Common Infrastructure for Neo Scientific and Planetary Defense Missions

NASA Technical Reports Server (NTRS)

Adams, Robert; Wilks, Rodney

2009-01-01

While defending the Earth against collisions with asteroids and comets has garnered increasing attention over the past few decades, our knowledge of the threats and methods of mitigation remain inadequate. There exists a considerable gap in knowledge regarding the size, composition, location, internal structure and formation of near earth asteroids and comets. Although estimates have been made, critical experiments have not yet been conducted on the effectiveness of various proposed mitigation techniques. Closing this knowledge gap is of interest to both the planetary defense and planetary science communities. Increased scientific knowledge of asteroid and comet composition and structure can confirm or advance current theories about the formation of the solar system. This proposal suggests a joint effort between these two communities to provide an economical architecture that supports multiple launches of characterization and mitigation payloads with minimal response time. The science community can use this architecture for characterization missions of opportunity when multiple scientific targets or targets of uncommon scientific value present themselves, while the planetary defense community would be able to fire characterization or mitigation payloads at targets that present a threat to the Earth. Both communities would benefit from testing potential mitigation techniques, which would reveal information on the internal structure of asteroids and comets. In return, the Earth would have the beginnings of a viable response system should an impact threat prove real in the near future.

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China

PubMed Central

Lin, Huirong; Zhang, Shuting; Gong, Song; Zhang, Shenghua; Yu, Xin

2015-01-01

The composition and microbial community structure of the drinking water system biofilms were investigated using microstructure analysis and 454 pyrosequencing technique in Xiamen city, southeast of China. SEM (scanning electron microscope) results showed different features of biofilm morphology in different fields of PVC pipe. Extracellular matrix material and sparse populations of bacteria (mainly rod-shaped and coccoid) were observed. CLSM (confocal laser scanning microscope) revealed different distributions of attached cells, extracellular proteins, α-polysaccharides, and β-polysaccharides. The biofilms had complex bacterial compositions. Differences in bacteria diversity and composition from different tap materials and ages were observed. Proteobacteria was the common and predominant group in all biofilms samples. Some potential pathogens (Legionellales, Enterobacteriales, Chromatiales, and Pseudomonadales) and corrosive microorganisms were also found in the biofilms. This study provides the information of characterization and visualization of the drinking water biofilms matrix, as well as the microbial community structure and opportunistic pathogens occurrence. PMID:26273617

COMMUNITY LEVEL ANALYSIS OF VECTOR-BORNE DISEASE

EPA Science Inventory

Ecological community structure is particularly important in vector-borne zoonotic diseases with complex life cycles. Single population models, such as the so-called Ross-Macdonald model (Baily, 1982), have been important in developing and characterizing our current understanding...

Diversity, structure and convergent evolution of the global sponge microbiome

PubMed Central

Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.

2016-01-01

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

PubMed Central

Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

2018-01-01

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient.

PubMed

Egan, Cameron P; Callaway, Ragan M; Hart, Miranda M; Pither, Jason; Klironomos, John

2017-04-01

Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.

Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor.

PubMed

Tao, Yong; Li, Jiabao; Rui, Junpeng; Xu, Zhancheng; Zhou, Yan; Hu, Xiaohong; Wang, Xiang; Liu, Menghua; Li, Daping; Li, Xiangzhen

2014-04-01

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.

Characterizing Urban Household Waste Generation and Metabolism Considering Community Stratification in a Rapid Urbanizing Area of China.

PubMed

Xiao, Lishan; Lin, Tao; Chen, Shaohua; Zhang, Guoqin; Ye, Zhilong; Yu, Zhaowu

2015-01-01

The relationship between social stratification and municipal solid waste generation remains uncertain under current rapid urbanization. Based on a multi-object spatial sampling technique, we selected 191 households in a rapidly urbanizing area of Xiamen, China. The selected communities were classified into three types: work-unit, transitional, and commercial communities in the context of housing policy reform in China. Field survey data were used to characterize household waste generation patterns considering community stratification. Our results revealed a disparity in waste generation profiles among different households. The three community types differed with respect to family income, living area, religious affiliation, and homeowner occupation. Income, family structure, and lifestyle caused significant differences in waste generation among work-unit, transitional, and commercial communities, respectively. Urban waste generation patterns are expected to evolve due to accelerating urbanization and associated community transition. A multi-scale integrated analysis of societal and ecosystem metabolism approach was applied to waste metabolism linking it to particular socioeconomic conditions that influence material flows and their evolution. Waste metabolism, both pace and density, was highest for family structure driven patterns, followed by lifestyle and income driven. The results will guide community-specific management policies in rapidly urbanizing areas.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

PubMed

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-06-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

PubMed Central

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-01-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function. PMID:23407312

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.

PubMed

Scola, Vincent; Ramond, Jean-Baptiste; Frossard, Aline; Zablocki, Olivier; Adriaenssens, Evelien M; Johnson, Riegardt M; Seely, Mary; Cowan, Don A

2018-01-01

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Social Landscapes of the Inter-Mountain West: A Comparison of "Old West" and "New West" Communities

ERIC Educational Resources Information Center

Winkler, Richelle; Field, Donald R.; Luloff, A. E.; Krannich, Richard S.; Williams, Tracy

2007-01-01

Rural communities have experienced dramatic demographic, social, and economic transformations over the past 30 years. Historically characterized by close links between natural resources and social, cultural, and economic structures, few of today's rural communities remain heavily dependent upon traditional extractive industries like ranching,…

Communities and classes in symmetric fractals

NASA Astrophysics Data System (ADS)

Krawczyk, Małgorzata J.

2015-07-01

Two aspects of fractal networks are considered: the community structure and the class structure, where classes of nodes appear as a consequence of a local symmetry of nodes. The analyzed systems are the networks constructed for two selected symmetric fractals: the Sierpinski triangle and the Koch curve. Communities are searched for by means of a set of differential equations. Overlapping nodes which belong to two different communities are identified by adding some noise to the initial connectivity matrix. Then, a node can be characterized by a spectrum of probabilities of belonging to different communities. Our main goal is that the overlapping nodes with the same spectra belong to the same class.

Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan

PubMed Central

Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

2016-01-01

Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments. PMID:26849440

Characterization and analysis of temporal and spatial variations in habitat and macroinvertebrate community structure, Fountain Creek basin, Colorado Springs and vicinity, Colorado, 1998-2001

USGS Publications Warehouse

Bruce, James F.

2002-01-01

The Fountain Creek Basin in and around Colorado Springs, Colorado, is affected by various land- and water-use activities. Biological, hydrological, water-quality, and land-use data were collected at 10 sites in the Fountain Creek Basin from April 1998 through April 2001 to provide a baseline characterization of macroinvertebrate communities and habitat conditions for comparison in subsequent studies; and to assess variation in macroinvertebrate community structure relative to habitat quality. Analysis of variance results indicated that instream and riparian variables were not affected by season, but significant differences were found among sites. Nine metrics were used to describe and evaluate macroinvertebrate community structure. Statistical analysis indicated that for six of the nine metrics, significant variability occurred between spring and fall seasons for 60 percent of the sites. Cluster analysis (unweighted pair group method average) using macroinvertebrate presence-absence data showed a well-defined separation between spring and fall samples. Six of the nine metrics had significant spatial variation. Cluster analysis using Sorenson?s Coefficient of Community values computed from macroinvertebrate density (number of organisms per square meter) data showed that macroinvertebrate community structure was more similar among tributary sites than main-stem sites. Canonical correspondence analysis identified a substrate particle-size gradient from site-specific species-abundance data and environmental correlates that decreased the 10 sites to 5 site clusters and their associated taxa.

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

PubMed Central

Staley, Christopher

2016-01-01

ABSTRACT Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P < 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P < 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gammaproteobacteria and Planctomycetes, and those from Florida had more Deltaproteobacteria and Firmicutes. Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P < 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment. IMPORTANCE This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives. PMID:26921429

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

PubMed Central

2011-01-01

Background Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing. Methods Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR. Results The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results. Conclusions This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis. PMID:22152152

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Towards a Dialogical Pedagogy: Some Characteristics of a Community of Mathematical Inquiry

ERIC Educational Resources Information Center

Kennedy, Nadia Stoyanova

2009-01-01

This paper discusses a teaching model called community of mathematical inquiry (CMI), characterized by dialogical and inquiry-driven communication and a dynamic structure of intertwined cognitive processes including distributed thinking, mathematical argumentation, integrated reasoning, conceptual transformation, internalization of critical…

Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities.

PubMed

Bradley, Ian M; Pinto, Ameet J; Guest, Jeremy S

2016-10-01

The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3' end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest. The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Prokaryotic Communities in Pit Mud from Different-Aged Cellars Used for the Production of Chinese Strong-Flavored Liquor

PubMed Central

Tao, Yong; Li, Jiabao; Rui, Junpeng; Xu, Zhancheng; Zhou, Yan; Hu, Xiaohong; Wang, Xiang; Liu, Menghua; Li, Daping

2014-01-01

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4+, lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor. PMID:24487528

Characterizing Urban Household Waste Generation and Metabolism Considering Community Stratification in a Rapid Urbanizing Area of China

PubMed Central

Xiao, Lishan; Lin, Tao; Chen, Shaohua; Zhang, Guoqin; Ye, Zhilong; Yu, Zhaowu

2015-01-01

The relationship between social stratification and municipal solid waste generation remains uncertain under current rapid urbanization. Based on a multi-object spatial sampling technique, we selected 191 households in a rapidly urbanizing area of Xiamen, China. The selected communities were classified into three types: work-unit, transitional, and commercial communities in the context of housing policy reform in China. Field survey data were used to characterize household waste generation patterns considering community stratification. Our results revealed a disparity in waste generation profiles among different households. The three community types differed with respect to family income, living area, religious affiliation, and homeowner occupation. Income, family structure, and lifestyle caused significant differences in waste generation among work-unit, transitional, and commercial communities, respectively. Urban waste generation patterns are expected to evolve due to accelerating urbanization and associated community transition. A multi-scale integrated analysis of societal and ecosystem metabolism approach was applied to waste metabolism linking it to particular socioeconomic conditions that influence material flows and their evolution. Waste metabolism, both pace and density, was highest for family structure driven patterns, followed by lifestyle and income driven. The results will guide community-specific management policies in rapidly urbanizing areas. PMID:26690056

Reticulate Structures Reveal the Significance of Cell Motility in the Morphogenesis of Complex Microbial Structures in Pavilion Lake, British Columbia

NASA Astrophysics Data System (ADS)

Shepard, R.

2008-12-01

Microbial communities are architects of incredibly complex and diverse morphological structures. Each morphology is a snapshot that reflects the complex interactions within the microbial community and between the community and its environment. Characterizing morphology as an emergent property of microbial communities is thus relevant to understanding the evolution of multicellularity and complexity in developmental systems, to the identification of biosignatures, and to furthering our understanding of modern and ancient microbial ecology. Recently discovered cyanobacterial mats in Pavilion Lake, British Columbia construct unusual complex architecture on the scale of decimeters that incorporates significant void space. Fundamental mesoscale morphological elements include terraces, arches, bridges, depressions, domes, and pillars. The mats themselves also exhibit several microscale morphologies, with reticulate structures being the dominant example. The reticulate structures exhibit a diverse spectrum of morphologies with endmembers characterized by either angular or curvilinear ridges. In laboratory studies, aggregation into reticulate structures occurs as a result of the random gliding and colliding among motile cyanobacterial filaments. Likewise, when Pavilion reticulate mats were sampled and brought to the surface, cyanobacteria invariably migrated out of the mat onto surrounding surfaces. Filaments were observed to move rapidly in clumps, preferentially following paths of previous filaments. The migrating filaments organized into new angular and ropey reticulate biofilms within hours of sampling, demonstrating that cell motility is responsible for the reticulate patterns. Because the morphogenesis of reticulate structures can be linked to motility behaviors of filamentous cyanobacteria, the Willow Point mats provide a unique natural laboratory in which to elucidate the connections between a specific microbial behavior and the construction of complex microbial community morphology. To this end, we identified and characterized fundamental building blocks of the mesoscale morphologies, including bridges, anchors, and curved edges. These morphological building blocks were compared with the suite of motility behaviors and patterns observed in reticulate morphogenesis. Results of this comparison suggest that cyanobacterial motility plays a significant and often dominant role in the morphogenesis of the entire suite of morphologies observed in the microbial mats of Pavilion Lake.

Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane

PubMed Central

Merlino, Giuseppe; Marzorati, Massimo; Rizzi, Aurora; Lavazza, Davide; de Ferra, Francesca; Carpani, Giovanna

2015-01-01

The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community. PMID:26273600

Functional Process Zones Characterizing Aquatic Insect Communities in Streams of the Brazilian Cerrado.

PubMed

Godoy, B S; Simião-Ferreira, J; Lodi, S; Oliveira, L G

2016-04-01

Stream ecology studies see to understand ecological dynamics in lotic systems. The characterization of streams into Functional Process Zones (FPZ) has been currently debated in stream ecology because aquatic communities respond to functional processes of river segments. Therefore, we tested if different functional process zones have different number of genera and trophic structure using the aquatic insect community of Neotropical streams. We also assessed whether using physical and chemical variables may complement the approach of using FPZ to model communities of aquatic insects in Cerrado streams. This study was conducted in 101 streams or rivers from the central region of the state of Goiás, Brazil. We grouped the streams into six FPZ associated to size of the river system, presence of riparian forest, and riverbed heterogeneity. We used Bayesian models to compare number of genera and relative frequency of the feeding groups between FPZs. Streams classified in different FPZs had a different number of genera, and the largest and best preserved rivers had an average of four additional genera. Trophic structure exhibited low variability among FPZs, with little difference both in the number of genera and in abundance. Using functional process zones in Cerrado streams yielded good results for Ephemeroptera, Plecoptera, and Trichoptera communities. Thus, species distribution and community structure in the river basin account for functional processes and not necessarily for the position of the community along a longitudinal dimension of the lotic system.

Hierarchical mutual information for the comparison of hierarchical community structures in complex networks

NASA Astrophysics Data System (ADS)

Perotti, Juan Ignacio; Tessone, Claudio Juan; Caldarelli, Guido

2015-12-01

The quest for a quantitative characterization of community and modular structure of complex networks produced a variety of methods and algorithms to classify different networks. However, it is not clear if such methods provide consistent, robust, and meaningful results when considering hierarchies as a whole. Part of the problem is the lack of a similarity measure for the comparison of hierarchical community structures. In this work we give a contribution by introducing the hierarchical mutual information, which is a generalization of the traditional mutual information and makes it possible to compare hierarchical partitions and hierarchical community structures. The normalized version of the hierarchical mutual information should behave analogously to the traditional normalized mutual information. Here the correct behavior of the hierarchical mutual information is corroborated on an extensive battery of numerical experiments. The experiments are performed on artificial hierarchies and on the hierarchical community structure of artificial and empirical networks. Furthermore, the experiments illustrate some of the practical applications of the hierarchical mutual information, namely the comparison of different community detection methods and the study of the consistency, robustness, and temporal evolution of the hierarchical modular structure of networks.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

PubMed

Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Characterizing species interactions to understand press perturbations: What is the community matrix?

USGS Publications Warehouse

Novak, Mark; Yeakel, Justin D.; Noble, Andrew E.; Doak, Daniel F.; Emmerson, Mark; Estes, James A.; Jacob, Ute; Tinker, M. Tim; Wootton, J. Timothy

2016-01-01

The community matrix is among ecology's most important mathematical abstractions, formally encapsulating the interconnected network of effects that species have on one another's populations. Despite its importance, the term `community matrix' has been applied to matrices having differing interpretations. This has hindered the application of theory for understanding community structure and perturbation responses, particularly in the contexts of ecosystem-based management and conservation. Here we clarify the correspondence and distinctions between the Interaction matrix, the Alpha matrix and the Jacobian matrix, terms which are frequently used interchangeably and have numerous synonyms, including the term Community matrix. We illustrate how these matrices correspond to different ways of characterizing interaction strengths, how they permit insights regarding different types of press perturbations of species growth rates or abundances, and how these are related by a simple scaling relationship. Connections to additional interaction strength characterizations encapsulated by the Beta matrix, the Gamma matrix, and the Removal matrix are also discussed. Our synthesis highlights the empirical challenges that remain in using these mathematical tools to understand actual communities.

Tidal Channel Diatom Assemblages Reflect within Wetland Environmental Conditions and Land Use at Multiple Scales

EPA Science Inventory

We characterized regional patterns of the tidal channel benthic diatom community and examined the relative importance of local wetland and surrounding landscape level factors measured at multiple scales in structuring this assemblage. Surrounding land cover was characterized at ...

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 were also related to habitat type, showing that communities from non-forest areas tend to be more clustered. Our study showed that both environmental filtering and spatial gradients play important roles in shaping the composition of Neotropical snake communities. PMID:26061038

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 were also related to habitat type, showing that communities from non-forest areas tend to be more clustered. Our study showed that both environmental filtering and spatial gradients play important roles in shaping the composition of Neotropical snake communities.

Approximation of Nash equilibria and the network community structure detection problem

PubMed Central

2017-01-01

Game theory based methods designed to solve the problem of community structure detection in complex networks have emerged in recent years as an alternative to classical and optimization based approaches. The Mixed Nash Extremal Optimization uses a generative relation for the characterization of Nash equilibria to identify the community structure of a network by converting the problem into a non-cooperative game. This paper proposes a method to enhance this algorithm by reducing the number of payoff function evaluations. Numerical experiments performed on synthetic and real-world networks show that this approach is efficient, with results better or just as good as other state-of-the-art methods. PMID:28467496

The type of carbohydrates specifically selects microbial community structures and fermentation patterns.

PubMed

Chatellard, Lucile; Trably, Eric; Carrère, Hélène

2016-12-01

The impact on dark fermentation of seven carbohydrates as model substrates of lignocellulosic fractions (glucose, cellobiose, microcrystalline cellulose, arabinose, xylose, xylan and wheat straw) was investigated. Metabolic patterns and bacterial communities were characterized at the end of batch tests inoculated with manure digestate. It was found that hydrogen production was linked to the sugar type (pentose or hexose) and the degree of polymerisation. Hexoses produced less hydrogen, with a specific selection of lactate-producing bacterial community structures. Maximal hydrogen production was five times higher on pentose-based substrates, with specific bacterial community structures producing acetate and butyrate as main metabolites. Low hydrogen amounts accumulated from complex sugars (cellulose, xylan and wheat straw). A relatively high proportion of the reads was affiliated to Ruminococcaceae suggesting an efficient hydrolytic activity. Knowing that the bacterial community structure is very specific to a particular substrate offers new possibilities to design more efficient H 2 -producing biological systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

PubMed Central

Messier, Christian; Kembel, Steven W.

2017-01-01

ABSTRACT Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. PMID:29238751

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity.

PubMed

Laforest-Lapointe, Isabelle; Messier, Christian; Kembel, Steven W

2017-01-01

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria . Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

Identifying and characterizing key nodes among communities based on electrical-circuit networks.

PubMed

Zhu, Fenghui; Wang, Wenxu; Di, Zengru; Fan, Ying

2014-01-01

Complex networks with community structures are ubiquitous in the real world. Despite many approaches developed for detecting communities, we continue to lack tools for identifying overlapping and bridging nodes that play crucial roles in the interactions and communications among communities in complex networks. Here we develop an algorithm based on the local flow conservation to effectively and efficiently identify and distinguish the two types of nodes. Our method is applicable in both undirected and directed networks without a priori knowledge of the community structure. Our method bypasses the extremely challenging problem of partitioning communities in the presence of overlapping nodes that may belong to multiple communities. Due to the fact that overlapping and bridging nodes are of paramount importance in maintaining the function of many social and biological networks, our tools open new avenues towards understanding and controlling real complex networks with communities accompanied with the key nodes.

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

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

Characterization of Metakaolin-Based Geopolymer (Briefing chart)

DTIC Science & Technology

2014-08-31

High Strain Rate Dynamic Characterization of Metakaolin and Fly Ash Bsed Geopolymers for Structural Applications The concrete community has...mechanical properties and microstructure of metakaolin geopolymer , obtain the static properties of metakaolin geopolymer for high strain rate Hopkinson...U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Metakaolin, fly ash, geopolymer , characterization, high strain rate

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Influence of different fertilizer types of zucchini (Cucurbita pepo) on the structure of nematode communities.

PubMed

Haytova, D; Bileva, T

2011-01-01

Increasing efficiency of production of vegetable crops is directly related to search for appropriate solution to increase their productivity. Organic amendments have been used for centuries to improve soil fertility and crop yield. Our study suggests that organic amendments can also be used as nematicidal agents. The survey was conducted on Experimental field of Department Horticulture at Agricultural University of Plovdiv, Bulgaria in 2009 on nematode infested sites. Combination with two types of fertilizers was used to investigate their effects on the community of soil nematodes. Characterization and comparative analysis among treatments of soil nematode community structure based on different ecological measures such as total nematode abundance, number of genera, trophic diversity and etc., was made. Changes in the composition and structure of nematode community as result of different fertilizer types were assessed.

Changes in community structure of active protistan assemblages from the lower Pearl River to coastal Waters of the South China Sea.

PubMed

Li, Ran; Jiao, Nianzhi; Warren, Alan; Xu, Dapeng

2018-04-01

Protists make up an important component of aquatic ecosystems, playing crucial roles in biogeochemical processes on local and global scales. To reveal the changes of diversity and community structure of protists along the salinity gradients, community compositions of active protistan assemblages were characterized along a transect from the lower Pearl River estuary to the open waters of the South China Sea (SCS), using high-throughput sequencing of the hyper-variable V9 regions of 18S rRNA. This study showed that the alpha diversity of protists, both in the freshwater and in the coastal SCS stations was higher than that in the estuary. The protist community structure also changed along the salinity gradient. The relative sequence abundance of Stramenopiles was highest at stations with lower salinity and decreased with the increasing of salinity. By contrast, the contributions of Alveolata, Hacrobia and Rhizaria to the protistan communities generally increased with the increasing of salinity. The composition of the active protistan community was strongly correlated with salinity, indicating that salinity was the dominant factor among measured environmental parameters affecting protistan community composition and structure. Copyright © 2018 Elsevier GmbH. All rights reserved.

Critical Multicultural Education and Teacher Sense of Agency

ERIC Educational Resources Information Center

Liggett, Tonda

2011-01-01

The interface between individual agency and subjectivity, and the hegemonic force of larger structures has brought many to characterize identity as not only being multiple and fluid but also as a site of struggle. Norton characterizes these aspects of our subjectivity in terms of "imagined communities", groups, intangible or not readily…

Subcommunities and Their Mutual Relationships in a Transaction Network

NASA Astrophysics Data System (ADS)

Iino, T.; Iyetomi, H.

We investigate a Japanese transaction network consisting ofabout 800 thousand firms (nodes) and four million business relations (links) with focus on its modular structure. Communities detected by maximizing modularity often are dominated by firms with common features or behaviors in the network, such as characterized by regions or industry sectors. However, it is well known that the modularity optimization approach has a resolution limit problem, that is, it fails in identifying fine communities buried in large communities. To unfold such hidden structures, we apply the community detection to each of subnetworks formed by isolating those communities from the whole body. Subcommunities thus identified are composed of firms with finer regions, more specified sectors or business affiliations. Also we introduce a new idea of reduced modularity matrix to measure the strength of relations between (sub)communities.

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats

USGS Publications Warehouse

Price, James T.; Paladino, Frank V.; Lamont, Margaret M.; Witherington, Blair E.; Bates, Scott T.; Soule, Tanya

2017-01-01

The gut microbiome of herbivorous animals consists of organisms that efficiently digest the structural carbohydrates of ingested plant material. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities because they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a neritic distribution and herbivorous diet. As an alternative to direct sampling of the gut, we investigated the cloacal microbiomes of juvenile green turtles before and after recruitment to neritic waters to observe any changes in their microbial community structure. Cloacal swabs were taken from individual turtles for analysis of the 16S rRNA gene sequences using Illumina sequencing. One fecal sample was also obtained, allowing for a preliminary comparison with the bacterial community of the cloaca. We found significant variation in the juvenile green turtle bacterial communities between pelagic and neritic habitats, suggesting that environmental and dietary factors support different bacterial communities in green turtles from these habitats. This is the first study to characterize the cloacal microbiome of green turtles in the context of their ontogenetic shifts, which could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.

Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

PubMed

Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

2014-12-01

Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms.

PubMed

Nagymáté, Zsuzsanna; Homonnay, Zalán G; Márialigeti, Károly

2016-01-01

Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution. Copyright © 2016 Elsevier GmbH. All rights reserved.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

PubMed Central

Basiliko, Nathan; Henry, Kevin; Gupta, Varun; Moore, Tim R.; Driscoll, Brian T.; Dunfield, Peter F.

2013-01-01

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses. PMID:23914185

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico.

PubMed

Ortmann, Alice C; Brannock, Pamela M; Wang, Lei; Halanych, Kenneth M

2018-04-17

Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.

Permafrost soil characteristics and microbial community structure across a boreal forest watershed vary over short spatial scales and dictate community responses to thaw.

NASA Astrophysics Data System (ADS)

Stegen, J.; Bottos, E. M.; Kennedy, D.; Romero, E. B.; Fansler, S.; Chu, R. K.; Tfaily, M.; Jansson, J.; Bernstein, H. C.; Brown, J. M.; Markillie, L. M.

2017-12-01

Understanding drivers of permafrost microbial community structure and function is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw; however, studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from the selective factors that influence non-permafrost soil communities, but that pre-thaw environmental and community characteristics will be strong determinants of community structure and function post-thaw. We characterized patterns of environmental variation and microbial community composition in sixty permafrost samples spanning landscape gradients in a boreal forest watershed, and monitored community responses to thaw. Consistent with our hypothesis, we found that, proportionally, the strongest process influencing permafrost community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21) and variable selection (0.16), and that deterministic selection arose primarily from energetic constraints of the permafrost environment. Our data supported a structural equation model in which organic carbon thermodynamics and organic acid content, influenced redox conditions and total selection. Post-thaw community composition was found to be driven primarily by pre-thaw community composition, indicating a strong influence of historical conditions. Together, these results suggest that community responses to thaw may be highly varied over short distances and that changes in community structure and function are likely to be drastic, as changes to system hydrology mobilize organisms and nutrients, thereby relieving the primary constraints on the system. These findings are being integrated with metabolomic and metatranscriptomic analyses to improve understanding of how pre-thaw conditions can be used to predict microbial activity post-thaw.

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

PubMed Central

Emerson, Brent C.; Cicconardi, Francesco; Fanciulli, Pietro P.; Shaw, Peter J. A.

2011-01-01

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages. PMID:21768154

Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species.

PubMed

Méndez, Verónica; Wood, Jamie R; Butler, Simon J

2018-05-01

Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater proportion of variance in native and exotic community characteristics than the number of habitat types present. Resource diversity and provenance should be explicitly accounted for when characterizing landscape structure and change as they offer additional mechanistic understanding of the links between environmental filtering and community structure. Manipulating resource diversity through the design and implementation of management actions could prove a powerful tool for the delivery of conservation objectives, be they to protect native species, control exotic species, or maintain ecosystem service provision.

Genetic characterization of uncultured fungal endophytes from Bouteloua eriopoda and Atriplex canescens

Treesearch

Mary E. Lucero; Jerry R. Barrow; Ruth Sedillo; Pedro Osuna-Avila; Isaac Reyes-Vera

2008-01-01

Obligate fungal endophytes form cryptic communities in vascular plants that can defy detection and isolation by microscopic examination of reproductive structures. Molecular detection by PCR amplification of fungal DNA sequences alone is insufficient, since target endophyte sequences are unknown and difficult to distinguish from sequences already characterized as plant...

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Treesearch

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

An Analysis of the Structure and Evolution of the Distance Education Research Area Community in Terms of Coauthorships

ERIC Educational Resources Information Center

Gomes, Rodrigo Richard; Barbosa, Marcelo Werneck

2018-01-01

This article aims at characterizing the research community of Distance Education (DE) with respect to coauthorship, a special kind of collaboration among researchers, according to publications of 11 relevant DE journals. This article identified who the central researchers are, the topological properties of the coauthorship networks analyzed, the…

Historical and contemporary factors generate unique butterfly communities on islands

NASA Astrophysics Data System (ADS)

Vodă, Raluca; Dapporto, Leonardo; Dincă, Vlad; Shreeve, Tim G.; Khaldi, Mourad; Barech, Ghania; Rebbas, Khellaf; Sammut, Paul; Scalercio, Stefano; Hebert, Paul D. N.; Vila, Roger

2016-06-01

The mechanisms shaping island biotas are not yet well understood mostly because of a lack of studies comparing eco-evolutionary fingerprints over entire taxonomic groups. Here, we linked community structure (richness, frequency and nestedness) and genetic differentiation (based on mitochondrial DNA) in order to compare insular butterfly communities occurring over a key intercontinental area in the Mediterranean (Italy-Sicily-Maghreb). We found that community characteristics and genetic structure were influenced by a combination of contemporary and historical factors, and among the latter, connection during the Pleistocene had an important impact. We showed that species can be divided into two groups with radically different properties: widespread taxa had high dispersal capacity, a nested pattern of occurrence, and displayed little genetic structure, while rare species were mainly characterized by low dispersal, high turnover and genetically differentiated populations. These results offer an unprecedented view of the distinctive butterfly communities and of the main processes determining them on each studied island and highlight the importance of assessing the phylogeographic value of populations for conservation.

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

PubMed Central

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.; Bible, Amber N.; Morrell-Falvey, Jennifer L.; Pelletier, Dale A.; Simpson, Michael L.; Doktycz, Mitchel J.; Retterer, Scott T.

2016-01-01

The structure and function of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment and the abundance of its community members. The complexity of this natural parameter space has made characterization of the key drivers of community development difficult. In order to facilitate these characterizations, we have developed a microwell platform designed to screen microbial growth and interactions across a wide variety of physical and initial conditions. Assembly of microbial communities into microwells was achieved using a novel biofabrication method that exploits well feature sizes for control of innoculum levels. Wells with incrementally smaller size features created populations with increasingly larger variations in inoculum levels. This allowed for reproducible growth measurement in large (20 μm diameter) wells, and screening for favorable growth conditions in small (5, 10 μm diameter) wells. We demonstrate the utility of this approach for screening and discovery using 5 μm wells to assemble P. aeruginosa colonies across a broad distribution of innoculum levels, and identify those conditions that promote the highest probability of survivial and growth under spatial confinement. Multi-member community assembly was also characterized to demonstrate the broad potential of this platform for studying the role of member abundance on microbial competition, mutualism and community succession. PMID:27152511

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Looking for hotspots of marine metacommunity connectivity: a methodological framework

PubMed Central

Melià, Paco; Schiavina, Marcello; Rossetto, Marisa; Gatto, Marino; Fraschetti, Simonetta; Casagrandi, Renato

2016-01-01

Seascape connectivity critically affects the spatiotemporal dynamics of marine metacommunities. Understanding how connectivity patterns emerge from physically and biologically-mediated interactions is therefore crucial to conserve marine ecosystem functions and biodiversity. Here, we develop a set of biophysical models to explore connectivity in assemblages of species belonging to a typical Mediterranean community (Posidonia oceanica meadows) and characterized by different dispersing traits. We propose a novel methodological framework to synthesize species-specific results into a set of community connectivity metrics and show that spatiotemporal variation in magnitude and direction of the connections, as well as interspecific differences in dispersing traits, are key factors structuring community connectivity. We eventually demonstrate how these metrics can be used to characterize the functional role of each marine area in determining patterns of community connectivity at the basin level and to support marine conservation planning. PMID:27029563

Looking for hotspots of marine metacommunity connectivity: a methodological framework

NASA Astrophysics Data System (ADS)

Melià, Paco; Schiavina, Marcello; Rossetto, Marisa; Gatto, Marino; Fraschetti, Simonetta; Casagrandi, Renato

2016-03-01

Seascape connectivity critically affects the spatiotemporal dynamics of marine metacommunities. Understanding how connectivity patterns emerge from physically and biologically-mediated interactions is therefore crucial to conserve marine ecosystem functions and biodiversity. Here, we develop a set of biophysical models to explore connectivity in assemblages of species belonging to a typical Mediterranean community (Posidonia oceanica meadows) and characterized by different dispersing traits. We propose a novel methodological framework to synthesize species-specific results into a set of community connectivity metrics and show that spatiotemporal variation in magnitude and direction of the connections, as well as interspecific differences in dispersing traits, are key factors structuring community connectivity. We eventually demonstrate how these metrics can be used to characterize the functional role of each marine area in determining patterns of community connectivity at the basin level and to support marine conservation planning.

Predictability of littoral-zone fish communities through ontogeny in Lake Texoma, Oklahoma-Texas, USA

USGS Publications Warehouse

Eggleton, M.A.; Ramirez, R.; Hargrave, C.W.; Gido, K.B.; Masoner, J.R.; Schnell, G.D.; Matthews, W.J.

2005-01-01

We sampled larval, juvenile and adult fishes from littoral-zone areas of a large reservoir (Lake Texoma, Oklahoma-Texas) (1) to characterize environmental factors that influenced fish community structure, (2) to examine how consistent fish-environment relationships were through ontogeny (i.e., larval vs. juvenile and adult), and (3) to measure the concordance of larval communities sampled during spring to juvenile and adult communities sampled at the same sites later in the year. Larval, juvenile and adult fish communities were dominated by Atherinidae (mainly inland silverside, Menidia beryllina) and Moronidae (mainly juvenile striped bass, Morone saxatilis) and were consistently structured along a gradient of site exposure to prevailing winds and waves. Larval, juvenile and adult communities along this gradient varied from atherinids and moronids at highly exposed sites to mostly centrarchids (primarily Lepomis and Micropterus spp.) at protected sites. Secondarily, zooplankton densities, water clarity, and land-use characteristics were related to fish community structure. Rank correlation analyses and Mantel tests indicated that the spatial consistency and predictability of fish communities was high as larval fishes sampled during spring were concordant with juvenile and adult fishes sampled at the same sites during summer and fall in terms of abundance, richness, and community structure. We propose that the high predictability and spatial consistency of littoral-zone fishes in Lake Texoma was a function of relatively simple communities (dominated by 1-2 species) that were structured by factors, such as site exposure to winds and waves, that varied little through time. ?? Springer 2005.

Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments.

PubMed

Almeida, C Marisa R; Oliveira, Tânia; Reis, Izabela; Gomes, Carlos R; Mucha, Ana P

2017-12-01

Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones. Copyright © 2017. Published by Elsevier Ltd.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

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

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

[The role of the floodplain gradient in structuring of testate amoebae communities in the Ilych River].

PubMed

Mazeĭ, Iu A; Malysheva, E A; Lapteva, E M; Komarov, A A; Taskaeva, A A

2012-01-01

Forty-two testate amoebae taxa were identified in alluvial soils of floodplain islands in the Ilych River. Among the pedo- and eurybionts, there were aquatic rhizopods. Along the floodplain transect (willow --> meadow --> deciduous forest --> coniferous forest), the testate amoebae community changed directly. There are spatially homogeneous (low beta-diversity) testacean communities but species rich on the local level (high alpha-diversity) within forests. Within willows and meadows, communities are characterized by low alpha-diversity and high heterogeneity that leads to high gamma-diversity.

Bioelectrochemical Systems Workshop:Standardized Analyses, Design Benchmarks, and Reporting

DTIC Science & Technology

2012-01-01

related to the exoelectrogenic biofilm activity, and to investigate whether the community structure is a function of design and operational parameters...where should biofilm samples be collected? The most prevalent methods of community characterization in BES studies have entailed phylogenetic ...of function associated with this genetic marker, and in methods that involve polymerase chain reaction (PCR) amplification the quantitative

Polychaetes of an artificial reef in the central mediterranean sea

NASA Astrophysics Data System (ADS)

Gravina, M. F.; Ardizzone, G. D.; Belluscio, A.

1989-02-01

The development of a polychaete community over five years on a man-made reef was analyzed. The reef was composed of 280 concrete blocks (2 × 2 × 2 m) and located in the Tyrrhenian Sea (Italy) 1.5 miles offshore and 12-14 m deep. Sixty-three species were collected—serpulids, nereids and cirratulids being the most abundant families. Ordination by Principal Components Analysis (PCA) technique showed three main stages in the colonization process: a pioneer phase, when mainly serpulids ( Pomatoceros triqueter, P. lamarckii, Hydroides pseuduncinata) occurred; a second phase, characterized by mussel ( Mytilus galloprovincialis) dominance and a more differentiated community structure with a lot of new species especially recurring on hard bottom ( Serpula concharum, H. dianthus, Ceratonereis costae); and a third phase, with an alteration of the substratum through soft deposits and the polychaete community characterized by also the occurrence of soft bottom species ( Heteromastus filiformis, Polydora ciliata, Dorvillea rubrovittata). From the trophic point of view, the structure of the community changed from dominance by filter feeders (97%) to a more differentiated situation with abundant detritic feeders ( c. 20%). The rates of immigration and extinction and the colonization curve showed that an actual stable steady-state was not reached.

LP-LPA: A link influence-based label propagation algorithm for discovering community structures in networks

NASA Astrophysics Data System (ADS)

Berahmand, Kamal; Bouyer, Asgarali

2018-03-01

Community detection is an essential approach for analyzing the structural and functional properties of complex networks. Although many community detection algorithms have been recently presented, most of them are weak and limited in different ways. Label Propagation Algorithm (LPA) is a well-known and efficient community detection technique which is characterized by the merits of nearly-linear running time and easy implementation. However, LPA has some significant problems such as instability, randomness, and monster community detection. In this paper, an algorithm, namely node’s label influence policy for label propagation algorithm (LP-LPA) was proposed for detecting efficient community structures. LP-LPA measures link strength value for edges and nodes’ label influence value for nodes in a new label propagation strategy with preference on link strength and for initial nodes selection, avoid of random behavior in tiebreak states, and efficient updating order and rule update. These procedures can sort out the randomness issue in an original LPA and stabilize the discovered communities in all runs of the same network. Experiments on synthetic networks and a wide range of real-world social networks indicated that the proposed method achieves significant accuracy and high stability. Indeed, it can obviously solve monster community problem with regard to detecting communities in networks.

A new Arctic seepage site? Preliminary evidence from benthic community

NASA Astrophysics Data System (ADS)

Caridi, Francesca; Sabbatini, Anna; Morigi, Caterina; Giulia Lucchi, Renata

2017-04-01

The Kveithola Trough is an abrupt and narrow sedimentary system located in the NW Barents Sea. The hydrographic, bio-geochemical conditions and the possible existence of gas seepage activity of the area have been investigated during the Eurofleets 2- BURSTER cruise, conducted on board the German icebreaker RV Polarstern. The aim of our work is to characterize the benthic biota and more specifically the macrofaunal community structure coupled to the study of benthic foraminiferal meiofauna. Preliminary qualitative results revealed that in the inner Kveithola Trough, the macrofaunal community is composed by abundant black worm tubes (Chaetopteridae worms and Siboglinidae-like taxa) with presence of Thyasiridae bivalve species. The occurrence of these macrofaunal taxa is usually associated to oxygen-reduced environments, hydrothermal vents and cold seeps. The living benthic foraminiferal assemblage in the same stations is characterized by the presence of typically oxygen-depleted environmental taxa including the calcareous species Nonionellina labradorica and Globobulimina spp.. Conversely, in the outer Kveithola trough, both benthic macrofauna and foraminiferal meiofauna assemblages are characterized by less opportunistic taxa with a higher biodiversity suggesting very distinct oceanographic sea bottom conditions. The organic matter richness plays a large role in the Kveithola Trough environmental setting and may bring anoxic conditions that could affect the biota of the area. In fact, the benthic community structure of this area inhabits suboxic, anoxic and organic-enriched sediments and disturbed environments, forming assemblages with low diversity and high abundances of a few tolerant and/or specialized species. This preliminary finding could be consistent with other studies examining benthic community structure around Svalbard and in particular cold seep and vents habitats where faunal characteristics are patchy, suggesting small-scale heterogeneity in the environment surrounding cold seeps. For said reasons we envisage the presence of a new Arctic seepage site having a strong local impact on the benthic system.

Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

PubMed Central

Staley, Christopher; Kaiser, Thomas; Gidley, Maribeth L.; Enochs, Ian C.; Jones, Paul R.; Goodwin, Kelly D.; Sinigalliano, Christopher D.

2017-01-01

ABSTRACT Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater. PMID:28341673

Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs.

PubMed

Staley, Christopher; Kaiser, Thomas; Gidley, Maribeth L; Enochs, Ian C; Jones, Paul R; Goodwin, Kelly D; Sinigalliano, Christopher D; Sadowsky, Michael J; Chun, Chan Lan

2017-05-15

Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater. Copyright © 2017 Staley et al.

Bioluminescence as an ecological factor during high Arctic polar night

NASA Astrophysics Data System (ADS)

Cronin, Heather A.; Cohen, Jonathan H.; Berge, Jørgen; Johnsen, Geir; Moline, Mark A.

2016-11-01

Bioluminescence commonly influences pelagic trophic interactions at mesopelagic depths. Here we characterize a vertical gradient in structure of a generally low species diversity bioluminescent community at shallower epipelagic depths during the polar night period in a high Arctic fjord with in situ bathyphotometric sampling. Bioluminescence potential of the community increased with depth to a peak at 80 m. Community composition changed over this range, with an ecotone at 20-40 m where a dinoflagellate-dominated community transitioned to dominance by the copepod Metridia longa. Coincident at this depth was bioluminescence exceeding atmospheric light in the ambient pelagic photon budget, which we term the bioluminescence compensation depth. Collectively, we show a winter bioluminescent community in the high Arctic with vertical structure linked to attenuation of atmospheric light, which has the potential to influence pelagic ecology during the light-limited polar night.

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.

The configuration of the Brazilian scientific field.

PubMed

Barata, Rita B; Aragão, Erika; de Sousa, Luis E P Fernandes; Santana, Taris M; Barreto, Mauricio L

2014-03-01

This article describes the configuration of the scientific field in Brazil, characterizing the scientific communities in every major area of knowledge in terms of installed capacity, ability to train new researchers, and capacity for academic production. Empirical data from several sources of information are used to characterize the different communities. Articulating the theoretical contributions of Pierre Bourdieu, Ludwik Fleck, and Thomas Kuhn, the following types of capital are analyzed for each community: social capital (scientific prestige), symbolic capital (dominant paradigm), political capital (leadership in S & T policy), and economic capital (resources). Scientific prestige is analyzed by taking into account the volume of production, activity index, citations, and other indicators. To characterize symbolic capital, the dominant paradigms that distinguish the natural sciences, the humanities, applied sciences, and technology development are analyzed theoretically. Political capital is measured by presidency in one of the main agencies in the S & T national system, and research resources and fellowships define the economic capital. The article discusses the composition of these different types of capital and their correspondence to structural capacities in various communities with the aim of describing the configuration of the Brazilian scientific field.

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

PubMed Central

Leung, Marcus H. Y.; Wilkins, David; Lee, Patrick K. H.

2015-01-01

Many studies have characterized microbiomes of western individuals. However, studies involving non-westerners are scarce. This study characterizes the skin microbiomes of Chinese individuals. Skin-associated genera, including Propionibacterium, Corynebacterium, Staphylococcus, and Enhydrobacter were prevalent. Extensive inter-individual microbiome variations were detected, with core genera present in all individuals constituting a minority of genera detected. Species-level analyses presented dominance of potential opportunistic pathogens in respective genera. Host properties including age, gender, and household were associated with variations in community structure. For all sampled sites, skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households. Network analyses highlighted general and skin-site specific relationships between genera. Comparison of microbiomes from different population groups revealed race-based clustering explained by community membership (Global R = 0.968) and structure (Global R = 0.589), contributing to enlargement of the skin pan-microbiome. This study provides the foundation for subsequent in-depth characterization and microbial interactive analyses on the skin and other parts of the human body in different racial groups, and an appreciation that the human skin pan-microbiome can be much larger than that of a single population. PMID:26177982

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

PubMed

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Alternative community structures in a kelp-urchin community: A qualitative modeling approach

USGS Publications Warehouse

Montano-Moctezuma, G.; Li, H.W.; Rossignol, P.A.

2007-01-01

Shifts in interaction patterns within a community may result from periodic disturbances and climate. The question arises as to the extent and significance of these shifting patterns. Using a novel approach to link qualitative mathematical models and field data, namely using the inverse matrix to identify the community matrix, we reconstructed community networks from kelp forests off the Oregon Coast. We simulated all ecologically plausible interactions among community members, selected the models whose outcomes match field observations, and identified highly frequent links to characterize the community network from a particular site. We tested all possible biologically reasonable community networks through qualitative simulations, selected those that matched patterns observed in the field, and further reduced the set of possibilities by retaining those that were stable. We found that a community can be represented by a set of alternative structures, or scenarios. From 11,943,936 simulated models, 0.23% matched the field observations; moreover, only 0.006%, or 748 models, were highly reliable in their predictions and met conditions for stability. Predator-prey interactions as well as non-predatory relationships were consistently found in most of the 748 models. These highly frequent connections were useful to characterize the community network in the study site. We suggest that alternative networks provide the community with a buffer to disturbance, allowing it to continuously reorganize to adapt to a variable environment. This is possible due to the fluctuating capacities of foraging species to consume alternate resources. This suggestion is sustained by our results, which indicate that none of the models that matched field observations were fully connected. This plasticity may contribute to the persistence of these communities. We propose that qualitative simulations represent a powerful technique to raise new hypotheses concerning community dynamics and to reconstruct guidelines that may govern community patterns. ?? 2007 Elsevier B.V. All rights reserved.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

PubMed Central

Pent, Mari; Põldmaa, Kadri; Bahram, Mohammad

2017-01-01

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales—the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements. PMID:28539921

Community Characteristics and Leaf Stoichiometric Traits of Desert Ecosystems Regulated by Precipitation and Soil in an Arid Area of China.

PubMed

Zhang, Xiaolong; Guan, Tianyu; Zhou, Jihua; Cai, Wentao; Gao, Nannan; Du, Hui; Jiang, Lianhe; Lai, Liming; Zheng, Yuanrun

2018-01-10

Precipitation is a key environmental factor determining plant community structure and function. Knowledge of how community characteristics and leaf stoichiometric traits respond to variation in precipitation is crucial for assessing the effects of global changes on terrestrial ecosystems. In this study, we measured community characteristics, leaf stoichiometric traits, and soil properties along a precipitation gradient (35-209 mm) in a desert ecosystem of Northwest China to explore the drivers of these factors. With increasing precipitation, species richness, aboveground biomass, community coverage, foliage projective cover (FPC), and leaf area index (LAI) all significantly increased, while community height decreased. The hyperarid desert plants were characterized by lower leaf carbon (C) and nitrogen/phosphorus (N/P) levels, and stable N and P, and these parameters did not change significantly with precipitation. The growth of desert plants was limited more by N than P. Soil properties, rather than precipitation, were the main drivers of desert plant leaf stoichiometric traits, whereas precipitation made the biggest contribution to vegetation structure and function. These results test the importance of precipitation in regulating plant community structure and composition together with soil properties, and provide further insights into the adaptive strategy of communities at regional scale in response to global climate change.

Community Characteristics and Leaf Stoichiometric Traits of Desert Ecosystems Regulated by Precipitation and Soil in an Arid Area of China

PubMed Central

Guan, Tianyu; Zhou, Jihua; Cai, Wentao; Gao, Nannan; Du, Hui; Jiang, Lianhe; Lai, Liming; Zheng, Yuanrun

2018-01-01

Precipitation is a key environmental factor determining plant community structure and function. Knowledge of how community characteristics and leaf stoichiometric traits respond to variation in precipitation is crucial for assessing the effects of global changes on terrestrial ecosystems. In this study, we measured community characteristics, leaf stoichiometric traits, and soil properties along a precipitation gradient (35–209 mm) in a desert ecosystem of Northwest China to explore the drivers of these factors. With increasing precipitation, species richness, aboveground biomass, community coverage, foliage projective cover (FPC), and leaf area index (LAI) all significantly increased, while community height decreased. The hyperarid desert plants were characterized by lower leaf carbon (C) and nitrogen/phosphorus (N/P) levels, and stable N and P, and these parameters did not change significantly with precipitation. The growth of desert plants was limited more by N than P. Soil properties, rather than precipitation, were the main drivers of desert plant leaf stoichiometric traits, whereas precipitation made the biggest contribution to vegetation structure and function. These results test the importance of precipitation in regulating plant community structure and composition together with soil properties, and provide further insights into the adaptive strategy of communities at regional scale in response to global climate change. PMID:29320458

Composition of fungal soil communities varies with plant abundance and geographic origin

PubMed Central

Reininger, Vanessa; Martinez-Garcia, Laura B.; Sanderson, Laura; Antunes, Pedro M.

2015-01-01

Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities. We also assessed whether these plants showed different symbiotic relationships with soil biota through their roots. We characterized the plant community and collected roots to investigate fungal communities using 454 pyrosequencing and assessed arbuscular mycorrhizal colonization and enemy-induced lesions. Differences in fungal communities were considered based on the assessment of α- and β diversity depending on plant ‘abundance’ and ‘origin’. Plant abundance and origin determined the fungal community. Fungal richness was higher for native abundant as opposed to relatively rare native plant species. However, this was not observed for exotics of contrasting abundance. Regardless of their origin, β diversity was higher for rare than for abundant species. Abundant exotics in the community, which happen to be grasses, were the least mycorrhizal whereas rare natives were most susceptible to enemy attack. Our results suggest that compared with exotics, the relative abundance of remnant native plant species in our old-field site is still linked to the structure of belowground fungal communities. In contrast, exotic species may act as a disturbing agent contributing towards the homogenization of soil fungal communities, potentially changing feedback interactions. PMID:26371291

Structure of Mesophotic Reef Fish Assemblages in the Northwestern Hawaiian Islands

PubMed Central

Kosaki, Randall K.; Wagner, Daniel; Kane, Corinne

2016-01-01

Mesophotic coral ecosystems (MCEs) support diverse communities of marine organisms with changes in community structure occurring along a depth gradient. In recent years, MCEs have gained attention due to their depths that provide protection from natural and anthropogenic stressors and their relative stability over evolutionary time periods, yet ecological structures of fish assemblages in MCEs remain largely un-documented. Here, we investigated composition and trophic structure of reef fish assemblages in the Northwestern Hawaiian Islands (NWHI) along a depth gradient from 1 to 67 m. The structure of reef fish assemblages as a whole showed a clear gradient from shallow to mesophotic depths. Fish assemblages at mesophotic depths had higher total densities than those in shallower waters, and were characterized by relatively high densities of planktivores and invertivores and relatively low densities of herbivores. Fishes that typified assemblages at mesophotic depths included six species that are endemic to the Hawaiian Islands. The present study showed that mesophotic reefs in the NWHI support unique assemblages of fish that are characterized by high endemism and relatively high densities of planktivores. Our findings underscore the ecological importance of these undersurveyed ecosystems and warrant further studies of MCEs. PMID:27383614

Inferring and analysis of social networks using RFID check-in data in China

PubMed Central

Liu, Tao; Liu, Shouyin; Ge, Shuangkui

2017-01-01

Social networks play an important role in our daily lives. However, social ties are rather elusive to quantify, especially for large groups of subjects over prolonged periods of time. In this work, we first propose a methodology for extracting social ties from long spatio-temporal data streams, where the subjects are 17,795 undergraduates from a university of China and the data streams are the 9,147,106 time-stamped RFID check-in records left behind by them during one academic year. By several metrics mentioned below, we then analyze the structure of the social network. Our results center around three main observations. First, we characterize the global structure of the network, and we confirm the small-world phenomenon on a global scale. Second, we find that the network shows clear community structure. And we observe that younger students at lower levels tend to form large communities, while students at higher levels mostly form smaller communities. Third, we characterize the assortativity patterns by studying the basic demographic and network properties of users. We observe clear degree assortativity on a global scale. Furthermore, we find a strong effect of grade and school on tie formation preference, but we do not find any strong region homophily. Our research may help us to elucidate the structural characteristics and the preference of the formation of social ties in college students’ social network. PMID:28570586

Characterization of Biofilm Community Structure by Ribosomal RNA sequences

DTIC Science & Technology

1989-12-01

for strains of Fibrobacter, 2) Desulfobacter genus-specific probe, 3) Desulfosarcina genus-specific probe, 4) archaebacterial kingdom -specific probes...and 5) eubacterial kingdom -specific probes 5) eukaryote kingdom -specific probe and 6) a general probe encompassing all characterized sulfate-reducing...sets have been fabricated. The group-specific primer sets selectively amplify either sulfate-reducing bacteria or archaebacteria . The SRB-specific

Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status

PubMed Central

Yang, Ching-Hong; Crowley, David E.

2000-01-01

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status. PMID:10618246

Using high throughput sequencing to explore the biodiversity in oral bacterial communities.

PubMed

Diaz, P I; Dupuy, A K; Abusleme, L; Reese, B; Obergfell, C; Choquette, L; Dongari-Bagtzoglou, A; Peterson, D E; Terzi, E; Strausbaugh, L D

2012-06-01

High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then characterized the bacterial communities in saliva and buccal mucosa of five healthy subjects to investigate the power of high throughput sequencing in revealing their diversity and biogeography patterns. Mock community analysis showed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities found a total of 455 OTUs (0.3% dissimilarity) with only 78 of these present in all subjects. We demonstrate that this variability was partly the result of incomplete richness coverage even at great sequencing depths, and so comparing communities by their structure was more effective than comparisons based solely on membership. With respect to oral biogeography, we found inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident at very low sequencing depths and were mostly caused by the abundance of Streptococcus mitis and Gemella haemolysans in mucosa. In summary, we present an experimental and data analysis framework that will facilitate design and interpretation of pyrosequencing-based studies. Despite challenges associated with this technique, we demonstrate its power for evaluation of oral diversity and biogeography patterns. © 2012 John Wiley & Sons A/S.

Cultural Psychiatry: A Spotlight on the Experience of Clinical Social Workers' Encounter with Jewish Ultra-Orthodox Mental Health Clients.

PubMed

Freund, Anat; Band-Winterstein, Tova

2017-07-01

Community is a complex issue, especially in two particular populations overlap: Haredi society, which embraces cultural codes common to closed communities, and the mental health population characterized by its own unique needs. The present study explores the encounter experience of social workers with the cultural perceptions of mental health clients in the Haredi community in light of Community Cultural Psychiatry. A qualitative-phenomenological approach was adopted. In-depth semi-structured interviews were conducted with 27 social workers, mental health professionals, who are in contact with ultra-Orthodox Jewish clients. Three major themes emerged from the data analysis: (1) Exclusion vs. grace and compassion. (2) Mental health: A professional or cultural arena? (3) Mental health help-seeking changing processes. This study shows that the attitude in the Haredi community toward mental health therapy undergoes a process of change. It is important to strengthen this process, together with preserving existing community informal structures of help.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

Local structuring factors of invertebrate communities in ephemeral freshwater rock pools and the influence of more permanent water bodies in the region

USGS Publications Warehouse

Jocque, M.; Graham, T.; Brendonck, L.

2007-01-01

We used three isolated clusters of small ephemeral rock pools on a sandstone flat in Utah to test the importance of local structuring processes on aquatic invertebrate communities. In the three clusters we characterized all ephemeral rock pools (total: 27) for their morphometry, and monitored their water quality, hydrology and community assemblage during a full hydrocycle. In each cluster we also sampled a set of more permanent interconnected freshwater systems positioned in a wash, draining the water from each cluster of rock pools. This design allowed additional testing for the potential role of more permanent water bodies in the region as source populations for the active dispersers and the effect on the community structure in the rock pools. Species richness and community composition in the rock pools correlated with level of permanence and the ammonia concentration. The length of the rock pool inundation cycle shaped community structure, most probably by inhibiting colonization by some taxa (e.g. tadpoles and insect larvae) through developmental constraints. The gradient in ammonia concentrations probably reflects differences in primary production. The more permanent water bodies in each wash differed both environmentally and in community composition from the connected set of rock pools. A limited set of active dispersers was observed in the rock pools. Our findings indicate that aquatic invertebrate communities in the ephemeral rock pools are mainly structured through habitat permanence, possibly linked with biotic interactions and primary production. ?? 2007 Springer Science+Business Media B.V.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

PubMed

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Anaerobic digestion of municipal solid waste composed of food waste, wastepaper, and plastic in a single-stage system: performance and microbial community structure characterization.

PubMed

Wan, Shungang; Sun, Lei; Douieb, Yaniv; Sun, Jian; Luo, Wensui

2013-10-01

The performance of municipal organic solid waste anaerobic digestion was investigated using a single-stage bioreactor, and the microbial community structures were characterized during the digestion. The results showed that the biogas and methane production rates were 592.4 and 370.1L/kg with volatile solid added at the ratio of 2:1:1 for food waste, wastepaper, and plastic based on dry weight. The methane volume concentration fluctuated between 44.3% and 75.4% at steady stage. Acetic acid, propionic acid, and butyric acid were the major volatile fatty acids produced during the digestion process. The anaerobic process was not inhibited by the accumulation of ammonia and free ammonia. The bacterial community was found to consist of at least 21 bands of bacteria and 12 bands of archaea at the steady state. All of the results indicated that the mixture of food waste, wastepaper, and plastic could be efficiently co-digested using the anaerobic digestion system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of Growing Soil Bacterial Communities across a pH gradient Using H218O DNA-Stable Isotope Probing

NASA Astrophysics Data System (ADS)

Welty-Bernard, A. T.; Schwartz, E.

2014-12-01

Recent studies have established consistent relationships between pH and bacterial diversity and community structure in soils from site-specific to landscape scales. However, these studies rely on DNA or PLFA extraction techniques from bulk soils that encompass metabolically active and inactive, or dormant, communities, and loose DNA. Dormant cells may comprise up to 80% of total live cells. If dormant cells dominate a particular environment, it is possible that previous interpretations of the soil variables assumed to drive communities could be profoundly affected. We used H218O stable isotope probing and bar-coded illumina sequencing of 16S rRNA genes to monitor the response of actively growing communities to changes in soil pH in a soil microcosm over 14 days. This substrate-independent approach has several advantages over 13C or 15N-labelled molecules in that all growing bacteria should be able to make use of water, allowing characterization of whole communities. We hypothesized that Acidobacteria would increasingly dominate the growing community and that Actinobacteria and Bacteroidetes would decline, given previously established responses by these taxa to soil pH. Instead, we observed the reverse. Actinobacteria abundance increased three-fold from 26 to 76% of the overall community as soil pH fell from pH 5.6 to pH 4.6. Shifts in community structure and decreases in diversity with declining soil pH were essentially driven by two families, Streptomyceaca and Microbacteracea, which collectively increased from 2 to 40% of the entire community. In contrast, Acidobacteria as a whole declined although numbers of subdivision 1 remained stable across all soil pH levels. We suggest that the brief incubation period in this SIP study selected for growth of acid-tolerant Actinobacteria over Acidobacteria. Taxa within Actinomycetales have been readily cultured over short time frames, suggesting rapid growth patterns. Conversely, taxa within Acidobacteria have been characterized as slow growers with low cell turnover and may represent a relatively quiescent portion of the bacterial community over the short-term. These results suggest that the short-term responses by individual taxa to pH may differ significantly from long-term responses reflecting variable life strategies within the community itself.

Fragmentation alters stream fish community structure in dendritic ecological networks.

PubMed

Perkin, Joshuah S; Gido, Keith B

2012-12-01

Effects of fragmentation on the ecology of organisms occupying dendritic ecological networks (DENs) have recently been described through both conceptual and mathematical models, but few hypotheses have been tested in complex, real-world ecosystems. Stream fishes provide a model system for assessing effects of fragmentation on the structure of communities occurring within DENs, including how fragmentation alters metacommunity dynamics and biodiversity. A recently developed habitat-availability measure, the "dendritic connectivity index" (DCI), allows for assigning quantitative measures of connectivity in DENs regardless of network extent or complexity, and might be used to predict fish community response to fragmentation. We characterized stream fish community structure in 12 DENs in the Great Plains, USA, during periods of dynamic (summer) and muted (fall) discharge regimes to test the DCI as a predictive model of fish community response to fragmentation imposed by road crossings. Results indicated that fish communities in stream segments isolated by road crossings had reduced species richness (alpha diversity) relative to communities that maintained connectivity with the surrounding DEN during summer and fall. Furthermore, isolated communities had greater dissimilarity (beta diversity) to downstream sites notisolated by road crossings during summer and fall. Finally, dissimilarity among communities within DENs decreased as a function of increased habitat connectivity (measured using the DCI) for summer and fall, suggesting that communities within highly connected DENs tend to be more homogeneous. Our results indicate that the DCI is sensitive to community effects of fragmentation in riverscapes and might be used by managers to predict ecological responses to changes in habitat connectivity. Moreover, our findings illustrate that relating structural connectivity of riverscapes to functional connectivity among communities might aid in maintaining metacommunity dynamics and biodiversity in complex dendritic ecosystems.

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

PubMed

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

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

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2015-03-01

We explored the impact of the starting community composition and structure on ecosystem response to perturbations using organic carbon amendment experiments. Subsurface sediment was partitioned into flow-through columns, and the microbial communities were initially stimulated in situ by addition of acetate as a carbon and electron donor source. This drove community richness and evenness down, and pushed the system into a new biogeochemical state characterized by iron reduction. Reconstructed near-full-length 16S rRNA gene sequence analysis indicated a concomitant enrichment of Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After 10 to 12 days, acetate was exchange for lactate in a subset of columns.more » Following the clear onset of sulfate reduction (35 days after acetate-amendment), acetate was substituted for lactate in additional columns. Acetatestimulated communities differed markedly during each biogeochemical regime and at each lactate-switch. Regardless, however, of when communities were switched to lactate, they followed comparable trajectories with respect to composition and structure, with convergence evident one week after each switch, and marked after one month of lactate amendment. During sulfate reduction all treatments were enriched in Firmicutes and a number of species likely involved in sulfate reduction (notably Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum). Lactate treatments were distinguished by substantially lower relative abundances of Desulfotomaculum and Bacteroidetes, and enrichments of Psychrosinus and Clostridiales species. Results imply that the structure of the starting community was not significant in controlling organism selection in community succession.« less

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

PubMed

Marzinelli, Ezequiel M; Campbell, Alexandra H; Zozaya Valdes, Enrique; Vergés, Adriana; Nielsen, Shaun; Wernberg, Thomas; de Bettignies, Thibaut; Bennett, Scott; Caporaso, J Gregory; Thomas, Torsten; Steinberg, Peter D

2015-10-01

Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

HARSHNESS: CHARACTERIZATION OF INTERMITTENT STREAM HABITAT OVER SPACE AND TIME

EPA Science Inventory

Frequently disturbed environments, such as intermittent streams, are ecologically useful for studying how disturbance characteristics (e.g., frequency, magnitude) affect community structure and succession. A harshness index summarizing spatial and temporal characteristics of pra...

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points: Microbial community succession and disturbance

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

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2014-04-18

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacteriummore » and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.« less

Pyrosequencing reveals regional differences in fruit-associated fungal communities

PubMed Central

Taylor, Michael W; Tsai, Peter; Anfang, Nicole; Ross, Howard A; Goddard, Matthew R

2014-01-01

We know relatively little of the distribution of microbial communities generally. Significant work has examined a range of bacterial communities, but the distribution of microbial eukaryotes is less well characterized. Humans have an ancient association with grape vines (Vitis vinifera) and have been making wine since the dawn of civilization, and fungi drive this natural process. While the molecular biology of certain fungi naturally associated with vines and wines is well characterized, complementary investigations into the ecology of fungi associated with fruiting plants is largely lacking. DNA sequencing technologies allow the direct estimation of microbial diversity from a given sample, avoiding culture-based biases. Here, we use deep community pyrosequencing approaches, targeted at the 26S rRNA gene, to examine the richness and composition of fungal communities associated with grapevines and test for geographical community structure among four major regions in New Zealand (NZ). We find over 200 taxa using this approach, which is 10-fold more than previously recovered using culture-based methods. Our analyses allow us to reject the null hypothesis of homogeneity in fungal species richness and community composition across NZ and reveal significant differences between major areas. PMID:24650123

Identifying Perceived Neighborhood Stressors Across Diverse Communities in New York City.

PubMed

Shmool, Jessie L C; Yonas, Michael A; Newman, Ogonnaya Dotson; Kubzansky, Laura D; Joseph, Evelyn; Parks, Ana; Callaway, Charles; Chubb, Lauren G; Shepard, Peggy; Clougherty, Jane E

2015-09-01

There is growing interest in the role of psychosocial stress in health disparities. Identifying which social stressors are most important to community residents is critical for accurately incorporating stressor exposures into health research. Using a community-academic partnered approach, we designed a multi-community study across the five boroughs of New York City to characterize resident perceptions of key neighborhood stressors. We conducted 14 community focus groups; two to three in each borough, with one adolescent group and one Spanish-speaking group per borough. We then used systematic content analysis and participant ranking data to describe prominent neighborhood stressors and identify dominant themes. Three inter-related themes regarding the social and structural sources of stressful experiences were most commonly identified across neighborhoods: (1) physical disorder and perceived neglect, (2) harassment by police and perceived safety and (3) gentrification and racial discrimination. Our findings suggest that multiple sources of distress, including social, political, physical and economic factors, should be considered when investigating health effects of community stressor exposures and psychological distress. Community expertise is essential for comprehensively characterizing the range of neighborhood stressors that may be implicated in psychosocial exposure pathways.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms. PMID:28095400

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.

Coexistence and community structure in a consumer resource model with implicit stoichiometry.

PubMed

Orlando, Paul A; Brown, Joel S; Wise, David H

2012-09-01

We combine stoichiometry theory and optimal foraging theory into the MacArthur consumer-resource model. This generates predictions for diet choice, coexistence, and community structure of heterotroph communities. Tradeoffs in consumer resource-garnering traits influence community outcomes. With scarce resources, consumers forage opportunistically for complementary resources and may coexist via tradeoffs in resource encounter rates. In contrast to single currency models, stoichiometry permits multiple equilibria. These alternative stable states occur when tradeoffs in resource encounter rates are stronger than tradeoffs in elemental conversion efficiencies. With abundant resources consumers exhibit partially selective diets for essential resources and may coexist via tradeoffs in elemental conversion efficiencies. These results differ from single currency models, where adaptive diet selection is either opportunistic or selective. Interestingly, communities composed of efficient consumers share many of the same properties as communities based on substitutable resources. However, communities composed of relatively inefficient consumers behave similarly to plant communities as characterized by Tilman's consumer resource theory. The results of our model indicate that the effects of stoichiometry theory on community ecology are dependent upon both consumer foraging behavior and the nature of resource garnering tradeoffs. Copyright © 2012 Elsevier Inc. All rights reserved.

Spatial variations in zooplankton community structure along the Japanese coastline in the Japan Sea: influence of the coastal current

NASA Astrophysics Data System (ADS)

Kodama, Taketoshi; Wagawa, Taku; Iguchi, Naoki; Takada, Yoshitake; Takahashi, Takashi; Fukudome, Ken-Ichi; Morimoto, Haruyuki; Goto, Tsuneo

2018-06-01

This study evaluates spatial variations in zooplankton community structure and potential controlling factors along the Japanese coast under the influence of the coastal branch of the Tsushima Warm Current (CBTWC). Variations in the density of morphologically identified zooplankton in the surface layer in May were investigated for a 15-year period. The density of zooplankton (individuals per cubic meter) varied between sampling stations, but there was no consistent west-east trend. Instead, there were different zooplankton community structures in the west and east, with that in Toyama Bay particularly distinct: Corycaeus affinis and Calanus sinicus were dominant in the west and Oithona atlantica was dominant in Toyama Bay. Distance-based redundancy analysis (db-RDA) was used to characterize the variation in zooplankton community structure, and four axes (RD1-4) provided significant explanation. RD2-4 only explained < 4.8 % of variation in the zooplankton community and did not show significant spatial difference; however, RD1, which explained 89.9 % of variation, did vary spatially. Positive and negative species scores on RD1 represent warm- and cold-water species, respectively, and their variation was mainly explained by water column mean temperature, and it is considered to vary spatially with the CBTWC. The CBTWC intrusion to the cold Toyama Bay is weak and occasional due to the submarine canyon structure of the bay. Therefore, the varying bathymetric characteristics along the Japanese coast of the Japan Sea generate the spatial variation in zooplankton community structure, and dominance of warm-water species can be considered an indicator of the CBTWC.

Relationships between Algae, Benthic Herbivorous Invertebrates and Fishes in Rocky Sublittoral Communities of a Temperate Sea (Mediterranean)

NASA Astrophysics Data System (ADS)

Ruitton, S.; Francour, P.; Boudouresque, C. F.

2000-02-01

In situ surveys were used to examine the contribution of benthic herbivorous invertebrates and fishes to the organization of Mediterranean rocky sublittoral communities. Shallow (1-3 m) and deep (6-8 m) sampling sites, in natural areas and on man-made structures, were characterized by a structural complexity index (cavity index and mean size of cavity aperture), algal cover (encrusting, turfy, shrubby and arborescent algae) and the density of benthic herbivorous invertebrates and fish. A relationship between structural complexity and biota was only evident for some fish species ( Diplodus spp. and Sarpa salpa) at deep sites, where they not only feed but also shelter. Three benthic herbivorous invertebrates, the sea urchins Paracentrotus lividus and Arbacia lixula, and the limpet Patella caerulea , are associated with communities dominated by encrusting algae. Variations in their abundance and role in structuring algal communities follow a depth gradient: P. caerulea and A. lixula are mainly present at shallow sites and P. lividus at deep sites. These benthic herbivorous invertebrates may account for the structure of shallow algal communities. In contrast, at deep sites, fishes (the omnivorous Diplodus spp. and the herbivorous S. salpa) have a potential importance in controlling sublittoral algae, in addition to invertebrates. It is suggested that the ecological impact of herbivorous and omnivorous fishes in temperate seas could be greater than is generally thought. Experiments should be designed to validate this postulate.

Urban slum structure: integrating socioeconomic and land cover data to model slum evolution in Salvador, Brazil.

PubMed

Hacker, Kathryn P; Seto, Karen C; Costa, Federico; Corburn, Jason; Reis, Mitermayer G; Ko, Albert I; Diuk-Wasser, Maria A

2013-10-20

The expansion of urban slums is a key challenge for public and social policy in the 21st century. The heterogeneous and dynamic nature of slum communities limits the use of rigid slum definitions. A systematic and flexible approach to characterize, delineate and model urban slum structure at an operational resolution is essential to plan, deploy, and monitor interventions at the local and national level. We modeled the multi-dimensional structure of urban slums in the city of Salvador, a city of 3 million inhabitants in Brazil, by integrating census-derived socioeconomic variables and remotely-sensed land cover variables. We assessed the correlation between the two sets of variables using canonical correlation analysis, identified land cover proxies for the socioeconomic variables, and produced an integrated map of deprivation in Salvador at 30 m × 30 m resolution. The canonical analysis identified three significant ordination axes that described the structure of Salvador census tracts according to land cover and socioeconomic features. The first canonical axis captured a gradient from crowded, low-income communities with corrugated roof housing to higher-income communities. The second canonical axis discriminated among socioeconomic variables characterizing the most marginalized census tracts, those without access to sanitation or piped water. The third canonical axis accounted for the least amount of variation, but discriminated between high-income areas with white-painted or tiled roofs from lower-income areas. Our approach captures the socioeconomic and land cover heterogeneity within and between slum settlements and identifies the most marginalized communities in a large, complex urban setting. These findings indicate that changes in the canonical scores for slum areas can be used to track their evolution and to monitor the impact of development programs such as slum upgrading.

Urban slum structure: integrating socioeconomic and land cover data to model slum evolution in Salvador, Brazil

PubMed Central

2013-01-01

Background The expansion of urban slums is a key challenge for public and social policy in the 21st century. The heterogeneous and dynamic nature of slum communities limits the use of rigid slum definitions. A systematic and flexible approach to characterize, delineate and model urban slum structure at an operational resolution is essential to plan, deploy, and monitor interventions at the local and national level. Methods We modeled the multi-dimensional structure of urban slums in the city of Salvador, a city of 3 million inhabitants in Brazil, by integrating census-derived socioeconomic variables and remotely-sensed land cover variables. We assessed the correlation between the two sets of variables using canonical correlation analysis, identified land cover proxies for the socioeconomic variables, and produced an integrated map of deprivation in Salvador at 30 m × 30 m resolution. Results The canonical analysis identified three significant ordination axes that described the structure of Salvador census tracts according to land cover and socioeconomic features. The first canonical axis captured a gradient from crowded, low-income communities with corrugated roof housing to higher-income communities. The second canonical axis discriminated among socioeconomic variables characterizing the most marginalized census tracts, those without access to sanitation or piped water. The third canonical axis accounted for the least amount of variation, but discriminated between high-income areas with white-painted or tiled roofs from lower-income areas. Conclusions Our approach captures the socioeconomic and land cover heterogeneity within and between slum settlements and identifies the most marginalized communities in a large, complex urban setting. These findings indicate that changes in the canonical scores for slum areas can be used to track their evolution and to monitor the impact of development programs such as slum upgrading. PMID:24138776

Functional identity and functional structure change through succession in a rocky intertidal marine herbivore assemblage.

PubMed

Aguilera, Moisés A; Navarrete, Sergio A

2012-01-01

Despite the great interest in characterizing the functional structure and resilience of functional groups in natural communities, few studies have examined in which way the roles and relationships of coexisting species change during community succession, a fundamental and natural process that follows the release of new resources in terrestrial and aquatic ecosystems. Variation in algal traits that characterize different phases and stages of community succession on rocky shores are likely to influence the magnitude, direction of effects, and the level of redundancy and complementarity in the diverse assemblage of herbivores. Two separate field experiments were conducted to quantify per capita and population effects and the functional relationship (i.e., redundancy or complementarity) of four herbivore species found in central Chile during early and late algal succession. The first experiment examined grazer effects on the colonization and establishment of early-succession algal species. The second experiment examined effects on the late-successional, dominant corticated alga Mazzaella laminarioides. Complementary laboratory experiments with all species and under natural environmental conditions allowed us to further characterize the collective effects of these species. We found that, during early community succession, all herbivore species had similar effects on the ephemeral algae, ulvoids, but only during the phase of colonization. Once these algae were established, only a subset of the species was able to control their abundance. During late succession, only the keyhole limpet Fissurella crassa could control corticated Mazzaella. The functional relationships among these species changed dramatically from redundant effects on ephemeral algae during early colonization, to a more complementary role on established early-successional algae, to a dominant (i.e., keystone) effect on late succession. This study highlights that functional relationship within consumer assemblages can vary at different phases and times of community succession. Differentiation in herbivore roles emphasizes the need to evaluate consumer's impacts through different times of community succession, and through experimental manipulations to make even broad predictions about the resilience or vulnerability of diverse intertidal assemblages to human disturbances.

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries.

PubMed

Aguirre, Mikel; Abad, David; Albaina, Aitor; Cralle, Lauren; Goñi-Urriza, María Soledad; Estonba, Andone; Zarraonaindia, Iratxe

2017-01-01

In this study, 16S rRNA gene sequencing was used to characterize the changes in taxonomic composition and environmental factors significantly influencing bacterial community structure across an annual cycle in the Estuary of Bilbao as well as its tributaries. In spite of this estuary being small and characterized by a short residence time, the environmental factors most highly correlated with the bacterial community mirrored those reported to govern larger estuaries, specifically salinity and temperature. Additionally, bacterial community changes in the estuary appeared to vary with precipitation. For example, an increase in freshwater bacteria (Comamonadaceae and Sphingobacteriaceae) was observed in high precipitation periods compared to the predominately marine-like bacteria (Rhodobacterales and Oceanospirillales) that were found in low precipitation periods. Notably, we observed a significantly higher relative abundance of Comamonadaceae than previously described in other estuaries. Furthermore, anthropic factors could have an impact on this particular estuary's bacterial community structure. For example, ecosystem changes related to the channelization of the estuary likely induced a low dissolved oxygen (DO) concentration, high temperature, and high chlorophyll concentration period in the inner euhaline water in summer (samples with salinity >30 ppt). Those samples were characterized by a high abundance of facultative anaerobes. For instance, OTUs classified as Cryomorphaceae and Candidatus Aquiluna rubra were negatively associated with DO concentration, while Oleiphilaceae was positively associated with DO concentration. Additionally, microorganisms related to biological treatment of wastewater (e.g Bdellovibrio and Zoogloea) were detected in the samples immediately downstream of the Bilbao Wastewater Treatment Plant (WWTP). There are several human activities planned in the region surrounding the Estuary of Bilbao (e.g. sediment draining, architectural changes, etc.) which will likely affect this ecosystem. Therefore, the addition of bacterial community profiling and diversity analysis into the estuary's ongoing monitoring program would provide a more comprehensive view of the ecological status of the Estuary of Bilbao.

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

PubMed Central

Abad, David; Albaina, Aitor; Cralle, Lauren; Goñi-Urriza, María Soledad; Estonba, Andone; Zarraonaindia, Iratxe

2017-01-01

In this study, 16S rRNA gene sequencing was used to characterize the changes in taxonomic composition and environmental factors significantly influencing bacterial community structure across an annual cycle in the Estuary of Bilbao as well as its tributaries. In spite of this estuary being small and characterized by a short residence time, the environmental factors most highly correlated with the bacterial community mirrored those reported to govern larger estuaries, specifically salinity and temperature. Additionally, bacterial community changes in the estuary appeared to vary with precipitation. For example, an increase in freshwater bacteria (Comamonadaceae and Sphingobacteriaceae) was observed in high precipitation periods compared to the predominately marine-like bacteria (Rhodobacterales and Oceanospirillales) that were found in low precipitation periods. Notably, we observed a significantly higher relative abundance of Comamonadaceae than previously described in other estuaries. Furthermore, anthropic factors could have an impact on this particular estuary’s bacterial community structure. For example, ecosystem changes related to the channelization of the estuary likely induced a low dissolved oxygen (DO) concentration, high temperature, and high chlorophyll concentration period in the inner euhaline water in summer (samples with salinity >30 ppt). Those samples were characterized by a high abundance of facultative anaerobes. For instance, OTUs classified as Cryomorphaceae and Candidatus Aquiluna rubra were negatively associated with DO concentration, while Oleiphilaceae was positively associated with DO concentration. Additionally, microorganisms related to biological treatment of wastewater (e.g Bdellovibrio and Zoogloea) were detected in the samples immediately downstream of the Bilbao Wastewater Treatment Plant (WWTP). There are several human activities planned in the region surrounding the Estuary of Bilbao (e.g. sediment draining, architectural changes, etc.) which will likely affect this ecosystem. Therefore, the addition of bacterial community profiling and diversity analysis into the estuary’s ongoing monitoring program would provide a more comprehensive view of the ecological status of the Estuary of Bilbao. PMID:28594872

Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

PubMed

Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

2017-06-15

This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids?

PubMed

Cevallos, Stefania; Sánchez-Rodríguez, Aminael; Decock, Cony; Declerck, Stéphane; Suárez, Juan Pablo

2017-04-01

In epiphytic orchids, distinctive groups of fungi are involved in the symbiotic association. However, little is known about the factors that determine the mycorrhizal community structure. Here, we analyzed the orchid mycorrhizal fungi communities associated with three sympatric Cymbidieae epiphytic tropical orchids (Cyrtochilum flexuosum, Cyrtochilum myanthum, and Maxillaria calantha) at two sites located within the mountain rainforest of southern Ecuador. To characterize these communities at each orchid population, the ITS2 region was analyzed by Illumina MiSeq technology. Fifty-five mycorrhizal fungi operational taxonomic units (OTUs) putatively attributed to members of Serendipitaceae, Ceratobasidiaceae and Tulasnellaceae were identified. Significant differences in mycorrhizal communities were detected between the three sympatric orchid species as well as among sites/populations. Interestingly, some mycorrhizal OTUs overlapped among orchid populations. Our results suggested that populations of studied epiphytic orchids have site-adjusted mycorrhizal communities structured around keystone fungal species. Interaction with multiple mycorrhizal fungi could favor orchid site occurrence and co-existence among several orchid species.

Variability of community interaction networks in marine reserves and adjacent exploited areas

USGS Publications Warehouse

Montano-Moctezuma, G.; Li, H.W.; Rossignol, P.A.

2008-01-01

Regional and small-scale local oceanographic conditions can lead to high variability in community structure even among similar habitats. Communities with identical species composition can depict distinct networks due to different levels of disturbance as well as physical and biological processes. In this study we reconstruct community networks in four different areas off the Oregon Coast by matching simulated communities with observed dynamics. We compared reserves with harvested areas. Simulations suggested that different community networks, but with the same species composition, can represent each study site. Differences were found in predator-prey interactions as well as non-predatory interactions between community members. In addition, each site can be represented as a set of models, creating alternative stages among sites. The set of alternative models that characterize each study area depicts a sequence of functional responses where each specific model or interaction structure creates different species composition patterns. Different management practices, either in the past or of the present, may lead to alternative communities. Our findings suggest that management strategies should be analyzed at a community level that considers the possible consequences of shifting from one community scenario to another. This analysis provides a novel conceptual framework to assess the consequences of different management options for ecological communities. ?? 2008 Elsevier B.V. All rights reserved.

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

PubMed Central

Sun, Li; Müller, Bettina; Ivarsson, Magnus; Hosgörmez, Hakan; Özcan, Dogacan; Broman, Curt; Schnürer, Anna

2017-01-01

ABSTRACT The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria. IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H2, which is poorly studied due to the rarity of these environments on Earth. PMID:28389534

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.

PubMed

Neubeck, Anna; Sun, Li; Müller, Bettina; Ivarsson, Magnus; Hosgörmez, Hakan; Özcan, Dogacan; Broman, Curt; Schnürer, Anna

2017-06-15

The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H 2 and CH 4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria , Actinobacteria , Chloroflexi , and Acidobacteria , accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria. IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H 2 , which is poorly studied due to the rarity of these environments on Earth. Copyright © 2017 Neubeck et al.

Microbial ecology of deep-water mid-Atlantic canyons

USGS Publications Warehouse

Kellogg, Christina A.

2011-01-01

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes.

PubMed

Vick-Majors, Trista J; Priscu, John C; Amaral-Zettler, Linda A

2014-04-01

High-latitude environments, such as the Antarctic McMurdo Dry Valley lakes, are subject to seasonally segregated light-dark cycles, which have important consequences for microbial diversity and function on an annual basis. Owing largely to the logistical difficulties of sampling polar environments during the darkness of winter, little is known about planktonic microbial community responses to the cessation of photosynthetic primary production during the austral sunset, which lingers from approximately February to April. Here, we hypothesized that changes in bacterial, archaeal and eukaryotic community structure, particularly shifts in favor of chemolithotrophs and mixotrophs, would manifest during the transition to polar night. Our work represents the first concurrent molecular characterization, using 454 pyrosequencing of hypervariable regions of the small-subunit ribosomal RNA gene, of bacterial, archaeal and eukaryotic communities in permanently ice-covered lakes Fryxell and Bonney, before and during the polar night transition. We found vertically stratified populations that varied at the community and/or operational taxonomic unit-level between lakes and seasons. Network analysis based on operational taxonomic unit level interactions revealed nonrandomly structured microbial communities organized into modules (groups of taxa) containing key metabolic potential capacities, including photoheterotrophy, mixotrophy and chemolithotrophy, which are likely to be differentially favored during the transition to polar night.

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 microbial communities on terrestrial C and N cycling.

Examining two epifaunal invertebrate communities using functional traits and environmental variables in and around Barrow canyon in the Chukchi and Beaufort seas

NASA Astrophysics Data System (ADS)

Rand, K.; Logerwell, E.; Bluhm, B.; Chenelot, H.; Danielson, S. L.; Iken, K.; Sousa, L.

2016-02-01

In the Arctic, benthic invertebrate communities are characterized by high species diversity and overall biomass when compared to corresponding benthic fish communities. Communities can be characterized with respect to their species diversity, biomass and the type of functions performed by the dominant organisms. Invertebrate communities with equally high species diversity may or may not have functionally similar traits. In this study, we examined basic functional traits of the dominant trawl-collected epifaunal invertebrates (e.g. mobility, feeding mode) along with environmental variables (e.g. sediment, salinity) in two high Arctic systems in and around Barrow Canyon; the northwest Chukchi Sea shelf (SHELFZ study, 2012) and the western Beaufort Sea shelf and upper slope (2008). The epifaunal communities are characterized by a large biomass of invertebrates (average of 5,000 kg/km2 in each) and species diversity ranged from 6-75 taxa per station in the Beaufort Sea (158 total) and 26-57 taxa per station in the Chukchi (215 total). These two communities share a commonality in taxonomic families, however, only 45 species occur in both. The top 2 dominant species within each community also differ; the filter-feeding basket star, Gorgonocephalus arcticus, and sea cucumber, Psolus peronii, dominate the offshore SHELFZ survey ( 60% of the biomass) while in the Beaufort Sea survey the primarily deposit feeding brittle star, Ophiura sarsi, and the mobile, predatory crab, Chionoecetes opilio, were the most biomass-prevalent species offshore (52% of the biomass). Oceanographic processes influencing water mass distribution in and around Barrow Canyon contribute to the benthic invertebrate community structure and the spatial variation in dominant functional traits. Finally, results from this study are discussed in the context of Arctic oil and gas development and climate change.

Characterization of Structure and Damage in Materials in Four Dimensions

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

Robertson, I. M.; Schuh, C. A.; Vetrano, J. S.

2010-09-30

The materials characterization toolbox has recently experienced a number of parallel revolutionary advances, foreshadowing a time in the near future when materials scientists can quantify material structure across orders of magnitude in length and time scales (i.e., in four dimensions) completely. This paper presents a viewpoint on the materials characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future development. Electron microscopy; atom-probe tomography; X-ray, neutron and electron tomography; serial sectioning tomography; and diffraction-based analysis methods are reviewed, and opportunities for their future development are highlighted. Particular attention is paid to studies that havemore » pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent the state-of-the-art in characterization, and suggest a trajectory for the continued development of the field. Based on this review, a set of grand challenges for characterization science is identified, including suggestions for instrumentation advances, scientific problems in microstructure analysis, and complex structure evolution problems involving materials damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.« less

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.

Emergence of bursts and communities in evolving weighted networks.

PubMed

Jo, Hang-Hyun; Pan, Raj Kumar; Kaski, Kimmo

2011-01-01

Understanding the patterns of human dynamics and social interaction and the way they lead to the formation of an organized and functional society are important issues especially for techno-social development. Addressing these issues of social networks has recently become possible through large scale data analysis of mobile phone call records, which has revealed the existence of modular or community structure with many links between nodes of the same community and relatively few links between nodes of different communities. The weights of links, e.g., the number of calls between two users, and the network topology are found correlated such that intra-community links are stronger compared to the weak inter-community links. This feature is known as Granovetter's "The strength of weak ties" hypothesis. In addition to this inhomogeneous community structure, the temporal patterns of human dynamics turn out to be inhomogeneous or bursty, characterized by the heavy tailed distribution of time interval between two consecutive events, i.e., inter-event time. In this paper, we study how the community structure and the bursty dynamics emerge together in a simple evolving weighted network model. The principal mechanisms behind these patterns are social interaction by cyclic closure, i.e., links to friends of friends and the focal closure, links to individuals sharing similar attributes or interests, and human dynamics by task handling process. These three mechanisms have been implemented as a network model with local attachment, global attachment, and priority-based queuing processes. By comprehensive numerical simulations we show that the interplay of these mechanisms leads to the emergence of heavy tailed inter-event time distribution and the evolution of Granovetter-type community structure. Moreover, the numerical results are found to be in qualitative agreement with empirical analysis results from mobile phone call dataset.

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater

EPA Science Inventory

Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when...

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Impact of oil on bacterial community structure in bioturbated sediments.

PubMed

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities.

Structure of Infaunal Communities on the Beaufort Sea Shelf and Slope: Insights from Morphological and Environmental DNA Sequencing Approaches

NASA Astrophysics Data System (ADS)

Hardy, S. M.; Bik, H.; Walker, A.; Sharma, J.; Blanchard, A.

2016-02-01

Rapid change is occurring in the Arctic concurrently with increased human activity, yet our knowledge of the structure and function of high-Arctic sediment communities is still rudimentary. The Beaufort Sea is particularly poorly sampled, and largely unexplored at slope depths, providing little information with which to assess the impacts of petroleum exploration activities now beginning in this area. We are investigating diversity and community structure of meio- and macrobenthic infauna on the continental shelf and slope of the Beaufort Sea across a range of depths (50 to 1000 m) using traditional taxonomic and environmental DNA sequencing approaches, and comparing results to additional sites in the adjacent NE Chukchi Sea petroleum lease-sale area. The Beaufort slope is topographically complex and characterized by an east-west gradient in benthic habitat characteristics, with heavy input of terrestrial organic matter particularly in the region of the Mackenzie River delta. Warmer, saltier subsurface Atlantic water masses impact benthic communities at mid-slope depths, likely influencing turnover in community structure observed with depth. Food resources are variable across the region, with very high sediment chlorophyll concentrations at 350 m depth in some areas. Differences in nematode assemblages were detected across the Beaufort Sea shelf/slope, across depths within the Beaufort Sea, and between the Beaufort and adjacent NE Chukchi Sea. These differences were apparent in both morphological and environmental sequencing data. Macrofaunal communities showed variable community structure among transects, with high abundance and high dominance in polychaete assemblages coincident with the chlorophyll maximum. Sequencing data also revealed an abundance of protists in sediments which have been mostly ignored in studies of ecosystem dynamics in this region, and may represent an important component of the food web.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

PubMed Central

Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

2016-01-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). PMID:26888080

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

PubMed

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield.

PubMed

Rime, Thomas; Hartmann, Martin; Brunner, Ivano; Widmer, Franco; Zeyer, Josef; Frey, Beat

2015-03-01

Spatial patterns of microbial communities have been extensively surveyed in well-developed soils, but few studies investigated the vertical distribution of micro-organisms in newly developed soils after glacier retreat. We used 454-pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils. © 2014 John Wiley & Sons Ltd.

Birds of Upland Oak Forests in the Arkansas Ozarks: Present Community Structure and Potential Impacts of Burning, Borers, and Forestry Practices

Treesearch

Kimberly Smith; Michael Mlodinow; Janet S. Self; Thomas M. Haggerty; Tamara R. Hocut

2004-01-01

Based on published works, our own research, and the U.S. Forest Service’s R8 Bird database, we characterize breeding bird communities in mesic and xeric upland hardwood forests of the Arkansas Ozarks. Although 59 species have been recorded as breeding, typical breeding assemblages in mesic forests are 20-25 species, with only 5 species commonly found in xeric forests....

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation

PubMed Central

Abusleme, Loreto; Dupuy, Amanda K; Dutzan, Nicolás; Silva, Nora; Burleson, Joseph A; Strausbaugh, Linda D; Gamonal, Jorge; Diaz, Patricia I

2013-01-01

The goals of this study were to better understand the ecology of oral subgingival communities in health and periodontitis and elucidate the relationship between inflammation and the subgingival microbiome. Accordingly, we used 454-pyrosequencing of 16S rRNA gene libraries and quantitative PCR to characterize the subgingival microbiome of 22 subjects with chronic periodontitis. Each subject was sampled at two sites with similar periodontal destruction but differing in the presence of bleeding, a clinical indicator of increased inflammation. Communities in periodontitis were also compared with those from 10 healthy individuals. In periodontitis, presence of bleeding was not associated with different α-diversity or with a distinct microbiome, however, bleeding sites showed higher total bacterial load. In contrast, communities in health and periodontitis largely differed, with higher diversity and biomass in periodontitis. Shifts in community structure from health to periodontitis resembled ecological succession, with emergence of newly dominant taxa in periodontitis without replacement of primary health-associated species. That is, periodontitis communities had higher proportions of Spirochetes, Synergistetes, Firmicutes and Chloroflexi, among other taxa, while the proportions of Actinobacteria, particularly Actinomyces, were higher in health. Total Actinomyces load, however, remained constant from health to periodontitis. Moreover, an association existed between biomass and community structure in periodontitis, with the proportion of specific taxa correlating with bacterial load. Our study provides a global-scale framework for the ecological events in subgingival communities that underline the development of periodontitis. The association, in periodontitis, between inflammation, community biomass and community structure and their role in disease progression warrant further investigation. PMID:23303375

Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia.

PubMed

Crane, Nicole L; Nelson, Peter; Abelson, Avigdor; Precoda, Kristin; Rulmal, John; Bernardi, Giacomo; Paddack, Michelle

2017-01-01

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1-oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2-oceanic and inhabited (high human impact); and cluster 3-lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.

Characterization of the ecological requirements for three plethodontid salamander species

Treesearch

Jessica A. Wooten; William B. Sutton; Thomas K. Pauley

2010-01-01

Increased availability of habitat and climate data has facilitated much research concerning the influence of these characteristics on the structure of salamander communities. We aimed to outline environmental requirements influencing the distribution of three sympatric plethodontid salamander species, including Plethodon cinereus, Desmognathus ochrophaeus...

Genomic heterogeneity and structural variation in soybean near-isogenic lines

USDA-ARS?s Scientific Manuscript database

Near-isogenic lines (NILs) are a critical genetic resource for the soybean research community. The ability to identify and characterize the genes driving the phenotypic differences between NILs is limited by the degree to which differential genetic introgressions can be resolved. Furthermore, the ...

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

PubMed Central

Kittelmann, Sandra; Seedorf, Henning; Walters, William A.; Clemente, Jose C.; Knight, Rob; Gordon, Jeffrey I.; Janssen, Peter H.

2013-01-01

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats. PMID:23408926

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

PubMed

Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

2013-01-01

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID:23536759

Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

PubMed

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments.

PubMed

Kunihiro, Tadao; Veuger, Bart; Vasquez-Cardenas, Diana; Pozzato, Lara; Le Guitton, Marie; Moriya, Kazuyoshi; Kuwae, Michinobu; Omori, Koji; Boschker, Henricus T S; van Oevelen, Dick

2014-01-01

Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.

The structure of bacterial communities in natural and anthropogenic brown forest soils of the Botanical Garden on Murav'eva-Amurskogo Peninsula

NASA Astrophysics Data System (ADS)

Kovaleva, G. V.; Dobrovol'Skaya, T. G.; Golovacheva, A. V.

2007-05-01

The microbiological characterization of the brown forest soils in the territory of the Botanical Garden-Institute of the Far East Division of the Russian Academy of Sciences in southern Primor’e is given. The high humus content and weakly acid reaction of these soils were shown to provide the optimal conditions for the development of bacteria. In the brown forest soils differing in the thickness of the humus horizons, all the ecologic-trophic groups of bacteria were present and the bacterial communities were highly diverse. The structure of the bacterial communities was identical in all the organomineral horizons of the soils and varied greatly by the seasons. In the anthropogenically disturbed soils, the share of corynebacteria, which are resistant to stress and capable of the destruction of xenobiotics, decreased.

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

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

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE PAGES

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

2015-06-28

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Vegetation, soil, and flooding relationships in a blackwater floodplain forest

USGS Publications Warehouse

Burke, M.K.; King, S.L.; Gartner, D.; Eisenbies, M.H.

2003-01-01

Hydroperiod is considered the primary determinant of plant species distribution in temperate floodplain forests, but most studies have focused on alluvial (sediment-laden) river systems. Few studies have evaluated plant community relationships in blackwater river systems of the South Atlantic Coastal Plain of North America. In this study, we characterized the soils, hydroperiod, and vegetation communities and evaluated relationships between the physical and chemical environment and plant community structure on the floodplain of the Coosawhatchie River, a blackwater river in South Carolina, USA. The soils were similar to previous descriptions of blackwater floodplain soils but had greater soil N and P availability, substantially greater clay content, and lower soil silt content than was previously reported for other blackwater river floodplains. Results of a cluster analysis showed there were five forest communities on the site, and both short-term (4 years) and long-term (50 years) flooding records documented a flooding gradient: water tupelo community > swamp tupelo > laurel oak = overcup oak > mixed oak. The long-term hydrologic record showed that the floodplain has flooded less frequently from 1994 to present than in previous decades. Detrended correspondence analysis of environmental and relative basal area values showed that 27% of the variation in overstory community structure could be explained by the first two axes; however, fitting the species distributions to the DCA axes using Gaussian regression explained 67% of the variation. Axes were correlated with elevation (flooding intensity) and soil characteristics related to rooting volume and cation nutrient availability. Our study suggests that flooding is the major factor affecting community structure, but soil characteristics also may be factors in community structure in blackwater systems. ?? 2003, The Society of Wetland Scientists.

Environmental and Spatial Influences on Biogeography and Community Structure of Benthic Diatoms

NASA Astrophysics Data System (ADS)

Plante, C.; Hill-Spanik, K.; Lowry, J.

2016-02-01

Several theoretical and practical reasons suggest that benthic microalgae could be useful bioindicators. For instance, an ideal indicator species or community would be associated with a given habitat due to local physical conditions or biotic interactions (i.e., `environmental filtering'), not due to dispersal limitation. Due to their small size, immense abundances, and reliance on passive dispersal, the popular notion about micro-organisms is that `Everything is everywhere, but, the environment selects' (Baas-Becking 1934). Although much recent research concerning planktonic bacteria and dispersal limitation has been conducted, very little in this regard is known about microeukaryotes, especially benthic microbes. The purpose of our study was to identify and compare spatial and environmental influences on benthic diatom community structure and biogeography. In summer 2015, sediment was sampled at various spatial scales from four barrier island beaches in South Carolina, USA, and high-throughput (Ion Torrent) DNA sequencing was used to characterize diatom assemblages. ANOSIM and principal coordinates analysis revealed that communities were statistically distinct on the four islands. Community dissimilarity was compared to both spatial distance and environmental differences to determine potential influences of these variables on community structure. We found that geographic distance had the strongest correlation with community similarity, with and without one anomalous location, while differences in temperature (air, water, and sediment), nutrients, organic matter, and turbidity also had significant but weaker relationships with community structure. Surprisingly, air temperature, which changes on very short time scales, appeared to be the environmental factor most strongly related to diatom species composition, potentially implicating some unmeasured variable (e.g., cloud cover). However, we also found that temperature and geographic distance were strongly correlated. Future research will expand the spatial scope of this preliminary study and employ techniques (partial Mantel tests) to control for co-variation among variables.

The role of banks in the Brazilian interbank market: Does bank type matter?

NASA Astrophysics Data System (ADS)

Cajueiro, Daniel O.; Tabak, Benjamin M.

2008-12-01

This paper analyzes the Brazilian interbank network structure using a complex network-based approach. Results suggest a weak evidence of community structure, high heterogeneity of the network and that this market is characterized by money centers having exposures to many banks. Furthermore, we go beyond the structure of the network using information about the characteristics of the nodes and a non-parametric test in order to understand the role of the banks in the interbanking market.

Mass coral bleaching causes biotic homogenization of reef fish assemblages.

PubMed

Richardson, Laura E; Graham, Nicholas A J; Pratchett, Morgan S; Eurich, Jacob G; Hoey, Andrew S

2018-04-06

Global climate change is altering community composition across many ecosystems due to nonrandom species turnover, typically characterized by the loss of specialist species and increasing similarity of biological communities across spatial scales. As anthropogenic disturbances continue to alter species composition globally, there is a growing need to identify how species responses influence the establishment of distinct assemblages, such that management actions may be appropriately assigned. Here, we use trait-based analyses to compare temporal changes in five complementary indices of reef fish assemblage structure among six taxonomically distinct coral reef habitats exposed to a system-wide thermal stress event. Our results revealed increased taxonomic and functional similarity of previously distinct reef fish assemblages following mass coral bleaching, with changes characterized by subtle, but significant, shifts toward predominance of small-bodied, algal-farming habitat generalists. Furthermore, while the taxonomic or functional richness of fish assemblages did not change across all habitats, an increase in functional originality indicated an overall loss of functional redundancy. We also found that prebleaching coral composition better predicted changes in fish assemblage structure than the magnitude of coral loss. These results emphasize how measures of alpha diversity can mask important changes in the structure and functioning of ecosystems as assemblages reorganize. Our findings also highlight the role of coral species composition in structuring communities and influencing the diversity of responses of reef fishes to disturbance. As new coral species configurations emerge, their desirability will hinge upon the composition of associated species and their capacity to maintain key ecological processes in spite of ongoing disturbances. © 2018 John Wiley & Sons Ltd.

Tree communities of lowland warm-temperate old-growth and neighboring shelterbelt forests in the Shikoku region of southwestern Japan

Treesearch

Shigeo Kuramoto; Shigenori Oshioka; Takahisa Hirayama; Kaori Sato; Yasumasa Hirata

2007-01-01

We characterized the tree species composition of a 30 ha old-growth and neighboring shelterbelt (reserved buffer strips among conifer plantations) in warm-temperate forests in the Shikoku region of southwestern Japan. Using a two-way indicator species analysis of data from 28 plots, we identified four structural groups in terms of relative basal area. These structural...

Ecological Structure of Recent and Last Glacial Mammalian Faunas in Northern Eurasia: The Case of Altai-Sayan Refugium

PubMed Central

Pavelková Řičánková, Věra; Robovský, Jan; Riegert, Jan

2014-01-01

Pleistocene mammalian communities display unique features which differ from present-day faunas. The paleocommunities were characterized by the extraordinarily large body size of herbivores and predators and by their unique structure consisting of species now inhabiting geographically and ecologically distinct natural zones. These features were probably the result of the unique environmental conditions of ice age ecosystems. To analyze the ecological structure of Last Glacial and Recent mammal communities we classified the species into biome and trophic-size categories, using Principal Component analysis. We found a marked similarity in ecological structure between Recent eastern Altai-Sayan mammalian assemblages and comparable Pleistocene faunas. The composition of Last Glacial and Recent eastern Altai-Sayan assemblages were characterized by the occurrence of large herbivore and predator species associated with steppe, desert and alpine biomes. These three modern biomes harbor most of the surviving Pleistocene mammals. None of the analyzed Palearctic Last Glacial faunas showed affinity to the temperate forest, taiga, or tundra biome. The Eastern part of the Altai-Sayan region could be considered a refugium of the Last Glacial-like mammalian assemblages. Glacial fauna seems to persist up to present in those areas where the forest belt does not separate alpine vegetation from the steppes and deserts. PMID:24454791

Measuring succession: methods for establishing long term vegetation monitoring sites

USDA-ARS?s Scientific Manuscript database

Successional stages are often characterized by dominant plant species (species with the highest cover) and their effect on the structure and function of an area through time. However, the plant species determining the ecosystem properties and plant community dynamics may not be the dominant, especia...

Microbial Community Structure in Relation to Water Quality in a Eutrophic Gulf of Mexico Estuary

EPA Science Inventory

Weeks Bay is a shallow, microtidal, eutrophic sub-estuary of Mobile Bay, AL. High watershed nutrient inputs to the estuary contribute to a eutrophic condition characterized by frequent summertime diel-cycling hypoxia and dissolved oxygen (DO) oversaturation. Spatial and seasonal ...

Genomic heterogeneity and structural variation in soybean near isogenic lines

USDA-ARS?s Scientific Manuscript database

Near-isogenic lines (NILs) are a critical genetic resource for the soybean research community. The ability to identify and characterize the genes driving the phenotypic differences between NILs is limited by the degree to which differential genetic introgressions can be resolved. Furthermore, the ge...

NEGLECTED COMPONENTS OF BIODIVERSITY: SOIL ORIBATID MITES, COMMUNITY STRUCTURE AND SOIL RECOVERY

EPA Science Inventory

Oribatid mites are an abundant and diverse component of soils in regional pine forests, and are valuable in characterizing the biodiversity of these forested lands. We sampled oribatid mites using soil cores and leaf litterbags, in young aggrading forest stands. Comparing these...

Climate Modeling Computing Needs Assessment

NASA Astrophysics Data System (ADS)

Petraska, K. E.; McCabe, J. D.

2011-12-01

This paper discusses early findings of an assessment of computing needs for NASA science, engineering and flight communities. The purpose of this assessment is to document a comprehensive set of computing needs that will allow us to better evaluate whether our computing assets are adequately structured to meet evolving demand. The early results are interesting, already pointing out improvements we can make today to get more out of the computing capacity we have, as well as potential game changing innovations for the future in how we apply information technology to science computing. Our objective is to learn how to leverage our resources in the best way possible to do more science for less money. Our approach in this assessment is threefold: Development of use case studies for science workflows; Creating a taxonomy and structure for describing science computing requirements; and characterizing agency computing, analysis, and visualization resources. As projects evolve, science data sets increase in a number of ways: in size, scope, timelines, complexity, and fidelity. Generating, processing, moving, and analyzing these data sets places distinct and discernable requirements on underlying computing, analysis, storage, and visualization systems. The initial focus group for this assessment is the Earth Science modeling community within NASA's Science Mission Directorate (SMD). As the assessment evolves, this focus will expand to other science communities across the agency. We will discuss our use cases, our framework for requirements and our characterizations, as well as our interview process, what we learned and how we plan to improve our materials after using them in the first round of interviews in the Earth Science Modeling community. We will describe our plans for how to expand this assessment, first into the Earth Science data analysis and remote sensing communities, and then throughout the full community of science, engineering and flight at NASA.

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site.

PubMed

Siles, José A; Margesin, Rosa

2018-05-01

The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.

How to become a superhero

NASA Astrophysics Data System (ADS)

Gleiser, Pablo M.

2007-09-01

We analyze a collaboration network based on the Marvel Universe comic books. First, we consider the system as a binary network, where two characters are connected if they appear in the same publication. The analysis of degree correlations reveals that, in contrast to most real social networks, the Marvel Universe presents a disassortative mixing on the degree. Then, we use a weight measure to study the system as a weighted network. This allows us to find and characterize well defined communities. Through the analysis of the community structure and the clustering as a function of the degree we show that the network presents a hierarchical structure. Finally, we comment on possible mechanisms responsible for the particular motifs observed.

Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.

PubMed

Bonilla, José O; Kurth, Daniel G; Cid, Fabricio D; Ulacco, José H; Gil, Raúl A; Villegas, Liliana B

2018-04-28

The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.

Understanding the local context and its possible influences on shaping, implementing and running social accountability initiatives for maternal health services in rural Democratic Republic of the Congo: a contextual factor analysis.

PubMed

Mafuta, Eric M; Hogema, Lisanne; Mambu, Thérèse N M; Kiyimbi, Pontien B; Indebe, Berthys P; Kayembe, Patrick K; De Cock Buning, Tjard; Dieleman, Marjolein A

2016-11-09

Social accountability has to be configured according to the context in which it operates. This paper aimed to identify local contextual factors in two health zones in the Democratic Republic of the Congo and discuss their possible influences on shaping, implementing and running social accountability initiatives. Data on local socio-cultural characteristics, the governance context, and socio-economic conditions related to social accountability enabling factors were collected in the two health zones using semi-structured interviews and document reviews, and were analyzed using thematic analysis. The contexts of the two health zones were similar and characterized by the existence of several community groups, similarly structured and using similar decision-making processes. They were not involved in the health sector's activities and had no link with the health committee, even though they acknowledged its existence. They were not networked as they focused on their own activities and did not have enough capacity in terms of social mobilization or exerting pressure on public authorities or providers. Women were not perceived as marginalized as they often occupied other positions in the community besides carrying out domestic tasks and participated in community groups. However, they were still subject to the local male dominance culture, which restrains their involvement in decision-making, as they tend to be less educated, unemployed and suffer from a lack of resources or specific skills. The socio-economic context is characterized by subsistence activities and a low employment rate, which limits the community members' incomes and increases their dependence on external support. The governance context was characterized by imperfect implementation of political decentralization. Community groups advocating community rights are identified as "political" and are not welcomed. The community groups seemed not to be interested in the health center's information and had no access to media as it is non-existent. The local contexts in the two health zones seemed not to be supportive of the operation of social accountability initiatives. However, they offer starting points for social accountability initiatives if better use is made of existing contextual factors, for instance by making community groups work together and improving their capacities in terms of knowledge and information.

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 streams had higher abundances of Sphingomonadaceae spp. and Nordella spp. (both Alphaproteobacteria). The cyanobacteria Chamaesiphon spp. was observed in highest abundance in the first and second order streams of the rock biofilm samples and the cyanobacteria Oscillatoria spp. was in highest abundance in the third order streams. Stream water samples from all orders had high lignin/tannin content and were enriched with carboxylic-rich alicyclic molecules (CRAM). There was an observable shift in in the molecular weight and relative abundance of the CRAM molecules with the CRAM molecules becoming less abundant and having lower molecular weight following the downstream gradient. Multivariate statistical analyses correlated the longitudinal patterns of changes in bacterial community structure to the DOM molecular structure and geochemical parameters across the river continuum.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.

PubMed

Liu, Jun; Chen, Xi; Shu, Hao-Yue; Lin, Xue-Rui; Zhou, Qi-Xing; Bramryd, Torleif; Shu, Wen-Sheng; Huang, Li-Nan

2018-04-01

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessment of ecological conditions and potential effects of water produced from coalbed natural gas development on biological communities in streams of the Powder River structural basin, Wyoming and Montana, 2005-08

USGS Publications Warehouse

Peterson, David A.; Clark, Melanie L.; Foster, Katharine; Wright, Peter R.; Boughton, Gregory K.

2010-01-01

Ongoing development of coalbed natural gas in the Powder River structural basin in Wyoming and Montana led to formation of an interagency task group to address concerns about the effects of the resulting production water on biological communities in streams of the area. The interagency task group developed a monitoring plan and conducted sampling of macroinvertebrate, algal, and fish communities at 47 sites during 2005-08 to document current ecological conditions and determine existing and potential effects of water produced from coalbed natural gas development on biological communities. Macroinvertebrate, algal, and fish community composition varied between drainage basins, among sites within drainage basins, and by year. Macroinvertebrate communities of the main-stem Tongue River were characterized by higher taxa richness and higher abundance of Ephemeroptera, for example, compared to macroinvertebrate communities in plains tributaries of the Tongue River and the main-stem Powder River. Fish communities of the Tongue River were characterized by higher taxa richness and abundance of introduced species compared to the Powder River where native species were dominant. Macroinvertebrate community metric values from sites in the middle reach of the main-stem Powder River, from below Willow Creek to below Crazy Woman Creek, differed from metric values in the upper and lower reaches of the Powder River. Metrics indicative of communitywide differences included measures of taxa richness, relative abundance, feeding mode, and tolerance. Some of the variation in the macroinvertebrate communities could be explained by variation in environmental variables, including physical (turbidity, embeddedness, bed substrate size, and streamflow) and chemical (alkalinity and specific conductance) variables. Of these environmental variables, alkalinity was the best indicator of coalbed natural gas development because of the sodiumbicarbonate signature of the production water. Algal samples from the main-stem Powder River generally confirmed the pattern observed in the macroinvertebrate communities. Algal communities at sites in the middle reach of the Powder River commonly were characterized by dominance by a single taxon and by low biovolume of algae compared to other sites. In contrast to the macroinvertebrate and algal communities, species richness of fish communities was highest in the middle reach of the Powder River. Although a few significant differences in fish metrics were determined along the main-stem Powder River, the differences did not correspond to the pattern observed for the macroinvertebrate and algae communities. Differences in biological communities were noted between years, potentially due to the effects of drought. Macroinvertebrate community metrics, such as Diptera taxa richness, were significantly different in the severe drought year of 2006 from metric values in 2005 and 2007-08. Waterquality data collected during the study indicated that, with few exceptions, water-quality constituents generally did not exceed State or Federal acute and chronic criteria for the protection of aquatic life.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium.

PubMed

Pereira, Arthur Prudêncio de Araujo; Andrade, Pedro Avelino Maia de; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

PubMed Central

de Andrade, Pedro Avelino Maia; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. PMID:28686690

Digital Reef Rugosity Estimates Coral Reef Habitat Complexity

PubMed Central

Dustan, Phillip; Doherty, Orla; Pardede, Shinta

2013-01-01

Ecological habitats with greater structural complexity contain more species due to increased niche diversity. This is especially apparent on coral reefs where individual coral colonies aggregate to give a reef its morphology, species zonation, and three dimensionality. Structural complexity is classically measured with a reef rugosity index, which is the ratio of a straight line transect to the distance a flexible chain of equal length travels when draped over the reef substrate; yet, other techniques from visual categories to remote sensing have been used to characterize structural complexity at scales from microhabitats to reefscapes. Reef-scale methods either lack quantitative precision or are too time consuming to be routinely practical, while remotely sensed indices are mismatched to the finer scale morphology of coral colonies and reef habitats. In this communication a new digital technique, Digital Reef Rugosity (DRR) is described which utilizes a self-contained water level gauge enabling a diver to quickly and accurately characterize rugosity with non-invasive millimeter scale measurements of coral reef surface height at decimeter intervals along meter scale transects. The precise measurements require very little post-processing and are easily imported into a spreadsheet for statistical analyses and modeling. To assess its applicability we investigated the relationship between DRR and fish community structure at four coral reef sites on Menjangan Island off the northwest corner of Bali, Indonesia and one on mainland Bali to the west of Menjangan Island; our findings show a positive relationship between DRR and fish diversity. Since structural complexity drives key ecological processes on coral reefs, we consider that DRR may become a useful quantitative community-level descriptor to characterize reef complexity. PMID:23437380

Digital reef rugosity estimates coral reef habitat complexity.

PubMed

Dustan, Phillip; Doherty, Orla; Pardede, Shinta

2013-01-01

Ecological habitats with greater structural complexity contain more species due to increased niche diversity. This is especially apparent on coral reefs where individual coral colonies aggregate to give a reef its morphology, species zonation, and three dimensionality. Structural complexity is classically measured with a reef rugosity index, which is the ratio of a straight line transect to the distance a flexible chain of equal length travels when draped over the reef substrate; yet, other techniques from visual categories to remote sensing have been used to characterize structural complexity at scales from microhabitats to reefscapes. Reef-scale methods either lack quantitative precision or are too time consuming to be routinely practical, while remotely sensed indices are mismatched to the finer scale morphology of coral colonies and reef habitats. In this communication a new digital technique, Digital Reef Rugosity (DRR) is described which utilizes a self-contained water level gauge enabling a diver to quickly and accurately characterize rugosity with non-invasive millimeter scale measurements of coral reef surface height at decimeter intervals along meter scale transects. The precise measurements require very little post-processing and are easily imported into a spreadsheet for statistical analyses and modeling. To assess its applicability we investigated the relationship between DRR and fish community structure at four coral reef sites on Menjangan Island off the northwest corner of Bali, Indonesia and one on mainland Bali to the west of Menjangan Island; our findings show a positive relationship between DRR and fish diversity. Since structural complexity drives key ecological processes on coral reefs, we consider that DRR may become a useful quantitative community-level descriptor to characterize reef complexity.

The human laryngeal microbiome: effects of cigarette smoke and reflux.

PubMed

Jetté, Marie E; Dill-McFarland, Kimberly A; Hanshew, Alissa S; Suen, Garret; Thibeault, Susan L

2016-10-24

Prolonged diffuse laryngeal inflammation from smoking and/or reflux is commonly diagnosed as chronic laryngitis and treated empirically with expensive drugs that have not proven effective. Shifts in microbiota have been associated with many inflammatory diseases, though little is known about how resident microbes may contribute to chronic laryngitis. We sought to characterize the core microbiota of disease-free human laryngeal tissue and to investigate shifts in microbial community membership associated with exposure to cigarette smoke and reflux. Using 454 pyrosequencing of the 16S rRNA gene, we compared bacterial communities of laryngeal tissue biopsies collected from 97 non-treatment-seeking volunteers based on reflux and smoking status. The core community was characterized by a highly abundant OTU within the family Comamonadaceae found in all laryngeal tissues. Smokers demonstrated less microbial diversity than nonsmokers, with differences in relative abundances of OTUs classified as Streptococcus, unclassified Comamonadaceae, Cloacibacterium, and Helicobacter. Reflux status did not affect microbial diversity nor community structure nor composition. Comparison of healthy laryngeal microbial communities to benign vocal fold disease samples revealed greater abundance of Streptococcus in benign vocal fold disease suggesting that mucosal dominance by Streptococcus may be a factor in disease etiology.

Patterns of Twitter Behavior Among Networks of Cannabis Dispensaries in California

PubMed Central

Chew, Robert F; Hsieh, Yuli P; Bieler, Gayle S; Bobashev, Georgiy V; Siege, Christopher; Zarkin, Gary A

2017-01-01

Background Twitter represents a social media platform through which medical cannabis dispensaries can rapidly promote and advertise a multitude of retail products. Yet, to date, no studies have systematically evaluated Twitter behavior among dispensaries and how these behaviors influence the formation of social networks. Objectives This study sought to characterize common cyberbehaviors and shared follower networks among dispensaries operating in two large cannabis markets in California. Methods From a targeted sample of 119 dispensaries in the San Francisco Bay Area and Greater Los Angeles, we collected metadata from the dispensary accounts using the Twitter API. For each city, we characterized the network structure of dispensaries based upon shared followers, then empirically derived communities with the Louvain modularity algorithm. Principal components factor analysis was employed to reduce 12 Twitter measures into a more parsimonious set of cyberbehavioral dimensions. Finally, quadratic discriminant analysis was implemented to verify the ability of the extracted dimensions to classify dispensaries into their derived communities. Results The modularity algorithm yielded three communities in each city with distinct network structures. The principal components factor analysis reduced the 12 cyberbehaviors into five dimensions that encompassed account age, posting frequency, referencing, hyperlinks, and user engagement among the dispensary accounts. In the quadratic discriminant analysis, the dimensions correctly classified 75% (46/61) of the communities in the San Francisco Bay Area and 71% (41/58) in Greater Los Angeles. Conclusions The most centralized and strongly connected dispensaries in both cities had newer accounts, higher daily activity, more frequent user engagement, and increased usage of embedded media, keywords, and hyperlinks. Measures derived from both network structure and cyberbehavioral dimensions can serve as key contextual indicators for the online surveillance of cannabis dispensaries and consumer markets over time. PMID:28676471

Ecosystem regime shifts disrupt trophic structure.

PubMed

Hempson, Tessa N; Graham, Nicholas A J; MacNeil, M Aaron; Hoey, Andrew S; Wilson, Shaun K

2018-01-01

Regime shifts between alternative stable ecosystem states are becoming commonplace due to the combined effects of local stressors and global climate change. Alternative states are characterized as substantially different in form and function from pre-disturbance states, disrupting the delivery of ecosystem services and functions. On coral reefs, regime shifts are typically characterized by a change in the benthic composition from coral to macroalgal dominance. Such fundamental shifts in the benthos are anticipated to impact associated fish communities that are reliant on the reef for food and shelter, yet there is limited understanding of how regime shifts propagate through the fish community over time, relative to initial or recovery conditions. This study addresses this knowledge gap using long-term data of coral reef regime shifts and recovery on Seychelles reefs following the 1998 mass bleaching event. It shows how trophic structure of the reef fish community becomes increasingly dissimilar between alternative reef ecosystem states (regime-shifted vs. recovering) with time since disturbance. Regime-shifted reefs developed a concave trophic structure, with increased biomass in base trophic levels as herbivorous species benefitted from increased algal resources. Mid trophic level species, including specialists such as corallivores, declined with loss of coral habitat, while biomass was retained in upper trophic levels by large-bodied, generalist invertivores. Recovering reefs also experienced an initial decline in mid trophic level biomass, but moved toward a bottom-heavy pyramid shape, with a wide range of feeding groups (e.g., planktivores, corallivores, omnivores) represented at mid trophic levels. Given the importance of coral reef fishes in maintaining the ecological function of coral reef ecosystems and their associated fisheries, understanding the effects of regime shifts on these communities is essential to inform decisions that enhance ecological resilience and economic sustainability. © 2017 by the Ecological Society of America.

The meaning of functional trait composition of food webs for ecosystem functioning.

PubMed

Gravel, Dominique; Albouy, Camille; Thuiller, Wilfried

2016-05-19

There is a growing interest in using trait-based approaches to characterize the functional structure of animal communities. Quantitative methods have been derived mostly for plant ecology, but it is now common to characterize the functional composition of various systems such as soils, coral reefs, pelagic food webs or terrestrial vertebrate communities. With the ever-increasing availability of distribution and trait data, a quantitative method to represent the different roles of animals in a community promise to find generalities that will facilitate cross-system comparisons. There is, however, currently no theory relating the functional composition of food webs to their dynamics and properties. The intuitive interpretation that more functional diversity leads to higher resource exploitation and better ecosystem functioning was brought from plant ecology and does not apply readily to food webs. Here we appraise whether there are interpretable metrics to describe the functional composition of food webs that could foster a better understanding of their structure and functioning. We first distinguish the various roles that traits have on food web topology, resource extraction (bottom-up effects), trophic regulation (top-down effects), and the ability to keep energy and materials within the community. We then discuss positive effects of functional trait diversity on food webs, such as niche construction and bottom-up effects. We follow with a discussion on the negative effects of functional diversity, such as enhanced competition (both exploitation and apparent) and top-down control. Our review reveals that most of our current understanding of the impact of functional trait diversity on food web properties and functioning comes from an over-simplistic representation of network structure with well-defined levels. We, therefore, conclude with propositions for new research avenues for both theoreticians and empiricists. © 2016 The Author(s).

The meaning of functional trait composition of food webs for ecosystem functioning

PubMed Central

Albouy, Camille

2016-01-01

There is a growing interest in using trait-based approaches to characterize the functional structure of animal communities. Quantitative methods have been derived mostly for plant ecology, but it is now common to characterize the functional composition of various systems such as soils, coral reefs, pelagic food webs or terrestrial vertebrate communities. With the ever-increasing availability of distribution and trait data, a quantitative method to represent the different roles of animals in a community promise to find generalities that will facilitate cross-system comparisons. There is, however, currently no theory relating the functional composition of food webs to their dynamics and properties. The intuitive interpretation that more functional diversity leads to higher resource exploitation and better ecosystem functioning was brought from plant ecology and does not apply readily to food webs. Here we appraise whether there are interpretable metrics to describe the functional composition of food webs that could foster a better understanding of their structure and functioning. We first distinguish the various roles that traits have on food web topology, resource extraction (bottom-up effects), trophic regulation (top-down effects), and the ability to keep energy and materials within the community. We then discuss positive effects of functional trait diversity on food webs, such as niche construction and bottom-up effects. We follow with a discussion on the negative effects of functional diversity, such as enhanced competition (both exploitation and apparent) and top-down control. Our review reveals that most of our current understanding of the impact of functional trait diversity on food web properties and functioning comes from an over-simplistic representation of network structure with well-defined levels. We, therefore, conclude with propositions for new research avenues for both theoreticians and empiricists. PMID:27114571

Characterizing Community Health Workers on Research Teams: Results From the Centers for Population Health and Health Disparities

PubMed Central

Thompson, Beti; Krok-Schoen, Jessica L.; Weier, Rory C.; Martin, Molly; Bone, Lee; McCarthy, William J.; Noel, Sabrina E.; Garcia, Beverly; Calderón, Nancy E.; Paskett, Electra D.

2016-01-01

Objectives. To quantify the characteristics of community health workers (CHWs) involved in community intervention research and, in particular, to characterize their job titles, roles, and responsibilities; recruitment and compensation; and training and supervision. Methods. We developed and administered a structured questionnaire consisting of 25 closed- and open-ended questions to staff on National Institutes of Health–funded Centers for Population Health and Health Disparities projects between March and April 2014. We report frequency distributions for CHW roles, sought-after skills, education requirements, benefits and incentives offered, and supervision and training activities. Results. A total of 54 individuals worked as CHWs across the 18 research projects and held a diverse range of job titles. The CHWs commonly collaborated on research project implementation, provided education and support to study participants, and collected data. Training was offered across projects to bolster CHW capacity to assist in intervention and research activities. Conclusions. Our experience suggests national benefit in supporting greater efforts to recruit, retain, and support the work of CHWs in community-engagement research. PMID:26794157

Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L.

PubMed

Jin, Hui; Yang, Xiao-Yan; Yan, Zhi-Qiang; Liu, Quan; Li, Xiu-Zhuang; Chen, Ji-Xiang; Zhang, Deng-Hong; Zeng, Li-Ming; Qin, Bo

2014-07-01

A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity. Copyright © 2014 Elsevier GmbH. All rights reserved.

Canopy structural alterations to nitrogen functions of the soil microbial community in a Quercus virginiana forest

NASA Astrophysics Data System (ADS)

Moore, L. D.; Van Stan, J. T., II; Rosier, C. L.; Gay, T. E.; Wu, T.

2014-12-01

Forest canopy structure controls the timing, amount and chemical character of precipitation supply to soils through interception and drainage along crown surfaces. Yet, few studies have examined forest canopy structural connections to soil microbial communities (SMCs), and none have measured how this affects SMC N functions. The maritime Quercus virginiana Mill. (southern live oak) forests of St Catherine's Island, GA, USA provide an ideal opportunity to examine canopy structural alterations to SMCs and their functioning, as their throughfall varies substantially across space due to dense Tillandsia usneoides L. (spanish moss) mats bestrewn throughout. To examine the impact of throughfall variability on SMC N functions, we examined points along the canopy coverage continuum: large canopy gaps (0%), bare canopy (50-60%), and canopy of heavy T. usneoides coverage (>=85%). Five sites beneath each of the canopy cover types were monitored for throughfall water/ions and soil leachates chemistry for one storm each month over the growing period (7 months, Mar-2014 to Sep-2014) to compare with soil chemistry and SMC communities sampled every two months throughout that same period (Mar, May, Jul, Sep). DGGE and QPCR analysis of the N functioning genes (NFGs) to characterize the ammonia oxidizing bacterial (AOB-amoA), archaea (AOA-amoA), and ammonification (chiA) communities were used to determine the nitrification and decomposition potential of these microbial communities. PRS™-probes (Western Ag Innovations Inc., Saskatoon, Canada) were then used to determine the availability of NO3-N and NH4+N in the soils over a 6-week period to evaluate whether the differing NFG abundance and community structures resulted in altered N cycling.

Microbiome analysis of dairy cows fed pasture or total mixed ration diets.

PubMed

de Menezes, Alexandre B; Lewis, Eva; O'Donovan, Michael; O'Neill, Brendan F; Clipson, Nicholas; Doyle, Evelyn M

2011-11-01

Understanding rumen microbial ecology is essential for the development of feed systems designed to improve livestock productivity, health and for methane mitigation strategies from cattle. Although rumen microbial communities have been studied previously, few studies have applied next-generation sequencing technologies to that ecosystem. The aim of this study was to characterize changes in microbial community structure arising from feeding dairy cows two widely used diets: pasture and total mixed ration (TMR). Bacterial, archaeal and protozoal communities were characterized by terminal restriction fragment length polymorphism of the amplified SSU rRNA gene and statistical analysis showed that bacterial and archaeal communities were significantly affected by diet, whereas no effect was observed for the protozoal community. Deep amplicon sequencing of the 16S rRNA gene revealed significant differences in the bacterial communities between the diets and between rumen solid and liquid content. At the family level, some important groups of rumen bacteria were clearly associated with specific diets, including the higher abundance of the Fibrobacteraceae in TMR solid samples and members of the propionate-producing Veillonelaceae in pasture samples. This study will be relevant to the study of rumen microbial ecology and livestock feed management. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Apple orchard pest control strategies affect bird communities in southeastern France.

PubMed

Bouvier, Jean-Charles; Ricci, Benoît; Agerberg, Julia; Lavigne, Claire

2011-01-01

Birds are regarded as appropriate biological indicators of how changes in agricultural practices affect the environment. They are also involved in the biocontrol of pests. In the present study, we provide an assessment of the impact of pest control strategies on bird communities in apple orchards in southeastern France. We compared the structure (abundance, species richness, and diversity) of breeding bird communities in 15 orchards under conventional or organic pest control over a three-year period (2003-2005). Pest control strategies and their evolution over time were characterized by analyzing farmers' treatment schedules. The landscape surrounding the orchards was characterized using a Geographic Information System. We observed 30 bird species overall. Bird abundance, species richness, and diversity were all affected by pest control strategies, and were highest in organic orchards and lowest in conventional orchards during the three study years. The pest control strategy affected insectivores more than granivores. We further observed a tendency for bird communities in integrated pest management orchards to change over time and become increasingly different from communities in organic orchards, which also corresponded to changes in treatment schedules. These findings indicate that within-orchard bird communities may respond quickly to changes in pesticide use and may, in turn, influence biocontrol of pests by birds. © 2010 SETAC.

Effects of farmhouse hotel and paper mill effluents on bacterial community structures in sediment and surface water of Nanxi River, China.

PubMed

Lu, Xiao-Ming; Lu, Peng-Zhen

2014-11-01

The pyrosequencing technique was used to evaluate bacterial community structures in sediment and surface water samples taken from Nanxi River receiving effluents from a paper mill and a farmhouse hotel, respectively. For each sample, 4,610 effective bacterial sequences were selected and used to do the analysis of diversity and abundance, respectively. Bacterial phylotype richness in the sediment sample without effluent input was higher than the other samples, and the surface water sample with addition of effluent from the paper mill contained the least richness. Effluents from both the paper mill and farmhouse hotel have a potential to reduce the bacterial diversity and abundance in the sediment and surface water, especially it is more significant in the sediment. The effect of the paper mill effluent on the sediment and surface water bacterial communities was more serious than that of the farmhouse hotel effluent. Characterization of microbial community structures in the sediment and surface water from two tributaries of the downstream river indicated that various effluents from the paper mill and farmhouse hotel have the similar potential to decrease the natural variability in riverine microbial ecosystems.

Impacts of feral horse use on riparian vegetation within the sagebrush steppe

USDA-ARS?s Scientific Manuscript database

Feral horses inhabit rangeland ecosystems around the world, but their impacts on riparian ecosystems are poorly understood. We characterized impacts of a free-ranging horse population on the structure and composition of riparian plant communities in the sagebrush steppe ecosystem in the western US....

Size Matters: The Contribution of Mega-Infauna to the Food Webs and Ecosystem Services of an Oregon Estuary

EPA Science Inventory

Large-bodied, invertebrates are common to infaunal communities of NE Pacific estuaries (e.g., bivalves, polychaetes, burrowing shrimps), but their contribution to the ecological structure, function and ecosystem services of most estuaries has been poorly characterized because the...

Rumen bacterial community structure impacts feed efficiency in beef cattle

USDA-ARS?s Scientific Manuscript database

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterize...

Institutionalizing Faculty Mentoring within a Community of Practice Model

ERIC Educational Resources Information Center

Smith, Emily R.; Calderwood, Patricia E.; Storms, Stephanie Burrell; Lopez, Paula Gill; Colwell, Ryan P.

2016-01-01

In higher education, faculty work is typically enacted--and rewarded--on an individual basis. Efforts to promote collaboration run counter to the individual and competitive reward systems that characterize higher education. Mentoring initiatives that promote faculty collaboration and support also defy the structural and cultural norms of higher…

Hillslope characterization: Identifying key controls on local-scale plant communities' distribution using remote sensing and subsurface data fusion.

NASA Astrophysics Data System (ADS)

Falco, N.; Wainwright, H. M.; Dafflon, B.; Leger, E.; Peterson, J.; Steltzer, H.; Wilmer, C.; Williams, K. H.; Hubbard, S. S.

2017-12-01

Mountainous watershed systems are characterized by extreme heterogeneity in hydrological and pedological properties that influence biotic activities, plant communities and their dynamics. To gain predictive understanding of how ecosystem and watershed system evolve under climate change, it is critical to capture such heterogeneity and to quantify the effect of key environmental variables such as topography, and soil properties. In this study, we exploit advanced geophysical and remote sensing techniques - coupled with machine learning - to better characterize and quantify the interactions between plant communities' distribution and subsurface properties. First, we have developed a remote sensing data fusion framework based on the random forest (RF) classification algorithm to estimate the spatial distribution of plant communities. The framework allows the integration of both plant spectral and structural information, which are derived from multispectral satellite images and airborne LiDAR data. We then use the RF method to evaluate the estimated plant community map, exploiting the subsurface properties (such as bedrock depth, soil moisture and other properties) and geomorphological parameters (such as slope, curvature) as predictors. Datasets include high-resolution geophysical data (electrical resistivity tomography) and LiDAR digital elevation maps. We demonstrate our approach on a mountain hillslope and meadow within the East River watershed in Colorado, which is considered to be a representative headwater catchment in the Upper Colorado Basin. The obtained results show the existence of co-evolution between above and below-ground processes; in particular, dominant shrub communities in wet and flat areas. We show that successful integration of remote sensing data with geophysical measurements allows identifying and quantifying the key environmental controls on plant communities' distribution, and provides insights into their potential changes in the future climate conditions.

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps.

PubMed

Gong, Hongli; Wang, Boyan; Shi, Yi; Shi, Yong; Xiao, Xiyan; Cao, Pengyu; Tao, Lei; Wang, Yuezhu; Zhou, Liang

2017-08-01

The pharynx is an important site of microbiota colonization, but the bacterial populations at this site have been relatively unexplored by culture-independent approaches. The aim of this study was to characterize the microbiota structure of the pharynx. Pyrosequencing of 16S rRNA gene libraries was used to characterize the pharyngeal microbiota using swab samples from 68 subjects with laryngeal cancer and 28 subjects with vocal cord polyps. Overall, the major phylum was Firmicutes, with Streptococcus as the predominant genus in the pharyngeal communities. Nine core operational taxonomic units detected from Streptococcus, Fusobacterium, Prevotella, Granulicatella, and Veillonella accounted for 21.3% of the total sequences detected. However, there was no difference in bacterial communities in the pharynx from patients with laryngeal cancer and vocal cord polyps. The relative abundance of Firmicutes was inversely correlated with Fusobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. The correlation was evident at the genus level, and the relative abundance of Streptococcus was inversely associated with Fusobacterium, Leptotrichia, Neisseria, Actinomyces, and Prevotella. This study presented a profile for the overall structure of the microbiota in pharyngeal swab samples. Inverse correlations were found between Streptococcus and other bacterial communities, suggesting that potential antagonism may exist among pharyngeal microbiota.

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus

PubMed Central

Libberton, Ben; Coates, Rosanna E.

2014-01-01

Nasal carriage of Staphylococcus aureus is a risk factor for infection, yet the bacterial determinants required for carriage are poorly defined. Interactions between S. aureus and other members of the bacterial flora may determine colonization and have been inferred in previous studies by using correlated species distributions. However, traits mediating species interactions are often polymorphic, suggesting that understanding how interactions structure communities requires a trait-based approach. We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. Across microbiomes, the cumulative community-level growth inhibition was negatively associated with S. aureus incidence. To fully understand the ecological processes structuring microbiomes, it will be crucial to account for intraspecific variation in the traits that mediate species interactions. PMID:24980973

Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

PubMed

Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

2014-11-01

Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output. Copyright © 2014 Elsevier Ltd. All rights reserved.

Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

PubMed Central

Nelson, Peter; Abelson, Avigdor; Precoda, Kristin; Rulmal, John; Bernardi, Giacomo; Paddack, Michelle

2017-01-01

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an ‘opportunistic’ scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities. PMID:28489903

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

PubMed

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

PubMed Central

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters. PMID:26648921

Discovering Network Structure Beyond Communities

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2011-11-01

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

Black grandmothers in multigenerational households: diversity in family structure and parenting involvement in the Woodlawn community.

PubMed

Pearson, J L; Hunter, A G; Ensminger, M E; Kellam, S G

1990-04-01

We report here the frequency of black grandmothers' coresidence in households with first-grade children, their patterns of involvement in parenting, and the degree to which family structure and employment affected the grandmothers' parenting involvement in a 1966/1967 community-defined population. Coresidence between grandmothers and their target first-grade grandchildren was found in 10% of the households. The 130 grandmothers' parenting involvement was substantial, second only to mother involvement, and was characterized by 2 parenting activity patterns: control and punishment, and support and punishment. The degree of grandmothers' parenting involvement differed by family structure, with grandmothers in mother-absent homes most likely to be involved. Grandmothers' employment did not moderate their engagement in parenting behaviors. These findings are consistent with previous reports of significant parenting involvement by black extended family members.

Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types.

PubMed

Xie, Yuwei; Wang, Jizhong; Yang, Jianghua; Giesy, John P; Yu, Hongxia; Zhang, Xiaowei

2017-04-01

Land-use intensification threatens freshwater biodiversity. Freshwater eukaryotic communities are affected by multiple chemical contaminants with a land-use specific manner. However, biodiversities of eukaryotes and their associations with multiple chemical contaminants are largely unknown. This study characterized in situ eukaryotic communities in sediments exposed to mixtures of chemical contaminants and assessed relationships between various environmental variables and eukaryotic communities in sediments from the Nanfei River. Eukaryotic communities in the sediment samples were dominated by Annelida, Arthropoda, Rotifera, Ochrophyta, Chlorophyta and Ciliophora. Alpha-diversities (Shannon entropy) and structures of eukaryotic communities were significantly different between land-use types. According to the results of multiple statistical tests (PCoA, distLM, Mantel and network analysis), dissimilarity of eukaryotic community structures revealed the key effects of pyrethroid insecticides, manganese, zinc, lead, chromium and polycyclic aromatic hydrocarbons (PAHs) on eukaryotic communities in the sediment samples from the Nanfei River. Furthermore, taxa associated with land-use types were identified and several sensitive eukaryotic taxa to some of the primary contaminants were identified as potential indicators to monitor effects of the primary chemical contaminants. Overall, environmental DNA metabarcoding on in situ eukaryotic communities provided a powerful tool for biomonitoring and identifying primary contaminants and their complex effects on benthic eukaryotic communities in freshwater sediments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.

PubMed

Nocadello, Salvatore; Minasov, George; Shuvalova, Ludmilla S; Dubrovska, Ievgeniia; Sabini, Elisabetta; Anderson, Wayne F

2016-07-15

Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production.

PubMed

Wang, Lin; Mao, Jiugeng; Zhao, Hejuan; Li, Min; Wei, Qishun; Zhou, Ying; Shao, Heping

2016-09-01

Rice straw (RS) is an important raw material for the preparation of Agaricus bisporus compost in China. In this study, the characterization of composting process from RS and wheat straw (WS) was compared for mushroom production. The results showed that the temperature in RS compost increased rapidly compared with WS compost, and the carbon (C)/nitrogen (N) ratio decreased quickly. The microbial changes during the Phase I and Phase II composting process were monitored using denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) analysis. Bacteria were the dominant species during the process of composting and the bacterial community structure dramatically changed during heap composting according to the DGGE results. The bacterial community diversity of RS compost was abundant compared with WS compost at stages 4-5, but no distinct difference was observed after the controlled tunnel Phase II process. The total amount of PLFAs of RS compost, as an indicator of microbial biomass, was higher than that of WS. Clustering by DGGE and principal component analysis of the PLFA compositions revealed that there were differences in both the microbial population and community structure between RS- and WS-based composts. Our data indicated that composting of RS resulted in improved degradation and assimilation of breakdown products by A. bisporus, and suggested that the RS compost was effective for sustaining A. bisporus mushroom growth as well as conventional WS compost.

A complex speciation–richness relationship in a simple neutral model

PubMed Central

Desjardins-Proulx, Philippe; Gravel, Dominique

2012-01-01

Speciation is the “elephant in the room” of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations. PMID:22957181

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils.

PubMed

Webster, Gordon; Embley, T Martin; Freitag, Thomas E; Smith, Zena; Prosser, James I

2005-05-01

Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.

Structural changes of TasA in biofilm formation of Bacillus subtilis.

PubMed

Diehl, Anne; Roske, Yvette; Ball, Linda; Chowdhury, Anup; Hiller, Matthias; Molière, Noel; Kramer, Regina; Stöppler, Daniel; Worth, Catherine L; Schlegel, Brigitte; Leidert, Martina; Cremer, Nils; Erdmann, Natalja; Lopez, Daniel; Stephanowitz, Heike; Krause, Eberhard; van Rossum, Barth-Jan; Schmieder, Peter; Heinemann, Udo; Turgay, Kürşad; Akbey, Ümit; Oschkinat, Hartmut

2018-03-27

Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics. Bacillus subtilis biofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, β-sheet-rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level. Copyright © 2018 the Author(s). Published by PNAS.

Structural changes of TasA in biofilm formation of Bacillus subtilis

PubMed Central

Diehl, Anne; Roske, Yvette; Ball, Linda; Chowdhury, Anup; Hiller, Matthias; Molière, Noel; Kramer, Regina; Stöppler, Daniel; Worth, Catherine L.; Schlegel, Brigitte; Leidert, Martina; Cremer, Nils; Erdmann, Natalja; Lopez, Daniel; Stephanowitz, Heike; Krause, Eberhard; Schmieder, Peter; Akbey, Ümit; Oschkinat, Hartmut

2018-01-01

Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics. Bacillus subtilis biofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, β-sheet–rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level. PMID:29531041

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

PubMed Central

Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E.; Adatte, Thierry; Guisan, Antoine; van der Meer, Jan Roelof

2016-01-01

ABSTRACT Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. PMID:27542929

Quantitative NDE of Composite Structures at NASA

NASA Technical Reports Server (NTRS)

Cramer, K. Elliott; Leckey, Cara A. C.; Howell, Patricia A.; Johnston, Patrick H.; Burke, Eric R.; Zalameda, Joseph N.; Winfree, William P.; Seebo, Jeffery P.

2015-01-01

The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. Ongoing work at NASA involves the use of the large-scale composite structures for spacecraft (payload shrouds, cryotanks, crew modules, etc). NASA is also working to enable the use and certification of composites in aircraft structures through the Advanced Composites Project (ACP). The rapid, in situ characterization of a wide range of the composite materials and structures has become a critical concern for the industry. In many applications it is necessary to monitor changes in these materials over a long time. The quantitative characterization of composite defects such as fiber waviness, reduced bond strength, delamination damage, and microcracking are of particular interest. The research approaches of NASA's Nondestructive Evaluation Sciences Branch include investigation of conventional, guided wave, and phase sensitive ultrasonic methods, infrared thermography and x-ray computed tomography techniques. The use of simulation tools for optimizing and developing these methods is also an active area of research. This paper will focus on current research activities related to large area NDE for rapidly characterizing aerospace composites.

Game Theory, Conditional Preferences, and Social Influence

PubMed Central

Stirling, Wynn C.; Felin, Teppo

2013-01-01

Neoclassical noncooperative game theory is based on a simple, yet powerful synthesis of mathematical and logical concepts: unconditional and immutable preference orderings and individual rationality. Although this structure has proven useful for characterizing competitive multi-player behavior, its applicability to scenarios involving complex social relationships is problematic. In this paper we directly address this limitation by the introduction of a conditional preference structure that permits players to modulate their preference orderings as functions of the preferences of other players. Embedding this expanded preference structure in a formal and graphical framework provides a systematic approach for characterizing a complex society. The result is an influence network that allows conditional preferences to propagate through the community, resulting in an emergent social model which characterizes all of the social relationships that exist and which leads to solution concepts that account for both group and individual interests. The Ultimatum game is presented as an example of how social influence can be modeled with conditional preferences. PMID:23451078

Game theory, conditional preferences, and social influence.

PubMed

Stirling, Wynn C; Felin, Teppo

2013-01-01

Neoclassical noncooperative game theory is based on a simple, yet powerful synthesis of mathematical and logical concepts: unconditional and immutable preference orderings and individual rationality. Although this structure has proven useful for characterizing competitive multi-player behavior, its applicability to scenarios involving complex social relationships is problematic. In this paper we directly address this limitation by the introduction of a conditional preference structure that permits players to modulate their preference orderings as functions of the preferences of other players. Embedding this expanded preference structure in a formal and graphical framework provides a systematic approach for characterizing a complex society. The result is an influence network that allows conditional preferences to propagate through the community, resulting in an emergent social model which characterizes all of the social relationships that exist and which leads to solution concepts that account for both group and individual interests. The Ultimatum game is presented as an example of how social influence can be modeled with conditional preferences.

Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters

PubMed Central

Ribalet, Francois; Marchetti, Adrian; Hubbard, Katherine A.; Brown, Kristina; Durkin, Colleen A.; Morales, Rhonda; Robert, Marie; Swalwell, Jarred E.; Tortell, Philippe D.; Armbrust, E. Virginia

2010-01-01

In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km–wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO2 and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans. PMID:20823224

Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters.

PubMed

Ribalet, Francois; Marchetti, Adrian; Hubbard, Katherine A; Brown, Kristina; Durkin, Colleen A; Morales, Rhonda; Robert, Marie; Swalwell, Jarred E; Tortell, Philippe D; Armbrust, E Virginia

2010-09-21

In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km-wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO(2) and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans.

Analysis of Composition and Structure of Coastal to Mesopelagic Bacterioplankton Communities in the Northern Gulf of Mexico

PubMed Central

King, Gary M.; Smith, Conor B.; Tolar, Bradley; Hollibaugh, James T.

2013-01-01

16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity, and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Thaumarchaeota, Firmicutes, and δ-Proteobacteria were relatively abundant in deeper waters, and α/γ ratios were low (<1). Canonical correlation analysis indicated that δ- and γ-Proteobacteria, Thaumarchaeota, and Firmicutes correlated positively with depth; α-Proteobacteria and Bacteroidetes correlated positively with temperature and dissolved oxygen; Actinobacteria, β-Proteobacteria, and Verrucomicrobia correlated positively with a measure of suspended particles. Diversity indices did not vary with depth or other factors, which indicated that richness and evenness elements of bacterioplankton communities might develop independently of nGoM physical-chemical variables. Phylogenetic community structure as measured by the net relatedness (NRI) and nearest taxon (NTI) indices also did not vary with depth. NRI values indicated that most of the communities were comprised of OTUs more distantly related to each other in whole community comparisons than expected by chance. NTI values derived from phylogenetic distances of the closest neighbor for each OTU in a given community indicated that OTUs tended to occur in clusters to a greater extent than expected by chance. This indicates that “habitat filtering” might play an important role in nGoM bacterioplankton species assembly, and that such filtering occurs throughout the water column. PMID:23346078

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

PubMed

Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

2015-11-15

Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

PubMed

Manel, Stéphanie; Couvreur, Thomas L P; Munoz, François; Couteron, Pierre; Hardy, Olivier J; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

Impact of Oil on Bacterial Community Structure in Bioturbated Sediments

PubMed Central

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g−1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities. PMID:23762350

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water.

PubMed

Kulkarni, Prachi; Olson, Nathan D; Paulson, Joseph N; Pop, Mihai; Maddox, Cynthia; Claye, Emma; Rosenberg Goldstein, Rachel E; Sharma, Manan; Gibbs, Shawn G; Mongodin, Emmanuel F; Sapkota, Amy R

2018-10-15

Water recycling continues to expand across the United States, from areas that have access to advanced, potable-level treated reclaimed water, to those having access only to reclaimed water treated at conventional municipal wastewater treatment plants. This expansion makes it important to further characterize the microbial quality of these conventionally-treated water sources. Therefore, we used 16S rRNA gene sequencing to characterize total bacterial communities present in differentially-treated wastewater and reclaimed water (n = 67 samples) from four U.S. wastewater treatment plants and one associated spray irrigation site conducting on-site ultraviolet treatment and open-air storage. The number of observed operational taxonomic units was significantly lower (p < 0.01) in effluent, compared to influent, after conventional treatment. Effluent community structure was influenced more by treatment method than by influent community structure. The abundance of Legionella spp. increased as treatment progressed in one treatment plant that performed chlorination and in another that seasonally chlorinated. Overall, the alpha-diversity of bacterial communities in reclaimed water decreased (p < 0.01) during wastewater treatment and spray irrigation site ultraviolet treatment (p < 0.01), but increased (p < 0.01) after open-air storage at the spray irrigation site. The abundance of Legionella spp. was higher at the sprinkler system pumphouse at the spray irrigation site than in the influent from the treatment plant supplying the site. Legionella pneumophila was detected in conventionally treated effluent samples and in samples collected after ultraviolet treatment at the spray irrigation site, while Legionella feeleii persisted throughout on-site treatment at the spray irrigation site, and, along with Mycobacterium gordonae, was also detected at the sprinkler system pumphouse at the spray irrigation site. These data could inform the development of future treatment technologies and reuse guidelines that address a broader assemblage of the bacterial community of reclaimed water, resulting in reuse practices that may be more protective of public health. Copyright © 2018 Elsevier B.V. All rights reserved.

Research Developments in Nondestructive Evaluation and Structural Health Monitoring for the Sustainment of Composite Aerospace Structures at NASA

NASA Technical Reports Server (NTRS)

Cramer, K. Elliott

2016-01-01

The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. Ongoing work at NASA involves the use of the large-scale composite structures for spacecraft (payload shrouds, cryotanks, crew modules, etc). NASA is also working to enable both the use and sustainment of composites in commercial aircraft structures. One key to the sustainment of these large composite structures is the rapid, in-situ characterization of a wide range of potential defects that may occur during the vehicle's life. Additionally, in many applications it is necessary to monitor changes in these materials over their lifetime. Quantitative characterization through Nondestructive Evaluation (NDE) of defects such as reduced bond strength, microcracking, and delamination damage due to impact, are of particular interest. This paper will present an overview of NASA's applications of NDE technologies being developed for the characterization and sustainment of advanced aerospace composites. The approaches presented include investigation of conventional, guided wave, and phase sensitive ultrasonic methods and infrared thermography techniques for NDE. Finally, the use of simulation tools for optimizing and validating these techniques will also be discussed.

Using a metagenomic approach to improve our understanding of Armillaria root disease

Treesearch

Amy Ross-Davis; Matt Settles; John W. Hanna; John D. Shaw; Andrew T. Hudak; Deborah S. Page-Dumroese; Ned B. Klopfenstein

2015-01-01

Metagenomics has illuminated our understanding of how microbial communities influence health and disease. Researchers are beginning to characterize what constitutes healthy microbiota in terms of structure, function, and diversity in a variety of environments. Although investigation lags behind the more well-studied human microbiome, a growing body of research is using...

Canopy gaps decrease microbial densities and disease risk for a shade-intolerant tree species

Treesearch

Kurt O. Reinhart; Alejandro A. Royo; Stacie A. Kageyama; Keith. Clay

2010-01-01

Canopy disturbances such as windthrowevents have obvious impacts on forest structure and composition aboveground, but changes in soil microbial communities and the consequences of these changes are less understood.We characterized the densities of a soil-borne pathogenic oomycete (Pythium) and a common saprotrophic zygomycete (Mortierella...

LANDSCAPE INFLUENCES ON LAKE CHEMISTRY AND OSTRACOD COMMUNITY STRUCTURE OF SMALL DIMICTIC LAKES IN SOUTHERN WISCONSIN DIMICTIC LAKES

EPA Science Inventory

The natural land cover patterns that characterize the southern part of Wisconsin are legacies of a

glaciated past. Land cover pattern and geomorphology control the hydrologic connections between water

resources and the land by which ecosystems, including lakes are o...

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

PubMed

Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

2016-10-01

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure.

PubMed

Stevenson, Bradley S; Drilling, Heather S; Lawson, Paul A; Duncan, Kathleen E; Parisi, Victoria A; Suflita, Joseph M

2011-04-01

The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Mathematical Ecology Analysis of Geographical Distribution of Soybean-Nodulating Bradyrhizobia in Japan

PubMed Central

Saeki, Yuichi; Shiro, Sokichi; Tajima, Toshiyuki; Yamamoto, Akihiro; Sameshima-Saito, Reiko; Sato, Takashi; Yamakawa, Takeo

2013-01-01

We characterized the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in Japan and their geographical distribution in an ecological study of indigenous soybean rhizobia. We isolated bradyrhizobia from three kinds of Rj-genotype soybeans. Their genetic diversity and community structure were analyzed by PCR-RFLP analysis of the 16S–23S rRNA gene internal transcribed spacer (ITS) region with 11 Bradyrhizobium USDA strains as references. We used data from the present study and previous studies to carry out mathematical ecological analyses, multidimensional scaling analysis with the Bray-Curtis index, polar ordination analysis, and multiple regression analyses to characterize the relationship between soybean-nodulating bradyrhizobial community structures and their geographical distribution. The mathematical ecological approaches used in this study demonstrated the presence of ecological niches and suggested the geographical distribution of soybean-nodulating bradyrhizobia to be a function of latitude and the related climate, with clusters in the order Bj123, Bj110, Bj6, and Be76 from north to south in Japan. PMID:24240318

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

PubMed Central

Gaheen, Sharon; Lijowski, Michal; Heiskanen, Mervi; Klemm, Juli

2015-01-01

Summary The cancer Nanotechnology Laboratory (caNanoLab) data portal is an online nanomaterial database that allows users to submit and retrieve information on well-characterized nanomaterials, including composition, in vitro and in vivo experimental characterizations, experimental protocols, and related publications. Initiated in 2006, caNanoLab serves as an established resource with an infrastructure supporting the structured collection of nanotechnology data to address the needs of the cancer biomedical and nanotechnology communities. The portal contains over 1,000 curated nanomaterial data records that are publicly accessible for review, comparison, and re-use, with the ultimate goal of accelerating the translation of nanotechnology-based cancer therapeutics, diagnostics, and imaging agents to the clinic. In this paper, we will discuss challenges associated with developing a nanomaterial database and recognized needs for nanotechnology data curation and sharing in the biomedical research community. We will also describe the latest version of caNanoLab, caNanoLab 2.0, which includes enhancements and new features to improve usability such as personalized views of data and enhanced search and navigation. PMID:26425409

Global-Scale Structure of the Eelgrass Microbiome.

PubMed

Fahimipour, Ashkaan K; Kardish, Melissa R; Lang, Jenna M; Green, Jessica L; Eisen, Jonathan A; Stachowicz, John J

2017-06-15

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments. IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina , or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host. Copyright © 2017 Fahimipour et al.

Initial insights into bacterial succession during human decomposition.

PubMed

Hyde, Embriette R; Haarmann, Daniel P; Petrosino, Joseph F; Lynne, Aaron M; Bucheli, Sibyl R

2015-05-01

Decomposition is a dynamic ecological process dependent upon many factors such as environment, climate, and bacterial, insect, and vertebrate activity in addition to intrinsic properties inherent to individual cadavers. Although largely attributed to microbial metabolism, very little is known about the bacterial basis of human decomposition. To assess the change in bacterial community structure through time, bacterial samples were collected from several sites across two cadavers placed outdoors to decompose and analyzed through 454 pyrosequencing and analysis of variable regions 3-5 of the bacterial 16S ribosomal RNA (16S rRNA) gene. Each cadaver was characterized by a change in bacterial community structure for all sites sampled as time, and decomposition, progressed. Bacteria community structure is variable at placement and before purge for all body sites. At bloat and purge and until tissues began to dehydrate or were removed, bacteria associated with flies, such as Ignatzschineria and Wohlfahrtimonas, were common. After dehydration and skeletonization, bacteria associated with soil, such as Acinetobacter, were common at most body sites sampled. However, more cadavers sampled through multiple seasons are necessary to assess major trends in bacterial succession.

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

PubMed Central

Zhang, Shaocun; Cao, Xiaocang; Huang, He

2017-01-01

Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research. PMID:28286741

Insights into biodegradation through depth-resolved microbial community functional and structural profiling of a crude-oil contaminant plume

USGS Publications Warehouse

Fahrenfeld, Nicole; Cozzarelli, Isabelle M.; Bailey, Zach; Pruden, Amy

2014-01-01

Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

PubMed Central

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

PubMed

Akmatov, Manas K; Koch, Nadine; Vital, Marius; Ahrens, Wolfgang; Flesch-Janys, Dieter; Fricke, Julia; Gatzemeier, Anja; Greiser, Halina; Günther, Kathrin; Illig, Thomas; Kaaks, Rudolf; Krone, Bastian; Kühn, Andrea; Linseisen, Jakob; Meisinger, Christine; Michels, Karin; Moebus, Susanne; Nieters, Alexandra; Obi, Nadia; Schultze, Anja; Six-Merker, Julia; Pieper, Dietmar H; Pessler, Frank

2017-05-12

We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

PubMed

Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

2018-04-06

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

PubMed Central

Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

2012-01-01

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

Nekton community structure varies in response to coastal urbanization near mangrove tidal tributaries

USGS Publications Warehouse

Krebs, Justin M.; McIvor, Carole C.; Bell, Susan S.

2014-01-01

To assess the potential influence of coastal development on estuarine-habitat quality, we characterized land use and the intensity of land development surrounding small tidal tributaries in Tampa Bay. Based on this characterization, we classified tributaries as undeveloped, industrial, urban, or man-made (i.e., mosquito-control ditches). Over one third (37 %) of the tributaries have been heavily developed based on landscape development intensity (LDI) index values >5.0, while fewer than one third (28 %) remain relatively undeveloped (LDI < 3.0). We then examined the nekton community from 11 tributaries in watersheds representing the four defined land-use classes. Whereas mean nekton density was independent of land use, species richness and nekton-community structure were significantly different between urban and non-urban (i.e., undeveloped, industrial, man-made) tributaries. In urban creeks, the community was species-poor and dominated by high densities of poeciliid fishes, Poecilia latipinna and Gambusia holbrooki, while typically dominant estuarine taxa including Menidia spp., Fundulus grandis, and Adinia xenica were in low abundance and palaemonid grass shrimp were nearly absent. Densities of economically important taxa in urban creeks were only half that observed in five of the six undeveloped or industrial creeks, but were similar to those observed in mosquito ditches suggesting that habitat quality in urban and mosquito-ditch tributaries is suboptimal compared to undeveloped tidal creeks. Furthermore, five of nine common taxa were rarely collected in urban creeks. Our results suggest that urban development in coastal areas has the potential to alter the quality of habitat for nekton in small tidal tributaries as reflected by variation in the nekton community.

Effect of thiram and of a hydrocarbon mixture on freshwater macroinvertebrate communities in outdoor stream and pond mesocosms: I. Study design, chemicals fate and structural responses.

PubMed

Bayona, Yannick; Roucaute, Marc; Cailleaud, Kevin; Lagadic, Laurent; Bassères, Anne; Caquet, Thierry

2015-11-01

Higher-tier ecological risk assessment (ERA) in mesocosms is commonly performed in lotic or lentic experimental systems. These systems differ in their physico-chemical and hydrological properties, leading to differences in chemical fate, community characteristics and potential recovery. This raises the issue of the relevance and sensitivity of community-level endpoints in different types of mesocosms. In this study, macroinvertebrate abundance and biomass estimates were used to assess the effects of a dithiocarbamate fungicide, thiram (35 and 170 µg l(-1)), and a petroleum middle distillate (PMD; 0.01, 0.4, 2 and 20 mg l(-1)) in outdoor stream and pond mesocosms. Streams were continuously treated during 3 weeks followed by a 2-month long post-treatment period. Ponds were treated weekly for 4 weeks, followed by a 10-month long post-treatment period. Taxonomic structure of macroinvertebrate communities was characterized using the α, β and γ components of taxa richness, Shannon and Gini-Simpson indices. Computations were based either on abundance or biomass data. Results clearly highlighted that the effects of chemicals depended on the exposure regime (for thiram) and type of system (for the PMD). Causes of the differences between streams and ponds in the magnitude and nature of effects include differential sensitivity of taxa dwelling in lentic and lotic systems and the influence of hydrology (e.g., drift from upstream) and mesocosm connectivity on recovery dynamics. This study also showed complementarities in the use of both types of mesocosms to improve the characterization of chemical effects on communities in ERA.

Identifying the Community Structure of the Food-Trade International Multi-Network

NASA Technical Reports Server (NTRS)

Torreggiani, S.; Mangioni, G.

2018-01-01

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of international food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the multi-network's community structure. Here we find that the individual crop-specific layers of the multi-network have densely connected trading groups, a consistent characteristic over the period 2001-2011. Further, the multi-network is characterized by low variability over this period but with substantial heterogeneity across layers in each year. In particular, the layers are mostly assortative: more-intensively connected countries tend to import from and export to countries that are themselves more connected. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors-such as geographical proximity and trade-agreement co-membership-than on country economic size and/or income. These community-structure findings of the multi-network are especially valuable for efforts to understand past and emerging dynamics in the global food system, especially those that examine potential 'shocks' to global food trade.

Identifying the community structure of the food-trade international multi-network

NASA Astrophysics Data System (ADS)

Torreggiani, S.; Mangioni, G.; Puma, M. J.; Fagiolo, G.

2018-05-01

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of international food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the multi-network’s community structure. Here we find that the individual crop-specific layers of the multi-network have densely connected trading groups, a consistent characteristic over the period 2001–2011. Further, the multi-network is characterized by low variability over this period but with substantial heterogeneity across layers in each year. In particular, the layers are mostly assortative: more-intensively connected countries tend to import from and export to countries that are themselves more connected. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors—such as geographical proximity and trade-agreement co-membership—than on country economic size and/or income. These community-structure findings of the multi-network are especially valuable for efforts to understand past and emerging dynamics in the global food system, especially those that examine potential ‘shocks’ to global food trade.

Development of a Fluid Structures Interaction Test Technique for Fabrics

NASA Technical Reports Server (NTRS)

Zilliac, Gregory G.; Heineck, James T.; Schairer, Edward T.; Mosher, Robert N.; Garbeff, Theodore Joseph

2012-01-01

Application of fluid structures interaction (FSI) computational techniques to configurations of interest to the entry, descent and landing (EDL) community is limited by two factors - limited characterization of the material properties for fabrics of interest and insufficient experimental data to validate the FSI codes. Recently ILC Dover Inc. performed standard tests to characterize the static stress-strain response of four candidate fabrics for use in EDL applications. The objective of the tests described here is to address the need for a FSI dataset for CFD validation purposes. To reach this objective, the structural response of fabrics was measured in a very simple aerodynamic environment with well controlled boundary conditions. Two test series were undertaken. The first series covered a range of tunnel conditions and the second focused on conditions that resulted in fabric panel buckling.

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.

Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities.

PubMed

Guo, Qingwei; Wan, Rui; Xie, Shuguang

2014-01-01

The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.

Changes in the structure of bacterial complexes of vegetable crops in the course of their growth on a cultivated soddy-podzolic soil

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Khusnetdinova, K. A.

2017-11-01

The dynamics of population density and taxonomic structure of epiphytic bacterial communities on the leaves and roots of potatoes, carrots, and beets have been studied. Significant changes take place in the ontogenesis of these vegetables with substitution of hydrolytic bacteria for eccrisotrophic bacteria feeding on products of plant exosmosis. The frequency of domination of representatives of different taxa of epiphytic bacteria on the studied plants has been determined for the entire period of their growth. Bacteria of different genera have been isolated from the aboveground and underground organs of vegetables; their functions are discussed. It is shown that the taxonomic structure of bacterial communities in the soil under studied plants is not subjected to considerable changes and is characterized by the domination of typical soil bacteria— Arthrobacter and bacilli—with the appearance of Rhodococcus as a codominant at the end of the season (before harvesting).

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics

DOE PAGES

Finstad, Kari M.; Probst, Alexander J.; Thomas, Brian C.; ...

2017-07-28

Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at themore » highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N 2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.« less

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics

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

Finstad, Kari M.; Probst, Alexander J.; Thomas, Brian C.

Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at themore » highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N 2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.« less

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco).

PubMed

Bruneel, Odile; Mghazli, N; Hakkou, R; Dahmani, I; Filali Maltouf, A; Sbabou, L

2017-07-01

In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics.

PubMed

Finstad, Kari M; Probst, Alexander J; Thomas, Brian C; Andersen, Gary L; Demergasso, Cecilia; Echeverría, Alex; Amundson, Ronald G; Banfield, Jillian F

2017-01-01

Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N 2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics.

PubMed

Niederdorfer, Robert; Peter, Hannes; Battin, Tom J

2016-10-03

Small-scale hydraulics affects microbial behaviour at the cell level 1 , trophic interactions in marine aggregates 2 and the physical structure and function of stream biofilms 3,4 . However, it remains unclear how hydraulics, predictably changing from small streams to large rivers, impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we present experimental evidence unveiling hydraulics as a hitherto poorly recognized control of microbial lifestyle differentiation in fluvial ecosystems. Exposing planktonic source communities from stream and floodplain ecosystems to different hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Only a few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous resident taxa characterized aggregate communities. Our findings unveil fundamental differences between biofilms and aggregates and build the basis for a mechanistic understanding of how hydraulics drives the distribution of microbial diversity along the fluvial continuum 5-7 .

Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China.

PubMed

Hu, Weigang; Zhang, Qi; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2014-12-01

While a vast number of studies have addressed the prokaryotic diversity in permafrost, characterized by subzero temperatures, low water activity, and extremely low rates of nutrient and metabolite transfer, fungal patterns have received surprisingly limited attention. Here, the fungal diversity and community structure were investigated by culture-dependent technique combined with cloning-restriction fragment length polymorphism (RFLP) analysis of sediments in a 10-m-long permafrost core from the Qinghai-Tibet Plateau of China. A total of 62 fungal phylotypes related to 10 distinct classes representing three phyla were recovered from 5031 clones generated in 13 environmental gene libraries. A large proportion of the phylotypes (25/62) that were distantly related to described fungal species appeared to be novel diversity. Ascomycota was the predominant group of fungi, with respect to both clone and phylotype number. Our results suggested there was the existence of cosmopolitan psychrophilic or psychrotolerant fungi in permafrost sediments, the community composition of fungi varied with increasing depth, while these communities largely distributed according to core layers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benthic megafaunal community structure of cobalt-rich manganese crusts on Necker Ridge

NASA Astrophysics Data System (ADS)

Morgan, Nicole B.; Cairns, Stephen; Reiswig, Henry; Baco, Amy R.

2015-10-01

In the North Pacific Ocean, the seamounts of the Hawaiian Archipelago and the Mid-Pacific Mountains are connected by Necker Ridge, a 600 km-long feature spanning a depth range of 1400-4000 m. The Necker Ridge is a part of a large area of the central and western Pacific under consideration for cobalt-rich manganese crust mining. We describe the fauna and community structure of the previously unsampled Necker Ridge based on explorations with the submersible Pisces IV. On five pinnacles and a portion of the Ridge ranging from 1400 to 2000 m deep, 27 transects were recorded using HD video, and voucher specimens were collected to aid in species identification. The video was analyzed to identify and count the megafauna found on each transect and to characterize the substrate. Diversity increased from south to north along the feature. There was a significant difference in community structure between southern and northern pinnacles, with southern pinnacles dominated by crinoids of the Family Charitometridae and northern pinnacles dominated by octocorals, especially the Families Isididae and Chrysogorgiidae. DistLM demonstrated a correlation between community structure on the pinnacles and at least six environmental variables, including latitude, sediment cover, and oxygen concentration, but not including depth. The discontinuous and patchy nature of these distinct megafaunal communities highlights growing evidence that cobalt-rich seamounts are highly heterogeneous habitats, and that managing seamounts may require more complex regulations than treating them as a single ecological unit. These results suggest that extensive community analysis should occur at a given site to determine management priority areas, prior to consideration of that site for exploitation of natural resources.

Diversity and community structure of Archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog.

PubMed

Cadillo-Quiroz, Hinsby; Yavitt, Joseph B; Zinder, Stephen H; Thies, Janice E

2010-05-01

Plant root exudates increase nutrient availability and influence microbial communities including archaeal members. We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the rhizoplane, MS was dominant on both plants although as a less variable fraction in S. purpurea. RC-I was significantly more abundant than E2 on S. purpurea, while the opposite was observed on D. arundinaceum, suggesting a plant-specific enrichment. Also, the statistical analyses of T-RFLP data showed that although both plants overlap in their community structure, factors such as plant type, patch location, and time could explain nearly a third of the variability in the dataset. Other factors such as water table, plant replicate, and root depth had a low contribution to the observed variance. The results of this study illustrate the general effects of roots and the specific effects of plant types on their nearby archaeal communities which in bog-inhabiting plants were mainly composed by methanogenic groups.

Enabling Community Through Social Media

PubMed Central

Haythornthwaite, Caroline

2013-01-01

Background Social network analysis provides a perspective and method for inquiring into the structures that comprise online groups and communities. Traces from interaction via social media provide the opportunity for understanding how a community is formed and maintained online. Objective The paper aims to demonstrate how social network analysis provides a vocabulary and set of techniques for examining interaction patterns via social media. Using the case of the #hcsmca online discussion forum, this paper highlights what has been and can be gained by approaching online community from a social network perspective, as well as providing an inside look at the structure of the #hcsmca community. Methods Social network analysis was used to examine structures in a 1-month sample of Twitter messages with the hashtag #hcsmca (3871 tweets, 486 unique posters), which is the tag associated with the social media–supported group Health Care Social Media Canada. Network connections were considered present if the individual was mentioned, replied to, or had a post retweeted. Results Network analyses revealed patterns of interaction that characterized the community as comprising one component, with a set of core participants prominent in the network due to their connections with others. Analysis showed the social media health content providers were the most influential group based on in-degree centrality. However, there was no preferential attachment among people in the same professional group, indicating that the formation of connections among community members was not constrained by professional status. Conclusions Network analysis and visualizations provide techniques and a vocabulary for understanding online interaction, as well as insights that can help in understanding what, and who, comprises and sustains a network, and whether community emerges from a network of online interactions. PMID:24176835

Ecospaces occupied by Homo erectus and Homo sapiens in insular Southeast Asia in the Pleistocene

NASA Astrophysics Data System (ADS)

Hertler, Christine; Haupt, Susanne; Volmer, Rebekka; Bruch, Angela

2014-05-01

Hominins migrated to the islands of the Sunda Shelf multiple times. At least two immigration events are evident, an early immigration of Homo erectus in the late Early Pleistocene and a second immigration of Homo sapiens during the Late Pleistocene. Regional environments changed considerably in the Pleistocene. Expansion patterns among hominins are at least co-determined by their ecologies and environmental change. We examine these expansion patterns on the basis of habitat reconstructions. Mammalian communities provide a geographically extensive record and permit to assess hominin ecospaces. Although chronological resolution is low, they represent the most complete record of habitat changes associated with hominin expansion patterns. In order to reconstruct and compare hominin ecospaces on a quantitative scale, we set up a reference sample consisting of mammalian communities of 117 national parks in South Asia and Sub-Saharan Africa. The diversity of such communities is assessed by ecological profiling of specialized herbivore taxa. Moreover, datasets on climate and vegetation correlate with the diversity structure of such specialized herbivore communities. Reconstructing the diversity structure of communities at key sites in Pleistocene Southeast Asia permits to infer features of the climatic and vegetation framework associated with different hominin taxa. Our results show that Homo erectus and Homo sapiens did not occupy similar ecospaces. The ecospace of Homo erectus is characterized by comparatively low diversity among frugivorous and folivorous taxa, while obligate grazers are part of the assemblages. Specialized herbivore communities with such a diversity structure occur at present in East Africa, while they are absent in Southeast Asia. In the reference sample, this type of ecospace corresponds to seasonal wetlands. Although Homo sapiens still inhabits this type of environment in Southeast Asia, his ecospace is wider. Homo sapiens is associated with specialized herbivore communities dominated by frugivorous and folivorous taxa. Specialized herbivore communities with such a diversity structure occur at present in rainforests on the Sunda Shelf.

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

PubMed Central

Dias, Armando Cavalcante Franco; Taketani, Rodrigo Gouveia; Andreote, Fernando Dini; Luvizotto, Danice Mazzer; da Silva, João Luis; Nascimento, Rosely dos Santos; de Melo, Itamar Soares

2012-01-01

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 104 in A. schaeriana and 6.26 x 103 in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere. PMID:24031877

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

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

Mobberley, Jennifer M.; Lindemann, Stephen R.; Bernstein, Hans C.

2017-03-21

Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements. Draft reconstructed genomes of abundantmore » organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence upon metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.« less

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests.

PubMed

Dias, Armando Cavalcante Franco; Taketani, Rodrigo Gouveia; Andreote, Fernando Dini; Luvizotto, Danice Mazzer; da Silva, João Luis; Nascimento, Rosely Dos Santos; de Melo, Itamar Soares

2012-04-01

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10(3) in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

Biotransformation of nitrogen- and sulfur-containing pollutants during coking wastewater treatment: Correspondence of performance to microbial community functional structure.

PubMed

Joshi, Dev Raj; Zhang, Yu; Gao, Yinxin; Liu, Yuan; Yang, Min

2017-09-15

Although coking wastewater is generally considered to contain high concentration of nitrogen- and sulfur-containing pollutants, the biotransformation processes of these compounds have not been well understood. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina MiSeq sequencing of the 16S rRNA gene were used to identify microbial functional traits and their role in biotransformation of nitrogen- and sulfur-containing compounds in a bench-scale aerobic coking wastewater treatment system operated for 488 days. Biotransformation of nitrogen and sulfur-containing pollutants deteriorated when pH of the bioreactor was increased to >8.0, and the microbial community functional structure was significantly associated with pH (Mantels test, P < 0.05). The release of ammonia nitrogen and sulfate was correlated with both the taxonomic and functional microbial community structure (P < 0.05). Considering the abundance and correlation with the release of ammonia nitrogen and sulfate, aromatic dioxygenases (e.g. xylXY, nagG), nitrilases (e.g. nhh, nitrilase), dibenzothiophene oxidase (DbtAc), and thiocyanate hydrolase (scnABC) were important functional genes for biotransformation of nitrogen- and sulfur-containing pollutants. Functional characterization of taxa and network analysis suggested that Burkholderiales, Actinomycetales, Rhizobiales, Pseudomonadales, and Hydrogenophiliales (Thiobacillus) were key functional taxa. Variance partitioning analysis showed that pH and influent ammonia nitrogen jointly explained 25.9% and 35.5% of variation in organic pollutant degrading genes and microbial community structure, respectively. This study revealed a linkage between microbial community functional structure and the likely biotransformation of nitrogen- and sulfur-containing pollutants, along with a suitable range of pH (7.0-7.5) for stability of the biological system treating coking wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome

PubMed Central

Fourie, Nicolaas H.; Wang, Dan; Abey, Sarah K.; Creekmore, Amy L.; Hong, Shuangsong; Martin, Christiana G.; Wiley, John W.

2017-01-01

ABSTRACT Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data. Microbial communities and functional profiles were compared between conditions. WA animals exhibited higher α-diversity and moderate divergence in community structure (β-diversity) compared with controls. Specific clades and taxa were consistently and significantly modified in the WA animals. The WA microbiome was particularly enriched in Proteobacteria and depleted in several beneficial taxa. A decreased capacity in metabolic domains, including energy- and lipid-metabolism, and an increased capacity for fatty acid and sulfur metabolism was inferred for the WA microbiome. The stressed condition favored the proliferation of a greater diversity of microbes that appear to be functionally similar, resulting in a functionally poorer microbiome with implications for epithelial health. Taxa, with known beneficial effects, were found to be depleted, which supports their relevance as therapeutic agents to restore microbial health. Microbial sulfur metabolism may form a key component of visceral nerve sensitization pathways and is therefore of interest as a target metabolic domain in microbial ecological restoration. PMID:28059627

Seasonal variations in the diversity and abundance of diazotrophic communities across soils.

PubMed

Pereira e Silva, Michele C; Semenov, Alexander V; van Elsas, Jan Dirk; Salles, Joana Falcão

2011-07-01

The nitrogen (N)-fixing community is a key functional community in soil, as it replenishes the pool of biologically available N that is lost to the atmosphere via anaerobic ammonium oxidation and denitrification. We characterized the structure and dynamic changes in diazotrophic communities, based on the nifH gene, across eight different representative Dutch soils during one complete growing season, to evaluate the amplitude of the natural variation in abundance and diversity, and identify possible relationships with abiotic factors. Overall, our results indicate that soil type is the main factor influencing the N-fixing communities, which were more abundant and diverse in the clay soils (n=4) than in the sandy soils (n=4). On average, the amplitude of variation in community size as well as the range-weighted richness were also found to be higher in the clay soils. These results indicate that N-fixing communities associated with sandy and clay soil show a distinct amplitude of variation under field conditions, and suggest that the diazotrophic communities associated with clay soil might be more sensitive to fluctuations associated with the season and agricultural practices. Moreover, soil characteristics such as ammonium content, pH and texture most strongly correlated with the variations observed in the diversity, size and structure of N-fixing communities, whose relative importance was determined across a temporal and spatial scale. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

NASA Astrophysics Data System (ADS)

Kojima, Hisaya; Tokizawa, Riho; Kogure, Kouhei; Kobayashi, Yuki; Itoh, Masayuki; Shiah, Fuh-Kwo; Okuda, Noboru; Fukui, Manabu

2014-07-01

Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer `Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of `M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition-fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

[Characterization of microbial community in produced water from a petroleum reservoir subjected to alkali-surfactant-polymer ASP flooding].

PubMed

Hao, Qin Qin; Shi, Rong Jiu; Hao, Jin Sheng; Zhao, Jin Yi; Li, Guo Qiao; Zhao, Feng; Han, Si Qin; Zhang, Ying

2017-10-01

Injection of alkali, surfactant and polymer (ASP) into oil reservoir can substantially increase oil recovery compared with water-flooding strategy. However, the effects of these agents on the microbial diversity and community structure, which is important for water management and corrosion control in oil industry, are hitherto poorly understood. Here, we disclosed the microbial diversity and community structure in the produced water collected from four producing wells of an ASP-flooded oilfield at Daqing, China, using high-throughput sequencing technique. Results showed that the average pH in produced water was as high as 9.65. The microbial diversity varied from well to well, and the Shannon diversity index was between 2.00 to 3.56. The Proteobacteria (85.5%-98.3%), γ-proteobacteria (83.7%-97.8%), and alkaliphilic Nitrincola (51.8%-82.5%) were the most dominant phylogenetic taxa at the phylum, class, and genus levels, respectively. A total of 12 potentially sulfide-producing genera were detected, and the most abundant taxon was Sulfurospirillum (0.4%-7.4%). The microbial community of ASP-flooded petroleum reservoir was distinct, showing an alkaliphilic or alkalitolerant potential; a reduced diversity and more simple structure were observed compared with those of the water-flooded petroleum reservoirs that were previously reported.

Spotting the differences in two-dimensional materials - the Raman scattering perspective.

PubMed

Zhang, Shishu; Zhang, Na; Zhao, Yan; Cheng, Ting; Li, Xiaobo; Feng, Rui; Xu, Hua; Liu, Zhirong; Zhang, Jin; Tong, Lianming

2018-05-08

Two-dimensional (2D) layered materials have attracted tremendous attention and led to a prosperous development in both fundamental investigation and device applications in various fields, such as nanoelectronics, flexible devices, sustainable energy and catalysts. The precise characterization of the structure and properties of 2D materials is in urgent need. Raman scattering spectroscopy is one of the most popular characterization tools that is convenient, rapid and non-invasive. It provides information on both the lattice structure from the frequency of phonon modes and the electronic band structure through the intensity due to electronic resonance Raman scattering. Although a few morphological characterization tools can image 2D materials with atomic resolution, Raman scattering measurements are more tolerant to the conditions of sample preparation such as the substrate and less technically demanding, and have been one of the routine tools for the characterization of 2D materials. In this review, we focus on the characterization of 2D materials using Raman scattering spectroscopy, in particular, the revealing of differences from primitive 2D materials, such as defects, doping effects, van der Waals heterostructures and the interaction with molecules. The characteristic Raman features of such differences and the corresponding interpretation will be discussed. We hope that this review will be useful for wide research communities of materials, physics, chemistry and engineering.

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

PubMed Central

Pepe-Ranney, Charles; Hall, Edward K.

2015-01-01

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm vs. planktonic) has a stronger influence on community composition. PMID:26236289

Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

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

Yang, Ziming; Yang, Sihang; Van Nostrand, Joy D.

Microbial decomposition of soil organic carbon (SOC) in the thawing Arctic permafrost is one of the most important, but poorly understood, processes in determining the greenhouse gases feedback of tundra ecosystems to climate. Here in this paper, we examine changes in microbial community structure during an anoxic incubation at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC chemistry, and GeoChips were used to determine microbial community structure and functional genes associated with C degradation andmore » Fe(III) reduction. We observed notable decreases in functional gene diversity (at P < 0.05) in response to warming at 8 °C, particularly in the organic soil. A number of genes associated with SOC degradation, fermentation, methanogenesis, and iron cycling decreased significantly (P < 0.05) after 122 days of incubation, which coincided well with decreasing labile SOC content, soil respiration, methane production, and iron reduction. The soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant environmental factors impacting the functional community structure. In contrast, the functional structure was largely unchanged in the –2 °C incubation due to low microbial activity resulting in less competition or exclusion. These results demonstrate the vulnerability of SOC in Arctic tundra to warming, facilitated by iron reduction and methanogenesis, and the importance of microbial communities in moderating such vulnerability.« less

Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

DOE PAGES

Yang, Ziming; Yang, Sihang; Van Nostrand, Joy D.; ...

2017-09-19

Microbial decomposition of soil organic carbon (SOC) in the thawing Arctic permafrost is one of the most important, but poorly understood, processes in determining the greenhouse gases feedback of tundra ecosystems to climate. Here in this paper, we examine changes in microbial community structure during an anoxic incubation at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC chemistry, and GeoChips were used to determine microbial community structure and functional genes associated with C degradation andmore » Fe(III) reduction. We observed notable decreases in functional gene diversity (at P < 0.05) in response to warming at 8 °C, particularly in the organic soil. A number of genes associated with SOC degradation, fermentation, methanogenesis, and iron cycling decreased significantly (P < 0.05) after 122 days of incubation, which coincided well with decreasing labile SOC content, soil respiration, methane production, and iron reduction. The soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant environmental factors impacting the functional community structure. In contrast, the functional structure was largely unchanged in the –2 °C incubation due to low microbial activity resulting in less competition or exclusion. These results demonstrate the vulnerability of SOC in Arctic tundra to warming, facilitated by iron reduction and methanogenesis, and the importance of microbial communities in moderating such vulnerability.« less

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment. PMID:27060115

Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR

PubMed Central

Jin, Tao; Yan, Qingmei

2010-01-01

Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 103 to 2.3 × 105 copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 102 to 3.8 × 103 copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen. PMID:20405121

Identifying functional groups for response to disturbance in an abandoned pasture

NASA Astrophysics Data System (ADS)

Lavorel, Sandra; Touzard, Blaise; Lebreton, Jean-Dominique; Clément, Bernard

1998-06-01

In an abandoned pasture in Brittany, we compared artificial small-scale disturbances to natural disturbances by wild boar and undisturbed vegetation. We developed a multivariate statistical approach which analyses how species biological attributes explain the response of community composition to disturbances. This technique, which reconciles the inductive and deductive approaches for functional classifications, identifies groups of species with similar responses to disturbance and characterizes their biological profiles. After 5 months of recolonization, artificial disturbances had a greater species richness than undisturbed vegetation as a result of recruitment of new species without the exclusion of pre-existing matrix species. Species morphology, described by canopy structure, canopy height and lateral spread, explained a large part (16 %) of community response to disturbance. Regeneration strategies, described by life history, seed mass, dispersal agent, dormancy and the existence of vegetative multiplication, explained a smaller part of community response to disturbance (8 %). Artificial disturbances were characterized by therophyte and compact rosettes with moderately dormant seeds, including a number of Asteraceae and other early successional species. Natural disturbances were colonized by leafy guerrilla species without seed dormancy. Few species were tightly related to undisturbed vegetation and were essentially grasses with a phalanx rosette morphology. The functional classification obtained is consistent with the classification of the community into fugitives, regenerators and persistors. These groups are structured according to Grubb's model for temperate grasslands, with regenerators and persistors in the matrix and fugitives taking advantage of gaps open by small-scale disturbances. The conjunction of functional diversity and species diversity within functional groups is the key to resilience to disturbance, an important ecosystem function.

Physical Habitat and Energy Inputs Determine Freshwater Invertebrate Communities in Reference and Cranberry Farm Impacted Northeastern Coastal Zone Streams

NASA Astrophysics Data System (ADS)

Lander, D. M. P.; McCanty, S. T.; Dimino, T. F.; Christian, A. D.

2016-02-01

The River Continuum Concept (RCC) predicts stream biological communities based on dominant physical structures and energy inputs into streams and predicts how these features and corresponding communities change along the stream continuum. Verifying RCC expectations is important for creating valid points of comparison during stream ecosystem evaluation. These reference expectations are critical for restoration projects, such as the restoration of decommissioned cranberry bogs. Our research compares the physical habitat and freshwater invertebrate functional feeding groups (FWIFFG) of reference, active cranberry farming, and cranberry farm passive restoration sites in Northeastern Coastal Zone streams of Massachusetts to the specific RCC FWIFFG predictions. We characterized stream physical habitat using a semi-quantitative habitat characterization protocol and sampled freshwater invertebrates using the U.S. EPA standard 20-jab multi-habitat protocol. We expected that stream habitat would be most homogeneous at active farming stations, intermediate at restoration stations, and most heterogeneous at reference stations. Furthermore, we expected reference stream FWIFFG would be accurately predicted by the RCC and distributions at restoration and active sites would vary significantly. Habitat data was analyzed using a principle component analysis and results confirmed our predictions showing more homogeneous habitat for the active and reference stations, while showing a more heterogeneous habitat at the reference stations. The FWIFFG chi-squared analysis showed significant deviation from our specific RCC FWIFFG predictions. Because published FWIFFG distributions did not match our empirical values for a least disturbed Northeastern Coastal Zone headwater stream, using our data as a community structure template for current and future restoration projects is not recommend without further considerations.

Biological support media influence the bacterial biofouling community in reverse osmosis water reclamation demonstration plants.

PubMed

Ferrera, Isabel; Mas, Jordi; Taberna, Elisenda; Sanz, Joan; Sánchez, Olga

2015-01-01

The diversity of the bacterial community developed in different stages of two reverse osmosis (RO) water reclamation demonstration plants designed in a wastewater treatment plant (WWTP) in Tarragona (Spain) was characterized by applying 454-pyrosequencing of the 16S rRNA gene. The plants were fed by secondary treated effluent to a conventional pretreatment train prior to the two-pass RO system. Plants differed in the material used in the filtration process, which was sand in one demonstration plant and Scandinavian schists in the second plant. The results showed the presence of a highly diverse and complex community in the biofilms, mainly composed of members of the Betaproteobacteria and Bacteroidetes in all stages, with the presence of some typical wastewater bacteria, suggesting a feed water origin. Community similarities analyses revealed that samples clustered according to filter type, highlighting the critical influence of the biological supporting medium in biofilm community structure.

Fine-scale spatial patterns in the demersal fish and invertebrate community in a northwest Atlantic ecosystem

NASA Astrophysics Data System (ADS)

Malek, Anna J.; Collie, Jeremy S.; Gartland, James

2014-06-01

The abundance, biomass, diversity, and species composition of the demersal fish and invertebrate community in Rhode Island Sound and Block Island Sound, an area identified for offshore renewable energy development, were evaluated for spatial and seasonal structure. We conducted 58 otter trawls and 51 beam trawls in the spring, summer and fall of 2009-2012, and incorporated additional data from 88 otter trawls conducted by the Northeast Area Monitoring and Assessment Program. We used regionally-grouped abundance, biomass, diversity, and size spectra to assess spatial patterns in the aggregate fish community, and hierarchical cluster analysis to evaluate trends in species assemblages. Our analyses revealed coherent gradients in fish community biomass, diversity and species composition extending from inshore to offshore waters, as well as patterns related to the differing bathymetry of Rhode Island and Block Island Sounds. The fish communities around Block Island and Cox's Ledge are particularly diverse, suggesting that the proximity of hard bottom habitat may be important in structuring fish communities in this area. Species assemblages in Rhode Island and Block Island Sounds are characterized by a combination of piscivores (silver hake, summer flounder, spiny dogfish), benthivores (American lobster, black sea bass, Leucoraja spp. skates, scup) and planktivores (sea scallop), and exhibit geographic patterns that are persistent from year to year, yet variable by season. Such distributions reflect the cross-shelf migration of fish and invertebrate species in the spring and fall, highlighting the importance of considering seasonal fish behavior when planning construction schedules for offshore development projects. The fine spatial scale (10 s of kms) of this research makes it especially valuable for local marine spatial planning efforts by identifying local-scale patterns in fish community structure that will enable future assessment of the ecological impacts of offshore development. As such, this knowledge of the spatial and temporal structure of the demersal fish community in Rhode Island and Block Island Sounds will help to guide the placement of offshore structures so as to preserve the ecological and economic value of the area.

National Forest Health Monitoring Program Maryland and Massachusetts Street Tree Monitoring Pilot Projects

Treesearch

Buckelew Cumming Anne; Daniel Twardus; William Smith

2006-01-01

Urban forests have many components: park trees, small woodlands, riparian buffers, street trees, and others. While some communities conduct city-wide inventories of street tree populations, there has been no comprehensive, statewide sampling to characterize the structure, health, and function of street tree populations. A statewide Street Tree Monitoring pilot study...

Patch based predation in a southern Appalachian stream

Treesearch

C.A. Gibson; R.E. Ratajezak; G.D. Grossman

2004-01-01

Streams are characterized by high degrees of patchiness that could influence the role of predators in these systems. Here we assess the impact of predatory benthic fishes on benthic macroinvertebrate density, biomass, and community structure at the patch scale in a fourth order stream in the southern Appalachians. We tested the role of predation in two different patch...

Changes in the Pincate Reserve ecosystems: Invasion of non-native plants

Treesearch

Denise Z. Avila-Jimenez

2005-01-01

Over the years, humans have modified the Sonoran Desert by introducing invasive plants that prosper in disturbed and non-disturbed habitats. These invaders modify the dynamics and structure of populations and the composition of communities, which in turn can result in radical changes in wildlife habitat. The natural landscape of the Sonoran Desert is characterized by...

Twenty-five years of vegetation change along a putative successional chronosequence on the Tanana River, Alaska

Treesearch

Teresa N. Hollingsworth; Andrea H. Lloyd; Dana R. Nossov; Roger W. Ruess; Brian A. Charlton; Knut Kielland

2010-01-01

Along the Tanana River floodplain, several turning points have been suggested to characterize the changes in ecosystem structure and function that accompany plant community changes through primary succession. In the past, much of tills research focused on a presumed chronosequence that uses space for time substitutions. Within this chronosequence, permanent vegetation...

Lift Every Voice and Sing: Constructing Community through Culturally Relevant Pedagogy in the University of Illinois Black Chorus

ERIC Educational Resources Information Center

Chadwick, Sheelagh

2011-01-01

For Gloria Ladson-Billings, culturally relevant pedagogy is characterized by three criteria: academic success, cultural competence and critical consciousness. Those engaged in culturally relevant pedagogy are connected by how they see themselves as teachers and how they see their students, how they view knowledge and how they structure social…

Characterization of the microbial community structure in Candidatus Liberibacter asiaticus-infected citrus plants treated with antibiotics in the field

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) is one of the most devastating diseases of citrus worldwide. There are no effective control measures for this newly emerging and century-old disease. Previously, we reported a combination of Penicillin G and Streptomycin were effective in eliminating or suppressing the HLB bacter...

Design and characterization of a 20 Gbit/s clock recovery circuit

NASA Astrophysics Data System (ADS)

Monteiro, Paulo M.; Matos, J. N.; Gameiro, Atilio M. S.; da Rocha, Jose F.

1995-02-01

In this communication we report the design of a clock recovery circuit produced for the 20 Gbit/s demonstrator of the RACE 2011 project `TRAVEL' of the European Community. The clock recovery circuit is based on an open loop structure using a dielectric resonator narrow bandpass filter with a high quality factor. A detailed electrical characterization of the circuit and also its sensitivity to temperature and detuning variations are presented. The experimental results show that the circuit is a very attractive solution for the forthcoming STM-128 optical links.

Homophyly/kinship hypothesis: Natural communities, and predicting in networks

NASA Astrophysics Data System (ADS)

Li, Angsheng; Li, Jiankou; Pan, Yicheng

2015-02-01

It has been a longstanding challenge to understand natural communities in real world networks. We proposed a community finding algorithm based on fitness of networks, two algorithms for prediction, accurate prediction and confirmation of keywords for papers in the citation network Arxiv HEP-TH (high energy physics theory), and the measures of internal centrality, external de-centrality, internal and external slopes to characterize the structures of communities. We implemented our algorithms on 2 citation and 5 cooperation graphs. Our experiments explored and validated a homophyly/kinship principle of real world networks. The homophyly/kinship principle includes: (1) homophyly is the natural selection in real world networks, similar to Darwin's kinship selection in nature, (2) real world networks consist of natural communities generated by the natural selection of homophyly, (3) most individuals in a natural community share a short list of common attributes, (4) natural communities have an internal centrality (or internal heterogeneity) that a natural community has a few nodes dominating most of the individuals in the community, (5) natural communities have an external de-centrality (or external homogeneity) that external links of a natural community homogeneously distributed in different communities, and (6) natural communities of a given network have typical structures determined by the internal slopes, and have typical patterns of outgoing links determined by external slopes, etc. Our homophyly/kinship principle perfectly matches Darwin's observation that animals from ants to people form social groups in which most individuals work for the common good, and that kinship could encourage altruistic behavior. Our homophyly/kinship principle is the network version of Darwinian theory, and builds a bridge between Darwinian evolution and network science.

Community variations in population exposure to near-field tsunami hazards as a function of pedestrian travel time to safety

USGS Publications Warehouse

Wood, Nathan J.; Schmidtlein, Mathew C.

2013-01-01

Efforts to characterize population exposure to near-field tsunami threats typically focus on quantifying the number and type of people in tsunami-hazard zones. To develop and prioritize effective risk-reduction strategies, emergency managers also need information on the potential for successful evacuations and how this evacuation potential varies among communities. To improve efforts to properly characterize and differentiate near-field tsunami threats among multiple communities, we assess community variations in population exposure to tsunamis as a function of pedestrian travel time to safety. We focus our efforts on the multiple coastal communities in Grays Harbor and Pacific Counties (State of Washington, USA), where a substantial resident and visitor population is threatened by near-field tsunamis related to a potential Cascadia subduction zone earthquake. Anisotropic, path-distance modeling is conducted to estimate travel times to safety and results are merged with various population data, including residents, employees, public venues, and dependent-care facilities. Results suggest that there is substantial variability among communities in the number of people that may have insufficient time to evacuate. Successful evacuations may be possible in some communities assuming slow-walking speeds, are plausible in others if travel speeds are increased, and are unlikely in another set of communities given the large distances and short time horizon. Emergency managers can use these results to prioritize the location and determine the most appropriate type of tsunami risk-reduction strategies, such as education and training in areas where evacuations are plausible and vertical-evacuation structures in areas where they are not.

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities.

PubMed

Frelat, Romain; Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs.

EDITORIAL: (Nano)characterization of semiconductor materials and structures (Nano)characterization of semiconductor materials and structures

NASA Astrophysics Data System (ADS)

Bonanni, Alberta

2011-06-01

The latest impressive advancements in the epitaxial fabrication of semiconductors and in the refinement of characterization techniques have the potential to allow insight into the deep relation between materials' structural properties and their physical and chemical functionalities. Furthermore, while the comprehensive (nano)characterization of semiconductor materials and structures is becoming more and more necessary, a compendium of the currently available techniques is lacking. We are positive that an overview of the hurdles related to the specific methods, often leading to deceptive interpretations, will be most informative for the broad community working on semiconductors, and will help in shining some light onto a plethora of controversial reports found in the literature. From this perspective, with this special issue we address and highlight the challenges and misinterpretations related to complementary local (nanoscale) and more global experimental methods for the characterization of semiconductors. The six topical reviews and the three invited papers by leading experts in the specific fields collected in here are intended to provide the required broad overview on the possibilities of actual (nano)characterization methods, from the microscopy of single quantum structures, over the synchrotron-based absorption and diffraction of nano-objects, to the contentious detection of tiny magnetic signals by quantum interference and resonance techniques. We are grateful to all the authors for their valuable contributions. Moreover, I would like to thank the Editorial Board of the journal for supporting the realization of this special issue and for inviting me to serve as Guest Editor. We greatly appreciate the work of the reviewers, of the editorial staff of Semiconductor Science and Technology and of IOP Publishing. In particular, the efforts of Alice Malhador in coordinating this special issue are acknowledged.

Feasibility and coexistence of large ecological communities.

PubMed

Grilli, Jacopo; Adorisio, Matteo; Suweis, Samir; Barabás, György; Banavar, Jayanth R; Allesina, Stefano; Maritan, Amos

2017-02-24

The role of species interactions in controlling the interplay between the stability of ecosystems and their biodiversity is still not well understood. The ability of ecological communities to recover after small perturbations of the species abundances (local asymptotic stability) has been well studied, whereas the likelihood of a community to persist when the conditions change (structural stability) has received much less attention. Our goal is to understand the effects of diversity, interaction strengths and ecological network structure on the volume of parameter space leading to feasible equilibria. We develop a geometrical framework to study the range of conditions necessary for feasible coexistence. We show that feasibility is determined by few quantities describing the interactions, yielding a nontrivial complexity-feasibility relationship. Analysing more than 100 empirical networks, we show that the range of coexistence conditions in mutualistic systems can be analytically predicted. Finally, we characterize the geometric shape of the feasibility domain, thereby identifying the direction of perturbations that are more likely to cause extinctions.

Feasibility and coexistence of large ecological communities

PubMed Central

Grilli, Jacopo; Adorisio, Matteo; Suweis, Samir; Barabás, György; Banavar, Jayanth R.; Allesina, Stefano; Maritan, Amos

2017-01-01

The role of species interactions in controlling the interplay between the stability of ecosystems and their biodiversity is still not well understood. The ability of ecological communities to recover after small perturbations of the species abundances (local asymptotic stability) has been well studied, whereas the likelihood of a community to persist when the conditions change (structural stability) has received much less attention. Our goal is to understand the effects of diversity, interaction strengths and ecological network structure on the volume of parameter space leading to feasible equilibria. We develop a geometrical framework to study the range of conditions necessary for feasible coexistence. We show that feasibility is determined by few quantities describing the interactions, yielding a nontrivial complexity–feasibility relationship. Analysing more than 100 empirical networks, we show that the range of coexistence conditions in mutualistic systems can be analytically predicted. Finally, we characterize the geometric shape of the feasibility domain, thereby identifying the direction of perturbations that are more likely to cause extinctions. PMID:28233768

Modeling Global Spatial-Temporal Evolution of Society: Hyperbolic Growth and Historical Cycles

NASA Astrophysics Data System (ADS)

Kurkina, E. S.

2011-09-01

The global historical processes are under consideration; and laws of global evolution of the world community are studied. The world community is considered as a united complex self-developing and self-organizing system. It supposed that the main driving force of social-economical evolution was the positive feedback between the population size and the level of technological development, which was a cause of growth in blow-up regime both of population and of global economic indexes. The study is supported by the results of mathematical modeling founded on a nonlinear heat equation with a source. Every social-economical epoch characterizes by own specific spatial distributed structures. So the global dynamics of world community during the whole history is investigated throughout the prism of the developing of spatial-temporal structures. The model parameters have been chosen so that 1) total population follows stable hyperbolic growth, consistently with the demographic data; 2) the evolution of the World-System goes through 11 stages corresponding to the main historical epochs.

Climate-driven regime shifts in Arctic marine benthos

PubMed Central

Kortsch, Susanne; Primicerio, Raul; Beuchel, Frank; Renaud, Paul E.; Rodrigues, João; Lønne, Ole Jørgen; Gulliksen, Bjørn

2012-01-01

Climate warming can trigger abrupt ecosystem changes in the Arctic. Despite the considerable interest in characterizing and understanding the ecological impact of rapid climate warming in the Arctic, few long time series exist that allow addressing these research goals. During a 30-y period (1980–2010) of gradually increasing seawater temperature and decreasing sea ice cover in Svalbard, we document rapid and extensive structural changes in the rocky-bottom communities of two Arctic fjords. The most striking component of the benthic reorganization was an abrupt fivefold increase in macroalgal cover in 1995 in Kongsfjord and an eightfold increase in 2000 in Smeerenburgfjord. Simultaneous changes in the abundance of benthic invertebrates suggest that the macroalgae played a key structuring role in these communities. The abrupt, substantial, and persistent nature of the changes observed is indicative of a climate-driven ecological regime shift. The ecological processes thought to drive the observed regime shifts are likely to promote the borealization of these Arctic marine communities in the coming years. PMID:22891319

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar

PubMed Central

Ji, Jun; Wu, Haiying; Meng, Fang; Zhang, Mingrong; Zheng, Xiaobo; Wu, Cunxiang; Zhang, Zhengguang

2014-01-01

Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91) that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample) were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars. PMID:25079947

Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics.

PubMed

Rodriguez-Caballero, A; Ramond, J-B; Welz, P J; Cowan, D A; Odlare, M; Burton, S G

2012-10-30

Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale biological sand filters (BSFs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the removal of pollutants through BSF systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented BSF showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two BSFs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of BSF sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect. Copyright © 2012 Elsevier Ltd. All rights reserved.

[Characterization of the Structure of the Prokaryotic Complex of Antarctic Permafrost by Molecular Genetic Techniques].

PubMed

Manucharova, N A; Trosheva, E V; Kol'tsova, E M; Demkina, E V; Karaevskaya, E V; Rivkina, E M; Mardanov, A V; El'-Registan, G I

2016-01-01

A prokaryotic mesophilic organotrophic community responsible for 10% of the total microbial number determined by epifluorescence microscopy was reactivated in the samples ofAntarctic permafrost retrieved from the environment favoring long-term preservation of microbial communities (7500 years). No culturable forms were obtained without resuscitation procedures (CFU = 0). Proteobacteria, Actinobacteria, and Firmicutes were the dominant microbial groups in the complex. Initiation of the reactivated microbial complex by addition of chitin (0.1% wt/vol) resulted in an increased share of metabolically active biomass (up to 50%) due to the functional domination of chitinolytics caused by the target resource. Thus, sequential application of resuscitation procedures and initiation of a specific physiological group (in this case, chitinolytics) to a permafrost-preserved microbial community made it possible to reveal a prokaryotic complex capable of reversion of metabolic activity (FISH data), to determine its phylogenetic structure by metagenomic anal-ysis, and to isolate a pure culture of the dominant microorganism with high chitinolytic activity.

Delineating ecological regions in marine systems: Integrating physical structure and community composition to inform spatial management in the eastern Bering Sea

NASA Astrophysics Data System (ADS)

Baker, Matthew R.; Hollowed, Anne B.

2014-11-01

Characterizing spatial structure and delineating meaningful spatial boundaries have useful applications to understanding regional dynamics in marine systems, and are integral to ecosystem approaches to fisheries management. Physical structure and drivers combine with biological responses and interactions to organize marine systems in unique ways at multiple scales. We apply multivariate statistical methods to define spatially coherent ecological units or ecoregions in the eastern Bering Sea. We also illustrate a practical approach to integrate data on species distribution, habitat structure and physical forcing mechanisms to distinguish areas with distinct biogeography as one means to define management units in large marine ecosystems. We use random forests to quantify the relative importance of habitat and environmental variables to the distribution of individual species, and to quantify shifts in multispecies assemblages or community composition along environmental gradients. Threshold shifts in community composition are used to identify regions with distinct physical and biological attributes, and to evaluate the relative importance of predictor variables to determining regional boundaries. Depth, bottom temperature and frontal boundaries were dominant factors delineating distinct biological communities in this system, with a latitudinal divide at approximately 60°N. Our results indicate that distinct climatic periods will shift habitat gradients and that dynamic physical variables such as temperature and stratification are important to understanding temporal stability of ecoregion boundaries. We note distinct distribution patterns among functional guilds and also evidence for resource partitioning among individual species within each guild. By integrating physical and biological data to determine spatial patterns in community composition, we partition ecosystems along ecologically significant gradients. This may provide a basis for defining spatial management units or serve as a baseline index for analyses of structural shifts in the physical environment, species abundance and distribution, and community dynamics over time.

Quantitative Characterization of Nanostructured Materials

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

Dr. Frank

The two-and-a-half day symposium on the "Quantitative Characterization of Nanostructured Materials" will be the first comprehensive meeting on this topic held under the auspices of a major U.S. professional society. Spring MRS Meetings provide a natural venue for this symposium as they attract a broad audience of researchers that represents a cross-section of the state-of-the-art regarding synthesis, structure-property relations, and applications of nanostructured materials. Close interactions among the experts in local structure measurements and materials researchers will help both to identify measurement needs pertinent to real-world materials problems and to familiarize the materials research community with the state-of-the-art local structuremore » measurement techniques. We have chosen invited speakers that reflect the multidisciplinary and international nature of this topic and the need to continually nurture productive interfaces among university, government and industrial laboratories. The intent of the symposium is to provide an interdisciplinary forum for discussion and exchange of ideas on the recent progress in quantitative characterization of structural order in nanomaterials using different experimental techniques and theory. The symposium is expected to facilitate discussions on optimal approaches for determining atomic structure at the nanoscale using combined inputs from multiple measurement techniques.« less

Microsatellite loci in two epiphytic lichens with contrasting dispersal modes: Nephroma laevigatum and N. parile (Nephromataceae).

PubMed

Belinchón, Rocío; Ellis, Christopher J; Yahr, Rebecca

2014-11-01

Microsatellite markers were characterized for two epiphytic cyanolichens, Nephroma laevigatum and N. parile (Nephromataceae), and will be used to investigate population structure and estimate gene flow among populations of these two closely related species with contrasting dispersal modes. • Twelve and 14 microsatellite loci were characterized for N. laevigatum and N. parile, respectively. Allele number in N. laevigatum ranged from three to 13 per locus, while in N. parile there were from two to six alleles per locus. As expected, the sexually reproducing N. laevigatum had higher genetic diversity than the predominantly asexual N. parile. • This new set of markers is suitable for studying population structure and providing insights into gene flow among populations and for understanding processes of diversification. Compared between the species, they will facilitate an understanding of the influence of contrasting reproductive strategies on population and community structure.

Influence of Thunderstorms on the Structure of the Ionosphere using Composite Analysis

NASA Astrophysics Data System (ADS)

Nava, O.; Sutherland, E.

2017-12-01

It is well known in the amateur (ham) radio community that thunderstorms have a significant influence on local and long-distance high-frequency (HF) communications. This study aims to characterize the structure of the ionosphere in response to strong convective activity and cloud electrification. Superposed Epoch Analysis is applied to surface weather observations and ionosonde data at Eglin Air Force Base, Florida from August 2014 to July 2017. Preliminary results indicate that thunderstorms significantly modify the structure of the ionosphere, generating statistically different measurements of several key parameters (e.g., foEs, hmF2, ITEC) compared to clear-sky observations. Seasonal and diurnal influences between the thunderstorm and clear sky cases are also explored. Accurate characterization of the ionosphere in response to thunderstorms has important implications for the effective use of HF communications in civilian and military operations, to include emergency services, aviation, amateur radio, and over-the-horizon radar.

Extracting information from multiplex networks

NASA Astrophysics Data System (ADS)

Iacovacci, Jacopo; Bianconi, Ginestra

2016-06-01

Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ ˜ S for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science.

Structural and compositional characterization of the adhesive produced by reef building oysters.

PubMed

Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

2015-04-29

Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem.

Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic.

PubMed

Pessi, Igor S; Pushkareva, Ekaterina; Lara, Yannick; Borderie, Fabien; Wilmotte, Annick; Elster, Josef

2018-05-23

Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

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

Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.

2014-04-07

Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retainedmore » in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.« less

Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient

PubMed Central

Campbell, Barbara J; Kirchman, David L

2013-01-01

Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment. PMID:22895159

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant.

PubMed

Oh, Seungdae; Hammes, Frederik; Liu, Wen-Tso

2018-01-01

Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interactions between Natural Organic Matter and Native Microbes in the Oak Ridge FRC Groundwater

NASA Astrophysics Data System (ADS)

Wu, X.; Hazen, T.; Fox, P. M.; Nico, P. S.; Li, Q.; Yang, W.; Liu, Y.; Hess, N. J.; Zhang, P.; Qin, Y.; Zhou, J.; Chakraborty, R.

2016-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of the carbon in NOM and its turnover by microbial communities. Microbial activity changes NOM's structure and properties, which may further influence the bioavailability of NOM. The change of NOM may reversely affect the microbial community structure as well. To date, our understanding of these interactions is insufficient, and it is critical to identify the role of NOM to carbon turnover, structure of microbial community and to the metabolic potential of that community. In this study, we aimed to study the interactions between NOM and native microbial communities present in groundwater at a background site (FW305 well) at Oak Ridge Field Research Center, TN. The total organic carbon and inorganic carbon in FW305 deep sediment samples were 0.071% and 0.011%, respectively. Water-soluble NOM was extracted from these sediment samples, the extraction efficiencies were 3.2% for organic carbon and 1.6% for inorganic carbon. The extracted NOM was then provided as the sole carbon source to native microbes present in groundwater. Subsamples were harvested several times from these incubations during a 50-day study. 16S rRNA gene amplicon sequencing and Geochip were used to identify the changes of microbial communities and expression of functional genes during transformation of the NOM. Several advanced chemical techniques including FTICR-MS and NEXAFS were used to characterize the C pool (i.e., NOM metabolites and microbial byproducts). Preliminary data clearly showed that microbial community responded to NOM, and shifted as functional groups in NOM transformed. Further detailed metabolite and gene-based analysis to elucidate these changes is currently being conducted.

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment.

PubMed

Wang, Haitao; Gilbert, Jack A; Zhu, Yongguan; Yang, Xiaoru

2018-08-01

Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres. Copyright © 2018 Elsevier B.V. All rights reserved.

Disentangling the role of management, vegetation structure, and plant quality for Orthoptera in lowland meadows.

PubMed

Schirmel, Jens; Gerlach, Rebekka; Buhk, Constanze

2017-08-17

Seminatural grasslands provide habitats for various species and are important for biodiversity conservation. The understanding of the diverse responses of species and traits to different grassland management methods is therefore urgently needed. We disentangled the role of grassland management (fertilization and irrigation), vegetation structure (biomass, sward height) and plant quality (protein and fiber content) for Orthoptera communities in lowland hay meadows in Germany. We found vegetation structure to be the most important environmental category in explaining community structure of Orthoptera (species richness, total individuals, functional diversity and species composition). Intensively used meadows (fertilized, irrigated, high plant biomass) were characterized by assemblages with few species, low functional diversity, and low conservation value. Thereby, the relatively moderate fertilizer inputs in our study system of up to ∼75 kg N/ha/year reduced functional diversity of Orthoptera, while this negative effect of fertilization was not detectable when solely considering taxonomic aspects. We found strong support for a prominent role of plant quality in shaping Orthoptera communities and especially the trait composition. Our findings demonstrate the usefulness of considering both taxonomic and functional components (functional diversity) in biodiversity research and we suggest a stronger involvement of plant quality measures in Orthoptera studies. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Nematode communities in sediments of the Kermadec Trench, Southwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Leduc, Daniel; Rowden, Ashley A.

2018-04-01

Hadal trenches are characterized by environmental conditions not found in any other deep-sea environment, such as steep topography and periodic disturbance by turbidity flows, which are likely responsible for the distinct nature of benthic communities of hadal trenches relative to those of the abyssal plain. Nematodes are the most abundant metazoans in the deep-sea benthos, but it is not yet clear if different trenches host distinct nematode communities, and no data are yet available on the communities of most trenches, including the Kermadec Trench in the Southwest Pacific. Quantitative core samples from the seafloor of the Kermadec Trench were recently obtained from four sites at 6000-9000 m depth which allowed for analyses of meiofauna, and nematodes in particular, for the first time. Nematode community and trophic structure was also compared with other trenches using published data. There was a bathymetric gradient in meiofauna abundance, biomass, and community structure within the Kermadec Trench, but patterns for species richness were ambiguous depending on which metric was used. There was a change in community structure from shallow to deep sites, as well as a consistent change in community structure from the upper sediment layers to the deeper sediment layers across the four sites. These patterns are most likely explained by variation in food availability within the trench, and related to trench topography. Together, deposit and microbial feeders represented 48-92% of total nematode abundance in the samples, which suggests that fine organic detritus and bacteria are major food sources. The relatively high abundance of epigrowth feeders at the 6000 and 9000 m sites (38% and 31%, respectively) indicates that relatively freshly settled microalgal cells represent another important food source at these sites. We found a significant difference in species community structure between the Kermadec and Tonga trenches, which was due to both the presence/absence of species as well as differences in relative abundances of shared species. The cluster and SIMPROF analyses of nematode genus community data across Pacific and Atlantic trenches identified two statistically significant natural groupings: the first group comprised all three Puerto Rico Trench samples, and the second comprised all remaining trenches (South Sandwich, Atacama, Tonga, and Kermadec). Our analyses show that differences in nematode between the adjacent Kermadec and Tonga trenches are observable when analyses are conducted with species-level identifications, but genera-based and trophic structure analyses revealed only limited heterogeneity among trenches. The present study contributes to the growing amount of information on hadal trench environments, which ultimately will build a greater understanding of these rarely sampled deep-sea habitats.

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

PubMed

Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

2016-11-01

Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km 2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km 2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

NASA Astrophysics Data System (ADS)

Ciobanu, M.-C.; Rabineau, M.; Droz, L.; Révillon, S.; Ghiglione, J.-F.; Dennielou, B.; Jorry, S.-J.; Kallmeyer, J.; Etoubleau, J.; Pignet, P.; Crassous, P.; Vandenabeele-Trambouze, O.; Laugier, J.; Guégan, M.; Godfroy, A.; Alain, K.

2012-09-01

An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG) and Halobacteria) within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence analyses (CCA) showed that the availability of electron acceptors and the quality of electron donors (indicated by age) strongly influenced the community structure. In contrast, within the Gulf of Lion core, characterized by a homogeneous lithological structure of upper-slope environment, most detected groups were Bacteroidetes and, to a lesser extent, Betaproteobacteria. At both site, the detection of Betaproteobacteria coincided with increased terrestrial inputs, as confirmed by the geochemical measurements (Si, Sr, Ti and Ca). In the Gulf of Lion, geochemical parameters were also found to drive microbial community composition. Taken together, our data suggest that the palaeoenvironmental history of erosion and deposition recorded in the Western Mediterranean Sea sediments has left its imprint on the sedimentological context for microbial habitability, and then indirectly on structure and composition of the microbial communities during the late Quaternary.

Racial Geography, Economic Growth and Natural Disaster Resilience

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

Li, Huiping; Fernandez, Steven J.; Ganguly, Auroop

Recent development of National Response Plans and National Incident Management Plans has emphasized the need for interoperability of plans, systems, technology, and command structures. However, much less emphasis has been placed on equally important elements such as the at-risk populations’ response to those plans, systems, and directions. The community-wide consequences of Hurricane Katrina demonstrated that the protection of communities should no longer be considered only a function of public organizations. Private organizations, nonprofit organizations and individual households have significant roles to play in these plans (Comfort 2006, Salamon 2002). This study is a first attempt to characterize the effect onmore » the resilience (recovery) of metropolitan areas by the presence (or absence) of separate small communities within a larger jurisdiction. These communities can be based on many different social cleavages (ethnic, racial, economic, social, geographic, linguistic, etc.).« less

Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea.

PubMed

Musat, Niculina; Werner, Ursula; Knittel, Katrin; Kolb, Steffen; Dodenhof, Tanja; van Beusekom, Justus E E; de Beer, Dirk; Dubilier, Nicole; Amann, Rudolf

2006-06-01

Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113-127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3 x 10(9) cells ml(-1) and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5 x 10(7)-1.8 x 10(8) cells ml(-1) accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).

Patterns of Twitter Behavior Among Networks of Cannabis Dispensaries in California.

PubMed

Peiper, Nicholas C; Baumgartner, Peter M; Chew, Robert F; Hsieh, Yuli P; Bieler, Gayle S; Bobashev, Georgiy V; Siege, Christopher; Zarkin, Gary A

2017-07-04

Twitter represents a social media platform through which medical cannabis dispensaries can rapidly promote and advertise a multitude of retail products. Yet, to date, no studies have systematically evaluated Twitter behavior among dispensaries and how these behaviors influence the formation of social networks. This study sought to characterize common cyberbehaviors and shared follower networks among dispensaries operating in two large cannabis markets in California. From a targeted sample of 119 dispensaries in the San Francisco Bay Area and Greater Los Angeles, we collected metadata from the dispensary accounts using the Twitter API. For each city, we characterized the network structure of dispensaries based upon shared followers, then empirically derived communities with the Louvain modularity algorithm. Principal components factor analysis was employed to reduce 12 Twitter measures into a more parsimonious set of cyberbehavioral dimensions. Finally, quadratic discriminant analysis was implemented to verify the ability of the extracted dimensions to classify dispensaries into their derived communities. The modularity algorithm yielded three communities in each city with distinct network structures. The principal components factor analysis reduced the 12 cyberbehaviors into five dimensions that encompassed account age, posting frequency, referencing, hyperlinks, and user engagement among the dispensary accounts. In the quadratic discriminant analysis, the dimensions correctly classified 75% (46/61) of the communities in the San Francisco Bay Area and 71% (41/58) in Greater Los Angeles. The most centralized and strongly connected dispensaries in both cities had newer accounts, higher daily activity, more frequent user engagement, and increased usage of embedded media, keywords, and hyperlinks. Measures derived from both network structure and cyberbehavioral dimensions can serve as key contextual indicators for the online surveillance of cannabis dispensaries and consumer markets over time. ©Nicholas C Peiper, Peter M Baumgartner, Robert F Chew, Yuli P Hsieh, Gayle S Bieler, Georgiy V Bobashev, Christopher Siege, Gary A Zarkin. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 04.07.2017.

Inferring the relative resilience of alternative states

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, Maria A.; Sanchez-Carrillo, Salvador

2013-01-01

Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or “temporal scales” in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing resilience of alternative states across ecological and other complex systems.

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics

USGS Publications Warehouse

Fahrenfeld, N.L.; Reyes, Hannah Delos; Eramo, Alessia; Akob, Denise M.; Mumford, Adam; Cozzarelli, Isabelle M.

2017-01-01

Unconventional oil and gas (UOG) production produces large quantities of wastewater with complex geochemistry and largely uncharacterized impacts on surface waters. In this study, we assessed shifts in microbial community structure and function in sediments and waters upstream and downstream from a UOG wastewater disposal facility. To do this, quantitative PCR for 16S rRNA and antibiotic resistance genes along with metagenomic sequencing were performed. Elevated conductivity and markers of UOG wastewater characterized sites sampled downstream from the disposal facility compared to background sites. Shifts in overall high level functions and microbial community structure were observed between background sites and downstream sediments. Increases in Deltaproteobacteria and Methanomicrobia and decreases in Thaumarchaeota were observed at downstream sites. Genes related to dormancy and sporulation and methanogenic respiration were 18–86 times higher at downstream, impacted sites. The potential for these sediments to serve as reservoirs of antimicrobial resistance was investigated given frequent reports of the use of biocides to control the growth of nuisance bacteria in UOG operations. A shift in resistance profiles downstream of the UOG facility was observed including increases in acrB and mexB genes encoding for multidrug efflux pumps, but not overall abundance of resistance genes. The observed shifts in microbial community structure and potential function indicate changes in respiration, nutrient cycling, and markers of stress in a stream impacted by UOG waste disposal operations.

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil.

PubMed

Sousa, O V; Macrae, A; Menezes, F G R; Gomes, N C M; Vieira, R H S F; Mendonça-Hagler, L C S

2006-12-01

The effects of shrimp farm effluents on bacterial communities in mangroves have been infrequently reported. Classic and molecular biology methods were used to survey bacterial communities from four mangroves systems. Water temperature, salinity, pH, total heterotrophic bacteria and maximum probable numbers of Vibrio spp. were investigated. Genetic profiles of bacterial communities were also characterized by polymerase chain reaction (PCR) amplification of eubacterial and Vibrio 16S rDNA using denaturing gradient gel electrophoresis (DGGE). Highest heterotrophic counts were registered in the mangrove not directly polluted by shrimp farming. The Enterobacteriaceae and Chryseomonas luteola dominated the heterotrophic isolates. Vibrio spp. pathogenic to humans and shrimps were identified. Eubacterial genetic profiles suggest a shared community structure independent of mangrove system. Vibrio genetic profiles were mangrove specific. Neither microbial counts nor genetic profiling revealed a significant decrease in species richness associated with shrimp farm effluent. The complex nature of mangrove ecosystems and their microbial communities is discussed.

Seasonal variation of zooplankton abundance and community structure in Prince William Sound, Alaska, 2009-2016

NASA Astrophysics Data System (ADS)

McKinstry, Caitlin A. E.; Campbell, Robert W.

2018-01-01

Large calanoid copepods and other zooplankters comprise the prey field for ecologically and economically important predators such as juvenile pink salmon, herring, and seabirds in Prince William Sound (PWS).​ From 2009-2016, the Gulf Watch Alaska program collected zooplankton 5-10 times each year at 12 stations in PWS to establish annual patterns. Surveys collected 188 species of zooplankton with Oithona similis, Limacina helicina, Pseudocalanus spp., and Acartia longiremis as the most common species present in 519 samples. Generalized additive models assessed seasonal abundance and showed peak abundance in July (mean: 9826 no. m-3 [95% CI: 7990-12,084]) and lowest abundance in January (503 no. m-3 [373 to 678]). Significantly higher zooplankton abundance occurred in 2010 (542 no. m-3 ± 55 SE) and lowest in 2013 (149 no. m-3 ± 13). The species composition of communities, determined via hierarchical cluster analysis and indicator species analysis, produced six distinct communities based on season and location. The winter community, characterized by warm-water indicator species including Mesocalanus tenuicornis, Calanus pacificus, and Corycaeus anglicus, diverged into four communities throughout the spring and summer. The first spring community, characterized by copepods with affinities for lower salinities, occurred sound-wide. The second spring community, comprised of planktonic larvae, appeared sporadically in PWS bays in 2011-2013. Spring and summer open water stations were defined by the presence of large calanoid copepods. A summer community including the most abundant taxa was common in 2010 and 2011, absent in 2013, then sporadically appeared in 2014 and 2015 suggesting interannual variability of zooplankton assemblages. The zooplankton community shifted to a uniform assemblage characterized by cnidarians in the early autumn. Community assemblages showed significant correlations to a set of environmental variables including SST, mixed layer depth, location, depth of chlorophyll-a max, mixed layer average salinity, chlorophyll-a maximum, and bottom depth (ρ = 0.24, p < 0.05). The disappearance of the summer community coincided with the appearance of the Gulf of Alaska warm water anomaly known as "The Blob". A shift in zooplankton community composition during critical grazing periods for predators such as juvenile Pacific herring (Clupea pallasi) could have energetic consequences for overwintering success.

Diet is the primary determinant of bacterial community structure in the guts of higher termites.

PubMed

Mikaelyan, Aram; Dietrich, Carsten; Köhler, Tim; Poulsen, Michael; Sillam-Dussès, David; Brune, Andreas

2015-10-01

The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches. © 2015 John Wiley & Sons Ltd.

Dynamics of communities of bacteria and ammonia-oxidizing microorganisms in response to simazine attenuation in agricultural soil.

PubMed

Wan, Rui; Wang, Zhao; Xie, Shuguang

2014-02-15

Autochthonous microbiota plays a crucial role in natural attenuation of s-triazine herbicides in agricultural soil. Soil microcosm study was carried out to investigate the shift in the structures of soil autochthonous microbial communities and the potential degraders associated with natural simazine attenuation. The relative abundance of soil autochthonous degraders and the structures of microbial communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. Phylogenetic composition of bacterial community was also characterized using clone library analysis. Soil autochthonous microbiota could almost completely clean up simazine (100 mg kg(-1)) in 10 days after herbicide application, indicating a strong self-remediation potential of agricultural soil. A significant increase in the proportion of s-triazine-degrading atzC gene was found in 6 days after simazine amendment. Simazine application could alter the community structures of total bacteria and ammonia-oxidizing archaea (AOA) and bacteria (AOB). AOA were more responsive to simazine application compared to AOB and bacteria. Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were the dominant bacterial groups either at the initial stage after simazine amendment or at the end stage of herbicide biodegradation, but Actinobacteria predominated at the middle stage of biodegradation. Microorganisms from several bacterial genera might be involved in simazine biodegradation. This work could add some new insights on the bioremediation of herbicides contaminated agricultural soils. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE.

PubMed

Ding, Xiao-Fei; Wu, Chong-De; Zhang, Li-Qiang; Zheng, Jia; Zhou, Rong-Qing

2014-02-01

The aim of this study was to investigate and compare the microbial community structures of eubacteria and archaea in the pit mud of Chinese Luzhou-flavor liquor from the wall (C(w)) and bottom (C(b)) of cellar through nested PCR-denaturing gradient gel electrophoresis (DGGE). The Shannon-Wiener index (H) calculated from the DGGE profiles showed that the community diversities of eubacteria and archaea in samples from C(b) were almost higher than that from C(w). In addition, cluster analysis of the DGGE profiles revealed that some differences were found in the microbial community structure in samples from different locations. The closely relative microorganisms of all eubacterial 16S rRNA gene sequences fell into four phyla (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), including 12 genera and 2 uncultured eubacteria. Moreover, 37.1% eubacteria were affiliated with Clostridium. Particularly, genus Acinetobacter was absent in all samples from C(b) but present in all samples from C(w). The closely relative microorganisms of all archaeal 16S rRNA gene sequences fell into four genera, which included Methanobrevibacter, Methanoculleus, Methanobacterium and Methanosaeta, while the dominant archaea in samples from C(w) and C(b) were similar. Results presented in this study provide further understanding of the spatial differences in microbial community structure in the pit mud, and is of great importance for the production and quality improvement of Luzhou-flavor liquor.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

Horizontal gene transfer and mobile genetic elements in marine systems.

PubMed

Sobecky, Patricia A; Hazen, Tracy H

2009-01-01

The pool of mobile genetic elements (MGE) in microbial communities consists of viruses, plasmids, and associated elements (insertion sequences, transposons, and integrons) that are either self-transmissible or use mobile plasmids and viruses as vehicles for their dissemination. This mobilome facilitates the horizontal transfer of genes that promote the evolution and adaptation of microbial communities. Efforts to characterize MGEs from microbial populations resident in a variety of ecological habitats have revealed a surprisingly novel and seemingly untapped biodiversity. To better understand the impact of horizontal gene transfer (HGT), as well as the agents that promote HGT in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of the mobilome in marine microbial communities, information on the distribution, diversity, and ecological traits of the marine mobilome is presented. In this chapter we discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea marine ecosystems.

Evaluation of methods for the extraction of DNA from drinking water distribution system biofilms.

PubMed

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-01-01

While drinking water biofilms have been characterized in various drinking water distribution systems (DWDS), little is known about the impact of different DNA extraction methods on the subsequent analysis of microbial communities in drinking water biofilms. Since different DNA extraction methods have been shown to affect the outcome of microbial community analysis in other environments, it is necessary to select a DNA extraction method prior to the application of molecular tools to characterize the complex microbial ecology of the DWDS. This study compared the quantity and quality of DNA yields from selected DWDS bacteria with different cell wall properties using five widely used DNA extraction methods. These were further selected and evaluated for their efficiency and reproducibility of DNA extraction from DWDS samples. Terminal restriction fragment length analysis and the 454 pyrosequencing technique were used to interpret the differences in microbial community structure and composition, respectively, from extracted DNA. Such assessments serve as a concrete step towards the determination of an optimal DNA extraction method for drinking water biofilms, which can then provide a reliable comparison of the meta-analysis results obtained in different laboratories.

Abundance and diversity of Archaea in heavy-metal-contaminated soils.

PubMed

Sandaa, R A; Enger, O; Torsvik, V

1999-08-01

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% +/- 0.3% of 4', 6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species.

Characterization of Mero-and Ichthyoplankton Communities within the Chesapeake Bay Plume off Virginia Beach, Virginia during 1983-1984.

DTIC Science & Technology

1985-03-01

A-A165 203 CHARACTERIZATION OF HERO-AND ICHTHYOPLANKTON 1/3 COMMUNITIES WITHIN THE CI4ESA..(U) OLD DOMINION UNIV INORFOLK VA APPLIED MARINE RESEARCH...UNIVERSITY N NORFOLK, VIRGINIA I--. CHARACTERIZATION OF MERO- A;ID ICHTHYOPLANKTONS0 COMMUNITIES WITHIN THE CHESAPEAKE BAY PLUMEL.L OFF VIRGINIA...Characterization of Mero- and Icthyoplankton Communities Within the Chesapeake Bay Plume Off Virginia Beach, Virginia During 1983-1984 12. PERSONAL AUTHOR(S

Parallel structure among environmental gradients and three trophic levels in a subarctic estuary

USGS Publications Warehouse

Speckman, Suzann G.; Piatt, John F.; Minte-Vera, C. V.; Parrish, Julia K.

2005-01-01

We assessed spatial and temporal variability in the physical environment of a subarctic estuary, and examined concurrent patterns of chlorophyll α abundance (fluorescence), and zooplankton and forage fish community structure. Surveys were conducted in lower Cook Inlet, Alaska, during late July and early August from 1997 through 1999. Principle components analysis (PCA) revealed that spatial heterogeneity in the physical oceanographic environment of lower Cook Inlet could be modeled as three marine-estuarine gradients characterized by temperature, salinity, bottom depth, and turbidity. The gradients persisted from 1997 through 1999, and PCA explained 68% to 92% of the variance in physical oceanography for each gradient-year combination. Correlations between chlorophyll α abundance and distribution and the PCA axes were weak. Chlorophyll was reduced by turbidity, and low levels occurred in areas with high levels of suspended sediments. Detrended correspondence analysis (DCA) was used to order the sample sites based on species composition and to order the zooplankton and forage fish taxa based on similarities among sample sites for each gradient-year. Correlations between the structure of the physical environment (PCA axis 1) and zooplankton community structure (DCA axis 1) were strong (r = 0.43-0.86) in all years for the three marine-estuarine gradients, suggesting that zooplankton community composition was structured by the physical environment. The physical environment (PCA) and forage fish community structure (DCA) were weakly correlated in all years along Gradient 2, defined by halocline intensity and surface temperature and salinity, even though these physical variables were more important for defining zooplankton habitats. However, the physical environment (PCA) and forage fish community structure (DCA) were strongly correlated along the primary marine-estuarine gradient (#1) in 1997 (r = 0.87) and 1998 (r = 0.82). The correlation was poor (r = 0.32) in 1999, when fish community structure changed markedly in lower Cook Inlet. Capelin (Mallotus villosus), walleye pollock (Theragra chalcogramma), and arrowtooth flounder (Atheresthes stomias) were caught farther north than in previous years. Waters were significantly colder and more saline in 1999, a La Nina year, than in other years of the study. Interannual fluctuations in environmental conditions in lower Cook Inlet did not have substantial effects on zooplankton community structure, although abundance of individual taxa varied significantly. The abundance and distribution of chlorophyll α, zooplankton and forage fish were affected much more by spatial variability in physical oceanography than by interannual variability. Our examination of physical-biological linkages in lower Cook Inlet supports the concept of "bottom-up control," i.e., that variability in the physical environment structures higher trophic-level communities by influencing their distribution and abundance across space.

Parallel structure among environmental gradients and three trophic levels in a subarctic estuary

NASA Astrophysics Data System (ADS)

Speckman, Suzann G.; Piatt, John F.; Minte-Vera, Carolina V.; Parrish, Julia K.

2005-07-01

We assessed spatial and temporal variability in the physical environment of a subarctic estuary, and examined concurrent patterns of chlorophyll α abundance (fluorescence), and zooplankton and forage fish community structure. Surveys were conducted in lower Cook Inlet, Alaska, during late July and early August from 1997 through 1999. Principle components analysis (PCA) revealed that spatial heterogeneity in the physical oceanographic environment of lower Cook Inlet could be modeled as three marine-estuarine gradients characterized by temperature, salinity, bottom depth, and turbidity. The gradients persisted from 1997 through 1999, and PCA explained 68% to 92% of the variance in physical oceanography for each gradient-year combination. Correlations between chlorophyll α abundance and distribution and the PCA axes were weak. Chlorophyll was reduced by turbidity, and low levels occurred in areas with high levels of suspended sediments. Detrended correspondence analysis (DCA) was used to order the sample sites based on species composition and to order the zooplankton and forage fish taxa based on similarities among sample sites for each gradient-year. Correlations between the structure of the physical environment (PCA axis 1) and zooplankton community structure (DCA axis 1) were strong ( r = 0.43-0.86) in all years for the three marine-estuarine gradients, suggesting that zooplankton community composition was structured by the physical environment. The physical environment (PCA) and forage fish community structure (DCA) were weakly correlated in all years along Gradient 2, defined by halocline intensity and surface temperature and salinity, even though these physical variables were more important for defining zooplankton habitats. However, the physical environment (PCA) and forage fish community structure (DCA) were strongly correlated along the primary marine-estuarine gradient (#1) in 1997 ( r = 0.87) and 1998 ( r = 0.82). The correlation was poor ( r = 0.32) in 1999, when fish community structure changed markedly in lower Cook Inlet. Capelin ( Mallotus villosus), walleye pollock ( Theragra chalcogramma), and arrowtooth flounder ( Atheresthes stomias) were caught farther north than in previous years. Waters were significantly colder and more saline in 1999, a La Niña year, than in other years of the study. Interannual fluctuations in environmental conditions in lower Cook Inlet did not have substantial effects on zooplankton community structure, although abundance of individual taxa varied significantly. The abundance and distribution of chlorophyll α, zooplankton and forage fish were affected much more by spatial variability in physical oceanography than by interannual variability. Our examination of physical-biological linkages in lower Cook Inlet supports the concept of “bottom-up control,” i.e., that variability in the physical environment structures higher trophic-level communities by influencing their distribution and abundance across space.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE PAGES

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; ...

2016-07-26

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

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

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm.

PubMed

Wang, Zhao; Yang, Yuyin; Sun, Weimin; Dai, Yu; Xie, Shuguang

2015-02-01

Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.

Unravel the submesoscale dynamics of the phytoplanktonic community in the NW Mediterranean Sea by in situ observations: the 2015 OSCAHR cruise

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Doglioli, Andrea M.; Grégori, Gérald; Della Penna, Alice; Wagener, Thibaut; Rougier, Gille; Bhairy, Nagib; Dugenne, Mathilde; Lahbib, Soumaya; Thyssen, Melilotus

2017-04-01

Submesoscale phenomena have been recently recognized as a key factor in physical-biological-biogeochemical interactions, even if it remains unclear how these processes affect the global state of the ocean. Significant large-scale impacts of submesoscale structures on primary production and influence on the phytoplankton community structure and diversity have also been reported. In the past decade submesoscale dynamics have been predominately studied through the analysis of numerical simulations. Observing the coupled physical and biogeochemical variability at this scale remains challenging due to the ephemeral nature of submesoscale structures. The in-situ study of such structures necessitates multidisciplinary approaches involving in situ observations, remote sensing and modeling. Last progresses in biogeochemical sensor development and advanced methodology including Lagrangian real-time adaptative strategies represent outstanding opportunities. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted thanks to a multidisciplinary approach in order to improve the understanding of submesoscale processes. An ephemeral submesoscale structure was first identified in the Ligurian Sea in fall 2015 using both satellite and numerical modeling data before the campaign. Afterwards, advanced observing systems for the physical, biological and biogeochemical characterization of the sea surface layer at a high spatial and temporal frequency were deployed during a 10-days cruise. A MVP (Moving Vessel Profiler) was used to obtain high resolution CTD profiles associated to a new pumping system with 1-m vertical resolution. Moreover, along the ship track, in addition to the standard measurements of seawater surface samples (Chl-a, nutrients, O2, SST, SSS …), we deployed an automated flow cytometer for near real-time characterization of phytoplankton functional groups (from micro-phytoplankton down to cyanobacteria). The observed submesoscale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Six phytoplankton groups were identified across the structure with an unprecedented spatial and temporal resolution. According to our observations, we could quantify the influence of the fast established physical structure on the spatial distribution of the phytoplankton functional groups, giving coherence to the observed community structuration. Moreover, the high resolution of our observations allows us to estimate the growth rate of the main phytoplankton groups. Our innovative adaptative strategy with a multidisciplinary and transversal approach provides a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

VA staff perceptions of the role of the extended care referral process in home and community-based services versus nursing home use posthospital discharge.

PubMed

Miller, Edward Alan; Intrator, Orna; Gadbois, Emily; Gidmark, Stefanie; Rudolph, James L

2017-01-01

Little is known about how the extended care referral process-its structure and participants-influences Veterans' use of home and community-based services (HCBS) over nursing home care within the Veterans Health Administration (VHA). This study thus characterizes the extended care referral process within the VHA and its impact on HCBS versus nursing home use at hospital discharge. Data derive from 35 semistructured interviews at 12 Veterans Affairs Medical Centers (VAMCs). Findings indicate that the referral process is characterized by a commitment by care teams to consider HCBS if possible, varied practice depending on the clinician that most heavily influences care team recommendations, and care team emphasis on respecting Veteran/family preferences even when they are contrary to care team recommendations. Potential modifications include adopting systematic assessment practices; improving Veteran, family, and provider education; and promoting informed selection through shared decision making.

Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis

PubMed Central

Leigh, Brittany; Karrer, Charlotte; Cannon, John P.; Breitbart, Mya; Dishaw, Larry J.

2017-01-01

Outnumbering all other biological entities on earth, bacteriophages (phages) play critical roles in structuring microbial communities through bacterial infection and subsequent lysis, as well as through horizontal gene transfer. While numerous studies have examined the effects of phages on free-living bacterial cells, much less is known regarding the role of phage infection in host-associated biofilms, which help to stabilize adherent microbial communities. Here we report the cultivation and characterization of a novel strain of Shewanella fidelis from the gut of the marine tunicate Ciona intestinalis, inducible prophages from the S. fidelis genome, and a strain-specific lytic phage recovered from surrounding seawater. In vitro biofilm assays demonstrated that lytic phage infection affects biofilm formation in a process likely influenced by the accumulation and integration of the extracellular DNA released during cell lysis, similar to the mechanism that has been previously shown for prophage induction. PMID:28327522

A New Approach to Predict Microbial Community Assembly and Function Using a Stochastic, Genome-Enabled Modeling Framework

NASA Astrophysics Data System (ADS)

King, E.; Brodie, E.; Anantharaman, K.; Karaoz, U.; Bouskill, N.; Banfield, J. F.; Steefel, C. I.; Molins, S.

2016-12-01

Characterizing and predicting the microbial and chemical compositions of subsurface aquatic systems necessitates an understanding of the metabolism and physiology of organisms that are often uncultured or studied under conditions not relevant for one's environment of interest. Cultivation-independent approaches are therefore important and have greatly enhanced our ability to characterize functional microbial diversity. The capability to reconstruct genomes representing thousands of populations from microbial communities using metagenomic techniques provides a foundation for development of predictive models for community structure and function. Here, we discuss a genome-informed stochastic trait-based model incorporated into a reactive transport framework to represent the activities of coupled guilds of hypothetical microorganisms. Metabolic pathways for each microbe within a functional guild are parameterized from metagenomic data with a unique combination of traits governing organism fitness under dynamic environmental conditions. We simulate the thermodynamics of coupled electron donor and acceptor reactions to predict the energy available for cellular maintenance, respiration, biomass development, and enzyme production. While `omics analyses can now characterize the metabolic potential of microbial communities, it is functionally redundant as well as computationally prohibitive to explicitly include the thousands of recovered organisms into biogeochemical models. However, one can derive potential metabolic pathways from genomes along with trait-linkages to build probability distributions of traits. These distributions are used to assemble groups of microbes that couple one or more of these pathways. From the initial ensemble of microbes, only a subset will persist based on the interaction of their physiological and metabolic traits with environmental conditions, competing organisms, etc. Here, we analyze the predicted niches of these hypothetical microbes and assess the ability of a stochastically assembled community of organisms to predict subsurface biogeochemical dynamics.

The Influence of Salmon Recolonization on Riparian Communities in the Cedar River, Washington, USA

NASA Astrophysics Data System (ADS)

Moravek, J.; Clipp, H.; Kiffney, P.

2016-02-01

Salmon are a valuable resource throughout the Pacific Northwest, but increasing human activity is degrading coastal ecosystems and threatening local salmon populations. Salmon conservation efforts often focus on habitat restoration, including the re-colonization of salmon into historically obstructed areas such as the Cedar River in Washington, USA. However, to assess the long term implications of salmon re-colonization on a landscape scale, it is critical to consider not only the river ecosystem but also the surrounding riparian habitat. Although prior studies suggest that salmon alter riparian food web dynamics, the riparian community on the Cedar River has not yet been characterized. To investigate possible connections between salmon and the riparian habitat after 12 years of re-colonization, we surveyed riparian spider communities along a gradient of salmon inputs (g/m2). In 10-m transects along the banks of the river, we identified spiders and spider webs, collected prey from webs, and characterized nearby aquatic macroinvertebrate communities. We found that the density of aquatic macroinvertebrates, as well as the density of spider prey, both had significant positive relationships with salmon inputs, supporting the hypothesis that salmon provide energy and nutrients for both aquatic and riparian food webs. We also found that spider diversity significantly decreased with salmon inputs, potentially due to confounding factors such as stream gradient or vegetation structure. Although additional information is needed to fully understand this relationship, the significant connection between salmon inputs and spider diversity is compelling motivation for further studies regarding the link between aquatic and riparian systems on the Cedar River. Understanding the connections between salmon and the riparian community is critical to characterizing the long term, landscape-scale implications of sustainable salmon management in the Pacific Northwest.

The Influence of Salmon Recolonization on Riparian Communities in the Cedar River, Washington, USA

NASA Astrophysics Data System (ADS)

Moravek, J.; Clipp, H.; Kiffney, P.

2015-12-01

Salmon are a valuable cultural and economic resource throughout the Pacific Northwest, but increasing human activity is degrading coastal ecosystems and threatening local salmon populations. Salmon conservation efforts often focus on habitat restoration, including the re-colonization of salmon into historically obstructed areas such as the Cedar River in Washington, USA. However, to assess the implications of salmon re-colonization on a landscape scale, it is critical to consider not only the river ecosystem but also the surrounding riparian habitat. Although prior studies suggest that salmon alter riparian food web dynamics, the riparian community on the Cedar River has not yet been characterized. To investigate possible connections between salmon and the riparian habitat, we surveyed riparian spider communities along a gradient of salmon inputs (g/m2). In 10-m transects along the banks of the river, we identified spiders and spider webs, collected prey from webs, and characterized nearby aquatic macroinvertebrate communities. We found that the density of aquatic macroinvertebrates, as well as the density of spider prey, both had significant positive relationships with salmon inputs, supporting the hypothesis that salmon provide energy and nutrients for both aquatic and riparian food webs. We also found that spider diversity significantly decreased with salmon inputs, potentially due to confounding factors such as stream gradient or vegetation structure. Although additional information is needed to fully understand this relationship, the significant connection between salmon inputs and spider diversity is compelling motivation for further studies regarding the link between aquatic and riparian systems on the Cedar River. Understanding the connections between salmon and the riparian community is critical to characterizing the landscape-scale implications of sustainable salmon management in the Pacific Northwest.

Molecular techniques revealed highly diverse microbial communities in natural marine biofilms on polystyrene dishes for invertebrate larval settlement.

PubMed

Lee, On On; Chung, Hong Chun; Yang, Jiangke; Wang, Yong; Dash, Swagatika; Wang, Hao; Qian, Pei-Yuan

2014-07-01

Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups.

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater.

PubMed

Kalenitchenko, Dimitri; Fagervold, Sonja K; Pruski, Audrey M; Vétion, Gilles; Yücel, Mustafa; Le Bris, Nadine; Galand, Pierre E

2015-12-01

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities.

PubMed

Lilleskov, Erik A; Bruns, Thomas D; Horton, Thomas R; Taylor, D; Grogan, Paul

2004-08-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied various measures of spatial pattern to characterize distributions at EMF community and species levels: Mantel tests, Mantel correlograms, variance/mean and standardized variograms. Mantel tests indicated that in four of eight sites community similarity decreased with distance, whereas Mantel correlograms also found spatial autocorrelation in those four plus two additional sites. In all but one of these sites elevated similarity was evident only at relatively small spatial scales (< 2.6 m), whereas one exhibited a larger scale pattern ( approximately 25 m). Evenness of biomass distribution among cores varied widely among taxa. Standardized variograms indicated that most of the dominant taxa showed patchiness at a scale of less than 3 m, with a range from 0 to < or =17 m. These results have implications for both sampling scale and intensity to achieve maximum efficiency of community sampling. In the systems we examined, cores should be at least 3 m apart to achieve the greatest sampling efficiency for stand-level community analysis. In some cases even this spacing may result in reduced sampling efficiency arising from patterns of spatial autocorrelation. Interpretation of the causes and significance of these patterns requires information on the genetic identity of individuals in the communities.

Strong coupling of plant and fungal community structure across western Amazonian rainforests

PubMed Central

Peay, Kabir G; Baraloto, Christopher; Fine, Paul VA

2013-01-01

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity. PMID:23598789

Assessing urban forest effects and values: Morgantown's Urban Forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Jack C. Stevens; Jonathan Cumming; Sandhya Mohen; Anne Buckelew. Cumming

2012-01-01

An analysis of the community forest in Morgantown, WV, was undertaken in 2004 to characterize the structural and functional attributes of this forest resource. The assessment revealed that this city has about 658,000 trees with canopies that cover 35.5 percent of the area. The most common tree species are sugar maple, black cherry, and hawthorn. The urban forest...

Backing onto sacred ground.

PubMed

Gunderson, G R

2000-01-01

It is widely recognized that the health of individuals and communities is determined by the interaction of physical, mental, social, and spiritual factors. Public health leaders can find precedent for the resulting holistic strategies in the collaboration with religious structures that characterized the early years of public health. The modern context is more pluralistic, democratic, and complex in terms of its institutional array of partners.

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Diversity and Variation of Bacterial Community Revealed by MiSeq Sequencing in Chinese Dark Teas

PubMed Central

Fu, Jianyu; Lv, Haipeng; Chen, Feng

2016-01-01

Chinese dark teas (CDTs) are now among the popular tea beverages worldwide due to their unique health benefits. Because the production of CDTs involves fermentation that is characterized by the effect of microbes, microorganisms are believed to play critical roles in the determination of the chemical characteristics of CDTs. Some dominant fungi have been identified from CDTs. In contrast, little, if anything, is known about the composition of bacterial community in CDTs. This study was set to investigate the diversity and variation of bacterial community in four major types of CDTs from China. First, the composition of the bacterial community of CDTs was determined using MiSeq sequencing. From the four typical CDTs, a total of 238 genera that belong to 128 families of bacteria were detected, including most of the families of beneficial bacteria known to be associated with fermented food. While different types of CDTs had generally distinct bacterial structures, the two types of brick teas produced from adjacent regions displayed strong similarity in bacterial composition, suggesting that the producing environment and processing condition perhaps together influence bacterial succession in CDTs. The global characterization of bacterial communities in CDTs is an essential first step for us to understand their function in fermentation and their potential impact on human health. Such knowledge will be important guidance for improving the production of CDTs with higher quality and elevated health benefits. PMID:27690376

Systematic evaluation of bias in microbial community profiles induced by whole genome amplification.

PubMed

Direito, Susana O L; Zaura, Egija; Little, Miranda; Ehrenfreund, Pascale; Röling, Wilfred F M

2014-03-01

Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement amplification (MDA)] and one new primer-free method [primase-based whole genome amplification (pWGA)] were compared using a polymerase chain reaction (PCR)-based method as control. Pyrosequencing of an environmental sample and principal component analysis revealed that MDA impacted community profiles more strongly than pWGA and indicated that this related to species GC content, although an influence of DNA integrity could not be excluded. Subsequently, biases by species GC content, DNA integrity and fragment size were separately analysed using defined mixtures of DNA from various species. We found significantly less amplification of species with the highest GC content for MDA-based templates and, to a lesser extent, for pWGA. DNA fragmentation also interfered severely: species with more fragmented DNA were less amplified with MDA and pWGA. pWGA was unable to amplify low molecular weight DNA (< 1.5 kb), whereas MDA was inefficient. We conclude that pWGA is the most promising method for characterization of microbial communities in low-biomass environments and for currently planned astrobiological missions to Mars. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.

PubMed

Rubio-Portillo, Esther; Santos, Fernando; Martínez-García, Manuel; de Los Ríos, Asunción; Ascaso, Carmen; Souza-Egipsy, Virginia; Ramos-Esplá, Alfonso A; Anton, Josefa

2016-12-01

Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

Crustacean communities in coastal ephemeral pools in the Araucanía region (38° S, Chile).

PubMed

De Los Ríos-Escalante, P; Acevedo, P

2016-01-01

The fauna communities of ephemeral pools in southern Chile are characterized by heterogeneity of crustacean taxa; nevertheless, no detailed studies exist of their community structure. The aim of the present study was to analyze the crustacean community structure in two groups of ephemeral pools (Puaucho and Nigue pools) in the coastal zone of the Araucanía region. A correlation matrix was made by species abundance against temperature, conductivity, pH and total dissolved solids. In a second step, a null model for species co-occurrence was applied to the total data and to each group. The results for total data revealed a significant direct relation between the abundance of H. costera, C. dubia and Mesocyclops. For the Puaucho pools, the same results were found together with direct associations with total dissolved solids, conductivity and pH. Finally, different results were found for the Nigue pools, with no clear significant associations, either direct or indirect, between the abundance of different crustacean taxa and abiotic parameters. These results were supported by the co-occurrence null model analysis, which revealed the presence of regulator factors for the total data, and for each of the two groups. Ecological topics are discussed with emphasis on meta-community dynamics.

Solid state NMR: The essential technology for helical membrane protein structural characterization

PubMed Central

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-01-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed – neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. PMID:24412099

Solid state NMR: The essential technology for helical membrane protein structural characterization

NASA Astrophysics Data System (ADS)

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-02-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

A multi-decade time series of kelp forest community structure at San Nicolas Island, California

USGS Publications Warehouse

Lafferty, Kevin D.; Kenner, Michael C.; Estes, James A.; Tinker, M. Tim; Bodkin, James L.; Cowen, Robert K.; Harrold, Christopher; Novak, Mark; Rassweiler, Andrew; Reed, Daniel C.

2013-01-01

San Nicolas Island is surrounded by broad areas of shallow subtidal habitat, characterized by dynamic kelp forest communities that undergo dramatic and abrupt shifts in community composition. Although these reefs are fished, the physical isolation of the island means that they receive less impact from human activities than most reefs in Southern California, making San Nicolas an ideal place to evaluate alternative theories about the dynamics of these communities. Here we present monitoring data from seven sampling stations surrounding the island, including data on fish, invertebrate, and algal abundance. These data are unusual among subtidal monitoring data sets in that they combine relatively frequent sampling (twice per year) with an exceptionally long time series (since 1980). Other outstanding qualities of the data set are the high taxonomic resolution captured and the monitoring of permanent quadrats and swaths where the history of the community structure at specific locations has been recorded through time. Finally, the data span a period that includes two of the strongest ENSO events on record, a major shift in the Pacific decadal oscillation, and the reintroduction of sea otters to the island in 1987 after at least 150 years of absence. These events provide opportunities to evaluate the effects of bottom-up forcing, top-down control, and physical disturbance on shallow rocky reef communities.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

PubMed

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

PubMed Central

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G.

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem. PMID:25078273

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

Voting behavior, coalitions and government strength through a complex network analysis.

PubMed

Dal Maso, Carlo; Pompa, Gabriele; Puliga, Michelangelo; Riotta, Gianni; Chessa, Alessandro

2014-01-01

We analyze the network of relations between parliament members according to their voting behavior. In particular, we examine the emergent community structure with respect to political coalitions and government alliances. We rely on tools developed in the Complex Network literature to explore the core of these communities and use their topological features to develop new metrics for party polarization, internal coalition cohesiveness and government strength. As a case study, we focus on the Chamber of Deputies of the Italian Parliament, for which we are able to characterize the heterogeneity of the ruling coalition as well as parties specific contributions to the stability of the government over time. We find sharp contrast in the political debate which surprisingly does not imply a relevant structure based on established parties. We take a closer look to changes in the community structure after parties split up and their effect on the position of single deputies within communities. Finally, we introduce a way to track the stability of the government coalition over time that is able to discern the contribution of each member along with the impact of its possible defection. While our case study relies on the Italian parliament, whose relevance has come into the international spotlight in the present economic downturn, the methods developed here are entirely general and can therefore be applied to a multitude of other scenarios.

How plants connect pollination and herbivory networks and their contribution to community stability.

PubMed

Sauve, Alix M C; Thébault, Elisa; Pocock, Michael J O; Fontaine, Colin

2016-04-01

Pollination and herbivory networks have mainly been studied separately, highlighting their distinct structural characteristics and the related processes and dynamics. However, most plants interact with both pollinators and herbivores, and there is evidence that both types of interaction affect each other. Here we investigated the way plants connect these mutualistic and antagonistic networks together, and the consequences for community stability. Using an empirical data set, we show that the way plants connect pollination and herbivory networks is not random and promotes community stability. Analyses of the structure of binary and quantitative networks show different results: the plants' generalism with regard to pollinators is positively correlated to their generalism with regard to herbivores when considering binary interactions, but not when considering quantitative interactions. We also show that plants that share the same pollinators do not share the same herbivores. However, the way plants connect pollination and herbivory networks promotes stability for both binary and quantitative networks. Our results highlight the relevance of considering the diversity of interaction types in ecological communities, and stress the need to better quantify the costs and benefits of interactions, as well as to develop new metrics characterizing the way different interaction types are combined within ecological networks.

Community detection, link prediction, and layer interdependence in multilayer networks.

PubMed

De Bacco, Caterina; Power, Eleanor A; Larremore, Daniel B; Moore, Cristopher

2017-04-01

Complex systems are often characterized by distinct types of interactions between the same entities. These can be described as a multilayer network where each layer represents one type of interaction. These layers may be interdependent in complicated ways, revealing different kinds of structure in the network. In this work we present a generative model, and an efficient expectation-maximization algorithm, which allows us to perform inference tasks such as community detection and link prediction in this setting. Our model assumes overlapping communities that are common between the layers, while allowing these communities to affect each layer in a different way, including arbitrary mixtures of assortative, disassortative, or directed structure. It also gives us a mathematically principled way to define the interdependence between layers, by measuring how much information about one layer helps us predict links in another layer. In particular, this allows us to bundle layers together to compress redundant information and identify small groups of layers which suffice to predict the remaining layers accurately. We illustrate these findings by analyzing synthetic data and two real multilayer networks, one representing social support relationships among villagers in South India and the other representing shared genetic substring material between genes of the malaria parasite.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.

PubMed

Yao, Xie-Feng; Zhang, Jiu-Ming; Tian, Li; Guo, Jian-Hua

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Community detection, link prediction, and layer interdependence in multilayer networks

NASA Astrophysics Data System (ADS)

De Bacco, Caterina; Power, Eleanor A.; Larremore, Daniel B.; Moore, Cristopher

2017-04-01

Complex systems are often characterized by distinct types of interactions between the same entities. These can be described as a multilayer network where each layer represents one type of interaction. These layers may be interdependent in complicated ways, revealing different kinds of structure in the network. In this work we present a generative model, and an efficient expectation-maximization algorithm, which allows us to perform inference tasks such as community detection and link prediction in this setting. Our model assumes overlapping communities that are common between the layers, while allowing these communities to affect each layer in a different way, including arbitrary mixtures of assortative, disassortative, or directed structure. It also gives us a mathematically principled way to define the interdependence between layers, by measuring how much information about one layer helps us predict links in another layer. In particular, this allows us to bundle layers together to compress redundant information and identify small groups of layers which suffice to predict the remaining layers accurately. We illustrate these findings by analyzing synthetic data and two real multilayer networks, one representing social support relationships among villagers in South India and the other representing shared genetic substring material between genes of the malaria parasite.

Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil.

PubMed

Militon, Cécile; Boucher, Delphine; Vachelard, Cédric; Perchet, Geoffrey; Barra, Vincent; Troquet, Julien; Peyretaillade, Eric; Peyret, Pierre

2010-12-01

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.

Arsenic(V) Reduction in Relation to Iron(III) Transformation and Molecular Characterization of the Structural and Functional Microbial Community in Sediments of a Basin-Fill Aquifer in Northern Utah

PubMed Central

Mirza, Babur S.; Muruganandam, Subathra; Meng, Xianyu; Sorensen, Darwin L.; Dupont, R. Ryan

2014-01-01

Basin-fill aquifers of the Southwestern United States are associated with elevated concentrations of arsenic (As) in groundwater. Many private domestic wells in the Cache Valley Basin, UT, have As concentrations in excess of the U.S. EPA drinking water limit. Thirteen sediment cores were collected from the center of the valley at the depth of the shallow groundwater and were sectioned into layers based on redoxmorphic features. Three of the layers, two from redox transition zones and one from a depletion zone, were used to establish microcosms. Microcosms were treated with groundwater (GW) or groundwater plus glucose (GW+G) to investigate the extent of As reduction in relation to iron (Fe) transformation and characterize the microbial community structure and function by sequencing 16S rRNA and arsenate dissimilatory reductase (arrA) genes. Under the carbon-limited conditions of the GW treatment, As reduction was independent of Fe reduction, despite the abundance of sequences related to Geobacter and Shewanella, genera that include a variety of dissimilatory iron-reducing bacteria. The addition of glucose, an electron donor and carbon source, caused substantial shifts toward domination of the bacterial community by Clostridium-related organisms, and As reduction was correlated with Fe reduction for the sediments from the redox transition zone. The arrA gene sequencing from microcosms at day 54 of incubation showed the presence of 14 unique phylotypes, none of which were related to any previously described arrA gene sequence, suggesting a unique community of dissimilatory arsenate-respiring bacteria in the Cache Valley Basin. PMID:24632255

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.

Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers

NASA Astrophysics Data System (ADS)

Zoccarato, Luca; Pallavicini, Alberto; Cerino, Federica; Fonda Umani, Serena; Celussi, Mauro

2016-12-01

Deep-sea environments host the largest pool of microbes and represent the last largely unexplored and poorly known ecosystems on Earth. The Ross Sea is characterized by unique oceanographic dynamics and harbors several water masses deeply involved in cooling and ventilation of deep oceans. In this study the V9 region of the 18S rDNA was targeted and sequenced with the Ion Torrent high-throughput sequencing technology to unveil differences in protist communities (>2 μm) correlated with biogeochemical properties of the water masses. The analyzed samples were significantly different in terms of environmental parameters and community composition outlining significant structuring effects of temperature and salinity. Overall, Alveolata (especially Dinophyta), Stramenopiles and Excavata groups dominated mesopelagic and bathypelagic layers, and protist communities were shaped according to the biogeochemistry of the water masses (advection effect and mixing events). Newly-formed High Salinity Shelf Water (HSSW) was characterized by high relative abundance of phototrophic organisms that bloom at the surface during the austral summer. Oxygen-depleted Circumpolar Deep Water (CDW) showed higher abundance of Excavata, common bacterivores in deep water masses. At the shelf-break, Antarctic Bottom Water (AABW), formed by the entrainment of shelf waters in CDW, maintained the eukaryotic genetic signature typical of both parental water masses.

Landscape characterization of peridomestic risk for Lyme disease using satellite imagery

NASA Technical Reports Server (NTRS)

Dister, S. W.; Fish, D.; Bros, S. M.; Frank, D. H.; Wood, B. L.

1997-01-01

Remotely sensed characterizations of landscape composition were evaluated for Lyme disease exposure risk on 337 residential properties in two communities of suburban Westchester County, New York. Properties were categorized as no, low, or high risk based on seasonally adjusted densities of Ixodes scapularis nymphs, determined by drag sampling during June and July 1990. Spectral indices based on Landsat Thematic Mapper data provided relative measures of vegetation structure and moisture (wetness), as well as vegetation abundance (greenness). A geographic information system (GIS) was used to spatially quantify and relate the remotely sensed landscape variables to risk category. A comparison of the two communities showed that Chappaqua, which had more high-risk properties (P < 0.001), was significantly greener and wetter than Armonk (P < 0.001). Furthermore, within Chappaqua, high-risk properties were significantly greener and wetter than lower-risk properties in this community (P < 0.01). The high-risk properties appeared to contain a greater proportion of broadleaf trees, while lower-risk properties were interpreted as having a greater proportion of nonvegetative cover and/or open lawn. The ability to distinguish these fine scale differences among communities and individual properties illustrates the efficiency of a remote sensing/GIS-based approach for identifying peridomestic risk of Lyme disease over large geographic areas.

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters.

PubMed

Wang, Wanfeng; Guo, Yanling; Yang, Qingxiang; Huang, Yao; Zhu, Chunyou; Fan, Jing; Pan, Feng

2015-07-15

Two biofilters were constructed using biological activated carbon (BAC) and nitrosamine-containing water from two drinking water treatment plants. The microbiome of each biofilter was characterized by 454 high-throughput pyrosequencing, and one nitrosamine-reducing bacterium was isolated. The results showed that nitrosamines changed the relative abundance at both the phylum and class levels, and the new genera were observed in the microbial communities of the two BAC filters after cultivation. As such, the genus Rhodococcus, which includes many nitrosamine-reducing strains reported in previous studies, was only detected in the BAC2 filter after cultivation. These findings indicate that nitrosamines can significantly affect the genus level in the microbial communities. Furthermore, the isolated bacterial culture Rhodococcus cercidiphylli A41 AS-1 exhibited the ability to reduce five nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodi-n-propylamine, N-nitrosopyrrolidine, and N-nitrosodi-n-butylamine) with removal ratios that ranged from 38.1% to 85.4%. The isolate exhibited a better biodegradation ability with nitrosamine as the carbon source when compared with nitrosamine as the nitrogen source. This study increases our understanding of the microbial community in drinking water biofilters with trace quantities of nitrosamines, and provides information on the metabolism of nitrosamine-reducing bacteria. Copyright © 2015. Published by Elsevier B.V.

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

PubMed Central

Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O.; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A.; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs. PMID:29136658

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

Techtmann, Stephen M.; Fortney, Julian L.; Ayers, Kati A.

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbialmore » community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Furthermore, our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.« less

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia.

PubMed

Sugitani, K; Mimura, K; Takeuchi, M; Yamaguchi, T; Suzuki, K; Senda, R; Asahara, Y; Wallis, S; Van Kranendonk, M J

2015-11-01

The 3.4-Ga Strelley Pool Formation (SPF) at the informally named 'Waterfall Locality' in the Goldsworthy greenstone belt of the Pilbara Craton, Western Australia, provides deeper insights into ancient, shallow subaqueous to possibly subaerial ecosystems. Outcrops at this locality contain a thin (<3 m) unit of carbonaceous and non-carbonaceous cherts and silicified sandstones that were deposited in a shallow-water coastal environment, with hydrothermal activities, consistent with the previous studies. Carbonaceous, sulfide-rich massive black cherts with coniform structures up to 3 cm high are characterized by diverse rare earth elements (REE) signatures including enrichment of light [light rare earth elements (LREE)] or middle rare earth elements and by enrichment of heavy metals represented by Zn. The massive black cherts were likely deposited by mixing of hydrothermal and non-hydrothermal fluids. Coniform structures in the cherts are characterized by diffuse laminae composed of sulfide particles, suggesting that unlike stromatolites, they were formed dominantly through physico-chemical processes related to hydrothermal activity. The cherts yield microfossils identical to previously described carbonaceous films, small and large spheres, and lenticular microfossils. In addition, new morphological types such as clusters composed of large carbonaceous spheroids (20-40 μm across each) with fluffy or foam-like envelope are identified. Finely laminated carbonaceous cherts are devoid of heavy metals and characterized by the enrichment of LREE. This chert locally contains conical to domal structures characterized by truncation of laminae and trapping of detrital grains and is interpreted as siliceous stromatolite formed by very early or contemporaneous silicification of biomats with the contribution of silica-rich hydrothermal fluids. Biological affinities of described microfossils and microbes constructing siliceous stromatolites are under investigation. However, this study emphasizes how diverse the microbial community in Paleoarchean coastal hydrothermal environment was. We propose the diversity is at least partially due to the availability of various energy sources in this depositional environment including reducing chemicals and sunlight. © 2015 John Wiley & Sons Ltd.

Characterizing the Phylogenetic Tree Community Structure of a Protected Tropical Rain Forest Area in Cameroon

PubMed Central

Munoz, François; Couteron, Pierre; Hardy, Olivier J.; Sonké, Bonaventure

2014-01-01

Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world. PMID:24936786

The BioPlex Network: A Systematic Exploration of the Human Interactome.

PubMed

Huttlin, Edward L; Ting, Lily; Bruckner, Raphael J; Gebreab, Fana; Gygi, Melanie P; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E; De Camilli, Pietro; Paulo, Joao A; Harper, J Wade; Gygi, Steven P

2015-07-16

Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors. Copyright © 2015 Elsevier Inc. All rights reserved.

The BioPlex Network: A Systematic Exploration of the Human Interactome

PubMed Central

Huttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K.; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A.; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E.; DeCamilli, Pietro; Paulo, Joao A.; Harper, J. Wade; Gygi, Steven P.

2015-01-01

SUMMARY Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally-related proteins. Finally, BioPlex, in combination with other approaches can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial Amyotrophic Lateral Sclerosis perturb a defined community of interactors. PMID:26186194

Phylogenetic Characterization of Fecal Microbial Communities of Dogs Fed Diets with or without Supplemental Dietary Fiber Using 454 Pyrosequencing

PubMed Central

Middelbos, Ingmar S.; Vester Boler, Brittany M.; Qu, Ani; White, Bryan A.; Swanson, Kelly S.; Fahey, George C.

2010-01-01

Background Dogs suffer from many of the same maladies as humans that may be affected by the gut microbiome, but knowledge of the canine microbiome is incomplete. This work aimed to use 16S rDNA tag pyrosequencing to phylogenetically characterize hindgut microbiome in dogs and determine how consumption of dietary fiber affects community structure. Principal Findings Six healthy adult dogs were used in a crossover design. A control diet without supplemental fiber and a beet pulp-supplemented (7.5%) diet were fed. Fecal DNA was extracted and the V3 hypervariable region of the microbial 16S rDNA gene amplified using primers suitable for 454-pyrosequencing. Microbial diversity was assessed on random 2000-sequence subsamples of individual and pooled DNA samples by diet. Our dataset comprised 77,771 reads with an average length of 141 nt. Individual samples contained approximately 129 OTU, with Fusobacteria (23 – 40% of reads), Firmicutes (14 – 28% of reads) and Bacteroidetes (31 – 34% of reads) being co-dominant phyla. Feeding dietary fiber generally decreased Fusobacteria and increased Firmicutes, but these changes were not equally apparent in all dogs. UniFrac analysis revealed that structure of the gut microbiome was affected by diet and Firmicutes appeared to play a strong role in by-diet clustering. Conclusions Our data suggest three co-dominant bacterial phyla in the canine hindgut. Furthermore, a relatively small amount of dietary fiber changed the structure of the gut microbiome detectably. Our data are among the first to characterize the healthy canine gut microbiome using pyrosequencing and provide a basis for studies focused on devising dietary interventions for microbiome-associated diseases. PMID:20339542

Characterization and structure of hypomania in a British nonclinical adolescent sample.

PubMed

Hosang, Georgina M; Cardno, Alastair G; Freeman, Daniel; Ronald, Angelica

2017-01-01

This study aimed to test the validity of using the Hypomania Checklist-16 [HCL-16] to measure hypomania in a British adolescent community sample. Limited research is available concerning the characterization of hypomania among community adolescent samples, particularly in the UK, despite its potential importance for early intervention policy development. To explore the structure and characterization of hypomania in a British adolescent nonclinical cohort, over 1400 17 year olds (Mean=17.05 years; SD=0.88) completed the HCL-16 along with measures of different psychological and psychopathological dimensions. Principal components analysis revealed a 2-component solution for the HCL-16, described as active-elated and irritable/risk-taking. Hypomanic symptoms were significantly correlated with many psychopathological dimensions. There were distinct correlation patterns for the two HCL-16 subscales, with the irritability/risk-taking subscale showing significantly stronger associations with psychotic-like experiences, internalizing and externalizing problems, and reduced life satisfaction relative to the active-elated dimension. Adolescents at 'high-risk' for bipolar disorder reported more psychopathology relative to the comparison group. Absence of the clinical diagnosis of bipolar disorder in the sample means that the classification of the 'high-risk' group cannot be confirmed. The structure of the HCL-16 in this UK adolescent sample mirrored that observed in adult and clinical cohorts. The observed links between the HCL-16 and psychopathological dimensions that have been previously associated with both hypomania and bipolar disorder lend support to the HCL-16's validity as a hypomania instrument for adolescents. Better understanding of hypomania prior to adulthood has considerable potential for informing early intervention approaches. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities.

PubMed

Zhao, Yang-Guo; Zhang, Yi; She, Zonglian; Shi, Yue; Wang, Min; Gao, Mengchun; Guo, Liang

2017-09-01

Performance of microbial fuel cells (MFCs) was monitored during the influent nutrient change from lactate to glucose/acetate/propionate and then to lactate. Meanwhile, anodic microbial communities were characterized by culture-independent molecular biotechnologies. Results showed MFC performance recovered rapidly when the lactate was replaced by one of its metabolic intermediates acetate, while it needed a longer time to recover if lactate substrate was converted to glucose/propionate or acetate to lactate. Secondary lactate feed enhanced the enrichment of bacterial populations dominating in first lactate feed. Electricity-producing bacteria, Geobacter spp., and beneficial helpers, Anaeromusa spp. and Pseudomonas spp., revived from a low abundance as lactate secondary supply, but microbial communities were hard to achieve former profiles in structure and composition. Hence, microbial community profiles tended to recover when outside environmental condition were restored. Different substrates selected unique functional microbial populations.

Family characteristics of anxious ADHD children: preliminary results.

PubMed

Kepley, Hayden O; Ostrander, Rick

2007-02-01

To investigate the family environments of children in a community sample with ADHD and co-occurring anxiety. Family Environment Scale, Behavioral Assessment System for Children, and Structured Clinical Interview are administered to parents of children with ADHD with and without anxiety. ADHD families are uniformly less cohesive and expressive and possess more conflict than families representing the community sample. In contrast to community or nonanxious ADHD families, anxious ADHD families do not encourage independence and tend to be distinctly less assertive, self-sufficient, and autonomous. Although anxious and nonanxious ADHD children tend to have a uniformly high incidence of maternal ADHD, mothers of anxious ADHD children tend to display a much higher incidence of substance/alcohol abuse than either nonanxious or community participants. Findings are consistent with the notion that an insular, dependent, and somewhat controlling family environment characterizes families of children with ADHD and comorbid childhood anxiety.

Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

PubMed Central

Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

2014-01-01

While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

The impact of anticyclonic mesoscale structures on microbial food webs in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Christaki, U.; van Wambeke, F.; Lefevre, D.; Lagaria, A.; Prieur, L.; Pujo-Pay, M.; Grattepanche, J.-D.; Colombet, J.; Psarra, S.; Dolan, J. R.; Sime-Ngando, T.; Conan, P.; Weinbauer, M. G.; Moutin, T.

2011-01-01

The abundance and activity of the major members of the heterotrophic microbial community - from viruses to ciliates - were studied along a longitudinal transect across the Mediterranean Sea in the summer of 2008. The Mediterranean Sea is characterized by a west to the east gradient of deepening of DCM (deep chlorophyll maximum) and increasing oligotrophy reflected in gradients of heterotrophic microbial biomass and production. However, within this longitudinal trend, hydrological mesoscale features exist and likely influence microbial dynamics. We show here the importance of mesoscale structures by a description of the structure and function of the microbial food web through an investigation of 3 geographically distant eddies within a longitudinal transect. Three selected sites each located in the center of an anticyclonic eddy were intensively investigated: in the Algero-Provencal Basin (St. A), the Ionian Basin (St. B), and the Levantine Basin (St. C). The 3 geographically distant eddies showed the lowest values of the different heterotrophic compartments of the microbial food web, and except for viruses in site C, all stocks were higher in the neighboring stations outside the eddies. During our study the 3 eddies showed equilibrium between GCP (Gross Community Production) and DCR (Dark Community Respiration); moreover, the west-east (W-E) gradient was evident in terms of heterotrophic biomass but not in terms of production. Means of integrated PPp values were higher at site B (~190 mg C m-2 d-1) and about 15% lower at sites A and C (~160 mg C m-2 d-1). Net community production fluxes were similar at all three stations exhibiting equilibrium between gross community production and dark community respiration.

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system.

PubMed

Revetta, R P; Gomez-Alvarez, V; Gerke, T L; Santo Domingo, J W; Ashbolt, N J

2016-07-01

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e. groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to 18 months. Differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity were associated with the classes Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Firmicutes. After 9 months the biofilm bacterial community from both GW and SW were dominated by Mycobacterium species. The distribution of the dominant operational taxonomic unit (OTU) (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature. In this study, the biofilm community structure observed between GW and SW were dissimilar, while communities from different locations receiving SW did not show significant differences. The results suggest that source water and/or the water quality shaped by their respective treatment processes may play an important role in shaping the bacterial communities in the distribution system. In addition, several bacterial groups were present in all samples, suggesting that they are an integral part of the core microbiota of this DWDS. These results provide an ecological insight into biofilm bacterial structure in chlorine-treated drinking water influenced by different water sources and their respective treatment processes. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

PubMed Central

Wang, Shaoguo; Hu, Xiaopan; Jiao, Kangli; He, Xiangyi; Li, Zhiqiang; Wang, Jizeng

2016-01-01

Recently, high-throughput sequencing has improved the understanding of the microbiological etiology of caries, but the characteristics of the microbial community structure in the human oral cavity with and without caries are not completely clear. To better understand these characteristics, Illumina MiSeq high-throughput sequencing was utilized to analyze 20 salivary samples (10 caries-free and 10 caries) from subjects from the same town in Dongxiang, Gansu, China. A total of 5,113 OTUs (Operational Taxonomic Units, 97% cutoff) were characterized in all of the salivary samples obtained from the 20 subjects. A comparison of the two groups revealed that (i) the predominant phyla were constant between the two groups; (ii) the relative abundance of the genera Veillonella, Bifidobacterium, Selenomonas, Olsenella, Parascardovia, Scardovia, Chryseobacterium, Terrimonas, Burkholderia and Sporobacter was significantly higher in the group with caries (P < 0.05); and (iii) four genera with low relative abundance (< 0.01% on average), including two characteristic genera in caries (Chryseobacterium and Scardovia), significantly influenced the microbial community structure at the genus and OTU levels. Moreover, via co-occurrence and principal component analyses, the co-prevalence of the pathogenic genera was detected in the caries samples, but in the caries-free samples, the function of clustered genera was more random. This result suggests that a synergistic effect may be influencing the assembly of the caries microbial community, whereas competition may play a more dominant role in governing the microbial community in the caries-free group. Our findings regarding the characteristics of the microbial communities of the groups with and without caries might improve the understanding of the microbiological etiology of caries and might improve the prevention and cure of caries in the future. PMID:26784334

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef.

PubMed

Marcelino, Vanessa Rossetto; Morrow, Kathleen M; van Oppen, Madeleine J H; Bourne, David G; Verbruggen, Heroen

2017-10-01

The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO 2 reef (avg. pCO 2 811 μatm) is not significantly different from corals inhabiting reference sites (avg. pCO 2 357 μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro-organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen-fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA. © 2017 John Wiley & Sons Ltd.

Characterisation of the physical composition and microbial community structure of biofilms within a model full-scale drinking water distribution system.

PubMed

Fish, Katherine E; Collins, Richard; Green, Nicola H; Sharpe, Rebecca L; Douterelo, Isabel; Osborn, A Mark; Boxall, Joby B

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS.

Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

PubMed Central

Roder, Cornelia; Arif, Chatchanit; Daniels, Camille; Weil, Ernesto; Voolstra, Christian R

2014-01-01

Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases. PMID:24350609

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

PubMed Central

Fish, Katherine E.; Collins, Richard; Green, Nicola H.; Sharpe, Rebecca L.; Douterelo, Isabel; Osborn, A. Mark; Boxall, Joby B.

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS. PMID:25706303

Predicting the consequences of species loss using size-structured biodiversity approaches.

PubMed

Brose, Ulrich; Blanchard, Julia L; Eklöf, Anna; Galiana, Nuria; Hartvig, Martin; R Hirt, Myriam; Kalinkat, Gregor; Nordström, Marie C; O'Gorman, Eoin J; Rall, Björn C; Schneider, Florian D; Thébault, Elisa; Jacob, Ute

2017-05-01

Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss. © 2016 Cambridge Philosophical Society.

High Contrast Imaging of Exoplanets and Exoplanetary Systems with JWST

NASA Astrophysics Data System (ADS)

Hinkley, Sasha; Skemer, Andrew; Biller, Beth; Baraffe, I.; Bonnefoy, M.; Bowler, B.; Carter, A.; Chen, C.; Choquet, E.; Currie, T.; Danielski, C.; Fortney, J.; Grady, C.; Greenbaum, A.; Hines, D.; Janson, M.; Kalas, P.; Kennedy, G.; Kraus, A.; Lagrange, A.; Liu, M.; Marley, M.; Marois, C.; Matthews, B.; Mawet, D.; Metchev, S.; Meyer, M.; Millar-Blanchaer, M.; Perrin, M.; Pueyo, L.; Quanz, S.; Rameau, J.; Rodigas, T.; Sallum, S.; Sargent, B.; Schlieder, J.; Schneider, G.; Stapelfeldt, K.; Tremblin, P.; Vigan, A.; Ygouf, M.

2017-11-01

JWST will transform our ability to characterize directly imaged planets and circumstellar debris disks, including the first spectroscopic characterization of directly imaged exoplanets at wavelengths beyond 5 microns, providing a powerful diagnostic of cloud particle properties, atmospheric structure, and composition. To lay the groundwork for these science goals, we propose a 39-hour ERS program to rapidly establish optimal strategies for JWST high contrast imaging. We will acquire: a) coronagraphic imaging of a newly discovered exoplanet companion, and a well-studied circumstellar debris disk with NIRCam & MIRI; b) spectroscopy of a wide separation planetary mass companion with NIRSPEC & MIRI; and c) deep aperture masking interferometry with NIRISS. Our primary goals are to: 1) generate representative datasets in modes to be commonly used by the exoplanet and disk imaging communities; 2) deliver science enabling products to empower a broad user base to develop successful future investigations; and 3) carry out breakthrough science by characterizing exoplanets for the first time over their full spectral range from 2-28 microns, and debris disk spectrophotometry out to 15 microns sampling the 3 micron water ice feature. Our team represents the majority of the community dedicated to exoplanet and disk imaging and has decades of experience with high contrast imaging algorithms and pipelines. We have developed a collaboration management plan and several organized working groups to ensure we can rapidly and effectively deliver high quality Science Enabling Products to the community.

Infaunal macrobenthic community dynamics in a manipulated hyperhaline ecosystem: a long-term study

PubMed Central

2013-01-01

Background Understanding the responses of ecological communities to human-induced perturbations is crucial for establishing conservation goals. Ecological communities are dynamic entities undergoing fluctuations due to their intrinsic characteristics as well as anthropogenic pressures varying over time. In this respect, long-term studies, based on large spatial and temporal datasets, may provide useful information in understanding patterns and processes influencing the communities’ structure. Theoretical evidence suggests that a role of biodiversity is acting as a compensatory buffer against environmental variability by decreasing the temporal variance in ecosystem functioning and by raising the level of community response to perturbations through the selection of better performing species. Therefore, the spatial and temporal changes in the specialization of the community components may be used as an effective tool to monitor the effects of natural and anthropogenic alterations of the environment in dynamic systems. We examined the temporal dynamics of macroinvertebrate community structure in the hyperhaline habitat of Tarquinia Saltworks (central Italy). We aimed at: (i) investigating the relationships between the level of community specialization and the alterations of the environment across fourteen years; (ii) comparing the ability of aggregate community parameters such as the average abundance vs. species specialization in describing patterns of community composition. Results We arranged the data in three sub-sets according to three periods, each characterized by different environmental conditions. The mean abundance of sampled macroinvertebrates showed a significant change (p < 0.01) only in the community inhabiting the saltwork basin closely connected to the sea, characterized by the highest environmental variation (i.e. the coefficient of variation, CV, of the aggregate environmental variability over the study period, CVrange = 0.010 - 0.2). Here we found marine species like Modiolus adriaticus (Lamarck, 1819), Neanthes irrorata (Malmgren, 1867), and Amphiglena mediterranea (Leydig, 1851), which inhabited the saltworks during the halt period but disappeared during the subsequent eutrophication phase. Conversely, species specialization showed a significant decrease for each sampled community in the presence of habitat degradation and a recovery after ecological restoration. The widest fluctuations of specialization were recorded for the community inhabiting the saltwork basin with the highest long-term environmental variability. Conclusions Recent advances have shown how the increased temporal and spatial variability of species’ abundance within the communities may be a signal of habitat disturbance, even in the absence of an apparent decline. Such approach could also be used as a sensitive monitoring tool, able to detect whether or not communities are subjected to increasing biotic homogenization. Also, the increased functional similarity triggered by habitat degradation may impact on species at higher trophic levels, such as the waterbirds wintering in the area or using it as a stopover during migration. PMID:24192133

Phylogenetic constrains on mycorrhizal specificity in eight Dendrobium (Orchidaceae) species.

PubMed

Xing, Xiaoke; Ma, Xueting; Men, Jinxin; Chen, Yanhong; Guo, Shunxing

2017-05-01

Plant phylogeny constrains orchid mycorrhizal (OrM) fungal community composition in some orchids. Here, we investigated the structures of the OrM fungal communities of eight Dendrobium species in one niche to determine whether similarities in the OrM fungal communities correlated with the phylogeny of the host plants and whether the Dendrobium-OrM fungal interactions are phylogenetically conserved. A phylogeny based on DNA data was constructed for the eight coexisting Dendrobium species, and the OrM fungal communities were characterized by their roots. There were 31 different fungal lineages associated with the eight Dendrobium species. In total, 82.98% of the identified associations belonging to Tulasnellaceae, and a smaller proportion involved members of the unknown Basidiomycota (9.67%). Community analyses revealed that phylogenetically related Dendrobium tended to interact with a similar set of Tulasnellaceae fungi. The interactions between Dendrobium and Tulasnellaceae fungi were significantly influenced by the phylogenetic relationships among the Dendrobium species. Our results provide evidence that the mycorrhizal specificity in the eight coexisting Dendrobium species was phylogenetically conserved.

Invertebrate Metacommunity Structure and Dynamics in an Andean Glacial Stream Network Facing Climate Change

PubMed Central

Cauvy-Fraunié, Sophie; Espinosa, Rodrigo; Andino, Patricio; Jacobsen, Dean; Dangles, Olivier

2015-01-01

Under the ongoing climate change, understanding the mechanisms structuring the spatial distribution of aquatic species in glacial stream networks is of critical importance to predict the response of aquatic biodiversity in the face of glacier melting. In this study, we propose to use metacommunity theory as a conceptual framework to better understand how river network structure influences the spatial organization of aquatic communities in glacierized catchments. At 51 stream sites in an Andean glacierized catchment (Ecuador), we sampled benthic macroinvertebrates, measured physico-chemical and food resource conditions, and calculated geographical, altitudinal and glaciality distances among all sites. Using partial redundancy analysis, we partitioned community variation to evaluate the relative strength of environmental conditions (e.g., glaciality, food resource) vs. spatial processes (e.g., overland, watercourse, and downstream directional dispersal) in organizing the aquatic metacommunity. Results revealed that both environmental and spatial variables significantly explained community variation among sites. Among all environmental variables, the glacial influence component best explained community variation. Overland spatial variables based on geographical and altitudinal distances significantly affected community variation. Watercourse spatial variables based on glaciality distances had a unique significant effect on community variation. Within alpine catchment, glacial meltwater affects macroinvertebrate metacommunity structure in many ways. Indeed, the harsh environmental conditions characterizing glacial influence not only constitute the primary environmental filter but also, limit water-borne macroinvertebrate dispersal. Therefore, glacier runoff acts as an aquatic dispersal barrier, isolating species in headwater streams, and preventing non-adapted species to colonize throughout the entire stream network. Under a scenario of glacier runoff decrease, we expect a reduction in both environmental filtering and dispersal limitation, inducing a taxonomic homogenization of the aquatic fauna in glacierized catchments as well as the extinction of specialized species in headwater groundwater and glacier-fed streams, and consequently an irreversible reduction in regional diversity. PMID:26308853

Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A Series of Hands-On Collaborative Practical Sessions for Undergraduate Students

ERIC Educational Resources Information Center

Rodrigues, João P. G. L. M.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.

2016-01-01

Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These…

Geochemical and physical drivers of microbial community structure in hot spring ecosystems

NASA Astrophysics Data System (ADS)

Havig, J. R.; Hamilton, T. L.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.

2012-12-01

Microbial communities in natural systems are typically characterized using samples collected from a single time point, thereby neglecting the temporal dynamics that characterize natural systems. The composition of these communities obtained from single point samples is then related to the geochemistry and physical parameters of the environment. Since most microbial life is adapted to a relatively narrow ecological niche (multiplicity of physical and chemical parameters that characterize a local habitat), these assessments provide only modest insight into the controls on community composition. Temporal variation in temperature or geochemical composition would be expected to add another dimension to the complexity of niche space available to support microbial diversity, with systems that experience greater variation supporting a greater biodiversity until a point where the variability is too extreme. . Hot springs often exhibit significant temporal variation, both in physical as well as chemical characteristics. This is a result of subsurface processes including boiling, phase separation, and differential mixing of liquid and vapor phase constituents. These characteristics of geothermal systems, which vary significantly over short periods of time, provide ideal natural laboratories for investigating how i) the extent of microbial community biodiversity and ii) the composition of those communities are shaped by temporal fluctuations in geochemistry. Geochemical and molecular samples were collected from 17 temporally variable hot springs across Yellowstone National Park, Wyoming. Temperature measurements using data-logging thermocouples, allowing accurate determination of temperature maximums, minimums, and ranges for each collection site, were collected in parallel, along with multiple geochemical characterizations as conditions varied. There were significant variations in temperature maxima (54.5 to 90.5°C), minima (12.5 to 82.5°C), and range (3.5 to 77.5°C) for the hot spring environments that spanned ranges of pH values (2.2 to 9.0) and geochemical compositions. We characterized the abundance, composition, and phylogenetic diversity of bacterial and archaeal 16S rRNA gene assemblages in sediment/biofilm samples collected from each site. 16S data can be used as proxy for metabolic dissimilarity. We predict that temporally fluctuating environments should provide additional complexity to the system (additional niche space) capable of supporting additional taxa, which should lead to greater 16S rRNA gene diversity. However, systems with too much variability should collapse the diversity. Thus, one would expect an optimal system for variability, with respect to 16S phylogenetic diversity. Community ecology tools were then applied to model the relative influence of physical and chemical characteristics (including temperature dynamics) on the local biodiversity. The results reveal unique insight into the role of temporal environmental variation in the development of biodiverse communities and provide a platform for predicting the response of an ecosystem to temperature perturbation.

Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure

USGS Publications Warehouse

Meador, M.R.; McIntyre, J.P.; Pollock, K.H.

2003-01-01

Two-pass backpack electrofishing data collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program were analyzed to assess the efficacy of single-pass backpack electrofishing. A two-capture removal model was used to estimate, within 10 river basins across the United States, proportional fish species richness from one-pass electrofishing and probabilities of detection for individual fish species. Mean estimated species richness from first-pass sampling (ps1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, ps1 values for individual sites ranged from 40% to 100% of estimated total species richness. Additional species unique to the second pass were collected in 50.3% of the samples. Of these, cyprinids and centrarchids were collected most frequently. Proportional fish species richness estimated for the first pass increased significantly with decreasing stream width for 1 of the 10 river basins. When used to calculate probabilities of detection of individual fish species, the removal model failed 48% of the time because the number of individuals of a species was greater in the second pass than in the first pass. Single-pass backpack electrofishing data alone may make it difficult to determine whether characterized fish community structure data are real or spurious. The two-pass removal model can be used to assess the effectiveness of sampling species richness with a single electrofishing pass. However, the two-pass removal model may have limited utility to determine probabilities of detection of individual species and, thus, limit the ability to assess the effectiveness of single-pass sampling to characterize species relative abundances. Multiple-pass (at least three passes) backpack electrofishing at a large number of sites may not be cost-effective as part of a standardized sampling protocol for large-geographic-scale studies. However, multiple-pass electrofishing at some sites may be necessary to better evaluate the adequacy of single-pass electrofishing and to help make meaningful interpretations of fish community structure.

Window Area and Development Drive Spatial Variation in Bird-Window Collisions in an Urban Landscape

PubMed Central

Hager, Stephen B.; Cosentino, Bradley J.; McKay, Kelly J.; Monson, Cathleen; Zuurdeeg, Walt; Blevins, Brian

2013-01-01

Collisions with windows are an important human-related threat to birds in urban landscapes. However, the proximate drivers of collisions are not well understood, and no study has examined spatial variation in mortality in an urban setting. We hypothesized that the number of fatalities at buildings varies with window area and habitat features that influence avian community structure. In 2010 we documented bird-window collisions (BWCs) and characterized avian community structure at 20 buildings in an urban landscape in northwestern Illinois, USA. For each building and season, we conducted 21 daily surveys for carcasses and nine point count surveys to estimate relative abundance, richness, and diversity. Our sampling design was informed by experimentally estimated carcass persistence times and detection probabilities. We used linear and generalized linear mixed models to evaluate how habitat features influenced community structure and how mortality was affected by window area and factors that correlated with community structure. The most-supported model was consistent for all community indices and included effects of season, development, and distance to vegetated lots. BWCs were related positively to window area and negatively to development. We documented mortalities for 16/72 (22%) species (34 total carcasses) recorded at buildings, and BWCs were greater for juveniles than adults. Based on the most-supported model of BWCs, the median number of annual predicted fatalities at study buildings was 3 (range = 0–52). These results suggest that patchily distributed environmental resources and levels of window area in buildings create spatial variation in BWCs within and among urban areas. Current mortality estimates place little emphasis on spatial variation, which precludes a fundamental understanding of the issue. To focus conservation efforts, we illustrate how knowledge of the structural and environmental factors that influence bird-window collisions can be used to predict fatalities in the broader landscape. PMID:23326420

Window area and development drive spatial variation in bird-window collisions in an urban landscape.

PubMed

Hager, Stephen B; Cosentino, Bradley J; McKay, Kelly J; Monson, Cathleen; Zuurdeeg, Walt; Blevins, Brian

2013-01-01

Collisions with windows are an important human-related threat to birds in urban landscapes. However, the proximate drivers of collisions are not well understood, and no study has examined spatial variation in mortality in an urban setting. We hypothesized that the number of fatalities at buildings varies with window area and habitat features that influence avian community structure. In 2010 we documented bird-window collisions (BWCs) and characterized avian community structure at 20 buildings in an urban landscape in northwestern Illinois, USA. For each building and season, we conducted 21 daily surveys for carcasses and nine point count surveys to estimate relative abundance, richness, and diversity. Our sampling design was informed by experimentally estimated carcass persistence times and detection probabilities. We used linear and generalized linear mixed models to evaluate how habitat features influenced community structure and how mortality was affected by window area and factors that correlated with community structure. The most-supported model was consistent for all community indices and included effects of season, development, and distance to vegetated lots. BWCs were related positively to window area and negatively to development. We documented mortalities for 16/72 (22%) species (34 total carcasses) recorded at buildings, and BWCs were greater for juveniles than adults. Based on the most-supported model of BWCs, the median number of annual predicted fatalities at study buildings was 3 (range = 0-52). These results suggest that patchily distributed environmental resources and levels of window area in buildings create spatial variation in BWCs within and among urban areas. Current mortality estimates place little emphasis on spatial variation, which precludes a fundamental understanding of the issue. To focus conservation efforts, we illustrate how knowledge of the structural and environmental factors that influence bird-window collisions can be used to predict fatalities in the broader landscape.

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

PubMed Central

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate. PMID:25202990

Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells.

PubMed

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status.

PubMed

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-04-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.

Structure and phylogenetic diversity of post-fire ectomycorrhizal communities of maritime pine.

PubMed

Rincón, A; Santamaría, B P; Ocaña, L; Verdú, M

2014-02-01

Environmental disturbances define the diversity and assemblage of species, affecting the functioning of ecosystems. Fire is a major disturbance of Mediterranean pine forests. Pines are highly dependent on the ectomycorrhizal (EM) fungal symbiosis, which is critical for tree recruitment under primary succession. To determine the effects of time since fire on the structure and recovery of EM fungal communities, we surveyed the young Pinus pinaster regenerate in three sites differing in the elapsed time after the last fire event. Pine roots were collected, and EM fungi characterized by sequencing the internal transcribed spacer (ITS) and the large subunit (LSU) regions of the nuclear ribosomal (nr)-DNA. The effects of the elapsed time after fire on the EM community structure (richness, presence/absence of fungi, phylogenetic diversity) and on soil properties were analysed.Fungal richness decreased with the elapsed time since the fire; although, the phylogenetic diversity of the EM community increased. Soil properties were different depending on the elapsed time after fire and particularly, the organic matter, carbon-to-nitrogen (C/N) ratio, nitrogen and iron significantly correlated with the assemblage of fungal species. Ascomycetes, particularly Tuberaceae and Pezizales, were significantly over-represented on saplings in the burned site. On seedlings, a significant over-representation of Rhizopogonaceae and Atheliaceae was observed in the most recently burned site, while other fungi (i.e. Cortinariaceae) were significantly under-represented. Our results are consistent with the hypothesis that fire can act as a selective agent by printing a phylogenetic signal on the EM fungal communities associated with naturally regenerated pines, pointing out to some groups as potential fire-adapted fungi.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

PubMed Central

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-01-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status. PMID:20927139

Spatio-temporal distribution patterns of the epibenthic community in the coastal waters of Suriname

NASA Astrophysics Data System (ADS)

Willems, Tomas; De Backer, Annelies; Wan Tong You, Kenneth; Vincx, Magda; Hostens, Kris

2015-10-01

This study aimed to characterize the spatio-temporal patterns of the epibenthic community in the coastal waters of Suriname. Data were collected on a (bi)monthly basis in 2012-2013 at 15 locations in the shallow (<40 m) coastal area, revealing three spatially distinct species assemblages, related to clear gradients in some environmental parameters. A species-poor coastal assemblage was discerned within the muddy, turbid-water zone (6-20 m depth), dominated by Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Penaeoidea). Near the 30 m isobath, sediments were much coarser (median grain size on average 345±103 μm vs. 128±53 μm in the coastal assemblage) and water transparency was much higher (on average 7.6±3.5 m vs. 2.4±2.1 m in the coastal assemblage). In this zone, a diverse offshore assemblage was found, characterized by brittle stars (mainly Ophioderma brevispina and Ophiolepis elegans) and a variety of crabs, sea stars and hermit crabs. In between both zones, a transition assemblage was noted, with epibenthic species typically found in either the coastal or offshore assemblages, but mainly characterized by the absence of X. kroyeri. Although the epibenthic community was primarily structured in an on-offshore gradient related to depth, sediment grain size and sediment total organic carbon content, a longitudinal (west-east) gradient was apparent as well. The zones in the eastern part of the Suriname coastal shelf seemed to be more widely stretched along the on-offshore gradient. Although clear seasonal differences were noted in the environmental characteristics (e.g. dry vs. rainy season), this was not reflected in the epibenthic community structure. X. kroyeri reached very high densities (up to 1383 ind 1000 m-²) in the shallow coastal waters of Suriname. As X. kroyeri is increasingly exploited throughout its range, the current study provides the ecological context for its presence and abundance, which is crucial for an ecosystem approach and the sustainable management of this commercially important species and its habitat.

Bacterial community changes in an industrial algae production system.

PubMed

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Echo Chambers: Emotional Contagion and Group Polarization on Facebook.

PubMed

Del Vicario, Michela; Vivaldo, Gianna; Bessi, Alessandro; Zollo, Fabiana; Scala, Antonio; Caldarelli, Guido; Quattrociocchi, Walter

2016-12-01

Recent findings showed that users on Facebook tend to select information that adhere to their system of beliefs and to form polarized groups - i.e., echo chambers. Such a tendency dominates information cascades and might affect public debates on social relevant issues. In this work we explore the structural evolution of communities of interest by accounting for users emotions and engagement. Focusing on the Facebook pages reporting on scientific and conspiracy content, we characterize the evolution of the size of the two communities by fitting daily resolution data with three growth models - i.e. the Gompertz model, the Logistic model, and the Log-logistic model. Although all the models appropriately describe the data structure, the Logistic one shows the best fit. Then, we explore the interplay between emotional state and engagement of users in the group dynamics. Our findings show that communities' emotional behavior is affected by the users' involvement inside the echo chamber. Indeed, to an higher involvement corresponds a more negative approach. Moreover, we observe that, on average, more active users show a faster shift towards the negativity than less active ones.

Evolution of network architecture in a granular material under compression

NASA Astrophysics Data System (ADS)

Bassett, Danielle

As a granular material is compressed, the particles and forces within the system arrange to form complex and heterogeneous collective structures. However, capturing and characterizing the dynamic nature of the intrinsic inhomogeneity and mesoscale architecture of granular systems can be challenging. Here, we utilize multilayer networks as a framework for directly quantifying the evolution of mesoscale architecture in a compressed granular system. We examine a quasi-two-dimensional aggregate of photoelastic disks, subject to biaxial compressions through a series of small, quasistatic steps. Treating particles as network nodes and inter-particle forces as network edges, we construct a multilayer network for the system by linking together the series of static force networks that exist at each strain step. We then extract the inherent mesoscale structure from the system by using a generalization of community detection methods to multilayer networks, and we define quantitative measures to characterize the reconfiguration and evolution of this structure throughout the compression process. To test the sensitivity of the network model to particle properties, we examine whether the method can distinguish a subsystem of low-friction particles within a bath of higher-friction particles. We find that this can be done by considering the network of tangential forces, and that the community structure is better able to separate the subsystem than consideration of the local inter-particle forces alone. The results discussed throughout this study suggest that these novel network science techniques may provide a direct way to compare and classify data from systems under different external conditions or with different physical makeup. National Science Foundation (BCS-1441502, PHY-1554488, and BCS-1631550).

Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere

PubMed Central

Stres, Blaz; Sul, Woo Jun; Murovec, Bostjan; Tiedje, James M.

2013-01-01

Background The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events. Methodology/Principal Findings Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4–12 µm) suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. Cyanobacteria represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (co)deposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria. Conclusions/Significance The spatial, environmental and temporal complexity of the high-altitude soils of the Himalaya generates ongoing disturbance and colonization events that subject heterogeneous microniches to stochastic colonization by far away dust associated microbes and result in the observed spatially divergent bacterial communities. PMID:24086740

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

PubMed

Bowman, Elizabeth A; Arnold, A Elizabeth

2018-04-01

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

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

PubMed Central

Oates, Lawrence G.; Read, Harry W.; Gutknecht, Jessica L. M.; Duncan, David S.; Balser, Teri B.; Jackson, Randall D.

2017-01-01

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step. PMID:28745639

Inferring community properties of benthic macroinvertebrates in streams using Shannon index and exergy

NASA Astrophysics Data System (ADS)

Nguyen, Tuyen Van; Cho, Woon-Seok; Kim, Hungsoo; Jung, Il Hyo; Kim, YongKuk; Chon, Tae-Soo

2014-03-01

Definition of ecological integrity based on community analysis has long been a critical issue in risk assessment for sustainable ecosystem management. In this work, two indices (i.e., Shannon index and exergy) were selected for the analysis of community properties of benthic macroinvertebrate community in streams in Korea. For this purpose, the means and variances of both indices were analyzed. The results found an extra scope of structural and functional properties in communities in response to environmental variabilities and anthropogenic disturbances. The combination of these two parameters (four indices) was feasible in identification of disturbance agents (e.g., industrial pollution or organic pollution) and specifying states of communities. The four-aforementioned parameters (means and variances of Shannon index and exergy) were further used as input data in a self-organizing map for the characterization of water quality. Our results suggested that Shannon index and exergy in combination could be utilized as a suitable reference system and would be an efficient tool for assessment of the health of aquatic ecosystems exposed to environmental disturbances.

Interconnected microbiomes and resistomes in low-income human habitats

PubMed Central

Pehrsson, Erica C.; Tsukayama, Pablo; Patel, Sanket; Mejía-Bautista, Melissa; Sosa-Soto, Giordano; Navarrete, Karla M.; Calderon, Maritza; Cabrera, Lilia; Hoyos-Arango, William; Bertoli, M. Teresita; Berg, Douglas E.; Gilman, Robert H.; Dantas, Gautam

2016-01-01

Summary Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by resistance gene exchange between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. We characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human fecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely-used excreta management strategies in reducing fecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance dissemination across interconnected habitats in settings representing over two-thirds of the world’s population. PMID:27172044

Microbial structure and chemical components of aerosols caused by rotating brushes in a wastewater treatment plant.

PubMed

Han, Yunping; Li, Lin; Liu, Junxin; Zhang, Mengzhu

2012-11-01

Bacterial community structure and the chemical components in aerosols caused by rotating brushes in an Orbal oxidation ditch were assessed in a Beijing municipal wastewater treatment plant. Air samples were collected at different distances from the aerosol-generating rotating brushes. Molecular culture-independent methods were used to characterize the community structure of the airborne bacteria in each sample regardless of cell culturability. A clone library of 16S rDNA directly amplified from air DNA of each sample was constructed and sequenced to analyze the community composition and diversity. Insoluble particles and water-soluble ions emitted with microorganisms in aerosols were analysis by a scanning electron microscope together with energy dispersive X-ray spectroscopy and ion chromatogram analyzer. In total, most of the identified bacteria were Proteobacteria. The majority of sequences near the rotating brushes (the main source of the bioaerosols) were Proteobacteria (62.97 %) with β-(18.52 %) and γ-(44.45 %) subgroups and Bacteroidetes (29.63 %). Complex patterns were observed for each sampling location, suggesting a highly diverse community structure, comparable to that found in water in the Orbal oxidation ditch. Accompany with microorganisms, 46.36 μg/m(3) of SO (4) (2-) , 29.35 μg/m(3) of Cl(-), 21.51 μg/m(3) of NO (3) (-) , 19.76 μg/m(3) of NH (4) (+) , 11.42 μg/m(3) of PO (4) (3-) , 6.18 μg/m(3) of NO (2) (-) , and elements of Mg, Cl, K, Na, Fe, S, and P were detected from the air near the aerosols source. Differences in the structure of the bacterial communities and chemical components in the aerosols observed between sampling sites indicated important site-related variability. The composition of microorganisms in water was one of the most important sources of bacterial communities in bioaerosols. Chemical components in bioaerosols may provide a media for airborne microorganism attachment, as well as a suitable microenvironment for their growth and survival in the air. This study will be benefit for the formulation of pollution standards, especially for aerosols, that take into account plant workers' health.

Mapping Plant Diversity and Composition Across North Carolina Piedmont Forest Landscapes Using Lidar-Hyperspectral Remote Sensing

NASA Astrophysics Data System (ADS)

Hakkenberg, Christopher R.

Forest modification, from local stress to global change, has given rise to efforts to model, map, and monitor critical properties of forest communities like structure, composition, and diversity. Predictive models based on data from spatially-nested field plots and LiDAR-hyperspectral remote sensing systems are one particularly effective means towards the otherwise prohibitively resource-intensive task of consistently characterizing forest community dynamics at landscape scales. However, to date, most predictive models fail to account for actual (rather than idealized) species and community distributions, are unsuccessful in predicting understory components in structurally and taxonomically heterogeneous forests, and may suffer from diminished predictive accuracy due to incongruity in scale and precision between field plot samples, remotely-sensed data, and target biota of varying size and density. This three-part study addresses these and other concerns in the modeling and mapping of emergent properties of forest communities by shifting the scope of prediction from the individual or taxon to the whole stand or community. It is, after all, at the stand scale where emergent properties like functional processes, biodiversity, and habitat aggregate and manifest. In the first study, I explore the relationship between forest structure (a proxy for successional demographics and resource competition) and tree species diversity in the North Carolina Piedmont, highlighting the empirical basis and potential for utilizing forest structure from LiDAR in predictive models of tree species diversity. I then extend these conclusions to map landscape pattern in multi-scale vascular plant diversity as well as turnover in community-continua at varying compositional resolutions in a North Carolina Piedmont landscape using remotely-sensed LiDAR-hyperspectral estimates of topography, canopy structure, and foliar biochemistry. Recognizing that the distinction between correlation and causation mirrors that between knowledge and understanding, all three studies distinguish between prediction of pattern and inference of process. Thus, in addition to advancing mapping methodologies relevant to a range of forest ecosystem management and monitoring applications, all three studies are noteworthy for assessing the ecological relationship between environmental predictors and emergent landscape patterns in plant composition and diversity in North Carolina Piedmont forests.

Sex worker-led structural interventions in India: a case study on addressing violence in HIV prevention through the Ashodaya Samithi collective in Mysore

PubMed Central

Reza-Paul, Sushena; Lorway, Rob; O’Brien, Nadia; Lazarus, Lisa; Jain, Jinendra; Bhagya, M.; Fathima, Mary P; Venukumar, KT; Raviprakash, K.N.; Baer, James; Steen, Richard

2012-01-01

Background & objectives: Structural interventions have the capacity to improve the outcomes of HIV/AIDS interventions by changing the social, economic, political or environmental factors that determine risk and vulnerability. Marginalized groups face disproportionate barriers to health, and sex workers are among those at highest risk of HIV in India. Evidence in India and globally has shown that sex workers face violence in many forms ranging from verbal, psychological and emotional abuse to economic extortion, physical and sexual violence and this is directly linked to lower levels of condom use and higher levels of sexually transmitted infections (STIs), the most critical determinants of HIV risk. We present here a case study of an intervention that mobilized sex workers to lead an HIV prevention response that addresses violence in their daily lives. Methods: This study draws on ethnographic research and project monitoring data from a community-led structural intervention in Mysore, India, implemented by Ashodaya Samithi. Qualitative and quantitative data were used to characterize baseline conditions, community responses and subsequent outcomes related to violence. Results: In 2004, the incidence of reported violence by sex workers was extremely high (> 8 incidents per sex worker, per year) but decreased by 84 per cent over 5 years. Violence by police and anti-social elements, initially most common, decreased substantially after a safe space was established for sex workers to meet and crisis management and advocacy were initiated with different stakeholders. Violence by clients, decreased after working with lodge owners to improve safety. However, initial increases in intimate partner violence were reported, and may be explained by two factors: (i) increased willingness to report such incidents; and (ii) increased violence as a reaction to sex workers’ growing empowerment. Trafficking was addressed through the establishment of a self-regulatory board (SRB). The community's progressive response to violence was enabled by advancing community mobilization, ensuring community ownership of the intervention, and shifting structural vulnerabilities, whereby sex workers increasingly engaged key actors in support of a more enabling environment. Interpretation & conclusions: Ashodaya's community-led response to violence at multiple levels proved highly synergistic and effective in reducing structural violence. PMID:22382190

Microbial Community Responses to Glycine Addition in Kansas Prairie Soils

NASA Astrophysics Data System (ADS)

Bottos, E.; Roy Chowdhury, T.; White, R. A., III; Brislawn, C.; Fansler, S.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.

2015-12-01

Advances in sequencing technologies are rapidly expanding our abilities to unravel aspects of microbial community structure and function in complex systems like soil; however, characterizing the highly diverse communities is problematic, due primarily to challenges in data analysis. To tackle this problem, we aimed to constrain the microbial diversity in a soil by enriching for particular functional groups within a community through addition of "trigger substrates". Such trigger substrates, characterized by low molecular weight, readily soluble and diffusible in soil solution, representative of soil organic matter derivatives, would also be rapidly degradable. A relatively small energy investment to maintain the cell in a state of metabolic alertness for such substrates would be a better evolutionary strategy and presumably select for a cohort of microorganisms with the energetics and cellular machinery for utilization and growth. We chose glycine, a free amino acid (AA) known to have short turnover times (in the range of hours) in soil. As such, AAs are a good source of nitrogen and easily degradable, and can serve as building blocks for microbial proteins and other biomass components. We hypothesized that the addition of glycine as a trigger substrate will decrease microbial diversity and evenness, as taxa capable of metabolizing it are enriched in relation to those that are not. We tested this hypothesis by incubating three Kansas native prairie soils with glycine for 24 hours at 21 degree Celsius, and measured community level responses by 16S rRNA gene sequencing, metagenomics, and metatranscriptomics. Preliminary evaluation of 16S rRNA gene sequences revealed minor changes in bacterial community composition in response to glycine addition. We will also present data on functional gene abundance and expression. The results of these analyses will be useful in designing sequencing strategies aimed at dissecting and deciphering complex microbial communities.

A new methodology to assess antimicrobial resistance of bacteria in coastal waters; pilot study in a Mediterranean hydrosystem

NASA Astrophysics Data System (ADS)

Almakki, Ayad; Estèves, Kevin; Vanhove, Audrey S.; Mosser, Thomas; Aujoulat, Fabien; Marchandin, Hélène; Toubiana, Mylène; Monfort, Patrick; Jumas-Bilak, Estelle; Licznar-Fajardo, Patricia

2017-10-01

The global resistome of coastal waters has been less studied than that of other waters, including marine ones. Here we develop an original method for characterizing the antimicrobial resistance of bacterial communities in coastal waters. The method combines the determination of a new parameter, the community Inhibitory Concentration (c-IC) of antibiotics (ATBs), and the description of the taxonomic richness of the resistant bacteria. We test the method in a Mediterranean hydrosystem, in the Montpellier region, France. Three types of waters are analyzed: near coastal river waters (Lez), lagoon brackish waters (Mauguio), and lake freshwaters (Salagou). Bacterial communities are grown in vitro in various conditions of temperature, salinity, and ATB concentrations. From these experiments, we determine the concentrations of ATB that decrease the bacterial community abundance by 50% (c-IC50) and by 90% (c-IC90). In parallel, we determine the taxonomic repertory of the resistant growing bacteria communities (repertory of Operational Taxonomic Units [OTU]). Temperature and salinity influence the abundance of the cultivable bacteria in presence of ATBs and hence the c-ICs. Very low ATB concentrations can decrease the bacterial abundance significantly. Beside a few ubiquitous genera (Bacillus, Pseudomonas, Shewanella, Vibrio), most resistant OTUs are specific of a type of water. In brackish water, resistant OTUs are more diverse and their community structure less vulnerable to ATBs than those in freshwater. We anticipate that c-IC measurement combined with taxonomic description can be applied to any littoral region to characterize the resistant bacterial communities in the coastal waters. This would help us to evaluate the vulnerability of aquatic ecosystems to antimicrobial pressure.

Microsatellite loci in two epiphytic lichens with contrasting dispersal modes: Nephroma laevigatum and N. parile (Nephromataceae)1

PubMed Central

Belinchón, Rocío; Ellis, Christopher J.; Yahr, Rebecca

2014-01-01

• Premise of the study: Microsatellite markers were characterized for two epiphytic cyanolichens, Nephroma laevigatum and N. parile (Nephromataceae), and will be used to investigate population structure and estimate gene flow among populations of these two closely related species with contrasting dispersal modes. • Methods and Results: Twelve and 14 microsatellite loci were characterized for N. laevigatum and N. parile, respectively. Allele number in N. laevigatum ranged from three to 13 per locus, while in N. parile there were from two to six alleles per locus. As expected, the sexually reproducing N. laevigatum had higher genetic diversity than the predominantly asexual N. parile. • Conclusions: This new set of markers is suitable for studying population structure and providing insights into gene flow among populations and for understanding processes of diversification. Compared between the species, they will facilitate an understanding of the influence of contrasting reproductive strategies on population and community structure. PMID:25383271

High resolution multi-facies realizations of sedimentary reservoir and aquifer analogs

PubMed Central

Bayer, Peter; Comunian, Alessandro; Höyng, Dominik; Mariethoz, Gregoire

2015-01-01

Geological structures are by nature inaccessible to direct observation. This can cause difficulties in applications where a spatially explicit representation of such structures is required, in particular when modelling fluid migration in geological formations. An increasing trend in recent years has been to use analogs to palliate this lack of knowledge, i.e., exploiting the spatial information from sites where the geology is accessible (outcrops, quarry sites) and transferring the observed properties to a study site deemed geologically similar. While this approach is appealing, it is difficult to put in place because of the lack of access to well-documented analog data. In this paper we present comprehensive analog data sets which characterize sedimentary structures from important groundwater hosting formations in Germany and Brazil. Multiple 2-D outcrop faces are described in terms of hydraulic, thermal and chemical properties and interpolated in 3-D using stochastic techniques. These unique data sets can be used by the wider community to implement analog approaches for characterizing reservoir and aquifer formations. PMID:26175910

Boundary Layer Characterization during Perdigão Field Campaign 2017

NASA Astrophysics Data System (ADS)

Leo, L. S.; Salvadore, J. J.; Belo-Pereira, M.; Menke, R.; Gomes, S.; Krishnamurthy, R.; Brown, W. O. J.; Creegan, E.; Klein, P. M.; Wildmann, N.; Oncley, S.; Fernando, J.; Mann, J.

2017-12-01

The depth and structure of the atmospheric boundary layer (ABL) significantly impact the performances of wind farms located in complex terrain environments, since low-level jets and other flow structures in the proximity of hills and mountains determine the weather extremes, such as shear layer instabilities, lee/internal wave breaking, etc. which in turn profoundly modify the turbulence profile at wind turbine relevant heights.A suite of instruments was deployed covering a double-ridge in central Portugal near the town of Perdigão in 2016-2017, and they are used here to characterize the ABL structure over complex terrain during the Intensive Observational Period (IOP, May 1- June 15, 2017) of the research field program dubbed "Perdigão". Firstly, the methodology adopted in this work to estimate the BL height will be discussed; secondly, an overview of the BL depth and characteristics during Perdigão-IOP campaign will be provided, with emphasis on case studies of interest for both the wind-power and boundary-layer communities.

Emergence of communities and diversity in social networks

PubMed Central

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross

2017-01-01

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics. PMID:28235785

Emergence of communities and diversity in social networks.

PubMed

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross; Stanley, H Eugene

2017-03-14

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics.

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

PubMed Central

Tang, Haixu; Li, Sujun; Ye, Yuzhen

2016-01-01

Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra. This approach is often limited because protein coding genes predicted from metagenomes are incomplete and fragmental. In this paper, we present a graph-centric approach to improving metagenome-guided peptide and protein identification in metaproteomics. Our method exploits the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensive database of protein sequences encoded in the community. We tested our method using several public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acquired from complex microbial communities in a biological wastewater treatment plant. The results showed that many more peptides and proteins can be identified when assembly graphs were utilized, improving the characterization of the proteins expressed in the microbial communities. The additional proteins we identified contribute to the characterization of important pathways such as those involved in degradation of chemical hazards. Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro. PMID:27918579

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

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.

Across a set of ecological communities connected to each other through organismal dispersal (a ‘meta-community’), turnover in composition is governed by (ecological) Drift, Selection, and Dispersal Limitation. Quantitative estimates of these processes remain elusive, but would represent a common currency needed to unify community ecology. Using a novel analytical framework we quantitatively estimate the relative influences of Drift, Selection, and Dispersal Limitation on subsurface, sediment-associated microbial meta-communities. The communities we study are distributed across two geologic formations encompassing ~12,500m3 of uranium-contaminated sediments within the Hanford Site in eastern Washington State. We find that Drift consistently governs ~25% of spatial turnovermore » in community composition; Selection dominates (governing ~60% of turnover) across spatially-structured habitats associated with fine-grained, low permeability sediments; and Dispersal Limitation is most influential (governing ~40% of turnover) across spatially-unstructured habitats associated with coarse-grained, highly-permeable sediments. Quantitative influences of Selection and Dispersal Limitation may therefore be predictable from knowledge of environmental structure. To develop a system-level conceptual model we extend our analytical framework to compare process estimates across formations, characterize measured and unmeasured environmental variables that impose Selection, and identify abiotic features that limit dispersal. Insights gained here suggest that community ecology can benefit from a shift in perspective; the quantitative approach developed here goes beyond the ‘niche vs. neutral’ dichotomy by moving towards a style of natural history in which estimates of Selection, Dispersal Limitation and Drift can be described, mapped and compared across ecological systems.« less

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

PubMed

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Are community-based pharmacists underused in the care of persons living with HIV? A need for structural and policy changes.

PubMed

Kibicho, Jennifer; Pinkerton, Steven D; Owczarzak, Jill; Mkandawire-Valhmu, Lucy; Kako, Peninnah M

2015-01-01

To describe community pharmacists' perceptions on their current role in direct patient care services, an expanded role for pharmacists in providing patient care services, and changes needed to optimally use pharmacists' expertise to provide high-quality direct patient care services to people living with human immunodeficiency virus (HIV) infections. Cross-sectional study. Four Midwestern cities in the United States in August through October 2009. 28 community-based pharmacists practicing in 17 pharmacies. Interviews. Opinions of participants about roles of specialty and nonspecialty pharmacists in caring for patients living with HIV infections. Pharmacists noted that although challenges in our health care system characterized by inaccessible health professionals presented opportunities for a greater pharmacist role, there were missed opportunities for greater level of patient care services in many community-based nonspecialty settings. Many pharmacists in semispecialty and nonspecialty pharmacies expressed a desire for an expanded role in patient care congruent with their pharmacy education and training. Structural-level policy changes needed to transform community-based pharmacy settings to patient-centered medical homes include recognizing pharmacists as important players in the multidisciplinary health care team, extending the health information exchange highway to include pharmacist-generated electronic therapeutic records, and realigning financial incentives. Comprehensive policy initiatives are needed to optimize the use of highly trained pharmacists in enhancing the quality of health care to an ever-growing number of Americans with chronic conditions who access care in community-based pharmacy settings.

Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses.

PubMed

Ben-David, Eric A; Zaady, Eli; Sher, Yoni; Nejidat, Ali

2011-06-01

Arid and semi-arid ecosystems are often characterized by vegetation patchiness and variable availability of resources. Phospholipid fatty acid (PLFA) and 16S rRNA gene fragment analyses were used to compare the bulk soil microbial community structure at patchy arid and semi-arid landscapes. Multivariate analyses of the PLFA data and the 16S rRNA gene fragments were in agreement with each other, suggesting that the differences between bulk soil microbial communities were primarily related to shrub vs intershrub patches, irrespective of climatic or site differences. This suggests that the mere presence of a living shrub is the dominant driving factor for the differential adaptation of the microbial communities. Lipid markers suggested as indicators of Gram-positive bacteria were higher in soils under the shrub canopies, while markers suggested as indicators of cyanobacteria and anaerobic bacteria were elevated in the intershrub soils. Secondary differences between soil microbial communities were associated with intershrub characteristics and to a lesser extent with the shrub species. This study provides an insight into the multifaceted nature of the factors that shape the microbial community structure in patchy desert landscapes. It further suggests that these drivers not only act in concert but also in a way that is dependent on the aridity level. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Cryptoendolithic lichen and cyanobacterial communities of the Ross Desert, Antarctica

NASA Technical Reports Server (NTRS)

Friedmann, E. I.; Hua, M.; Ocampo-Friedmann, R.

1988-01-01

Cryptoendolithic microbial communities in the Ross Desert (McMurdo Dry Valleys) are characterized on the basis of photosynthetic microorganisms and fungi. Two eukaryotic communities (the lichen-dominated and Hemichloris communities) and three cyanobacterial communities (the red Gloeocapsa, Hormathonema-Gloeocapsa, and Chroococcidiopsis communities) are described. Eleven coccoid, one pleurocapsoid, and five filamentous cyanobacteria occurring in these communities are characterized and illustrated. The moisture grade of the rock substrate seems to affect pH, formation of primary iron stain, and the distribution of microbial communities.

Characterization of the gut microbiota in the red panda (Ailurus fulgens).

PubMed

Kong, Fanli; Zhao, Jiangchao; Han, Shushu; Zeng, Bo; Yang, Jiandong; Si, Xiaohui; Yang, Benqing; Yang, Mingyao; Xu, Huailiang; Li, Ying

2014-01-01

The red panda is the only living species of the genus Ailurus. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo.

Characterization of the Gut Microbiota in the Red Panda (Ailurus fulgens)

PubMed Central

Han, Shushu; Zeng, Bo; Yang, Jiandong; Si, Xiaohui; Yang, Benqing; Yang, Mingyao; Xu, Huailiang; Li, Ying

2014-01-01

The red panda is the only living species of the genus Ailurus. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo. PMID:24498390

Evaluation of Methods for the Extraction of DNA from Drinking Water Distribution System Biofilms

PubMed Central

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L.; LeChevallier, Mark W.; Liu, Wen-Tso

2012-01-01

While drinking water biofilms have been characterized in various drinking water distribution systems (DWDS), little is known about the impact of different DNA extraction methods on the subsequent analysis of microbial communities in drinking water biofilms. Since different DNA extraction methods have been shown to affect the outcome of microbial community analysis in other environments, it is necessary to select a DNA extraction method prior to the application of molecular tools to characterize the complex microbial ecology of the DWDS. This study compared the quantity and quality of DNA yields from selected DWDS bacteria with different cell wall properties using five widely used DNA extraction methods. These were further selected and evaluated for their efficiency and reproducibility of DNA extraction from DWDS samples. Terminal restriction fragment length analysis and the 454 pyrosequencing technique were used to interpret the differences in microbial community structure and composition, respectively, from extracted DNA. Such assessments serve as a concrete step towards the determination of an optimal DNA extraction method for drinking water biofilms, which can then provide a reliable comparison of the meta-analysis results obtained in different laboratories. PMID:22075624

Microbiological investigation of an industrial ultra pure supply water plant using cultivation-based and cultivation-independent methods.

PubMed

Bohus, Veronika; Tóth, Erika M; Székely, Anna J; Makk, Judit; Baranyi, Krisztián; Patek, Gábor; Schunk, János; Márialigeti, Károly

2010-12-01

Ultra pure waters (UPW), characterized by extremely low salt and nutrient concentrations, can suffer from microbial contamination which causes biofouling and biocorrosion, possibly leading to reduced lifetime and increased operational costs. Samples were taken from an ultra pure supply water producing plant of a power plant. Scanning electron microscopic examination was carried out on the biofilms formed in the system. Biofilm, ion exchange resin, and water samples were characterized by culture-based methods and molecular fingerprinting (terminal restriction fragment length polymorphism [T-RFLP] analysis and molecular cloning). Identification of bacteria was based on 16S rDNA sequence comparison. A complex microbial community structure was revealed. Nearly 46% of the clones were related to as yet uncultured bacteria. The community profiles of the water samples were the most diverse and most of bacteria were recruited from bacterial communities of tube surface and ion exchange resin biofilms. Microbiota of different layers of the mixed bed ion exchange resin showed the highest similarity. Most of the identified taxa (dominated by β-Proteobacteria) could take part in microbially influenced corrosion. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microbial Community Structure in the Rhizosphere of Rice Plants

PubMed Central

Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

2016-01-01

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes.

PubMed

Pechal, Jennifer L; Benbow, M Eric

2016-05-01

Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Manure Refinement Affects Apple Rhizosphere Bacterial Community Structure: A Study in Sandy Soil

PubMed Central

Zhang, Qiang; Sun, Jian; Liu, Songzhong; Wei, Qinping

2013-01-01

We used DNA-based pyrosequencing to characterize the bacterial community structure of the sandy soil of an apple orchard with different manure ratios. Five manure percentages (5%, 10%, 15%, 20% and 25%) were examined. More than 10,000 valid reads were obtained for each replicate. The communities were composed of five dominant groups (Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Bacteroidetes), of which Proteobacteria content gradually decreased from 41.38% to 37.29% as manure ratio increased from 0% to 25%, respectively. Redundancy analysis showed that 37 classes were highly correlated with manure ratio, 18 of which were positively correlated. Clustering revealed that the rhizosphere samples were grouped into three components: low manure (control, 5%) treatment, medium manure (10%, 15%) treatment and high manure (20%, 25%) treatment. Venn analysis of species types of these three groups revealed that the bacteria community difference was primarily reflected by quantity ratio rather than species variety. Although greater manure content led to higher soil organic matter content, the medium manure improved soil showed the highest urease activity and saccharase activity, while 5% to 20% manure ratio improvement also resulted in higher bacteria diversity than control and 25% manure ratio treatment. Our experimental results suggest that the use of a proper manure ratio results in significantly higher soil enzyme activity and different bacteria community patterns, whereas the use of excessive manure amounts has negative effect on soil quality. PMID:24155909

Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities.

PubMed

Pham, Hoang Nam; Michalet, Serge; Bodillis, Josselin; Nguyen, Tien Dat; Nguyen, Thi Kieu Oanh; Le, Thi Phuong Quynh; Haddad, Mohamed; Nazaret, Sylvie; Dijoux-Franca, Marie-Geneviève

2017-07-01

Plants adapt to metal stress by modifying their metabolism including the production of secondary metabolites in plant tissues. Such changes may impact the diversity and functions of plant associated microbial communities. Our study aimed to evaluate the influence of metals on the secondary metabolism of plants and the indirect impact on rhizosphere bacterial communities. We then compared the secondary metabolites of the hyperaccumulator Pteris vittata L. collected from a contaminated mining site to a non-contaminated site in Vietnam and identified the discriminant metabolites. Our data showed a significant increase in chlorogenic acid derivatives and A-type procyanidin in plant roots at the contaminated site. We hypothesized that the intensive production of these compounds could be part of the antioxidant defense mechanism in response to metals. In parallel, the structure and diversity of bulk soil and rhizosphere communities was studied using high-throughput sequencing. The results showed strong differences in bacterial composition, characterized by the dominance of Proteobacteria and Nitrospira in the contaminated bulk soil, and the enrichment of some potential human pathogens, i.e., Acinetobacter, Mycobacterium, and Cupriavidus in P. vittata's rhizosphere at the mining site. Overall, metal pollution modified the production of P. vittata secondary metabolites and altered the diversity and structure of bacterial communities. Further investigations are needed to understand whether the plant recruits specific bacteria to adapt to metal stress.

Barcoded NS31/AML2 primers for sequencing of arbuscular mycorrhizal communities in environmental samples1

PubMed Central

Morgan, Benjamin S. T.; Egerton-Warburton, Louise M.

2017-01-01

Premise of the study: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples. Methods: Libraries of small subunit ribosomal RNA fragment amplicons were amplified from environmental DNA using a single-step PCR reaction with barcoded NS31/AML2 primers. Amplicons were sequenced on an Illumina MiSeq sequencer using version 2, 2 × 250-bp paired-end chemistry, and analyzed using QIIME and RDP Classifier. Results: Sequencing captured 196 to 6416 operational taxonomic units (OTUs; depending on clustering parameters) representing nine AMF genera. Regardless of clustering parameters, ∼20 OTUs dominated AMF communities (78–87% reads) with the remaining reads distributed among other OTUs. Analyses also showed significant biogeographic differences in AMF communities and that community composition could be linked to specific edaphic factors. Discussion: Barcoded NS31/AML2 primers and Illumina MiSeq sequencing provide a powerful approach to address AMF diversity and variations in fungal assemblages across host plants, ecosystems, and responses to environmental drivers including global change. PMID:28924511

Spatial scaling of bacterial community diversity at shallow hydrothermal vents: a global comparison

NASA Astrophysics Data System (ADS)

Pop Ristova, P.; Hassenrueck, C.; Molari, M.; Fink, A.; Bühring, S. I.

2016-02-01

Marine shallow hydrothermal vents are extreme environments, often characterized by discharge of fluids with e.g. high temperatures, low pH, and laden with elements toxic to higher organisms. They occur at continental margins around the world's oceans, but represent fragmented, isolated habitats of locally small areal coverage. Microorganisms contribute the main biomass at shallow hydrothermal vent ecosystems and build the basis of the food chain by autotrophic fixation of carbon both via chemosynthesis and photosynthesis, occurring simultaneously. Despite their importance and unique capacity to adapt to these extreme environments, little is known about the spatial scales on which the alpha- and beta-diversity of microbial communities vary at shallow vents, and how the geochemical habitat heterogeneity influences shallow vent biodiversity. Here for the first time we investigated the spatial scaling of microbial biodiversity patterns and their interconnectivity at geochemically diverse shallow vents on a global scale. This study presents data on the comparison of bacterial community structures on large (> 1000 km) and small (0.1 - 100 m) spatial scales as derived from ARISA and Illumina sequencing. Despite the fragmented global distribution of shallow hydrothermal vents, similarity of vent bacterial communities decreased with geographic distance, confirming the ubiquity of distance-decay relationship. Moreover, at all investigated vents, pH was the main factor locally structuring these communities, while temperature influenced both the alpha- and beta-diversity.

eDNA-based bioassessment of coastal sediments impacted by an oil spill.

PubMed

Xie, Yuwei; Zhang, Xiaowei; Yang, Jianghua; Kim, Seonjin; Hong, Seongjin; Giesy, John P; Yim, Un Hyuk; Shim, Won Joon; Yu, Hongxia; Khim, Jong Seong

2018-07-01

Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Archaeal community structure in leachate and solid waste is correlated to methane generation and volume reduction during biodegradation of municipal solid waste.

PubMed

Fei, Xunchang; Zekkos, Dimitrios; Raskin, Lutgarde

2015-02-01

Duplicate carefully-characterized municipal solid waste (MSW) specimens were reconstituted with waste constituents obtained from a MSW landfill and biodegraded in large-scale landfill simulators for about a year. Repeatability and relationships between changes in physical, chemical, and microbial characteristics taking place during the biodegradation process were evaluated. Parameters such as rate of change of soluble chemical oxygen demand in the leachate (rsCOD), rate of methane generation (rCH4), rate of specimen volume reduction (rVt), DNA concentration in the leachate, and archaeal community structures in the leachate and solid waste were monitored during operation. The DNA concentration in the leachate was correlated to rCH4 and rVt. The rCH4 was related to rsCOD and rVt when waste biodegradation was intensive. The structures of archaeal communities in the leachate and solid waste of both simulators were very similar and Methanobacteriaceae were the dominant archaeal family throughout the testing period. Monitoring the chemical and microbial characteristics of the leachate was informative of the biodegradation process and volume reduction in the simulators, suggesting that leachate monitoring could be informative of the extent of biodegradation in a full-scale landfill. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

PubMed

Ducey, T F; Johnson, P R; Shriner, A D; Matheny, T A; Hunt, P G

2013-01-01

Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

NASA Astrophysics Data System (ADS)

Ivanova, E. A.; Kutovaya, O. V.; Tkhakakhova, A. K.; Chernov, T. I.; Pershina, E. V.; Markina, L. G.; Andronov, E. E.; Kogut, B. M.

2015-11-01

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of <0.25, 2-5, and >7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined in the fractions <0.25 and aggregates 2-5 mm; the bacterial and archaeal biomass decreased in the following series: fallow > permanent black fallow > permanent winter wheat. The greatest number of fungi was recorded in the fraction <0.25 mm from the soils of the permanent black fallow and in all the studied aggregate fractions in the variant with permanent wheat. The system of agricultural use affected more significantly the structure of the prokaryote community in the chernozem than the size of aggregate fractions did. The most diverse microbial community was recorded in the soil samples of the fallow; the statistically significant maximums of the Shannon diversity indices and indices of phylogenetic diversity (PD) were recorded in the fractions <0.25 and 2-5 mm from the fallow soil. On the whole, the fine soil fractions (<0.25 mm) were characterized by higher diversity indices in comparison with those of the coarser aggregate fractions.

Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach

USGS Publications Warehouse

Tenore, K.R.; Zajac, R.N.; Terwin, J.; Andrade, F.; Blanton, J.; Boynton, W.; Carey, D.; Diaz, R.; Holland, Austin F.; Lopez-Jamar, E.; Montagna, P.; Nichols, F.; Rosenberg, R.; Queiroga, H.; Sprung, M.; Whitlatch, R.B.

2006-01-01

Ecologists studying coastal and estuarine benthic communities have long taken a macroecological view, by relating benthic community patterns to environmental factors across several spatial scales. Although many general ecological patterns have been established, often a significant amount of the spatial and temporal variation in soft-sediment communities within and among systems remains unexplained. Here we propose a framework that may aid in unraveling the complex influence of environmental factors associated with the different components of coastal systems (i.e. the terrestrial and benthic landscapes, and the hydrological seascape) on benthic communities, and use this information to assess the role played by benthos in coastal ecosystems. A primary component of the approach is the recognition of system modules (e.g. marshes, dendritic systems, tidal rivers, enclosed basins, open bays, lagoons). The modules may differentially interact with key forcing functions (e.g. temperature, salinity, currents) that influence system processes and in turn benthic responses and functions. Modules may also constrain benthic characteristics and related processes within certain ecological boundaries and help explain their overall spatio-temporal variation. We present an example of how benthic community characteristics are related to the modular structure of 14 coastal seas and estuaries, and show that benthic functional group composition is significantly related to the modular structure of these systems. We also propose a framework for exploring the role of benthic communities in coastal systems using this modular approach and offer predictions of how benthic communities may vary depending on the modular composition and characteristics of a coastal system. ?? 2006 Elsevier B.V. All rights reserved.

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

PubMed Central

Green, Stefan J.; Prakash, Om; Jasrotia, Puja; Overholt, Will A.; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2012-01-01

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment. PMID:22179233

Structural Genomics and Drug Discovery for Infectious Diseases

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

Anderson, W.F.

The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging,more » or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.« less

Influence of seabird colonies and other environmental variables on benthic community structure, Lancaster Sound Region, Canadian Arctic

NASA Astrophysics Data System (ADS)

Bouchard Marmen, Mariève; Kenchington, Ellen; Ardyna, Mathieu; Archambault, Philippe

2017-03-01

The Canadian Arctic shelters millions of seabirds each year during the breeding season. By the excretion of important quantities of guano, seabirds locally concentrate nutrient-rich organic matter in the marine areas surrounding colonies. Seabirds, acting as biological vectors of nutrients, can markedly affect terrestrial ecosystems, but their influence on the structure of marine benthic communities is still under-studied. Sessile and long-lived megabenthic species can integrate environmental variation into marine food webs over long time frames. The objectives of this study were (1) to characterize the epifaunal and infaunal communities of the Lancaster Sound Region (LSR) and (2) to test the influence of the presence of seabird colonies and other environmental parameters on the structure of those benthic communities. Our prediction was that benthic diversity, number of taxa, total biomass of infauna and total density of epifauna and infauna, would be higher in areas with colonies present. Photos of the seafloor (data on epifauna) and grab samples (data on infauna) were taken at three control areas and at five areas near seabird colonies, within a depth range of 122 to 442 m. A database of 26 environmental parameters was built to study the environment-benthos relationships. Infauna, which was relatively uniform across the LSR, was numerically dominated by Annelida. Epifauna was much patchier, with each study area having unique epibenthic assemblages. Brittle stars were highly abundant in epifaunal communities, reaching 600 individuals per square meter. The presence of seabird colonies was not a major driver of benthic community structure in the LSR at the depths studied. Negative effects of colonies were detected on the density and number of taxa of infauna, perhaps due to top-down effects transmitted by the seabirds which feed in the water column and can directly reduce the quantity of food reaching the seabed. Sediment concentration of pigment, percent cover of gravel and boulders, depth, temperature and duration of open water explained a substantial part of the observed variation across the LSR. Food availability, as expressed by sediment pigment concentration, is a factor driving benthic communities, even if potential pathways through seabirds did not broadly affect the benthos at the point source.

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

PubMed Central

Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

2015-01-01

Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

PubMed

Munson-McGee, Jacob H; Peng, Shengyun; Dewerff, Samantha; Stepanauskas, Ramunas; Whitaker, Rachel J; Weitz, Joshua S; Young, Mark J

2018-06-01

The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.

Host tree phenology affects vascular epiphytes at the physiological, demographic and community level

PubMed Central

Einzmann, Helena J. R.; Beyschlag, Joachim; Hofhansl, Florian; Wanek, Wolfgang; Zotz, Gerhard

2015-01-01

The processes that govern diverse tropical plant communities have rarely been studied in life forms other than trees. Structurally dependent vascular epiphytes, a major part of tropical biodiversity, grow in a three-dimensional matrix defined by their hosts, but trees differ in their architecture, bark structure/chemistry and leaf phenology. We hypothesized that the resulting seasonal differences in microclimatic conditions in evergreen vs. deciduous trees would affect epiphytes at different levels, from organ physiology to community structure. We studied the influence of tree leaf phenology on vascular epiphytes on the Island of Barro Colorado, Panama. Five tree species were selected, which were deciduous, semi-deciduous or evergreen. The crowns of drought-deciduous trees, characterized by sunnier and drier microclimates, hosted fewer individuals and less diverse epiphyte assemblages. Differences were also observed at a functional level, e.g. epiphyte assemblages in deciduous trees had larger proportions of Crassulacean acid metabolism species and individuals. At the population level a drier microclimate was associated with lower individual growth and survival in a xerophytic fern. Some species also showed, as expected, lower specific leaf area and higher δ13C values when growing in deciduous trees compared with evergreen trees. As hypothesized, host tree leaf phenology influences vascular epiphytes at different levels. Our results suggest a cascading effect of tree composition and associated differences in tree phenology on the diversity and functioning of epiphyte communities in tropical lowland forests. PMID:25392188

Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

PubMed

Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

2015-01-01

Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

Custom Super-Resolution Microscope for the Structural Analysis of Nanostructures

DTIC Science & Technology

2018-05-29

research community. As part of our validation of the new design approach, we performed two - color imaging of pairs of adjacent oligo probes hybridized...nanostructures and biological targets. Our microscope features a large field of view and custom optics that facilitate 3D imaging and enhanced contrast in...our imaging throughput by creating two microscopy platforms for high-throughput, super-resolution materials characterization, with the AO set-up being

Microorganisms in small patterned ground features and adjacent vegetated soils along topographic and climatic gradients in the High Arctic, Canada

Treesearch

G. Gonzalez; F.J. Rivera-Figueroa; W. Gould; S.A. Cantrell; J.R. Pérez-Jiménez

2014-01-01

In this study, we determine differences in total biomass of soil microorganisms and community structure (using the most probable number of bacteria (MPN) and the number of fungal genera) in patterned ground features (PGF) and adjacent vegetated soils (AVS) in mesic sites from three High Arctic islands in order to characterize microbial dynamics as affected by...

Mineralogic control on abundance and diversity of surface-adherent microbial communities

USGS Publications Warehouse

Mauck, Brena S.; Roberts, Jennifer A.

2007-01-01

In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated activities in subsurface environments extend to the microscale and cautions over-interpretation of highly sample-dependent measurements in the context of interpreting field data.

Linking genes to ecosystem trace gas fluxes in a large-scale model system

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Cueva, A.; Volkmann, T. H. M.; Sengupta, A.; Troch, P. A.

2017-12-01

Soil microorganisms mediate biogeochemical cycles through biosphere-atmosphere gas exchange with significant impact on atmospheric trace gas composition. Improving process-based understanding of these microbial populations and linking their genomic potential to the ecosystem-scale is a challenge, particularly in soil systems, which are heterogeneous in biodiversity, chemistry, and structure. In oligotrophic systems, such as the Landscape Evolution Observatory (LEO) at Biosphere 2, atmospheric trace gas scavenging may supply critical metabolic needs to microbial communities, thereby promoting tight linkages between microbial genomics and trace gas utilization. This large-scale model system of three initially homogenous and highly instrumented hillslopes facilitates high temporal resolution characterization of subsurface trace gas fluxes at hundreds of sampling points, making LEO an ideal location to study microbe-mediated trace gas fluxes from the gene to ecosystem scales. Specifically, we focus on the metabolism of ubiquitous atmospheric reduced trace gases hydrogen (H2), carbon monoxide (CO), and methane (CH4), which may have wide-reaching impacts on microbial community establishment, survival, and function. Additionally, microbial activity on LEO may facilitate weathering of the basalt matrix, which can be studied with trace gas measurements of carbonyl sulfide (COS/OCS) and carbon dioxide (O-isotopes in CO2), and presents an additional opportunity for gene to ecosystem study. This work will present initial measurements of this suite of trace gases to characterize soil microbial metabolic activity, as well as links between spatial and temporal variability of microbe-mediated trace gas fluxes in LEO and their relation to genomic-based characterization of microbial community structure (phylogenetic amplicons) and genetic potential (metagenomics). Results from the LEO model system will help build understanding of the importance of atmospheric inputs to microorganisms pioneering fresh mineral matrix. Additionally, the measurement and modeling techniques that will be developed at LEO will be relevant for other investigators linking microbial genomics to ecosystem function in more well-developed soils with greater complexity.

Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs

PubMed Central

Delparte, D; Gates, RD; Takabayashi, M

2015-01-01

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems. PMID:26207190

Transformation of soil and vegetable conditions at oil production territories

NASA Astrophysics Data System (ADS)

Gatina, Evgeniia

2017-04-01

On the territory of modern oil production soil, vegetation, ecosystem conditions of the environment are significantly transformed. Researches have been conducted on the oil production territories located in a boreal coniferous forest natural zone from 2005 to 2015. Standard geobotanical and soil methods are used. Mechanical destruction of a plant cover, change of the water conditions, intake of oil products and salty waters in ecosystems, pollution of the atmosphere are considered as the major technology-related factors defining transformation of land ecosystems at operation of the oil field. Under the mechanical destruction of a plant cover the pioneer plant communities are formed. These communities are characterized by most reduced specific wealth with prevalence of types of meadow groups of plants and presence of types of wetland groups of plants. The biodiversity of biocenosis which are affected linear infrastructure facilities of oil production territories and change of the water conditions, decreases. It is observed decrease in species wealth, simplification of structure of communities. Under the salting of soils in ecosystems there is a decrease species diversity of communities to prevalence nitrophilous and meadow plant species. At the increased content of organic substances in the soils that is a consequence of intake of oil products, is characteristic increase in specific richness of communities, introduction of types of wetland and oligotrophic groups of plants in forest communities. Influence depends on distance to an influence source. In process of removal from a source of atmospheric pollution in forest communities there is a decrease in species diversity and complication of structure of community. It is caused by introduction of types of meadow groups of plants in ecotone sites of the forest communities located near a source of influence and restoration of structural features of forest communities in process of removal from an influence source. Operation of oil fields leads to introduction of the synanthropes relating to meadow and wetland groups of plants. Transformation depends on loading time. At the initial stage of operation of the oil field the synantropization of a plant cover leads to increase in species diversity. At long technogenic loading decrease in values of indexes of a biodiversity due to oppression of native species of plants is observed. Technology-related influence of oil fields is a regional factor of change of specific structure of plant communities. Modern oil production has to be followed by purposeful formation of the operated natural and technology-related ecosystems with adjustable parameters and higher stability in relation to a complex of technogenic oil-field influence.

Soil microbial community profiles and functional diversity in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea.

PubMed

Khalil, Maha T; Bouwmeester, Jessica; Berumen, Michael L

2017-01-01

Local-scale ecological information is critical as a sound basis for spatial management and conservation and as support for ongoing research in relatively unstudied areas. We conducted visual surveys of fish and benthic communities on nine reefs (3-24 km from shore) in the Thuwal area of the central Saudi Arabian Red Sea. Fish biomass increased with increasing distance from shore, but was generally low compared to reefs experiencing minimal human influence around the world. All reefs had a herbivore-dominated trophic structure and few top predators, such as sharks, jacks, or large groupers. Coral cover was considerably lower on inshore reefs, likely due to a 2010 bleaching event. Community analyses showed inshore reefs to be characterized by turf algae, slower-growing corals, lower herbivore diversity, and highly abundant turf-farming damselfishes. Offshore reefs had more planktivorous fishes, a more diverse herbivore assemblage, and faster-growing corals . All reefs appear to be impacted by overfishing, and inshore reefs seem more vulnerable to thermal bleaching. The study provides a description of the spatial variation in biomass and community structure in the central Saudi Arabian Red Sea and provides a basis for spatial prioritization and subsequent marine protected area design in Thuwal.

Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea

PubMed Central

Bouwmeester, Jessica; Berumen, Michael L.

2017-01-01

Local-scale ecological information is critical as a sound basis for spatial management and conservation and as support for ongoing research in relatively unstudied areas. We conducted visual surveys of fish and benthic communities on nine reefs (3–24 km from shore) in the Thuwal area of the central Saudi Arabian Red Sea. Fish biomass increased with increasing distance from shore, but was generally low compared to reefs experiencing minimal human influence around the world. All reefs had a herbivore-dominated trophic structure and few top predators, such as sharks, jacks, or large groupers. Coral cover was considerably lower on inshore reefs, likely due to a 2010 bleaching event. Community analyses showed inshore reefs to be characterized by turf algae, slower-growing corals, lower herbivore diversity, and highly abundant turf-farming damselfishes. Offshore reefs had more planktivorous fishes, a more diverse herbivore assemblage, and faster-growing corals. All reefs appear to be impacted by overfishing, and inshore reefs seem more vulnerable to thermal bleaching. The study provides a description of the spatial variation in biomass and community structure in the central Saudi Arabian Red Sea and provides a basis for spatial prioritization and subsequent marine protected area design in Thuwal. PMID:28603671

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth.

PubMed

Techtmann, Stephen M; Fortney, Julian L; Ayers, Kati A; Joyner, Dominique C; Linley, Thomas D; Pfiffner, Susan M; Hazen, Terry C

2015-01-01

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.

The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth

PubMed Central

Techtmann, Stephen M.; Fortney, Julian L.; Ayers, Kati A.; Joyner, Dominique C.; Linley, Thomas D.; Pfiffner, Susan M.; Hazen, Terry C.

2015-01-01

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column. PMID:25807542

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

DOE PAGES

Techtmann, Stephen M.; Fortney, Julian L.; Ayers, Kati A.; ...

2015-03-25

The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbialmore » community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Furthermore, our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.« less

Forest strata drive spatial structure of bacterial and archaeal communities and microbial methane cycling in neotropical bromeliad wetlands

NASA Astrophysics Data System (ADS)

Martinson, Guntars; Brandt, Franziska; Conrad, Ralf

2016-04-01

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that harbors diverse communities of archaea and bacteria and emit substantial amounts of methane. We studied spatial distribution of archaeal and bacterial communities, microbial methane cycling and their environmental drivers in tank bromeliad wetlands. We selected tank bromeliads of different species and functional types (terrestrial and canopy bromeliads) in a neotropical montane forest of Southern Ecuador and sampled the organic tank slurry. Archaeal and bacterial communities were characterized using terminal-restriction fragment length polymorphism (T-RFLP) and Illumina MiSeq sequencing, respectively, and linked with physico-chemical tank-slurry properties. Additionally, we performed tank-slurry incubations to measure methane production potential, stable carbon isotope fractionation and pathway of methane formation. Archaeal and bacterial community composition in bromeliad wetlands was dominated by methanogens and by Alphaproteobacteria, respectively, and did not differ between species but between functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens among all bromeliads but the relative abundance of aceticlastic Methanosaetaceae increased in terrestrial bromeliads. Complementary, hydrogenotrophic methanogenesis was the dominant pathway of methane formation but the relative contribution of aceticlastic methanogenesis increased in terrestrial bromeliads and led to a concomitant increase in total methane production. Rhodospirillales were characteristic for canopy bromeliads, Planctomycetales and Actinomycetalis for terrestrial bromeliads. While nitrogen concentration and pH explained 32% of the archaeal community variability, 29% of the bacterial community variability was explained by nitrogen, acetate and propionate concentrations. Our study demonstrates that bromeliad functional types, associated with different forest strata, and their constrained environmental characteristics shape the spatial structure of archaeal and bacterial communities and microbial methane cycling in neotropical bromeliad wetlands.

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment

PubMed Central

Krolicka, Adriana; Boccadoro, Catherine; Nilsen, Mari Mæland; Baussant, Thierry

2017-01-01

The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring. After an incubation for 1 d, the distribution of the individual ribotypes of bacterial communities in control and oil-treated (O and OD) tanks differed. Differences related to the structures of bacterial communities were observed at later stages of the incubation. Among the early responders identified (Pseudoalteromonas, Sulfitobacter, Vibrio, Pseudomonas, Glaciecola, Neptunomonas, Methylophaga, and Pseudofulvibacter), genera that utilize a disintegrated biomass or hydrocarbons as well as biosurfactant producers were detected. None of these genera included obligate hydrocarbonoclastic bacteria (OHCB). After an incubation for 1 d, the abundances of Glaciecola and Pseudofulvibacter were approximately 30-fold higher in the OD and O tanks than in the control tank. OTUs assigned to the Glaciecola genus were represented more in the OD tank, while those of Pseudofulvibacter were represented more in the O tank. We also found that 2 to 3% of the structural community shift originated from the bacterial community in the oil itself, with Polaribacter being a dominant bacterium. PMID:29187706

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment.

PubMed

Krolicka, Adriana; Boccadoro, Catherine; Nilsen, Mari Mæland; Baussant, Thierry

2017-12-27

The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring.After an incubation for 1 d, the distribution of the individual ribotypes of bacterial communities in control and oil-treated (O and OD) tanks differed. Differences related to the structures of bacterial communities were observed at later stages of the incubation. Among the early responders identified (Pseudoalteromonas, Sulfitobacter, Vibrio, Pseudomonas, Glaciecola, Neptunomonas, Methylophaga, and Pseudofulvibacter), genera that utilize a disintegrated biomass or hydrocarbons as well as biosurfactant producers were detected. None of these genera included obligate hydrocarbonoclastic bacteria (OHCB). After an incubation for 1 d, the abundances of Glaciecola and Pseudofulvibacter were approximately 30-fold higher in the OD and O tanks than in the control tank. OTUs assigned to the Glaciecola genus were represented more in the OD tank, while those of Pseudofulvibacter were represented more in the O tank. We also found that 2 to 3% of the structural community shift originated from the bacterial community in the oil itself, with Polaribacter being a dominant bacterium.

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery.

PubMed

Chu, Derrick M; Ma, Jun; Prince, Amanda L; Antony, Kathleen M; Seferovic, Maxim D; Aagaard, Kjersti M

2017-03-01

Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R 2 = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R 2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R 2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.

Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery

PubMed Central

Chu, Derrick M.; Ma, Jun; Prince, Amanda L.; Antony, Kathleen M.; Seferovic, Maxim D.; Aagaard, Kjersti M.

2017-01-01

Human microbial communities are characterized by their taxonomic, metagenomic, and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to assess the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites, and assess the impact of mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early 3rd trimester (n=81) were prospectively enrolled for longitudinal sampling through 6 weeks post-delivery, and a second matched cross-sectional cohort (n=81) was additionally recruited for sampling once at delivery. Samples were collected for each maternal-infant dyad across multiple body sites, including stool, oral gingiva, nares, skin and vagina. 16S rRNA gene sequencing analysis and whole genome shotgun sequencing was performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogenous across all body sites at delivery, with the notable exception of neonatal meconium. However, by 6 weeks, the infant microbiota structure and function had significantly expanded and diversified, with body site serving as the primary determinant of the bacterial community composition and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with Cesarean delivery in some body sites (oral, nares, and skin; R2 = 0.038), this was not true in neonatal stool (meconium, Mann-Whitney p>0.05) and there was no observable difference in community function regardless of delivery mode. By 6 weeks of age, the infant microbiota structure and function had expanded and diversified with demonstrable body site specificity (p<0.001, R2 = 0.189), and no discernable differences in neither community structure nor function by Cesarean delivery were identifiable (p=0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes significant reorganization that is primarily driven by body site and not by mode of delivery. PMID:28112736

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

PubMed

Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

2014-03-01

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Ecosystem screening approach for pathogen-associated microorganisms affecting host disease.

PubMed

Galiana, Eric; Marais, Antoine; Mura, Catherine; Industri, Benoît; Arbiol, Gilles; Ponchet, Michel

2011-09-01

The microbial community in which a pathogen evolves is fundamental to disease outcome. Species interacting with a pathogen on the host surface shape the distribution, density, and genetic diversity of the inoculum, but the role of these species is rarely determined. The screening method developed here can be used to characterize pathogen-associated species affecting disease. This strategy involves three steps: (i) constitution of the microbial community, using the pathogen as a trap; (ii) community selection, using extracts from the pathogen as the sole nutrient source; and (iii) molecular identification and the screening of isolates focusing on their effects on the growth of the pathogen in vitro and host disease. This approach was applied to a soilborne plant pathogen, Phytophthora parasitica, structured in a biofilm, for screening the microbial community from the rhizosphere of Nicotiana tabacum (the host). Two of the characterized eukaryotes interfered with the oomycete cycle and may affect the host disease. A Vorticella species acted through a mutualistic interaction with P. parasitica, disseminating pathogenic material by leaving the biofilm. A Phoma species established an amensal interaction with P. parasitica, strongly suppressing disease by inhibiting P. parasitica germination. This screening method is appropriate for all nonobligate pathogens. It allows the definition of microbial species as promoters or suppressors of a disease for a given biotope. It should also help to identify important microbial relationships for ecology and evolution of pathogens.

Methods for collecting algal samples as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Porter, Stephen D.; Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic algae (periphyton) and phytoplankton communities are characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. This multidisciplinary approach provides multiple lines of evidence for evaluating water-quality status and trends, and for refining an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. Water quality can be characterized by evaluating the results of qualitative and quantitative measurements of the algal community. Qualitative periphyton samples are collected to develop of list of taxa present in the sampling reach. Quantitative periphyton samples are collected to measure algal community structure within selected habitats. These samples of benthic algal communities are collected from natural substrates, using the sampling methods that are most appropriate for the habitat conditions. Phytoplankton samples may be collected in large nonwadeable streams and rivers to meet specific program objectives. Estimates of algal biomass (chlorophyll content and ash-free dry mass) also are optional measures that may be useful for interpreting water-quality conditions. A nationally consistent approach provides guidance on site, reach, and habitat selection, as well as information on methods and equipment for qualitative and quantitative sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data locally, regionally, and nationally.

The effect of Hurricane Katrina on nekton communities in the tidal freshwater marshes of Breton Sound, Louisiana, USA

USGS Publications Warehouse

Piazza, Bryan P.; La Peyre, M.K.

2009-01-01

Hurricanes are climatically-induced resource pulses that affect community structure through the combination of physical and chemical habitat change. Estuaries are susceptible to hurricane pulses and are thought to be resilient to habitat change, because biotic communities often return quickly to pre-hurricane conditions. Although several examples provide evidence of quick recovery of estuarine nekton communities following a hurricane, few studies take place in tidal freshwater habitat where physical habitat effects can be extensive and may not be readily mitigated. We examined nekton communities (density, biomass, ?? and ?? diversity, % occurrence by residence status) in tidal freshwater marshes in Breton Sound, Louisiana, before and after a direct hit by Hurricane Katrina (2005). Vegetative marsh loss in the study area was extensive, and elevated salinity persisted for almost 6 months. Post-Katrina nekton density and biomass increased significantly, and the nekton community shifted from one of tidal freshwater/resident species to one containing brackish/migrant species, many of which are characterized by pelagic and benthic life history strategies. By spring 2007, the nekton community had shifted back to tidal freshwater/resident species, despite the enduring loss of vegetated marsh habitat. ?? 2009 Elsevier Ltd.

Community mapping and respondent-driven sampling of gay and bisexual men’s communities in Vancouver, Canada

PubMed Central

Forrest, Jamie I; Stevenson, Benjamin; Rich, Ashleigh; Michelow, Warren; Pai, Jayaram; Jollimore, Jody; Raymond, H. Fisher; Moore, David; Hogg, Robert S; Roth, Eric A

2014-01-01

Literature suggests formative research is vital for those using respondent-driven sampling (RDS) to study hidden populations of interest. However, few authors have described in detail how different qualitative methodologies can address the objectives of formative research for understanding the social network properties of the study population, selecting seeds, and adapting survey logistics to best fit the population. In this paper we describe the use of community mapping exercises as a tool within focus groups to collect data on social and sexual network characteristics of gay and bisexual men in the metropolitan area of Vancouver, Canada. Three key themes emerged from analyzing community maps along with other formative research data: (a) connections between physical spaces and social networks of gay and bisexual men, (b) diversity in communities, and (c) substance use connected with formation of sub-communities. We discuss how these themes informed the planning and operations of a longitudinal epidemiological cohort study recruited by RDS. We argue that using community mapping within formative research is a valuable qualitative tool for characterizing network structures of a diverse and differentiated population of gay and bisexual men in a highly developed urban setting. PMID:24512070

Dynamic robustness of knowledge collaboration network of open source product development community

NASA Astrophysics Data System (ADS)

Zhou, Hong-Li; Zhang, Xiao-Dong

2018-01-01

As an emergent innovative design style, open source product development communities are characterized by a self-organizing, mass collaborative, networked structure. The robustness of the community is critical to its performance. Using the complex network modeling method, the knowledge collaboration network of the community is formulated, and the robustness of the network is systematically and dynamically studied. The characteristics of the network along the development period determine that its robustness should be studied from three time stages: the start-up, development and mature stages of the network. Five kinds of user-loss pattern are designed, to assess the network's robustness under different situations in each of these three time stages. Two indexes - the largest connected component and the network efficiency - are used to evaluate the robustness of the community. The proposed approach is applied in an existing open source car design community. The results indicate that the knowledge collaboration networks show different levels of robustness in different stages and different user loss patterns. Such analysis can be applied to provide protection strategies for the key users involved in knowledge dissemination and knowledge contribution at different stages of the network, thereby promoting the sustainable and stable development of the open source community.

Biological Diversity Comprising Microbial Structures of Antarctic Ice Covered Lakes

NASA Astrophysics Data System (ADS)

Matys, E. D.

2015-12-01

Analysis of microbial membrane lipids is a rapid and non-selective method for evaluating the composition of microbial communities. To fully realise the diagnostic potential of these lipids, we must first understand their structural diversity, biological sources, physiological functions, and pathways of preservation. Particular environmental conditions likely prompt the production of different membrane lipid structures. Antarctica's McMurdo Dry Valleys host numerous ice-covered lakes with sharp chemical gradients that vary in illumination, geochemical structure, and benthic mat morphologies that are structured by nutrient availability and water chemistry. The lipid contents of these benthic mats have not received extensive study nor have the communities yet been thoroughly characterized. Accordingly, a combination of lipid biomarker and nucleic acid sequence data provides the means of assessing species diversity and environmental controls on the composition and diversity of membrane lipid assemblages. We investigated the richness and diversity of benthic microbial communities and accumulated organic matter in Lake Vanda of the McMurdo Dry Valleys. We have identified diverse glycolipids, aminolipids, and phospholipids in addition to many unknown compounds that may be specific to these particular environments. Light levels fluctuate seasonally, favoring low-light-tolerant cyanobacteria and specific lipid assemblages. Adaptations to nutrient limitations are reflected in contrasting intact polar lipid assemblages. For example, under P-limiting conditions, phospholipids are subsidiary to membrane-forming lipids that do not contain P (i.e. ornithine, betaine, and sulfolipids). The bacteriohopanepolyol (BHP) composition is dominated by bacteriohopanetetrol (BHT), a ubiquitous BHP, and 2-methylhopanoids. The relative abundance of 2-methylhopanoids is unprecedented and may reflect the unusual seasonal light regime of this polar environment. By establishing correlations between environmental conditions, microbial community composition and the lipid assemblages of microbial structures in ice-covered lakes of Antarctica's McMurdo Dry Valleys, our data provides important ecological and evolutionary insights into these unusual environments.

Nitrifying biomass characterization and monitoring during bioaugmentation in a membrane bioreactor.

PubMed

D'Anteo, Sibilla; Mannucci, Alberto; Meliani, Matteo; Verni, Franco; Petroni, Giulio; Munz, Giulio; Lubello, Claudio; Mori, Gualtiero; Vannini, Claudia

2015-01-01

A membrane bioreactor (MBR), fed with domestic wastewater, was bioaugmented with nitrifying biomass selected in a side-stream MBR fed with a synthetic high nitrogen-loaded influent. Microbial communities evolution was monitored and comparatively analysed through an extensive bio-molecular investigation (16S rRNA gene library construction and terminal-restriction fragment length polymorphism techniques) followed by statistical analyses. As expected, a highly specialized nitrifying biomass was selected in the side-stream reactor fed with high-strength ammonia synthetic wastewater. The bioaugmentation process caused an increase of nitrifying bacteria of the genera Nitrosomonas (up to more than 30%) and Nitrobacter in the inoculated MBR reactor. The overall structure of the microbial community changed in the mainstream MBR as a result of bioaugmentation. The effect of bioaugmentation in the shift of the microbial community was also verified through statistical analysis.

Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats.

PubMed

Omelon, Christopher R; Pollard, Wayne H; Ferris, F Grant

2007-11-01

Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum).

PubMed

Benucci, Gian Maria Niccolò; Lefevre, Charles; Bonito, Gregory

2016-07-01

Many truffle species in the genus Tuber are endemic to North America. Some of these have commercial value such as Tuber oregonense and Tuber gibbosum, commonly known as Oregon white truffles. Most of what is known about the ecology of these truffles comes from observational data. These truffle species form ectomycorrhizas with Douglas-fir (Pseudotsuga menziesii) and sometimes fruit abundantly in early successional forest regrowth. The goal of this study was to characterize fungal communities and soils associated with truffle-producing Douglas-fir sites. We extracted DNA from roots of five trees at four different truffle-producing Douglas-fir sites (n = 20). We amplified the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) and sequenced amplicons with 454 pyrosequencing. After quality filtering, we assembled 15,713 sequences into 150 fungal operational taxonomic units (OTUs). Pezizomycetes (Tuber and Pyronemataceae) were the most abundant taxa detected followed by Helotiales. Agaricomycetes represented most by Thelephoraceae, Russulaceae, and Inocybaceae were also abundant. A total of five Tuber species were detected. T. oregonense was the most abundant OTU, followed by T. gibbosum and Wilcoxina mikolae. Fungal root endophytes were also detected and well represented by Chalara and Phialocephala spp. Fungal community structure and soil chemistry differed between sites. This study represents the first characterization of the fungal communities in Douglas-fir stands producing Oregon white truffles. We found that Tuber species can be dominant ectomycorrhizal symbionts of Douglas-fir. Truffle fungi are also important in forest health, food webs, and as a non-timber forest resource that can contribute to rural economies.

Diversity and composition of sediment bacteria in subtropical coastal wetlands of North Stradbroke Island, Queensland, Australia

NASA Astrophysics Data System (ADS)

Chuvochina, Maria; Sampayo, Eugenia; Welti, Nina; Hayes, Matthew; Lu, Yang; Lovelock, Catherine; Lockington, David

2013-04-01

Coastal wetlands provide a wide variety of important ecosystem services but continue to suffer disturbance, degradation and deforestation. Sediment bacteria are responsible for major nutrient transformation and recycling in these ecosystems. Insight into microbial community composition and the factors that determine them may improve our understanding of biogeochemical processes, food web dynamics, biodegradation processes and, thus, help to develop the management strategies for preserving the ecosystem health and services. Characterizing shifts in community taxa along environmental gradients has been shown to provide a useful tool for determining the major drivers affecting community structure and function. North Stradbroke Island (NSI) in Southern Queensland presents considerable habitat diversity including variety of groundwater dependent ecosystems such as lakes, swamps, sedge-like salt marshes and mangroves. Ecological responses of continuous groundwater extraction for municipal purposes and sand mining operations on NSI are still need to be assessed in order to protect its unique environment. Changes in coastal hydrology due to either climate change or human activity may directly affect microbial populations and, thus, biogeochemical cycles of nutrients. These may result in altering/losing some ecosystem services provided by coastal wetlands. In this study we examine microbial diversity and determine environmental controls on bacterial community structure along a natural transition from freshwater forested wetland (melaleuca woodland), sedge-like salt marsh and into mangroves located at NSI. The study area is characterized by significant groundwater flow, nutrient limitation and sharp transition from one ecosystem type to another. Sediment cores (0-5 cm and 20-25 cm depth) were collected from three representative sites of each zone (mangroves - salt marsh - freshwater wetland) along the salinity gradient in August 2012. Subsamples were set aside for use in chemical analyses, microbiological analysis and for porewater extraction. Microbial community structure and diversity are assessed using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments and barcoded pyrosequencing. To evaluate the relationships between microbial communities and environmental variables we use bioinformatical and statistical tools. Physico-chemical parameters included measurements of sediment pH, temperature, salinity and nutrients composition. Background information regarding hydrology and vegetation is incorporated in the study. Sediment bacteria play a vital role in wetland ecological function, and they are very sensitive to environmental changes. Considering coastal wetlands of NSI as a model area, our study may contribute to the knowledge of factors shaping microbial diversity in tropical wetlands, help to gain insight into the microbe-nutrient-plant relationships, and also serve as background for conservation plans to safeguard these ecosystems.

Rationale and design of a multicenter echocardiographic study to assess the relationship between cardiac structure and function and heart failure risk in a biracial cohort of community-dwelling elderly persons: the Atherosclerosis Risk in Communities study.

PubMed

Shah, Amil M; Cheng, Susan; Skali, Hicham; Wu, Justina; Mangion, Judy R; Kitzman, Dalane; Matsushita, Kunihiro; Konety, Suma; Butler, Kenneth R; Fox, Ervin R; Cook, Nakela; Ni, Hanyu; Coresh, Josef; Mosley, Thomas H; Heiss, Gerardo; Folsom, Aaron R; Solomon, Scott D

2014-01-01

Heart failure is an important public health concern, particularly among persons>65 years of age. Women and blacks are critically understudied populations that carry a sizeable portion of the heart failure burden. Limited normative and prognostic data exist on measures of cardiac structure, diastolic function, and novel measures of systolic deformation in older adults living in the community. The Atherosclerosis Risk in Communities (ARIC) study is a large, predominantly biracial, National Heart, Lung, and Blood Institute-sponsored epidemiological cohort study. Between 2011 and 2013, ≈6000 surviving participants, now in their seventh to ninth decade of life, are expected to return for a fifth study visit during which comprehensive 2-dimensional, Doppler, tissue Doppler, and speckle-tracking echocardiography will be performed uniformly in all cohort clinic visit participants. The following objectives will be addressed: (1) to characterize cardiac structural and functional abnormalities among the elderly and to determine how they differ by sex and race/ethnicity, (2) to determine the relationship between ventricular and vascular abnormalities, and (3) to prospectively examine the extent to which these noninvasive measures associate with incident heart failure. We describe the design, imaging acquisition and analysis methods, and quality assurance metrics for echocardiography in visit 5 of the ARIC cohort. A better understanding of the differences in cardiac structure and function through the spectrum of heart failure stages in elderly persons generally, and between sexes and racial/ethnic groups specifically, will deepen our understanding of the pathophysiology driving heart failure progression in these at-risk populations and may inform novel prevention or therapeutic strategies.

Collaboration between non-governmental organizations and public services in health - a qualitative case study from rural Ecuador.

PubMed

Biermann, Olivia; Eckhardt, Martin; Carlfjord, Siw; Falk, Magnus; Forsberg, Birger C

2016-01-01

Non-governmental organizations (NGOs) have a key role in improving health in low- and middle-income countries. Their work needs to be synergistic, complementary to public services, and rooted in community mobilization and collective action. The study explores how an NGO and its health services are perceived by the population that it serves, and how it can contribute to reducing barriers to care. A qualitative exploratory study was conducted in remote Ecuador, characterized by its widespread poverty and lack of official governance. An international NGO collaborated closely with the public services to deliver preventative and curative health services. Data were collected using focus group discussions and semistructured interviews with purposively sampled community members, healthcare personnel, and community health workers based on their links to the health services. Conventional qualitative content analysis was used, focusing on manifest content. Emerging themes relate to the public private partnership (PPP), the NGO and its services, and community participation. The population perceives the NGO positively, linking it to healthcare improvements. Their priority is to get services, irrespective of the provider's structure. The presence of an NGO in the operation may contribute to unrealistic expectations of health services, affecting perceptions of the latter negatively. To avoid unrealistic expectations and dissatisfaction, and to increase and sustain the population's trust in the organization, an NGO should operate in a manner that is as integrated as possible within the existing structure. The NGO should work close to the population it serves, with services anchored in the community. PPP parties should develop a common platform with joint messages to the target population on the provider's structure, and regarding partners' roles and responsibilities. Interaction between the population and the providers on service content and their expectations is key to positive outcomes of PPP operations.

Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites▿†

PubMed Central

Lazzaro, Anna; Gauer, Andreas; Zeyer, Josef

2011-01-01

Studies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3− showed a seasonal pattern, increasing from 1 to 3 μg NO3− (g soil dry weight)−1 after the melting of snow but decreasing to <1 μg NO3− (g soil dry weight)−1 in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field. PMID:21965395

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

USGS Publications Warehouse

Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes.

PubMed

Chun, Chan Lan; Peller, Julie R; Shively, Dawn; Byappanahalli, Muruleedhara N; Whitman, Richard L; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines. Copyright © 2016 Elsevier B.V. All rights reserved.

Community structure of free-floating filamentous cyanobacterial mats from the Wonder Lake geothermal springs in the Philippines.

PubMed

Lacap, Donnabella C; Smith, Gavin J D; Warren-Rhodes, Kimberley; Pointing, Stephen B

2005-07-01

Cyanobacterial mats were characterized from pools of 45-60 degrees C in near-neutral pH, low-sulphide geothermal springs in the Philippines. Mat structure did not vary with temperature. All mats possessed highly ordered layers of airspaces at both the macroscopic and microscopic level, and these appear to be an adaptation to a free-floating growth habit. Upper mat layers supported biomass with elevated carotenoid:chlorophyll a ratios and an as yet uncharacterized waxy layer on the dorsal surface. Microscopic examination revealed mats comprised a single Fischerella morphotype, with abundant heterocysts throughout mats at all temperatures. Molecular analysis of mat community structure only partly matched morphological identification. All samples supported greater 16S rDNA-defined diversity than morphology suggested, with a progressive loss in the number of genotypes with increasing temperature. Fischerella-like sequences were recovered from mats occurring at all temperatures, but some mats also yielded Oscillatoria-like sequences, although corresponding phenotypes were not observed. Phylogenetic analysis revealed that Fischerella-like sequences were most closely affiliated with Fischerella major and the Oscillatoria-like sequences with Oscillatoria amphigranulata.

[What to do to avoid death by starvation? Domestic dynamics and childhood feeding practices in a rural area of extreme poverty in Mexico].

PubMed

Pelcastre-Villafuerte, Blanca; Riquer-Fernández, Florinda; de León-Reyes, Verónica; Reyes-Morales, Hortensia; Gutiérrez-Trujillo, Gonzalo; Bronfman, Mario

2006-01-01

To describe and compare household dynamics in terms of structure, beliefs and nutrition-related behavior in the homes of malnourished and well-nourished children less than five years of age. The authors carried out a qualitative ethnographic study using participant observation, and in depth interviews. Interviews were conducted with the child's caretaker or key informants, prior oral informed consent. Child care and childhood feeding practices at home and in the community were the focus of observations. The study included two periods of field work conducted in 2001, in three rural municipalities from the Río Balsas region, in Guerrero state, Mexico. The study's ethical and methodological aspects were approved by the National Research Commission of the Mexican Institute of Social Security. Households were differentially characterized by number of members, composition, type of relationship, source of income, and interactions among household members and with the community. Monoparental structures, in an early stage of the household cycle, give rise to conditions that render the child prone to malnutrition. Extended family structure represented more favorable household dynamics.

Structure and evolution of a European Parliament via a network and correlation analysis

NASA Astrophysics Data System (ADS)

Puccio, Elena; Pajala, Antti; Piilo, Jyrki; Tumminello, Michele

2016-11-01

We present a study of the network of relationships among elected members of the Finnish parliament, based on a quantitative analysis of initiative co-signatures, and its evolution over 16 years. To understand the structure of the parliament, we constructed a statistically validated network of members, based on the similarity between the patterns of initiatives they signed. We looked for communities within the network and characterized them in terms of members' attributes, such as electoral district and party. To gain insight on the nested structure of communities, we constructed a hierarchical tree of members from the correlation matrix. Afterwards, we studied parliament dynamics yearly, with a focus on correlations within and between parties, by also distinguishing between government and opposition. Finally, we investigated the role played by specific individuals, at a local level. In particular, whether they act as proponents who gather consensus, or as signers. Our results provide a quantitative background to current theories in political science. From a methodological point of view, our network approach has proven able to highlight both local and global features of a complex social system.

Characterizing the Use of Research-Community Partnerships in Studies of Evidence-Based Interventions in Children's Community Services

ERIC Educational Resources Information Center

Frazee-Brookman, Lauren; Stahmer, Aubyn; Stadnick, Nicole; Chlebowski, Colby; Herschel, Amy; Garland, Ann F.

2015-01-01

This study characterized the use of research community partnerships (RCPs) to tailor evidence-based intervention, training, and implementation models for delivery across different childhood problems and service contexts using a survey completed by project principal investigators and community partners. To build on previous RCP research and to…

Influence of a dominant consumer species reverses at increased diversity.

PubMed

Brandt, Margarita; Witman, Jon D; Chiriboga, Angel I

2012-04-01

Theory and experiments indicate that changes in consumer diversity affect benthic community structure and ecosystem functioning. Although the effects of consumer diversity have been tested in the laboratory and the field, little is known about effects of consumer diversity in the subtidal zone, one of the largest marine habitats. We investigated the grazing effects of sea urchins on algal abundance and benthic community structure in a natural subtidal habitat of the Galápagos Islands. Three species of urchins (Eucidaris, Lytechinus, and Tripneustes) were manipulated in inclusion cages following a replacement design with three levels of species richness (one, two, and three species) with all possible two-species urchin combinations. Identity was the main factor accounting for changes in the percentage of substrate grazed and benthic community structure. Two out of the three two-species assemblages grazed more than expected, suggesting a richness effect, but analyses revealed that this increased grazing was due to a sampling effect of the largest and commercially valued urchin species, Tripneustes. Benthic community structure in treatments with Eucidaris, Lytechinus, and Tripneustes alone was significantly different at the end of the experiment, suggesting that resource use differentiation occurred. Communities in Tripneustes enclosures were characterized by abundant crustose coralline algae and grazed substrate, while those without it contained abundant green foliose algae (Ulva sp.). An unexpected emergent property of the system was that the most species-rich urchin assemblage underyielded, grazing less than any other assemblage with Tripneustes, effectively reversing its dominant influence observed in the two-species treatments. While further experiments are needed to discern the mechanisms of underyielding, it may be related to changing interspecific interactions as richness increases from two to three species or to density-dependent Tripneustes grazing. This study highlights the general importance of evaluating consumer richness effects across the entire range of species richness considered, as the performance of the most species-rich consumer assemblage could not be predicted by manipulations of intermediate levels of consumer species richness.

Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios

PubMed Central

Fagúndez, Jaime

2013-01-01

Background Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Scope Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Conclusions Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios. PMID:23223202

Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios.

PubMed

Fagúndez, Jaime

2013-02-01

Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios.