 sites) from March 2009 through February 2010, representing 5 forest age classes approximately 0, 10, 50, 85, and 150 years old. A total of 2,568 individuals, representing 30 genera and 63 species, were collected. Carabid species diversity, as estimated by six diversity indices, was significantly different between the oldest and youngest forest age classes for four of the six indices. Most carabid species were habitat generalists, occurring in all or most of the forest age classes. Carabid species composition varied across forest age classes. Seventeen carabid species were identified as potential candidates for ecological indicators of forest age. Non-metric multidimensional scaling (NMDS) showed separation among forest age classes in terms of carabid beetle community composition. The proportion of individuals capable of flight decreased significantly with forest age.

Changes in ground beetle diversity and community composition in age structured forests (Coleoptera, Carabidae)

PubMed Central

Riley, Kathryn N.; Browne, Robert A.

2011-01-01

Abstract We examined diversity, community composition, and wing-state of Carabidae as a function of forest age in Piedmont North Carolina. Carabidae were collected monthly from 396 pitfall traps (12×33 sites) from March 2009 through February 2010, representing 5 forest age classes approximately 0, 10, 50, 85, and 150 years old. A total of 2,568 individuals, representing 30 genera and 63 species, were collected. Carabid species diversity, as estimated by six diversity indices, was significantly different between the oldest and youngest forest age classes for four of the six indices. Most carabid species were habitat generalists, occurring in all or most of the forest age classes. Carabid species composition varied across forest age classes. Seventeen carabid species were identified as potential candidates for ecological indicators of forest age. Non-metric multidimensional scaling (NMDS) showed separation among forest age classes in terms of carabid beetle community composition. The proportion of individuals capable of flight decreased significantly with forest age. PMID:22371677

Evaluation of phytoplankton community composition in the eutrophic Masan Bay by HPLC pigment analysis.

PubMed

Kim, Jeong Bae; Hong, Sokjin; Lee, Won-Chan; Lee, Yong-Woo; Kim, Hyung Chul; Cho, Yoonsik

2015-03-01

To assess the spatiotemporal changes in phytoplankton community composition in relation to the environment of Masan Bay, a semi-enclosed bay on the southern coast of Korea, photosynthetic pigments and environmental variables were analyzed in seawater, every month between March and November 2010. The level of dissolved inorganic nutrients was highest between July and September when the freshwater influx was at its peak, whereas chlorophyll a level was highest in April and August. Phosphate concentration was low in April (average: 0.22 +/- 0.17 microM), indicating the role of phosphate as a growth-limiting factor for phytoplankton. The results of pigment analysis indicate that dinoflagellate blooms occurred under favorable conditions, where competition with diatoms occurred. Fucoxanthin- and chlorophyll b-containing phytoplankton dominated the surface layer of Masan Bay from July to September. The composition of phytoplankton community in Masan Bay changed dramatically each month according to variations in the amount and composition of nutrients introduced through surface runoff.

Vertical distribution of chlorophyll a concentration and phytoplankton community composition from in situ fluorescence profiles: a first database for the global ocean

NASA Astrophysics Data System (ADS)

Sauzède, R.; Lavigne, H.; Claustre, H.; Uitz, J.; Schmechtig, C.; D'Ortenzio, F.; Guinet, C.; Pesant, S.

2015-10-01

In vivo chlorophyll a fluorescence is a proxy of chlorophyll a concentration, and is one of the most frequently measured biogeochemical properties in the ocean. Thousands of profiles are available from historical databases and the integration of fluorescence sensors to autonomous platforms has led to a significant increase of chlorophyll fluorescence profile acquisition. To our knowledge, this important source of environmental data has not yet been included in global analyses. A total of 268 127 chlorophyll fluorescence profiles from several databases as well as published and unpublished individual sources were compiled. Following a robust quality control procedure detailed in the present paper, about 49 000 chlorophyll fluorescence profiles were converted into phytoplankton biomass (i.e., chlorophyll a concentration) and size-based community composition (i.e., microphytoplankton, nanophytoplankton and picophytoplankton), using a method specifically developed to harmonize fluorescence profiles from diverse sources. The data span over 5 decades from 1958 to 2015, including observations from all major oceanic basins and all seasons, and depths ranging from the surface to a median maximum sampling depth of around 700 m. Global maps of chlorophyll a concentration and phytoplankton community composition are presented here for the first time. Monthly climatologies were computed for three of Longhurst's ecological provinces in order to exemplify the potential use of the data product. Original data sets (raw fluorescence profiles) as well as calibrated profiles of phytoplankton biomass and community composition are available on open access at PANGAEA, Data Publisher for Earth and Environmental Science. Raw fluorescence profiles: http://doi.pangaea.de/10.1594/PANGAEA.844212 and Phytoplankton biomass and community composition:

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

PubMed

Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

2016-10-01

The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river. Copyright © 2016 Elsevier Inc. All rights reserved.

Cultural patterns in children's learning through keen observation and participation in their communities.

PubMed

Correa-Chávez, Maricela; Roberts, Amy L D; Pérez, Margarita Martínez

2011-01-01

This chapter examines children's learning through careful attention and participation in the ongoing activities of their community. This form of learning, which has been called learning through Intent Community Participation, seems to be especially common in Mesoamerican Indigenous communities. In these communities, children are integrated into the everyday work and lives of adults and their learning may not be the central focus. We contrast this pattern with that of middle-class European American communities where children are segregated from the primary adult functions of the community. In middle-class communities and schools, children are often encouraged to engage in abstract lessons where their attention is explicitly directed to specific events. In contrast, learning through keen attention and observation may rely on learning through attention to instructions not specifically directed to the learner. Studies demonstrate Mesoamerican Indigenous children's ability to learn through simultaneous and open attention to overheard or observed activities. This form of learning is supported through multiple modalities of communication and interaction. Motivation to learn stems from the learner's inclusion into the major activities and goals of the community. Implications of research and future directions for the study of learning through keen observation are discussed.

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

PubMed

Hagen, Live Heldal; Vivekanand, Vivekanand; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

2015-07-01

A new biogas process is initiated by adding a microbial community, typically in the form of a sample collected from a functional biogas plant. This inoculum has considerable impact on the initial performance of a biogas reactor, affecting parameters such as stability, biogas production yields and the overall efficiency of the anaerobic digestion process. In this study, we have analyzed changes in the microbial composition and performance of an inoculum during storage using barcoded pyrosequencing of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, and determination of the biomethane potential, respectively. The inoculum was stored at room temperature, 4 and -20 °C for up to 11 months and cellulose was used as a standard substrate to test the biomethane potential. Storage up to 1 month resulted in similar final methane yields, but the rate of methane production was reduced by storage at -20 °C. Longer storage times resulted in reduced methane yields and slower production kinetics for all storage conditions, with room temperature and frozen samples consistently giving the best and worst performance, respectively. Both storage time and temperature affected the microbial community composition and methanogenic activity. In particular, fluctuations in the relative abundance of Bacteroidetes were observed. Interestingly, a shift from hydrogenotrophic methanogens to methanogens with the capacity to perform acetoclastic methanogensis was observed upon prolonged storage. In conclusion, this study suggests that biogas inocula may be stored up to 1 month with low loss of methanogenic activity, and identifies bacterial and archaeal species that are affected by the storage.

Top predators affect the composition of naive protist communities, but only in their early-successional stage.

PubMed

Zander, Axel; Gravel, Dominique; Bersier, Louis-Félix; Gray, Sarah M

2016-02-01

Introduced top predators have the potential to disrupt community dynamics when prey species are naive to predation. The impact of introduced predators may also vary depending on the stage of community development. Early-succession communities are likely to have small-bodied and fast-growing species, but are not necessarily good at defending against predators. In contrast, late-succession communities are typically composed of larger-bodied species that are more predator resistant relative to small-bodied species. Yet, these aspects are greatly neglected in invasion studies. We therefore tested the effect of top predator presence on early- and late-succession communities that were either naive or non-naive to top predators. We used the aquatic community held within the leaves of Sarracenia purpurea. In North America, communities have experienced the S. purpurea top predator and are therefore non-naive. In Europe, this predator is not present and its niche has not been filled, making these communities top-predator naive. We collected early- and late-succession communities from two non-naive and two naive sites, which are climatically similar. We then conducted a common-garden experiment, with and without the presence of the top predator, in which we recorded changes in community composition, body size spectra, bacterial density, and respiration. We found that the top predator had no statistical effect on global measures of community structure and functioning. However, it significantly altered protist composition, but only in naive, early-succession communities, highlighting that the state of community development is important for understanding the impact of invasion.

Changes in plant community composition lag behind climate warming in lowland forests.

PubMed

Bertrand, Romain; Lenoir, Jonathan; Piedallu, Christian; Riofrío-Dillon, Gabriela; de Ruffray, Patrice; Vidal, Claude; Pierrat, Jean-Claude; Gégout, Jean-Claude

2011-10-19

Climate change is driving latitudinal and altitudinal shifts in species distribution worldwide, leading to novel species assemblages. Lags between these biotic responses and contemporary climate changes have been reported for plants and animals. Theoretically, the magnitude of these lags should be greatest in lowland areas, where the velocity of climate change is expected to be much greater than that in highland areas. We compared temperature trends to temperatures reconstructed from plant assemblages (observed in 76,634 surveys) over a 44-year period in France (1965-2008). Here we report that forest plant communities had responded to 0.54 °C of the effective increase of 1.07 °C in highland areas (500-2,600 m above sea level), while they had responded to only 0.02 °C of the 1.11 °C warming trend in lowland areas. There was a larger temperature lag (by 3.1 times) between the climate and plant community composition in lowland forests than in highland forests. The explanation of such disparity lies in the following properties of lowland, as compared to highland, forests: the higher proportion of species with greater ability for local persistence as the climate warms, the reduced opportunity for short-distance escapes, and the greater habitat fragmentation. Although mountains are currently considered to be among the ecosystems most threatened by climate change (owing to mountaintop extinction), the current inertia of plant communities in lowland forests should also be noted, as it could lead to lowland biotic attrition. ©2011 Macmillan Publishers Limited. All rights reserved

Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

PubMed Central

Oved, Tamar; Shaviv, Avi; Goldrath, Tal; Mandelbaum, Raphi T.; Minz, Dror

2001-01-01

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein. PMID:11472914

SPRUCE: Sphagnum Productivity and Community Composition in the SPRUCE Experimental Plots

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

Norby, R.J.; Childs, J.

This data set reports annual dry matter production of Sphagnum in replicated growth columns, the composition of the moss community, and plot-average Sphagnum productivity in the SPRUCE experimental study plots located in the S1-Bog. Data are reported for 2016 (October 2015 to October 2016) and 2017 (October 2016 to October 2017). Additional data will be appended as they become available.

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

PubMed Central

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C.

2017-01-01

ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of Py

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment.

PubMed

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C; Xu, Jianming

2017-01-01

Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria , particularly Actinomycetales , was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and

Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

PubMed

Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

2017-12-01

Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

USDA-ARS?s Scientific Manuscript database

Changing environmental conditions result in substantial shifts in the composition of communities. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, most studies on environmental change quantify the biotic responses at single spat...

COMMUNITY SCALE STREAM TAXA SENSITIVITIES TO DIFFERENT COMPOSITIONS OF EXCESS TOTAL DISSOLVED SOLIDS

EPA Science Inventory

Model stream chronic dosing studies (42 d) were conducted with three total dissolved solids (TDS) recipes. The recipes differed in composition of major ions. Community scale emergence was compared with single-species responses conducted simultaneously using the whole effluent tox...

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition.

PubMed

Castaño, Carles; Parladé, Javier; Pera, Joan; Martínez de Aragón, Juan; Alday, Josu G; Bonet, José Antonio

2016-11-01

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Winter Waterbird Community Composition and Use at Created Wetlands in West Virginia, USA

PubMed Central

Peters, Michael L.

2017-01-01

Information on nonbreeding waterbirds using created wetlands in the Central Appalachian region of the United States is limited. We compared waterbird communities of two managed wetlands, created in 2013 and 2001, in West Virginia. We observed 27 species of waterbirds. Species richness and diversity were generally similar between the wetlands, but species composition and use differed. Branta canadensis (Canada Geese), Anas strepera (Gadwall), Bucephala albeola (Buffleheads), Aythya affinis (Lesser Scaup), and Aythya collaris (Ring-Necked Ducks) used the older wetland most frequently. Disparities in species use were the highest in March. The older wetland differed from the younger in supporting species such as diving ducks, possibly due to differences in size, vegetation, water depth, and microtopography. However, the ability to provide habitat for waterbirds during the winter was determined to be comparable between wetlands, despite their age difference. PMID:28386513

High similarity between bacterioneuston and airborne bacterial community compositions in a high mountain lake area.

PubMed

Hervas, Anna; Casamayor, Emilio O

2009-02-01

The bacterioneuston (bacteria inhabiting the air-water interface) is poorly characterized and possibly forms a unique community in the aquatic environment. In high mountain lakes, the surface film is subjected to extreme conditions of life, suggesting the development of a specific and adapted bacterioneuston community. We have studied the surface film of a remote high mountain lake in the Pyrenees by cloning the PCR-amplified 16S rRNA gene and comparing with bacteria present in underlying waters (UW), and airborne bacteria from the dust deposited on the top of the snow pack. We did not detect unusual taxa in the neuston but rather very common and widespread bacterial groups. Betaproteobacteria and Actinobacteria accounted for >75% of the community composition. Other minor groups were Gammaproteobacteria (between 8% and 12%), Alphaproteobacteria (between 1% and 5%), and Firmicutes (1%). However, we observed segregated populations in neuston and UW for the different clades within each of the main phylogenetic groups. The soil bacterium Acinetobacter sp. was only detected in the snow-dust sample. Overall, higher similarities were found between bacterioneuston and airborne bacteria than between the former and bacterioplankton. The surface film in high mountain lakes appears as a direct interceptor of airborne bacteria useful for monitoring long-range bacterial dispersion.

Effect of biostimulants on 2,4,6-trinitrotoluene (TNT) degradation and bacterial community composition in contaminated aquifer sediment enrichments.

PubMed

Fahrenfeld, Nicole; Zoeckler, Jeffrey; Widdowson, Mark A; Pruden, Amy

2013-04-01

2,4,6-Trinitrotoluene (TNT) is a toxic and persistent explosive compound occurring as a contaminant at numerous sites worldwide. Knowledge of the microbial dynamics driving TNT biodegradation is limited, particularly in native aquifer sediments where it poses a threat to water resources. The purpose of this study was to quantify the effect of organic amendments on anaerobic TNT biodegradation rate and pathway in an enrichment culture obtained from historically contaminated aquifer sediment and to compare the bacterial community dynamics. TNT readily biodegraded in all microcosms, with the highest biodegradation rate obtained under the lactate amended condition followed by ethanol amended and naturally occurring organic matter (extracted from site sediment) amended conditions. Although a reductive pathway of TNT degradation was observed across all conditions, denaturing gradient gel electrophoresis (DGGE) analysis revealed distinct bacterial community compositions. In all microcosms, Gram-negative γ- or β-Proteobacteria and Gram-positive Negativicutes or Clostridia were observed. A Pseudomonas sp. in particular was observed to be stimulated under all conditions. According to non-metric multidimensional scaling analysis of DGGE profiles, the microcosm communities were most similar to heavily TNT-contaminated field site sediment, relative to moderately and uncontaminated sediments, suggesting that TNT contamination itself is a major driver of microbial community structure. Overall these results provide a new line of evidence of the key bacteria driving TNT degradation in aquifer sediments and their dynamics in response to organic carbon amendment, supporting this approach as a promising technology for stimulating in situ TNT bioremediation in the subsurface.

Community composition and diversity of ground beetles (Coleoptera: Carabidae) in Yaoluoping National Nature Reserve

PubMed Central

Li, Wen-Bo; Liu, Nai-Yi; Wu, Yun-He; Zhang, Yu-Cai; Xu, Qin; Chu, Jun; Wang, Shu-Yan

2017-01-01

Abstract This study used pitfall trapping to examine community composition and diversity of ground beetles in five different habitats (coniferous, deciduous, mixed coniferous, farmland, and settlements) within Anhui Yaoluoping National Nature Reserve from May to September 2014. In total, 1,352 ground beetles were collected, belonging to 16 genera and 44 species. Of these, four dominant species Dolichus halensis, Harpalus pastor, Carabus casaleianus, and Pheropsophus jessoensis were identified, respectively, comprising 370, 177, 131, and 123 individuals. The deciduous forest showed greater diversity (3.78 according to Shannon–Weiner index), equitability (0.80 according to Pielou’s index), and dominance (9.52 according to Simpson’s index) when compared with farmland, but species richness in the deciduous forest (27) was lower than that in farmland (35). One-way analysis of variance showed that ground beetle species composition and abundance among different habitats varied significantly. Cluster analysis and principal coordinate analysis showed that farmland shared low community similarity with other habitat types, and coniferous and mixed coniferous forests shared similar community types. Our results indicate that species composition, abundance, and diversity of ground beetles are affected by different habitat types, with deciduous forest types being critical in maintaining the diversity of rare species. We recommend reducing cultivated farmland area and increasing the area of carefully planned deciduous forest in order to better protect ground beetle diversity in the region.

Vegetation community composition in wetlands created following oil sand mining in Alberta, Canada.

PubMed

Roy, Marie-Claude; Foote, Lee; Ciborowski, Jan J H

2016-05-01

Reclaiming wetlands following open pit mining for industrial oil sand extraction is challenging due to the physical and chemical conditions of the post-mined landscape. The aim of our study was to examine and compare the influence of oil sands process water (OSPW) and material (fine fluid tails or FFT) on the plant community composition of created wetlands. Compared to created-unamended and natural wetlands, the created wetlands amended with OSPW and/or FFT (created-tailings wetlands) had significantly higher water salinity, conductivity, dissolved oxygen concentration and lower oxidative-reductive potential. Water chemistry parameters of created-unamended did not differ significantly from those of natural wetlands. The sediment of created wetlands had significantly less moisture, total nitrogen, and organic content than the natural wetlands. The application of OSPW/FFT in created wetlands will likely lead to initial vegetation composition atypical of natural regional wetlands. For the objective of reclaiming vegetation composition to the status of natural regional wetlands, unamended wetlands were the best reclamation option, based on the physical and chemical parameters measured. Despite being the favored reclamation option, created-unamended wetlands' physical and chemical characteristics remain atypical of natural wetlands. Most significantly, the basin morphometry of created wetlands was significantly different from that of naturally-formed wetlands in the region, and this appears to partly explain difference in vegetation composition. We also demonstrate that species richness alone is not a useful measure in wetland monitoring. Instead, plant community composition is a better indicator of wetland conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of Microbial Community Composition and Methane Production From Northern Peatlands Across a Climate Gradient

NASA Astrophysics Data System (ADS)

Sarno, A. F.; Humphreys, E.; Olefeldt, D.; Heffernan, L.; Roman, T. D.; Sebestyen, S.; Kolka, R.; Yavitt, J. B.; Finn, D.; Cadillo-Quiroz, H.

2017-12-01

Northern peatland ecosystems allow for the accumulation of a carbon (C) pool as the rate of photosynthesis exceeds the rate of organic carbon decomposition. Under current climate conditions, many northern peatlands act as a C sink; however, changes in climate and other environmental conditions, such as soil permafrost melting, are capable of changing the decomposition cascade. Here we take advantage of four peatlands situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess how the relative abundance of microbial functional groups and substrate availability within the microbial community might impact the decomposition of soil organic matter to methane. The four peatlands had similar hydrology and geochemistry and were poor fen types. Soil, water and gas samples were collected at the water table level. Microbial community composition, derived from Illumina amplicon sequencing of the 16S rRNA gene, and geochemical and climate variables were analyzed with principal component regression analysis to determine major drivers of community variation. Mean annual temperature (r2=0.53), mean annual precipitation (r2=0.36), water table level (r2=0.43) and soil temperature (r2=0.49), were all statistically significant drivers of both general microbial and methanogen community composition (p value < 0.001). The relative abundance of Methanocella, Methanosarcina and Methanobacterium varied significantly across the climate gradient (p value < 0.05), however the majority of methanogen genera did not. Interestingly, dissolved methane (r2=0.24) was statistically significant at the general community level (p value < 0.001), but not significant when tested against only the methanogen community. The results demonstrate that environmental factors predicted to change over time due to climate change will have a significant impact on microbial community

Sensitivity of grassland plant community composition to spatial vs. temporal variation in precipitation

USDA-ARS?s Scientific Manuscript database

Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the magnitudes of these changes, it is important to determine how temporal variation in climate influences...

Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan, Indonesia.

PubMed

Isobe, Kazuo; Otsuka, Shigeto; Sudiana, Imade; Nurkanto, Arif; Senoo, Keishi

2009-10-01

Soil bacterial community compositions in burnt and unburnt areas in a tropical rainforest in East Kalimantan, Indonesia, were investigated 8 and 9 years after a fire by denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene. Three study sites were set in the forest area devoid of fire damage (control), and in the lightly damaged and heavily damaged forest areas. Succession of aboveground vegetation in the two damaged areas had clearly proceeded after the fire, but the vegetation types still differed from the unburnt area at the time of this study. Community composition of total soil bacteria was similar among the three areas, and so was that of actinobacteria. However, the composition of ammonia oxidizing bacteria clearly differed depending on the presence or absence of past fire damage. These results indicate that even nearly a decade after the forest fire, impacts of the fire remained on the community composition of ammonia oxidizing bacteria, but not apparently on those of dominant bacteria and actinobacteria.

Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

PubMed Central

Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

2016-01-01

We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses. PMID:27892507

Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

NASA Astrophysics Data System (ADS)

Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

2016-11-01

We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

Relationships between cognitive function and body composition among community-dwelling older adults: a cross-sectional study.

PubMed

Noh, Hye-Mi; Oh, Sohee; Song, Hong Ji; Lee, Eun Young; Jeong, Jin-Young; Ryu, Ohk-Hyun; Hong, Kyung-Soon; Kim, Dong-Hyun

2017-11-02

Previous studies reported mixed results regarding the association between cognition and body weight in late life. We evaluated the relationships between cognitive function and body composition among community-dwelling older adults. Three hundred twenty subjects (≥65 years, women 53%) with available data of cognitive function and body composition from 2010 Hallym Aging Study. Cognitive function was assessed using Korean Mini-Mental State Examination (K-MMSE). Dual-energy X-ray absorptiometry (DEXA) was used for measuring body composition including body fat and lean body mass. Anthropometric measurements and laboratory data were collected in clinical examination. Body composition variables were divided into sex-specific tertiles, and examined by multivariable logistic regression. Among female, the highest tertile group of fat mass and second tertile group of total lean body mass were associated with lower risk for cognitive impairment compared to the respective first tertile groups (odds ratios, 0.23 and 0.09, respectively; 95% confidence intervals, 0.04-0.88 and 0.01-0.44, respectively) after adjusting for confounding factors. In male, higher arm bone mineral content was associated with lower risk for cognitive impairment, but significance was lost after adjusting for adiponectin, age, and education. Higher fat mass and lean body mass were associated with lower risk of cognitive impairment in older women. These observations suggest that body fat and lean mass later in life might be beneficial for cognition.

Effects of triclosan on bacterial community composition and ...

EPA Pesticide Factsheets

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

PubMed

Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

2016-04-01

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange.

PubMed

Williams, Alwyn; Manoharan, Lokeshwaran; Rosenstock, Nicholas P; Olsson, Pål Axel; Hedlund, Katarina

2017-01-01

Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon ( 13 C) and 33 P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

PubMed Central

Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Rodney T.; Moore, John C.

2014-01-01

The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-Proteobacteria and β-Proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming. PMID:25324836

Nitrogen Forms Influence Microcystin Concentration and Composition via Changes in Cyanobacterial Community Structure

PubMed Central

Monchamp, Marie-Eve; Pick, Frances R.; Beisner, Beatrix E.; Maranger, Roxane

2014-01-01

The eutrophication of freshwaters is a global health concern as lakes with excess nutrients are often subject to toxic cyanobacterial blooms. Although phosphorus is considered the main element regulating cyanobacterial biomass, nitrogen (N) concentration and more specifically the availability of different N forms may influence the overall toxicity of blooms. In this study of three eutrophic lakes prone to cyanobacterial blooms, we examined the effects of nitrogen species and concentrations and other environmental factors in influencing cyanobacterial community structure, microcystin (MC) concentrations and MC congener composition. The identification of specific MC congeners was of particular interest as they vary widely in toxicity. Different nitrogen forms appeared to influence cyanobacterial community structure leading to corresponding effects on MC concentrations and composition. Total MC concentrations across the lakes were largely explained by a combination of abiotic factors: dissolved organic nitrogen, water temperature and ammonium, but Microcystis spp. biomass was overall the best predictor of MC concentrations. Environmental factors did not appear to affect MC congener composition directly but there were significant associations between specific MC congeners and particular species. Based on redundancy analyses (RDA), the relative biomass of Microcystis aeruginosa was associated with MC-RR, M. wesenbergii with MC-LA and Aphanizomenon flos-aquae with MC-YR. The latter two species are not generally considered capable of MC production. Total nitrogen, water temperature, ammonium and dissolved organic nitrogen influenced the cyanobacterial community structure, which in turn resulted in differences in the dominant MC congener and the overall toxicity. PMID:24427318

Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone

PubMed Central

Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J.

2017-01-01

ABSTRACT Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON. IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and

Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.

PubMed

de Voogd, Nicole J; Cleary, Daniel F R; Polónia, Ana R M; Gomes, Newton C M

2015-04-01

In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

PubMed

Munoz, François; Ramesh, B R; Couteron, Pierre

2014-08-01

Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

Seasonal variation in the biochemical compositions of phytoplankton and zooplankton communities in the southwestern East/Japan Sea

NASA Astrophysics Data System (ADS)

Jo, Naeun; Kang, Jae Joong; Park, Won Gyu; Lee, Bo Ram; Yun, Mi Sun; Lee, Jang Han; Kim, Su Min; Lee, Dasom; Joo, HuiTae; Lee, Jae Hyung; Ahn, So Hyun; Lee, Sang Heon

2017-09-01

The macromolecular composition of phytoplankton communities and the proximate composition of zooplankton communities were measured monthly in the southwestern East/Japan Sea from April to November 2014 in order to identify seasonal changes in, and relationships among, the biochemical compositions in both phytoplankton and zooplankton. The carbohydrate content of phytoplankton was highest in June, whereas the protein content was highest in August and lipids were highest in April. Overall, carbohydrates were dominant (53.2 ± 12.5%) in the macromolecular composition of phytoplankton during the study period. This composition is believed to result from the dominance of diatoms and/or nutrient-depleted conditions. In comparison, the protein level of zooplankton was highest in November, whereas lipids were slightly higher in May than other months. Overall, proteins were the dominant organic compounds (47.9±8.6% DW) in zooplankton communities, whereas lipids were minor components (5.5±0.6% DW). The high protein content of zooplankton might be related to the abundance of copepods, whereas the low lipid content might be due to a relatively high primary production that could provide a sufficient food supply for zooplankton so that they do not require high lipid storage. A significant positive correlation (r=0.971, n=7, p<0.01) was found between the lipid compositions of phytoplankton and zooplankton during our study period with a time lag, which is consistent with the findings from previous studies. More detailed studies on the biochemical composition of phytoplankton and zooplankton are needed to better understand the East/Japan Sea ecosystem's response to the many environmental changes associated with global warming.

Transfer to forest nurseries significantly affects mycorrhizal community composition of Asteropeia mcphersonii wildings.

PubMed

Henry, Charline; Raivoarisoa, Jeanne-Françoise; Razafimamonjy, Angélo; Ramanankierana, Heriniaina; Andrianaivomahefa, Paul; Ducousso, Marc; Selosse, Marc-André

2017-05-01

Mycorrhizal symbiosis is extremely important for tree growth, survival and resistance after transplantation particularly in Madagascar where deforestation is a major concern. The importance of mycorrhizal symbiosis is further increased when soil conditions at the planting site are limiting. To identify technical itineraries capable of improving ecological restoration in Madagascar, we needed to obtain native ectomycorrhizal (ECM) saplings with a wide diversity of ECM fungi. To this end, we transplanted ECM seedlings from the wild (wildlings) to a nursery. Using molecular characterisation of internal transcribed spacer (ITS) rDNA, we tested the effect of transplanting Asteropeia mcphersonii wildlings on ECM communities after 8 months of growth in the nursery. With or without the addition of soil from the site where the seedlings were sampled to the nursery substrate, we observed a dramatic change in the composition of fungal communities with a decrease in the ECM infection rate, a tremendous increase in the abundance of an operational taxonomic unit (OTU) taxonomically close to the order Trechisporales and the disappearance of all OTUs of Boletales. Transplanting to the nursery and/or to nursery conditions was shown to be incompatible with the survival and even less with the development in the nursery of most ECM fungi naturally associated with A. mcphersonii wildings.

Light availability affects stream biofilm bacterial community composition and function, but not diversity

PubMed Central

Wagner, Karoline; Besemer, Katharina; Burns, Nancy R.; Battin, Tom J.

2015-01-01

Summary Changes in riparian vegetation or water turbidity and browning in streams alter the local light regime with potential implications for stream biofilms and ecosystem functioning. We experimented with biofilms in microcosms grown under a gradient of light intensities (range: 5–152 μmole photons s−1 m−2) and combined 454‐pyrosequencing and enzymatic activity assays to evaluate the effects of light on biofilm structure and function. We observed a shift in bacterial community composition along the light gradient, whereas there was no apparent change in alpha diversity. Multifunctionality, based on extracellular enzymes, was highest under high light conditions and decoupled from bacterial diversity. Phenol oxidase activity, involved in the degradation of polyphenolic compounds, was twice as high on average under the lowest compared with the highest light condition. This suggests a shift in reliance of microbial heterotrophs on biofilm phototroph‐derived organic matter under high light availability to more complex organic matter under low light. Furthermore, extracellular enzyme activities correlated with nutrient cycling and community respiration, supporting the link between biofilm structure–function and biogeochemical fluxes in streams. Our findings demonstrate that changes in light availability are likely to have significant impacts on biofilm structure and function, potentially affecting stream ecosystem processes. PMID:26013911

Titan's Atmospheric Composition from Observations by the Cassini Infrared Spectrometer

NASA Technical Reports Server (NTRS)

Abbas, M. M.; LeClair, A.; Flasar, F. M.; Kunde, V. G.; Conrath, B. J.; Coustenis, A.; Jennings, D. J.; Nixon, C. A.; Brasunas, J.; Achterberg, R. K.

2006-01-01

The Composite Infrared Spectrometer (CIRS) aboard the Cassini spacecraft has been making observations during the fly-bys of Titan since the Saturn-Orbit-Insertion in July 2004. The observations provide infrared them1 emission spectra of Titan s atmosphere in three spectral channels covering the 10/cm to 1400/cm spectral region, with variable spectral resolutions of 0.53/cm and 2.8/cm. The uniquely observed spectra exhibit rotational and vibrational-rotational spectral lines of the molecular constituents of Titan s atmosphere that may be analyzed to retrieve information about the composition, thermal structure, and physical and dynamical processes in the remotely sensed atmosphere. We present an analysis of Titan's infrared spectra observed during July 2004 (TO), December 2004 (Tb) and February 2005 (T3), for retrieval of the stratospheric thermal structure, distribution of the hydrocarbons, nitriles, and oxygen bearing constituents, such as C2H2, C2H4, C2H6, C3H8, HCN, HC3N, CO, and CO2 . Preliminary results on the distribution and opacity of haze in Titan s atmosphere are discussed.

Summer phytoplankton pigments and community composition related to water mass properties in the Gulf of Gabes

NASA Astrophysics Data System (ADS)

Bel Hassen, M.; Drira, Z.; Hamza, A.; Ayadi, H.; Akrout, F.; Issaoui, H.

2008-05-01

Variations in phytoplankton pigments and community composition were examined in the Gulf of Gabes in relationship to water mass properties, characterised by the influence of the Modified Atlantic Water and by the thermal stratification. Data were collected on board the R/V Hannibal during July 2005. Distinct water masses were identified using cluster analysis of temperature-salinity ( T- S) characteristics. Three major clusters appeared based on the combined effects of temperature and salinity. The first cluster was identified as the cool and less salty bottom Modified Atlantic Water (MAW). The warmer and saltier Mediterranean Mixed Water (MMW) represented the second cluster. The third cluster was the Transition Water (TW) separating the two previous clusters. The pigment and taxonomic composition of these water masses were examined. Chlorophyll a was rather low (<200 ng l -1). Chlorophyll b was generally the most abundant accessory pigment and fucoxanthin dominated the accessory pigments in the MAW. Proportions of chlorophyll a associated with different phytoplankton classes were estimated using CHEMTAX software, and did not present significant variations among water groups. The results pointed out variations in the relative contribution of each phytoplankton taxa in each station group. Chlorophytes and prasinophytes accounted for 65% of chlorophyll a in the MMW. Diatoms and chlorophytes were relatively abundant in the MAW contributing to almost 63% of chlorophyll a. An unstructured community, slightly dominated by prasinophytes, chlorophytes and cryptophytes, characterised the TW. Different trophic statuses were observed in these water masses, the MMW and the MAW being characterised by mesotrophy, while an oligotrophy was observed in the TW. Nutrient availability, particularly the P-limitation supported by the summer stratification, as revealed by the high N:P ratio (greater than 20), seems to enhance the development of small-sized phytoplankton, thereby

Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes

PubMed Central

Scherer, Pia I.; Millard, Andrew D.; Miller, Andreas; Schoen, Renate; Raeder, Uta; Geist, Juergen; Zwirglmaier, Katrin

2017-01-01

Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the correlation of a genetic marker with microcystin concentration and aimed to identify the main microcystin producer. We used Illumina MiSeq sequencing to study the bacterioplankton in two recreational lakes in South Germany. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of microcystin biosynthesis genes. Bloom toxicity did not alter the bacterial community composition, which was highly dynamic at the lowest taxonomic level for some phyla such as Cyanobacteria. At the OTU level, we found distinctly different degrees of temporal variation between major bacteria phyla. Cyanobacteria and Bacteroidetes showed drastic temporal changes in their community compositions, while the composition of Actinobacteria remained rather stable in both lakes. The bacterial community composition of Alpha- and Beta-proteobacteria remained stable over time in Lake Klostersee, but it showed temporal variations in Lake Bergknappweiher. The presence of potential microcystin degraders and potential algicidal bacteria amongst prevalent Bacteroidetes and Alphaproteobacteria implied a role of those co-occurring heterotrophic bacteria in cyanobacterial bloom dynamics. Comparison of both lakes studied revealed a large shared microbiome, which was shaped toward the lake specific community composition by environmental factors. Microcystin

Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

PubMed Central

Paz, Henry A.; Anderson, Christopher L.; Muller, Makala J.; Kononoff, Paul J.; Fernando, Samodha C.

2016-01-01

The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

DOE PAGES

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.; ...

2018-03-20

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

PubMed Central

Moon, JiWon; Veach, Allison M.; Mosher, Jennifer J.; Wymore, Ann M.; van Nostrand, Joy D.; Zhou, Jizhong; Hazen, Terry C.; Arkin, Adam P.; Elias, Dwayne A.

2018-01-01

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems. PMID:29558522

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

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

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents.

PubMed

Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Bowker, Matthew A; Jeffries, Thomas C; Singh, Brajesh K

2018-04-02

Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Spacecraft observations of the solar wind composition

NASA Technical Reports Server (NTRS)

Bame, S. J.

1972-01-01

Solar wind composition studies by means of plasma analyzers carried on various spacecraft are reviewed. The average ratio of helium to hydrogen over the solar cycle is close to 0.045; values as low as 0.0025 and as high as 0.25 have been observed. High values have been observed following solar flares and interplanetary shock waves when the flare gas driving the shock arrives at the spacecraft. Ions of He-3(+2), O-16(+6), and O-16(+7) have been observed with Vela 3 electrostatic analyzers. Further measurements with Vela 5 analyzers have shown the presence of N-14(+6), Si-28(+7) to Si-28(+9) and Fe-56(+7) to Fe-56(+12) ions. The relative abundance of oxygen, silicon, and iron in the solar wind of July 6, 1969, was 1.00, 0.21, and 0.17, which is very similar to reported values for the corona. The ratio of helium to oxygen is variable; the average value of He/O is close to 100, but values between 30 and 400 have been observed.

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils.

PubMed

Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

2018-01-01

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity ( P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi ( P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline–Alkaline Soils

PubMed Central

Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

2018-01-01

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi. PMID:29535703

Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

PubMed Central

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

2012-01-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

PubMed

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid; Höfle, Manfred G

2012-05-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

NASA Astrophysics Data System (ADS)

Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

2018-02-01

Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time.

PubMed

Noble, Peter A; Park, Hee-Deung; Olson, Betty H; Asvapathanagul, Pitiporn; Hunter, M Colby; Garrido-Baserba, Manel; Lee, Sang-Hoon; Rosso, Diego

2016-07-01

Aeration diffusers in wastewater treatment plants generate air bubbles that promote mixing, distribution of dissolved oxygen, and microbial processing of dissolved and suspended matter in bulk solution. Biofouling of diffusers represents a significant problem to wastewater treatment plants because biofilms decrease oxygen transfer efficiency and increase backpressure on the blower. To better understand biofouling, we conducted a pilot study to survey the bacterial community composition and function of biofilms on different diffuser substrates and compare them to those in the bulk solution. DNA was extracted from the surface of ethylene-propylene-diene monomer (EPDM), polyurethane, and silicone diffusers operated for 15 months in a municipal treatment plant and sampled at 3 and 9 months. The bacterial community composition and function of the biofilms and bulk solution were determined by amplifying the 16S rRNA genes and pyrosequencing the amplicons and raw metagenomic DNA. The ordination plots and dendrograms of the 16S rRNA and functional genes showed that while the bacterial community composition and function of the bulk solution was independent of sampling time, the composition and function of the biofilms differed by diffuser type and testing time. For the EPDM and silicone diffusers, the biofilm communities were more similar in composition to the bulk solution at 3 months than 9 months. In contrast, the bacteria on the polyurethane diffusers were more dissimilar to the bulk solution at 3 months than 9 months. Taken together, the survey showed that the community composition and function of bacterial biofilms depend on the diffuser substrate and testing time, which warrants further elucidation.

Small mammal community composition in cornfields, roadside ditches, and prairies in eastern Nebraska

USGS Publications Warehouse

Kirsch, E.M.

1997-01-01

Community composition of small mammals was examined in prairies, cornfields, and their adjacent roadside ditches in eastern Nebraska. Western harvest mice (Reithrodontomys megalotis) and meadow voles (Microtus pennsylvanicus) were associated with prairie habitat, were common in ditches, but avoided cornfields. Prairie voles (M. Ochrogaster) and white-footed mice (Peromyscus leucopus) were associated with ditch habitat, were common in prairies, but avoided cornfields. Short-tailed shrews (Blarina brevicauda) avoided cornfields, were associated with ditches next to cornfields, but were common in prairies and ditches next to prairies. Deer mice (P. Maniculatus) were associated with cornfields but were relatively common in prairies and ditches. House mice (Mus musculus) were most common in ditches next to cornfields, occurred in cornfields and ditches next to prairies, but were not captured in prairies. Although community composition appears to differ among prairies, ditches, and cornfields, ditches support a more complete suite of the native small mammal species in large and relatively even numbers, whereas cornfields only support deer mice in large numbers.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Long-term effects of disinfectants on the community composition of drinking water biofilms.

PubMed

Roeder, Rosemarie S; Lenz, Johannes; Tarne, Peter; Gebel, Jürgen; Exner, Martin; Szewzyk, Ulrich

2010-06-01

Numerous investigations have demonstrated efficiencies of different disinfection methods, but until now only little is known about long-term effects on community compositions of drinking water biofilms. Changes in the community structure, especially regrowth of hygienically relevant microorganisms could be critical for the drinking water quality. In this study the long-term effect of disinfection methods on biofilm communities in drinking water systems was analysed. Old drinking water biofilms grown in silicone tubes were exposed to different preparations of disinfectants (free chlorine, chlorine dioxide, hydrogen peroxide combined with fruit acid, silver and silver with peracetic acid, respectively) and subsequently further exposed in the original drinking water. The comparison of the treated and regrown biofilm populations with untreated ones by the DNA-fingerprinting method denaturing gradient gel electrophoresis (DGGE) revealed a considerable population shift caused by the disinfectants. The disinfection methods induced a selection pressure on the biofilm populations depending on the composition and concentrations. The similarities between the treated and untreated biofilms were generally low. Compared to preparations with peracetic acid the disinfection with hydrogen peroxide and silver resulted in higher similarities of the treated and untreated biofilms, but the microbial diversity increased. It can be concluded that the disinfectants have a major impact on the drinking water biofilm communities and that possibly the intervention selects persisters and microorganisms, which can live on the residuals of the dead biofilm cells. For the evaluation of the efficiency of disinfection methods in drinking water installations it is necessary not only to consider reduction of certain bacteria but also to pay attention to the biofilm community. Copyright 2010 Elsevier GmbH. All rights reserved.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

PubMed Central

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila; Glavina del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A.; Tringe, Susannah G.; Currie, Cameron R.; Kolter, Roberto

2017-01-01

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans. PMID:28545131

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

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

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant speciesmore » Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.« less

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

DOE PAGES

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila; ...

2017-05-18

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant speciesmore » Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.« less

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

PubMed

Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

2017-01-01

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Assessment of beetle diversity, community composition and potential threats to forestry using kairomone-baited traps.

PubMed

Olivier-Espejel, S; Hurley, B P; Garnas, J

2017-02-01

Traps designed to capture insects during normal movement/dispersal, or via attraction to non-specific (plant) volatile lures, yield by-catch that carries valuable information about patterns of community diversity and composition. In order to identify potential native/introduced pests and detect predictors of colonization of non-native pines, we examined beetle assemblages captured in intercept panel traps baited with kairomone lures used during a national monitoring of the woodwasp, Sirex noctilio, in Southern Africa. We identified 50 families and 436 morphospecies of beetles from nine sites sampled in both 2008 and 2009 and six areas in 2007 (trap catch pooled by region) across a latitudinal and elevational gradient. The most diverse groups were mainly those strongly associated with trees, known to include damaging pests. While native species dominated the samples in terms of richness, the dominant species was the introduced bark beetle Orthotomicus erosus (Curculionidae: Scolytinae) (22 ± 34 individuals/site). Four Scolytinae species without previous records in South Africa, namely Coccotrypes niger, Hypocryphalus robustus (formerly Hypocryphalus mangiferae), Hypothenemus birmanus and Xyleborus perforans, were captured in low abundances. Communities showed temporal stability within sites and strong biogeographic patterns across the landscape. The strongest single predictors of community composition were potential evaporation, latitude and maximum relative humidity, while the strongest multifactor model contained elevation, potential evaporation and maximum relative humidity. Temperature, land use variables and distance to natural areas did not significantly correlate with community composition. Non-phytophagous beetles were also captured and were highly diverse (32 families) perhaps representing important beneficial insects.

Ocean acidification alters early successional coral reef communities and their rates of community metabolism.

PubMed

Noonan, Sam H C; Kluibenschedl, Anna; Fabricius, Katharina E

2018-01-01

Ocean acidification is expected to alter community composition on coral reefs, but its effects on reef community metabolism are poorly understood. Here we document how early successional benthic coral reef communities change in situ along gradients of carbon dioxide (CO2), and the consequences of these changes on rates of community photosynthesis, respiration, and light and dark calcification. Ninety standardised benthic communities were grown on PVC tiles deployed at two shallow-water volcanic CO2 seeps and two adjacent control sites in Papua New Guinea. Along the CO2 gradient, both the upward facing phototrophic and the downward facing cryptic communities changed in their composition. Under ambient CO2, both communities were dominated by calcifying algae, but with increasing CO2 they were gradually replaced by non-calcifying algae (predominantly green filamentous algae, cyanobacteria and macroalgae, which increased from ~30% to ~80% cover). Responses were weaker in the invertebrate communities, however ascidians and tube-forming polychaetes declined with increasing CO2. Differences in the carbonate chemistry explained a far greater amount of change in communities than differences between the two reefs and successional changes from five to 13 months, suggesting community successions are established early and are under strong chemical control. As pH declined from 8.0 to 7.8, rates of gross photosynthesis and dark respiration of the 13-month old reef communities (upper and cryptic surfaces combined) significantly increased by 10% and 20%, respectively, in response to altered community composition. As a consequence, net production remained constant. Light and dark calcification rates both gradually declined by 20%, and low or negative daily net calcification rates were observed at an aragonite saturation state of <2.3. The study demonstrates that ocean acidification as predicted for the end of this century will strongly alter reef communities, and will significantly

Ocean acidification alters early successional coral reef communities and their rates of community metabolism

PubMed Central

Kluibenschedl, Anna; Fabricius, Katharina E.

2018-01-01

Ocean acidification is expected to alter community composition on coral reefs, but its effects on reef community metabolism are poorly understood. Here we document how early successional benthic coral reef communities change in situ along gradients of carbon dioxide (CO2), and the consequences of these changes on rates of community photosynthesis, respiration, and light and dark calcification. Ninety standardised benthic communities were grown on PVC tiles deployed at two shallow-water volcanic CO2 seeps and two adjacent control sites in Papua New Guinea. Along the CO2 gradient, both the upward facing phototrophic and the downward facing cryptic communities changed in their composition. Under ambient CO2, both communities were dominated by calcifying algae, but with increasing CO2 they were gradually replaced by non-calcifying algae (predominantly green filamentous algae, cyanobacteria and macroalgae, which increased from ~30% to ~80% cover). Responses were weaker in the invertebrate communities, however ascidians and tube-forming polychaetes declined with increasing CO2. Differences in the carbonate chemistry explained a far greater amount of change in communities than differences between the two reefs and successional changes from five to 13 months, suggesting community successions are established early and are under strong chemical control. As pH declined from 8.0 to 7.8, rates of gross photosynthesis and dark respiration of the 13-month old reef communities (upper and cryptic surfaces combined) significantly increased by 10% and 20%, respectively, in response to altered community composition. As a consequence, net production remained constant. Light and dark calcification rates both gradually declined by 20%, and low or negative daily net calcification rates were observed at an aragonite saturation state of <2.3. The study demonstrates that ocean acidification as predicted for the end of this century will strongly alter reef communities, and will significantly

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

PubMed

Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

2013-12-01

Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights

Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols.

PubMed

Ma, Mingchao; Jiang, Xin; Wang, Qingfeng; Ongena, Marc; Wei, Dan; Ding, Jianli; Guan, Dawei; Cao, Fengming; Zhao, Baisuo; Li, Jun

2018-03-23

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition. © 2018 The Authors

Dissolved organic matter (DOM) in pore water of Arctic Ocean sediments: linking DOM molecular composition with microbial community structure

NASA Astrophysics Data System (ADS)

Rossel, P. E.; Bienhold, C.; Boetius, A.; Dittmar, T.

2016-02-01

Marine organic matter (OM) that sinks from surface waters to the seafloor is the energy and carbon source for benthic communities. These communities produce dissolved organic matter (DOM) in the process of remineralization, enriching the sediment porewater with fresh DOM compounds. In the Arctic Ocean, primary production is limited by nutrients and light and is thus strongly influenced by sea ice cover. Ice cover is expected to further decrease due to global warming, which may have important consequences for primary production and the quantity and quality of OM exported to the seafloor. This study focused on: 1) the molecular composition of the DOM in sediment pore waters of the deep Eurasian Arctic basins, 2) whether there is any relation between Arctic Ocean ice cover and DOM composition and 3) whether the DOM composition correlates with microbial community structure. Molecular data, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were statistically correlated with environmental parameters. The productive ice margin stations showed higher abundances of molecular formulae of peptides, unsaturated aliphatics and saturated fatty acids. This molecular trend is indicative of fresh OM and phytodetritus deposition, compared to the northernmost, ice-covered stations which had stronger aromatic signals. Benthic bacterial community structure, as assessed with the fingerprinting method ARISA, was significantly correlated with DOM molecular composition. Further analyses using Illumina next-generation sequencing will enable the taxonomic identification of specific bacterial groups and their interdependence with DOM compounds. This study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and provides first insights into potential links between microbial community structure and DOM molecular composition in Arctic sediments

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

PubMed

McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

2012-05-01

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

Decadal variability in coastal phytoplankton community composition in a changing West Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Schofield, Oscar; Saba, Grace; Coleman, Kaycee; Carvalho, Filipa; Couto, Nicole; Ducklow, Hugh; Finkel, Zoe; Irwin, Andrew; Kahl, Alex; Miles, Travis; Montes-Hugo, Martin; Stammerjohn, Sharon; Waite, Nicole

2017-06-01

The coastal waters of the West Antarctic Peninsula (WAP) are associated with large phytoplankton blooms dominated by large (>20 μm) diatoms however, nanoplankton (<20 μm) are also an important component of the food web. The dominant nanoflagellates in the WAP are cryptomonad algae. Using a twenty-year time series collected by the Palmer Long Term Ecological Research program at the United States Palmer Research Station, we assessed long-term patterns and stability in the coastal phytoplankton communities in the WAP. There was significant interannual variability in the integrated water column chlorophyll a (chl-a) concentrations, which varied by a factor of 5 over the 20-year time series. There has been a significant positive increase in the seasonally integrated concentration of chl-a over the time series. The dominant phytoplankton were diatoms, with cryptophytes the second most abundant. Mixed flagellates also constituted a significant fraction of the chl-a but showed less interannual variability than diatoms and cryophytes. Peak phytoplankton biomass was observed in summer months, when monthly averaged wind speed was lower than in the fall and autumn. Cryptophytes were most abundant during the summer months (December-January) after the seasonal retreat of sea ice. While diatoms were observed over the full range of observed salinities 32-34.5) as well as over the full range of in situ temperatures (-1.5 to 2.5 °C), the cryptophyte populations were observed in locations with lower salinity 32.5-33.75) and colder water (-1 to 1 °C). Environmental factors that favored a shallower seasonal mixed layer resulted in larger diatom blooms compared to the other phytoplankton taxa. During summer with lower phytoplankton biomass, a larger proportion of the chlorophyll a was associated with cryptophytes. These results demonstrate that continued temperature changes along the West Antarctic Peninsula will result in changes in phytoplankton concentration and community

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.

The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale.

PubMed

Hazard, Christina; Gosling, Paul; van der Gast, Christopher J; Mitchell, Derek T; Doohan, Fiona M; Bending, Gary D

2013-03-01

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis ('everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

PubMed Central

Hazard, Christina; Gosling, Paul; van der Gast, Christopher J; Mitchell, Derek T; Doohan, Fiona M; Bending, Gary D

2013-01-01

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition. PMID:23096401

Forecasting climate change impacts to plant community composition in the Sonoran Desert region

USGS Publications Warehouse

Munson, Seth M.; Webb, Robert H.; Belnap, Jayne; Hubbard, J. Andrew; Swann, Don E.; Rutman, Sue

2012-01-01

Hotter and drier conditions projected for the southwestern United States can have a large impact on the abundance and composition of long-lived desert plant species. We used long-term vegetation monitoring results from 39 large plots across four protected sites in the Sonoran Desert region to determine how plant species have responded to past climate variability. This cross-site analysis identified the plant species and functional types susceptible to climate change, the magnitude of their responses, and potential climate thresholds. In the relatively mesic mesquite savanna communities, perennial grasses declined with a decrease in annual precipitation, cacti increased, and there was a reversal of the Prosopis velutina expansion experienced in the 20th century in response to increasing mean annual temperature (MAT). In the more xeric Arizona Upland communities, the dominant leguminous tree, Cercidium microphyllum, declined on hillslopes, and the shrub Fouquieria splendens decreased, especially on south- and west-facing slopes in response to increasing MAT. In the most xeric shrublands, the codominant species Larrea tridentata and its hemiparasite Krameria grayi decreased with a decrease in cool season precipitation and increased aridity, respectively. This regional-scale assessment of plant species response to recent climate variability is critical for forecasting future shifts in plant community composition, structure, and productivity.

Lead Toxicity to the Performance, Viability, And Community Composition of Activated Sludge Microorganisms

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

Yuan, L; Zhi, W; Liu, YS

Lead (Pb) is a prominent toxic metal in natural and engineered systems. Current knowledge on Pb toxicity to the activated sludge has been limited to short-term (<= 24 h) toxicity. The effect of extended Pb exposure on process performance, bacterial viability, and community compositions remains unknown. We quantified the 24-h and 7-day Pb toxicity to chemical oxygen demand (COD) and NH3-N removal, bacterial viability, and community compositions using lab-scale experiments. Our results showed that 7-day toxicity was significantly higher than the short-term 24-h toxicity. Ammonia-oxidizing bacteria were more susceptible than the heterotrophs to Pb toxicity. The specific oxygen uptake ratemore » responded quickly to Pb addition and could serve as a rapid indicator for detecting Pb pollutions. Microbial viability decreased linearly with the amount of added Pb at extended exposure. The bacterial community diversity was markedly reduced with elevated Pb concentrations. Surface analysis suggested that the adsorbed form of Pb could have contributed to its toxicity along with the dissolved form. Our study provides for the first time a systematic investigation of the effect of extended exposure of Pb on the performance and microbiology of aerobic treatment processes, and it indicates that long-term Pb toxicity has been underappreciated by previous studies.« less

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

PubMed

Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

2013-03-01

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

PubMed Central

Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth

2015-01-01

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels.

PubMed

Nielsen, Lene Nørby; Roager, Henrik M; Casas, Mònica Escolà; Frandsen, Henrik L; Gosewinkel, Ulrich; Bester, Kai; Licht, Tine Rask; Hendriksen, Niels Bohse; Bahl, Martin Iain

2018-02-01

Recently, concerns have been raised that residues of glyphosate-based herbicides may interfere with the homeostasis of the intestinal bacterial community and thereby affect the health of humans or animals. The biochemical pathway for aromatic amino acid synthesis (Shikimate pathway), which is specifically inhibited by glyphosate, is shared by plants and numerous bacterial species. Several in vitro studies have shown that various groups of intestinal bacteria may be differently affected by glyphosate. Here, we present results from an animal exposure trial combining deep 16S rRNA gene sequencing of the bacterial community with liquid chromatography mass spectrometry (LC-MS) based metabolic profiling of aromatic amino acids and their downstream metabolites. We found that glyphosate as well as the commercial formulation Glyfonova ® 450 PLUS administered at up to fifty times the established European Acceptable Daily Intake (ADI = 0.5 mg/kg body weight) had very limited effects on bacterial community composition in Sprague Dawley rats during a two-week exposure trial. The effect of glyphosate on prototrophic bacterial growth was highly dependent on the availability of aromatic amino acids, suggesting that the observed limited effect on bacterial composition was due to the presence of sufficient amounts of aromatic amino acids in the intestinal environment. A strong correlation was observed between intestinal concentrations of glyphosate and intestinal pH, which may partly be explained by an observed reduction in acetic acid produced by the gut bacteria. We conclude that sufficient intestinal levels of aromatic amino acids provided by the diet alleviates the need for bacterial synthesis of aromatic amino acids and thus prevents an antimicrobial effect of glyphosate in vivo. It is however possible that the situation is different in cases of human malnutrition or in production animals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Effect of ocean acidification on the fatty acid composition of a natural plankton community

NASA Astrophysics Data System (ADS)

Leu, E.; Daase, M.; Schulz, K. G.; Stuhr, A.; Riebesell, U.

2012-07-01

The effect of ocean acidification on the fatty acid composition of a natural plankton community in the Arctic was studied in a large-scale mesocosm experiment, carried out in Kongsfjorden (Svalbard, Norway) at 79° N. Nine mesocosms of ~50 cbm each were exposed to different pCO2 levels (from natural background conditions to ~1420 μatm), yielding pH values (on the total scale) from ~8.3 to 7.5. Inorganic nutrients were added on day 13. The phytoplankton development during this 30 days experiment passed three distinct phases: (1) prior to the addition of inorganic nutrients, (2) first bloom after nutrient addition, and (3) second bloom after nutrient addition. The fatty acid composition of the natural plankton community was analysed and showed, in general, high percentages of polyunsaturated fatty acids (PUFAs): 44-60% of total fatty acids. Positive correlations with pCO2 were found for most PUFAs during phases 2 and/or 3, with the exception of 20:5n3 (eicosapentaenoic acid, EPA), an important diatom marker. There are strong indications for these correlations being mediated indirectly through taxonomic changes and the natural development of the communities in the mesocosms exposed to different pCO2 levels. While diatoms increased during phase 3 mainly in the low and intermediate pCO2 treatments, dinoflagellates were favoured by high CO2 concentrations during the same time period. This is reflected in the development of group-specific fatty acid trophic markers. No indications were found for a generally detrimental effect of ocean acidification on the planktonic food quality in terms of essential fatty acids. The significant positive correlations between most PUFAs and pCO2 reflected treatment-dependent differences in the community composition between the mesocosms rather than a direct positive effect of pCO2 on specific fatty acids.

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

PubMed

Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

2015-03-01

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.

PubMed

Sun, Ruibo; Dsouza, Melissa; Gilbert, Jack A; Guo, Xisheng; Wang, Daozhong; Guo, Zhibin; Ni, Yingying; Chu, Haiyan

2016-12-01

Organic matter application is a widely used practice to increase soil carbon content and maintain soil fertility. However, little is known about the effect of different types of organic matter, or the input of exogenous species from these materials, on soil fungal communities. In this study, fungal community composition was characterized from soils amended with three types of organic matter over a 30-year fertilization experiment. Chemical fertilization significantly changed soil fungal community composition and structure, which was exacerbated by the addition of organic matter, with the direction of change influenced by the type of organic matter used. The addition of organic matter significantly increased soil fungal richness, with the greatest richness achieved in soils amended with pig manure. Importantly, following addition of cow and pig manure, fungal taxa associated with these materials could be found in the soil, suggesting that these exogenous species can augment soil fungal composition. Moreover, the addition of organic matter decreased the relative abundance of potential pathogenic fungi. Overall, these results indicate that organic matter addition influences the composition and structure of soil fungal communities in predictable ways. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Fungal community composition and diversity vary with soil depths and landscape position in a no-till wheat cropping system.

USDA-ARS?s Scientific Manuscript database

Fungal communities in soil are critical to plant health and ecosystem processes in agricultural systems. Although the composition of fungal communities is often related to soil edaphic characteristic and host plant identity, there is a paucity of information on how communities vary with soil depth a...

Elephants, fire, and frost can determine community structure and composition in Kalahari Woodlands.

PubMed

Holdo, Ricardo M

2007-03-01

Fire, elephants, and frost are important disturbance factors in many African savannas, but the relative magnitude of their effects on vegetation and their interactions have not been quantified. Understanding how disturbance shapes savanna structure and composition is critical for predicting changes in tree cover and for formulating management and conservation policy. A simulation model was used to investigate how the disturbance regime determines vegetation structure and composition in a mixed Kalahari sand woodland savanna in western Zimbabwe. The model consisted of submodels for tree growth, tree damage caused by disturbance, mortality, and recruitment that were parameterized from field data collected over a two-year period. The model predicts that, under the current disturbance regime, tree basal area in the study area will decline by two-thirds over the next two decades and become dominated by species unpalatable to elephants. Changes in the disturbance regime are predicted to greatly modify vegetation structure and community composition. Elephants are the primary drivers of woodland change in this community at present-day population densities, and their impacts are exacerbated by the effects of fire and frost. Frost, in particular, does not play an important role when acting independently but appears to be a key secondary factor in the presence of elephants and/or fire. Unlike fire and frost, which cannot suppress the woodland phase on their own in this ecosystem, elephants can independently drive the vegetation to the scrub phase. The results suggest that elephant and fire management may be critical for the persistence of certain woodland communities within dry-season elephant habitats in the eastern Kalahari, particularly those dominated by Brachystegia spiciformis and other palatable species.

nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

PubMed

Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

2016-10-01

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

Species- and community-level responses combine to drive phenology of lake phytoplankton

USGS Publications Warehouse

Walters, Annika; Sagrario, María de los Ángeles González; Schindler, Daniel E.

2013-01-01

Global change is leading to shifts in the seasonal timing of growth and maturation for primary producers. Remote sensing is increasingly used to measure the timing of primary production in both aquatic and terrestrial ecosystems, but there is often a poor correlation between these results and direct observations of life-history responses of individual species. One explanation may be that in addition to phenological shifts, global change is also causing shifts in community composition among species with different seasonal timing of growth and maturation. We quantified how shifts in species phenology and in community composition translated into phenological change in a diverse phytoplankton community from 1962-2000. During this time the aggregate community spring-summer phytoplankton peak has shifted 63 days earlier. The mean taxon shift was only 3 days earlier and shifts in taxa phenology explained only 40% of the observed community phenological shift. The remaining community shift was attributed to dominant early season taxa increasing in abundance while a dominant late season taxon decreased in abundance. In diverse producer communities experiencing multiple stressors, changes in species composition must be considered to fully understand and predict shifts in the seasonal timing of primary production.

Observed use of standard precautions in Chilean community clinics.

PubMed

Ferrer, Lilian Marcela; Cianelli, Rosina; Norr, Kathleen F; Cabieses, Baltica; Araya, Alejandra; Irarrázabal, Lisette; Bernales, Margarita

2009-01-01

In Chile, little information about the use of standard precautions (SP) among health care workers (HCWs) exists. As part of a larger study to tailor and test an HIV prevention intervention for community HCWs, this study describes the observed frequency with which appropriate SP were used by HCWs in low-income community clinics of Santiago. Also, the availability of supplies is described. A total of 52 structured observations with potential contamination with body fluids were done. HCWs used SP inconsistently, especially neglecting hand washing, surface cleaning, and cleaning of shared materials. Lack of materials contributed in some instances of failure to use SPs, especially wiping surfaces and safe disposal of sharp instruments, as shown by a positive correlation between use of SP and availability of materials. Essential materials were usually available. Although more education should relate to a better understanding of the importance of SP, no difference was found between professionals and paraprofessionals in the use of SP. It is clear that the initial training, continuing education, and ongoing support for practicing SP are not adequate. Training should be offered to HCWs involved in caring for clients at community clinics to stop the spread of HIV or other infectious diseases in health care settings.

The American Association of Variable Star Observers: Serving the Research Community in 2010 and Beyond

NASA Astrophysics Data System (ADS)

Templeton, Matthew R.; Henden, A. A.; Davis, K.; Kinne, R.; Watson, C.; Saladyga, M.; Waagen, E.; Beck, S.; Menali, G.; Price, A.; Turner, R.

2010-05-01

The American Association of Variable Star Observers (AAVSO) holds the largest single online database of variable star data in the world, collected from thousands of amateur and professional observers during the past century. One of our core missions is to preserve and distribute these data to the research community in service to the science of variable star astronomy. But as an organization, the AAVSO is much more than a data archive. Our services to the research community include: monitoring for and announcement of major astronomical events like novae and supernovae; organization and management of observing campaigns; support for satellite and other TOO observing programs by the professional community; creation of comparison star sequences and generation of charts for the observer community; and observational and other support for the amateur, professional, and educator communities in all things related to variable stars. As we begin a new century of variable star astronomy we invite you to take advantage of the services the AAVSO can provide, and to become a part of our organization yourselves. In this poster, we highlight some of the most important services the AAVSO can provide to the professional research community, as well as suggest ways in which your research may be enhanced with support from the AAVSO.

A multistate dynamic site occupancy model for spatially aggregated sessile communities

USGS Publications Warehouse

Fukaya, Keiichi; Royle, J. Andrew; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2017-01-01

Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e. a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations.We developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error.By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real data set of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account.Results suggest the importance of accounting for resampling error and local community structure for developing management plans that are based on Markovian models. Our approach provides a solution to this problem that is applicable to broad sessile communities. It can even accommodate an anisotropic spatial correlation of species composition, and may also serve as a basis for inferring complex nonlinear ecological dynamics.

Demonstrating the value of community-based ('citizen science') observations for catchment modelling and characterisation

NASA Astrophysics Data System (ADS)

Starkey, Eleanor; Parkin, Geoff; Birkinshaw, Stephen; Large, Andy; Quinn, Paul; Gibson, Ceri

2017-05-01

Despite there being well-established meteorological and hydrometric monitoring networks in the UK, many smaller catchments remain ungauged. This leaves a challenge for characterisation, modelling, forecasting and management activities. Here we demonstrate the value of community-based ('citizen science') observations for modelling and understanding catchment response as a contribution to catchment science. The scheme implemented within the 42 km2 Haltwhistle Burn catchment, a tributary of the River Tyne in northeast England, has harvested and used quantitative and qualitative observations from the public in a novel way to effectively capture spatial and temporal river response. Community-based rainfall, river level and flood observations have been successfully collected and quality-checked, and used to build and run a physically-based, spatially-distributed catchment model, SHETRAN. Model performance using different combinations of observations is tested against traditionally-derived hydrographs. Our results show how the local network of community-based observations alongside traditional sources of hydro-information supports characterisation of catchment response more accurately than using traditional observations alone over both spatial and temporal scales. We demonstrate that these community-derived datasets are most valuable during local flash flood events, particularly towards peak discharge. This information is often missed or poorly represented by ground-based gauges, or significantly underestimated by rainfall radar, as this study clearly demonstrates. While community-based observations are less valuable during prolonged and widespread floods, or over longer hydrological periods of interest, they can still ground-truth existing traditional sources of catchment data to increase confidence during characterisation and management activities. Involvement of the public in data collection activities also encourages wider community engagement, and provides important

Observing Classroom Engagement in Community College: A Systematic Approach

ERIC Educational Resources Information Center

Alicea, Stacey; Suárez-Orozco, Carola; Singh, Sukhmani; Darbes, Tasha; Abrica, Elvira Julia

2016-01-01

Despite decades of research indicating classrooms shape student engagement, learning, and development, there is a dearth of empirically grounded research focusing specifically on observed classroom engagement as a predictor of student outcomes in community colleges. This article describes the development of a qualitatively grounded, quantitative…

Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

PubMed

Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J; Casotti, Raffaella

2017-09-01

Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON. IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific

PubMed Central

Sun, Xin; Jayakumar, Amal; Ward, Bess B.

2017-01-01

The ozone-depleting and greenhouse gas, nitrous oxide (N2O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water. PMID:28702012

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific.

PubMed

Sun, Xin; Jayakumar, Amal; Ward, Bess B

2017-01-01

The ozone-depleting and greenhouse gas, nitrous oxide (N 2 O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N 2 O consumption is the last step in canonical denitrification, and is also the least O 2 tolerant step. Community composition of total and active N 2 O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase ( nosZ ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N 2 O concentration but not O 2 . Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N 2 O consumption even in the oxygenated surface water.

GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

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

He, Z.; Deng, Y.; Van Nostrand, J.D.

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets.more » Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.« less

The composition of M-type asteroids: Synthesis of spectroscopic and radar observations

NASA Astrophysics Data System (ADS)

Neeley, J. R.; Ockert-Bell, M. E.; Clark, B. E.; Shepard, M. K.; Cloutis, E. A.; Fornasier, S.; Bus, S. J.

2011-10-01

This work updates our and expands our long term radar-driven observational campaign of 27 main-belt asteroids (MBAs) focused on Bus-DeMeo Xc- and Xk-type objects (Tholen X and M class asteroids) using the Arecibo radar and NASA Infrared Telescope Facilities (IRTF). Seventeen of our targets were near-simultaneously observed with radar and those observations are described in companion paper (Shepard et al., 2010). We utilized visible wavelength for a more complete compositional analysis of our targets. Compositional evidence is derived from our target asteroid spectra using three different methods: 1) a χ2 search for spectral matches in the RELAB database, 2) parametric comparisons with meteorites and 3) linear discriminant analysis. This paper synthesizes the results of the RELAB search, parametric comparisons, and linear discriminant analysis with compositional suggestions based on radar observations. We find that for six of seventeen targets with radar data, our spectral results are consistent with their radar analog (16 Psyche, 21 Lutetia, 69 Hesperia, 135 Hertha, 216 Kleopatra, and 497 Iva). For twenty out of twenty-seven objects our statistical comparisons with RELAB meteorites result in consistent analog identification, providing a degree of confidence in our parametric methods.

The relationship between observational scale and explained variance in benthic communities

PubMed Central

Flood, Roger D.; Frisk, Michael G.; Garza, Corey D.; Lopez, Glenn R.; Maher, Nicole P.

2018-01-01

This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces). Redundancy analysis was coupled with spatial variograms generated by multiscale ordination to quantify the explained and residual variance at different spatial scales and within and between acoustic provinces. The amount of community variation below the sampling interval of the surveys (< 100 m) was estimated to be 36–59% of the total. Once adjusted for this small-scale variation, > 71% of the remaining variance was explained by the environmental and province variables. Furthermore, these variables effectively explained the spatial structure present in the infaunal community. Overall, no scale problems remained to compromise inferences, and unexplained infaunal community variation had no apparent spatial structure within the observational scale of the surveys (> 100 m), although small-scale gradients (< 100 m) below the observational scale may be present. PMID:29324746

Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

USGS Publications Warehouse

Harris, Theodore D.; Graham, Jennifer L.

2015-01-01

The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

Inorganic phosphorus and nitrogen modify composition and diversity of microbial communities in water of mesotrophic lake.

PubMed

Chróst, Ryszard J; Adamczewski, Tomasz; Kalinowska, Krystyna; Skowrońska, Agnieszka

2009-01-01

The effects of inorganic nutrients (N, P) enrichment of mesotrophic lake water on changes in bacterial and protistan (heterotrophic nanoflagellates and ciliates) communities compositions were studied in the mesocosm experiment. Phosphorus (PO4(3-)) and nitrogen (NH4+) alone and in combination were added to three types of experimental mesocosms. Mesocosms results suggested that simultaneous addition of P and N stimulated phytoplankton growth and production rates of bacterial biomass its turnover rate. Strong positive correlations between chlorophyll a and bacterial secondary production rates suggested that bacteria were mainly controlled by organic substrates released in course ofphytoplankton photosynthesis. Both nutrients increased distinctly protistan biomass and resulted in the shift in ciliate community composition from algivorous to large omnivorous species. The response of bacterial numbers and biomass to nutrients addition was less evident. However, intensive grazing caused their dynamic changes. Fluorescence in situ hybridization (FISH) revealed only small changes in bacterial taxonomic composition. There was an apparent shift in dominance from Cytophaga-Flavobacterium to the Alphaproteobacteria group in the mesocosm with simultaneous addition of P and N, which positively related to increased abundance of bacterivorous protists. Experiment demonstrated that inorganic N and P nutrients directly influenced the bottom-down control of microbial communities, which had a crucial effect on morphological diversity of bacteria.

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

Microbial Community Shifts due to Hydrofracking: Observations from Field-Scale Observations and Laboratory-Scale Incubations

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Ansari, M.; Hartsock, A.; Lui, S.; Lenhart, J.

2012-12-01

The use of fluids containing chemicals and variable water sources during the hydrofracking of unconventional shale is the source of considerable controversy due to perceived risks from altered subsurface biogeochemistry and the potential for contaminating potable water supplies. Rapid shifts in subsurface biogeochemistry are often driven by available macronutrients combined with the abundance and metabolic condition of the subsurface microbiota. While the depth that fracturing occurs in the Marcellus formation is reasonably deep to pose little risk to groundwater supplies, no published studies have systematically characterized the indigenous microbial population and how this community is altered through variable fluid management practices (e.g., chemical composition, source water makeup). In addition, limited information is available on how shallower microbial communities and geochemical conditions might be affected through the accidental release of these fluids to groundwater aquifers. Our measurements indicate field-applied and laboratory-generated fracking fluids contain levels of organic carbon greater than 300 mg/l and nitrogen concentrations greater than 80 mg/l that may differentially stimulate microbial growth in subsurface formations. In contrast to certain inorganic constituents (e.g., chloride) which increase in concentration through the flowback period; dissolved organic carbon levels decrease with time after the fracturing process through multiple attenuation processes (dilution, sorption, microbial utilization). Pyrosequencing data of the 16S rRNA gene indicate a shift from a more diverse source water microbial community to a less diverse community typical of a brine formation as time after fracturing increases. The introduction of varying percentages of a laboratory-generated fracking fluid to microcosm bottles containing groundwater and aquifer media stimulated biogeochemical changes similar to the introduction of landfill leachate, another

From source to filter: changes in bacterial community composition during potable water treatment.

PubMed

Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

2017-06-01

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

NASA Astrophysics Data System (ADS)

Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

2015-12-01

Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

USGS Publications Warehouse

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

2017-01-01

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

Algal and Invertebrate Community Composition along Agricultural Gradients: A Comparative Study from Two Regions of the Eastern United States

USGS Publications Warehouse

Calhoun, Daniel L.; Gregory, M. Brian; Weyers, Holly S.

2008-01-01

Benthic algal and invertebrate communities in two Coastal Plain regions of the Eastern United States?the Delmarva Peninsula (27 sites) and Georgia Upper Coastal Plain (29 sites)?were assessed to determine if aspects of agricultural land use and nutrient conditions (dissolved and whole-water nitrogen and phosphorus) could be linked to biological community compositions. Extensive effort was made to compile land-use data describing the basin and riparian conditions at multiple scales to determine if scale played a role in these relations. Large differences in nutrient condition were found between the two study areas, wherein on average, the Delmarva sites had three times the total phosphorus and total nitrogen as did the sites in the Georgia Upper Coastal Plain. A statistical approach was undertaken that included multivariate correlations between Bray-Curtis similarity matrices of the biological communities and Euclidean similarity matrices of instream nutrients and land-use categories. Invertebrate assemblage composition was most associated with land use near the sampled reach, and algal diatom assemblage composition was most associated with land use farther from the streams and into the watersheds. Link tree analyses were conducted to isolate portions of nonmetric multidimensional scaling ordinations of community compositions that could be explained by break points in abiotic datasets. Invertebrate communities were better defined by factors such as agricultural land use near streams and geographic position. Algal communities were better defined by agricultural land use at the basin scale and instream nutrient chemistry. Algal autecological indices were more correlated with gradients of nutrient condition than were typically employed invertebrate metrics and may hold more promise in indicating nutrient impairment in these regions. Nutrient conditions in the respective study areas are compared to draft nutrient criteria established by the U.S. Environmental Protection

Observations of climate change among subsistence-oriented communities around the world

NASA Astrophysics Data System (ADS)

Savo, V.; Lepofsky, D.; Benner, J. P.; Kohfeld, K. E.; Bailey, J.; Lertzman, K.

2016-05-01

The study of climate change has been based strongly on data collected from instruments, but how local people perceive such changes remains poorly quantified. We conducted a meta-analysis of climatic changes observed by subsistence-oriented communities. Our review of 10,660 observations from 2,230 localities in 137 countries shows that increases in temperature and changes in seasonality and rainfall patterns are widespread (~70% of localities across 122 countries). Observations of increased temperature show patterns consistent with simulated trends in surface air temperature taken from the ensemble average of CMIP5 models, for the period 1955-2005. Secondary impacts of climatic changes on both wild and domesticated plants and animals are extensive and threaten the food security of subsistence-oriented communities. Collectively, our results suggest that climate change is having profound disruptive effects at local levels and that local observations can make an important contribution to understanding the pervasiveness of climate change on ecosystems and societies.

From flint to stainless steel: observations on surgical instrument composition.

PubMed Central

Kirkup, J.

1993-01-01

Man's failure to extract deeply embedded thorns and arrowheads, with bare hands and teeth, stimulated 'instrument substitutes' mimicking these appendages. Evidence from primitive communities suggest animal, plant and mineral items were employed, both before and after metal became the standard material of today's armamentarium. Changing surgical instrument composition has mirrored concurrent technology and manufacturing methods both of which are reviewed. Particular significance is accorded flint, bronze, crucible steel, thermal sterilisation, nickel-plate, stainless steel and disposable plastics. The paper is based on an exhibition From Flint to Stainless Steel on display at the College. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8215156

Use of a cable-based system for observing the heterogeneity of vegetation communities in arctic tundra

NASA Astrophysics Data System (ADS)

Ahrends, H. E.; Oberbauer, S. F.; Tweedie, C.; Hollister, R. D.

2010-12-01

Knowledge of changing tundra vegetation and its response to climate variability is critical for understanding the land-atmosphere-interactions for the Arctic and the global system. However, vegetation characteristics, such as phenology, structure and species composition, are characterized by an extreme heterogeneity at a small scale. Manual observations of these variables are highly time-consuming, labor intensive, subjective, and disturbing to the vegetation. In contrast, recently developed robotic systems (networked infomechanical systems, NIMS) allow for performing non-intrusive spatially integrated measurements of vegetation communities. Within the ITEX (International Tundra Experiment) AON (Arctic Observation Network) project we installed a cable-based sensor system, running over a transect of approximately 50 m length and 2 m width, at two long-term arctic research sites in Alaska. The trolley was initially equipped with instruments recording the distance to vegetation canopy, up- and downwelling short- and longwave radiation, air and surface temperature and spectral reflection. We aim to study the thermal and spectral response of the vegetation communities over a wide range of ecosystem types. We expect that automated observations, covering the spatial heterogeneity of vegetation and surface characteristics, can give a deeper insight in ecosystem functioning and vegetation response to climate. The data can be used for scaling up vegetation characteristics derived from manual measurements and for linking them to aircraft and satellite data and to carbon, water and surface energy budgets measured at the ecosystem scale. Sampling errors due to cable sag are correctable and effects of wind-driven movements can be offset by repeat measurements. First hand-pulled test measurements during summer 2010 show strong heterogeneity of the observation parameters and a variable spectral and thermal response of the plants within the transects. Differences support the

Potential nitrification and denitrification and the corresponding composition of the bacterial communities in a compact constructed wetland treating landfill leachates.

PubMed

Sundberg, C; Tonderski, K; Lindgren, P E

2007-01-01

Constructed wetlands can be used to decrease the high ammonium concentrations in landfill leachates. We investigated nitrification/denitrification activity and the corresponding bacterial communities in landfill leachate that was treated in a compact constructed wetland, Tveta Recycling Facility, Sweden. Samples were collected at three depths in a filter bed and the sediment from a connected open pond in July, September and November 2004. Potential ammonia oxidation was measured by short-term incubation method and potential denitrification by the acetylene inhibition technique. The ammonia-oxidising and the denitrifying bacterial communities were investigated using group-specific PCR primers targeting 16S rRNA genes and the functional gene nosZ, respectively. PCR products were analysed by denaturing gradient gel electrophoresis and nucleotide sequencing. The same degree of nitrification activity was observed in the pond sediment and at all levels in the filter bed, whereas the denitrification activity decreased with filter bed depth. Denitrification rates were higher in the open pond, even though the denitrifying bacterial community was more diverse in the filter bed. The ammonia-oxidising community was also more varied in the filter bed. In the filter bed and the open pond, there was no obvious relationship between the nitrification/denitrification activities and the composition of the corresponding bacterial communities.

Comparison of Microbial Community Compositions of Injection and Production Well Samples in a Long-Term Water-Flooded Petroleum Reservoir

PubMed Central

Ren, Hong-Yan; Zhang, Xiao-Jun; Song, Zhi-yong; Rupert, Wieger; Gao, Guang-Jun; Guo, Sheng-xue; Zhao, Li-Ping

2011-01-01

Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water. PMID:21858049

Tree specie effects on soil microbial community composition and greenhouse gases emissions in a Mediterranean ecotone forest

NASA Astrophysics Data System (ADS)

Fernandez, Maria Jose; Ortiz, Carlos; Kitzler, Barbara; Curiel, Jorge; Rubio, Agustin

2016-04-01

Over recent decades in the Iberian Peninsula, altitudinal shifts from Pinus sylvestris L. to Quercus pyrenaica Willd species has been observed as a consequence of Global Change, meaning changes in temperature, precipitation, land use and forestry. The forest conversion from pine to oak can alter the litter quality and quantity provided to the soil and thereby the soil microbial community composition and functioning. Since soil microbiota plays an important role in organic matter decomposition, and this in turn is key in biogeochemical cycles and forest ecosystems productivity, the rate in which forests produce and consume greenhouse gases can be also affected by changes in forest composition. In other words, changes in litter decomposition will ultimately affect downstream carbon and nitrogen dynamics although this impact is uncertain. In order to predict changes in carbon and nitrogen stocks in Global Change scenarios, it is necessary to deepen the impact of vegetation changes on soil microbial communities, litter decomposition dynamics (priming effect) and the underlying interactions between these factors. To test this, we conducted a full-factorial transplant microcosms experiment mixing both fresh soils and litter from Pyrenean oak, Scots pine and mixed stands collected inside their transitional area in Central Spain. The microcosms consisted in soil cylinders inside Kilner jars used as chambers inside an incubator. In this experiment, we investigated how and to what extent the addition of litter with different quality (needles, oak leaves and mixed needles-leaves) to soil inoculums with contrasting soil microbiota impact on (i) soil CO2, NO, N2O and CH4 efflux rates, (ii) total organic carbon and nitrogen and (iii) dissolved organic carbon and nitrogen. Furthermore, we assessed if these responses were controlled by changes in the microbial community structure using the PLFA analyses prior and after the incubation period of 54 days.

Absence of snow cover reduces understory plant cover and alters plant community composition in boreal forests.

PubMed

Kreyling, Juergen; Haei, Mahsa; Laudon, Hjalmar

2012-02-01

Snow regimes affect biogeochemistry of boreal ecosystems and are altered by climate change. The effects on plant communities, however, are largely unexplored despite their influence on relevant processes. Here, the impact of snow cover on understory community composition and below-ground production in a boreal Picea abies forest was investigated using a long-term (8-year) snow cover manipulation experiment consisting of the treatments: snow removal, increased insulation (styrofoam pellets), and control. The snow removal treatment caused longer (118 vs. 57 days) and deeper soil frost (mean minimum temperature -5.5 vs. -2.2°C) at 10 cm soil depth in comparison to control. Understory species composition was strongly altered by the snow cover manipulations; vegetation cover declined by more than 50% in the snow removal treatment. In particular, the dominant dwarf shrub Vaccinium myrtillus (-82%) and the most abundant mosses Pleurozium schreberi (-74%) and Dicranum scoparium (-60%) declined strongly. The C:N ratio in V. myrtillus leaves and plant available N in the soil indicated no altered nitrogen nutrition. Fine-root biomass in summer, however, was negatively affected by the reduced snow cover (-50%). Observed effects are attributed to direct frost damage of roots and/ or shoots. Besides the obvious relevance of winter processes on plant ecology and distribution, we propose that shifts in the vegetation caused by frost damage may be an important driver of the reported alterations in biogeochemistry in response to altered snow cover. Understory plant performance clearly needs to be considered in the biogeochemistry of boreal systems in the face of climate change.

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes.

PubMed

Rofner, Carina; Peter, Hannes; Catalán, Núria; Drewes, Fabian; Sommaruga, Ruben; Pérez, María Teresa

2017-06-01

Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in-lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate-change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon-specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil-derived carbon and phosphorus. Our work suggests that climate-induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident.

PubMed

Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth; Greer, Charles W

2015-09-01

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Shifts of community composition and population density substantially affect ecosystem function despite invariant richness.

PubMed

Spaak, Jurg W; Baert, Jan M; Baird, Donald J; Eisenhauer, Nico; Maltby, Lorraine; Pomati, Francesco; Radchuk, Viktoriia; Rohr, Jason R; Van den Brink, Paul J; De Laender, Frederik

2017-10-01

There has been considerable focus on the impacts of environmental change on ecosystem function arising from changes in species richness. However, environmental change may affect ecosystem function without affecting richness, most notably by affecting population densities and community composition. Using a theoretical model, we find that, despite invariant richness, (1) small environmental effects may already lead to a collapse of function; (2) competitive strength may be a less important determinant of ecosystem function change than the selectivity of the environmental change driver and (3) effects on ecosystem function increase when effects on composition are larger. We also present a complementary statistical analysis of 13 data sets of phytoplankton and periphyton communities exposed to chemical stressors and show that effects on primary production under invariant richness ranged from -75% to +10%. We conclude that environmental protection goals relying on measures of richness could underestimate ecological impacts of environmental change. © 2017 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.

PubMed

Edberg, Frida; Andersson, Anders F; Holmström, Sara J M

2012-11-01

Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

Learning How to Feel: Conversion Narratives and Community Membership in First-Year Composition

ERIC Educational Resources Information Center

Kurtyka, Faith M.

2017-01-01

This article examines the rhetoric of the conversion narratives told by a group of women joining a new social sorority on campus. I argue that these sorority conversion narratives are of interest to composition scholars because they document the emotional work involved in entering a community in one's first year of college. My close analysis of…

UHECR mass composition measurement at Telescope Array via stereoscopic observation

NASA Astrophysics Data System (ADS)

Stroman, Thomas; Telescope Array Collaboration

2015-04-01

The masses of primary ultra-high-energy cosmic-ray (UHECR) nuclei cannot be measured directly on an individual basis, but constraints on the chemical composition can be inferred from the distributions of observable properties. The atmospheric slant depth at which a UHECR-induced extensive air shower reaches its maximum number of particles, Xmax, is particularly sensitive to the mass of the incident nucleus, occurring earlier in the shower's longitudinal development for heavier nuclei at a given energy. The Telescope Array in west-central Utah, the northern hemisphere's largest UHECR detector, is equipped for accurate Xmax and energy measurements via stereoscopic fluorescence observation. Using data from seven years of operation, we will present Xmax distributions at several energies E >10 18 . 2eV , and compare them to distributions predicted by detailed detector simulations under an assortment of assumed UHECR compositions and high-energy hadronic interaction models.

Effect of investigator disturbance in experimental forensic entomology: succession and community composition.

PubMed

De Jong, G D; Hoback, W W

2006-06-01

Carrion insect succession studies have historically used repeated sampling of single or a few carcasses to produce data, either weighing the carcasses, removing a qualitative subsample of the fauna present, or both, on every visit over the course of decomposition and succession. This study, conducted in a set of related experimental hypotheses with two trials in a single season, investigated the effect that repeated sampling has on insect succession, determined by the number of taxa collected on each visit and by community composition. Each trial lasted at least 21 days, with daily visits on the first 14 days. Rat carcasses used in this study were all placed in the field on the same day, but then either sampled qualitatively on every visit (similar to most succession studies) or ignored until a given day of succession, when they were sampled qualitatively (a subsample) and then destructively sampled in their entirety. Carcasses sampled on every visit were in two groups: those from which only a sample of the fauna was taken and those from which a sample of fauna was taken and the carcass was weighed for biomass determination. Of the carcasses visited only once, the number of taxa in subsamples was compared to the actual number of taxa present when the carcass was destructively sampled to determine if the subsamples adequately represented the total carcass fauna. Data from the qualitative subsamples of those carcasses visited only once were also compared to data collected from carcasses that were sampled on every visit to investigate the effect of the repeated sampling. A total of 39 taxa were collected from carcasses during the study and the component taxa are discussed individually in relation to their role in succession. Number of taxa differed on only one visit between the qualitative subsamples and the actual number of taxa present, primarily because the organisms missed by the qualitative sampling were cryptic (hidden deep within body cavities) or rare (only

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.