Shifts in microbial community structure during in situ surfactant-enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil.

PubMed

Wang, Lingwen; Li, Feng; Zhan, Yu; Zhu, Lizhong

2016-07-01

This study aims to reveal the microbial mechanism of in situ surfactant-enhanced bioremediation (SEBR). Various concentrations of rhamnolipids, Tween 80, and sodium dodecyl benzenesulfonate (SDBS) were separately sprayed onto soils contaminated with polycyclic aromatic hydrocarbons (PAHs) for years. Within 90 days, the highest level of degradation (95 %) was observed in the soil treated with rhamnolipids (10 mg/kg), followed by 92 % degradation with Tween 80 (50 mg/kg) and 90 % degradation with SDBS (50 mg/kg). The results of the microbial phospholipid fatty acids (PLFAs) suggest that bacteria dominated the enhanced PAH biodegradation (94 % of the maximum contribution). The shift of bacterial community structure during the surfactant treatment was analyzed by using the 16S rRNA gene high-throughput sequencing. In the presence of surfactants, the number of the operational taxonomic units (OTUs) associated with Bacillus, Pseudomonas, and Sphingomonas increased from 2-3 to 15-30 % at the end of the experiment (two to three times of control). Gene prediction with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) shows that the PAH-degrading genes, such as 1-hydroxy-2-naphthoate dioxygenase and PAH dioxygenase large subunit, significantly increased after the surfactant applications (p < 0.05). The findings of this study provide insights into the surfactant-induced shifts of microbial community, as well as critical factors for efficient bioremediation.

Nematode community shifts in response to experimental warming and canopy conditions are associated with plant community changes in the temperate-boreal forest ecotone.

PubMed

Thakur, Madhav Prakash; Reich, Peter B; Fisichelli, Nicholas A; Stefanski, Artur; Cesarz, Simone; Dobies, Tomasz; Rich, Roy L; Hobbie, Sarah E; Eisenhauer, Nico

2014-06-01

Global climate warming is one of the key forces driving plant community shifts, such as range shifts of temperate species into boreal forests. As plant community shifts are slow to observe, ecotones, boundaries between two ecosystems, are target areas for providing early evidence of ecological responses to warming. The role of soil fauna is poorly explored in ecotones, although their positive and negative effects on plant species can influence plant community structure. We studied nematode communities in response to experimental warming (ambient, +1.7, +3.4 °C) in soils of closed and open canopy forest in the temperate-boreal ecotone of Minnesota, USA and calculated various established nematode indices. We estimated species-specific coverage of understory herbaceous and shrub plant species from the same experimental plots and tested if changes in the nematode community are associated with plant cover and composition. Individual nematode trophic groups did not differ among warming treatments, but the ratio between microbial-feeding and plant-feeding nematodes increased significantly and consistently with warming in both closed and open canopy areas and at both experimental field sites. The increase in this ratio was positively correlated with total cover of understory plant species, perhaps due to increased predation pressure on soil microorganisms causing higher nutrient availability for plants. Multivariate analyses revealed that temperature treatment, canopy conditions and nematode density consistently shaped understory plant communities across experimental sites. Our findings suggest that warming-induced changes in nematode community structure are associated with shifts in plant community composition and productivity in the temperate-boreal forest ecotones.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

Experimental whole-stream warming alters community size structure.

PubMed

Nelson, Daniel; Benstead, Jonathan P; Huryn, Alexander D; Cross, Wyatt F; Hood, James M; Johnson, Philip W; Junker, James R; Gíslason, Gísli M; Ólafsson, Jón S

2017-07-01

How ecological communities respond to predicted increases in temperature will determine the extent to which Earth's biodiversity and ecosystem functioning can be maintained into a warmer future. Warming is predicted to alter the structure of natural communities, but robust tests of such predictions require appropriate large-scale manipulations of intact, natural habitat that is open to dispersal processes via exchange with regional species pools. Here, we report results of a two-year whole-stream warming experiment that shifted invertebrate assemblage structure via unanticipated mechanisms, while still conforming to community-level metabolic theory. While warming by 3.8 °C decreased invertebrate abundance in the experimental stream by 60% relative to a reference stream, total invertebrate biomass was unchanged. Associated shifts in invertebrate assemblage structure were driven by the arrival of new taxa and a higher proportion of large, warm-adapted species (i.e., snails and predatory dipterans) relative to small-bodied, cold-adapted taxa (e.g., chironomids and oligochaetes). Experimental warming consequently shifted assemblage size spectra in ways that were unexpected, but consistent with thermal optima of taxa in the regional species pool. Higher temperatures increased community-level energy demand, which was presumably satisfied by higher primary production after warming. Our experiment demonstrates how warming reassembles communities within the constraints of energy supply via regional exchange of species that differ in thermal physiological traits. Similar responses will likely mediate impacts of anthropogenic warming on biodiversity and ecosystem function across all ecological communities. © 2016 John Wiley & Sons Ltd.

Population and community structure shifts of ammonia oxidizers after four-year successive biochar application to agricultural acidic and alkaline soils.

PubMed

He, Lili; Bi, Yucui; Zhao, Jin; Pittelkow, Cameron M; Zhao, Xu; Wang, Shenqiang; Xing, Guangxi

2018-04-01

Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2.25 (BC2.25) and 11.3 (BC11.3) Mgha -1 per cropping season for eight consecutive wheat/millet seasons. Quantitative polymerase chain reaction (qPCR) and 454 high-throughput pyrosequencing techniques were performed to quantify and sequence amoA gene copies and composition of AOA and AOB. Results showed that QU had lower PNR and a higher ratio of amoA gene copies of AOA to AOB than YU, PNR of QU with BC application was significantly associated with the amoA gene of AOB. Similar to previous short-term findings, BC application enhanced QU soil nitrification, which may be explained by the significant increase in AOB abundance and a shift in AOB community structure from Nitrosospira cluster 2 toward cluster 3, along with the disappearance of some obligate acidophile AOA groups, leading to the appearance of ammonia-oxidizers from neutral-alkaline soils in BC-amended acid soils. Canonical correspondence analysis (CCA) showed that soil pH was the most important factor driving shifts in ammonia-oxidizers composition. Although BC application did not have significant effects on PNR in YU, BC11.3 decreased AOA and AOB gene copies and influenced the relative abundance of community structure. Our findings represent the first investigation of long-term BC effects on AOA and AOB communities in agricultural soils using 454 high-throughput pyrosequencing, showing that BC application can alter soil

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

PubMed

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

The shifting dynamics of social roles and project ownership over the lifecycle of a community-based participatory research project.

PubMed

Salsberg, Jon; Macridis, Soultana; Garcia Bengoechea, Enrique; Macaulay, Ann C; Moore, Spencer

2017-06-01

. Community based participatory research (CBPR) is often initiated by academic researchers, yet relies on meaningful community engagement and ownership to have lasting impact. Little is understood about how ownership shifts from academic to community partners. . We examined a CBPR project over its life course and asked: what does the evolution of ownership look like from project initiation by an academic (non-community) champion (T1); to maturation-when the intervention is ready to be deployed (T2); to independence-the time when the original champion steps aside (T3); and finally, to its maintenance-when the community has had an opportunity to function independently of the original academic champion (T4)? . Using sociometric (whole network) social network analysis, knowledge leadership was measured using 'in-degree centrality'. Stakeholder network structure was measured using 'centralisation' and 'core-periphery analysis'. Friedman rank sum test was used to measure change in actor roles over time from T1 to T4. . Project stakeholder roles were observed to shift significantly (P < 0.005) from initiation (T1) to project maintenance (T4). Community stakeholders emerged into positions of knowledge leadership, while the roles of academic partners diminished in importance. The overall stakeholder network demonstrated a structural shift towards a core of densely interacting community stakeholders. . This was the first study to use Social network analysis to document a shift in ownership from academic to community partners, indicating community self-determination over the research process. Further analysis of qualitative data will determine which participatory actions or strategies were responsible for this observed change. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conservation of forest birds: evidence of a shifting baseline in community structure.

PubMed

Rittenhouse, Chadwick D; Pidgeon, Anna M; Albright, Thomas P; Culbert, Patrick D; Clayton, Murray K; Flather, Curtis H; Huang, Chengquan; Masek, Jeffrey G; Stewart, Susan I; Radeloff, Volker C

2010-08-02

Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance. We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period) and modest losses in abundance (-28.7 - -10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States. Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., approximately 22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these findings suggest some regions of the United States may

Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests.

PubMed

Pérez-Izquierdo, Leticia; Zabal-Aguirre, Mario; Flores-Rentería, Dulce; González-Martínez, Santiago C; Buée, Marc; Rincón, Ana

2017-04-01

Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughput sequencing and enzymatic approaches, we studied the fungal communities associated with three genotypic variants of Pinus pinaster trees, in 45-year-old common garden plantations. We aimed to determine the impact of biotic (i.e., tree genotype) and abiotic (i.e., season, site) factors on the fungal community structure, and to explore whether structural shifts triggered functional responses affecting relevant ecosystem processes. Tree genotype and spatial-temporal factors were pivotal structuring fungal communities, mainly by influencing their assemblage and selecting certain fungi. Diversity variations of total fungal community and of that of specific fungal guilds, together with edaphic properties and tree's productivity, explained relevant ecosystem services such as processes involved in carbon turnover and phosphorous mobilization. A mechanistic model integrating relations of these variables and ecosystem functional outcomes is provided. Our results highlight the importance of structural shifts in fungal communities because they may have functional consequences for key ecosystem processes in Mediterranean forests. © 2017 Society for Applied Microbiology and John Wiley and Sons Ltd.

First steps of ecological restoration in Mediterranean lagoons: Shifts in phytoplankton communities

NASA Astrophysics Data System (ADS)

Leruste, A.; Malet, N.; Munaron, D.; Derolez, V.; Hatey, E.; Collos, Y.; De Wit, R.; Bec, B.

2016-10-01

Along the French Mediterranean coast, a complex of eight lagoons underwent intensive eutrophication over four decades, mainly related to nutrient over-enrichment from continuous sewage discharges. The lagoon complex displayed a wide trophic gradient from mesotrophy to hypertrophy and primary production was dominated by phytoplankton communities. In 2005, the implementation of an 11 km offshore outfall system diverted the treated sewage effluents leading to a drastic reduction of anthropogenic inputs of nitrogen and phosphorus into the lagoons. Time series data have been examined from 2000 to 2013 for physical, chemical and biological (phytoplankton) variables of the water column during the summer period. Since 2006, total nitrogen and phosphorus concentrations as well as chlorophyll biomass strongly decreased revealing an improvement in lagoon water quality. In summertime, the decline in phytoplankton biomass was accompanied by shifts in community structure and composition that could be explained by adopting a functional approach by considering the common functional traits of the main algal groups. These phytoplankton communities were dominated by functional groups of small-sized and fast-growing algae (diatoms, cryptophytes and green algae). The trajectories of summer phytoplankton communities displayed a complex response to changing nutrient loads over time. While diatoms were the major group in 2006 in all the lagoons, the summer phytoplankton composition in hypertrophic lagoons has shifted towards green algae, which are particularly well adapted to summertime conditions. All lagoons showed increasing proportion and occurrence of peridinin-rich dinophytes over time, probably related to their capacity for mixotrophy. The diversity patterns were marked by a strong variability in eutrophic and hypertrophic lagoons whereas phytoplankton community structure reached the highest diversity and stability in mesotrophic lagoons. We observe that during the re

Changes in Soil Microbial Community Structure with Flooding

USDA-ARS?s Scientific Manuscript database

Flooding disturbs both above- and below-ground ecosystem processes. Although often ignored, changes in below-ground environments are no less important than those that occur above-ground. Shifts in soil microbial community structure are expected when anaerobic conditions develop from flooding. The ...

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Shift in a Large River Fish Assemblage: Body-Size and Trophic Structure Dynamics

PubMed Central

Broadway, Kyle J.; Pyron, Mark; Gammon, James R.; Murry, Brent A.

2015-01-01

As the intensity and speed of environmental change increase at both local and global scales it is imperative that we gain a better understanding of the ecological implications of community shifts. While there has been substantial progress toward understanding the drivers and subsequent responses of community change (e.g. lake trophic state), the ecological impacts of food web changes are far less understood. We analyzed Wabash River fish assemblage data collected from 1974-2008, to evaluate temporal variation in body-size structure and functional group composition. Two parameters derived from annual community size-spectra were our major response variables: (1) the regression slope is an index of ecological efficiency and predator-prey biomass ratios, and (2) spectral elevation (regression midpoint height) is a proxy for food web capacity. We detected a large assemblage shift, over at least a seven year period, defined by dramatic changes in abundance (measured as catch-per-unit-effort) of the dominant functional feeding groups among two time periods; from an assemblage dominated by planktivore-omnivores to benthic invertivores. There was a concurrent increase in ecological efficiency (slopes increased over time) following the shift associated with an increase in large-bodied low trophic level fish. Food web capacity remained relatively stable with no clear temporal trends. Thus, increased ecological efficiency occurred simultaneous to a compensatory response that shifted biomass among functional feeding groups. PMID:25902144

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.

Structural shifts of fecal microbial communities in rats with acute rejection after liver transplantation.

PubMed

Xie, Yirui; Luo, Zhuanbo; Li, Zhengfeng; Deng, Min; Liu, Hao; Zhu, Biao; Ruan, Bing; Li, Lanjuan

2012-08-01

Bacterial translocation and the development of sepsis after orthotopic liver transplantation (OLT) may be promoted by immunological damage to the intestinal mucosa or by quantitative and qualitative changes in intestinal microbiota. This study monitored structural shifts of gut microbiota in rats with OLT using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (RT-qPCR). RT-qPCR targets six major microorganisms (Domain Bacteria, Bacteroides, Bifidobacteria, Enterobacteriaceae, Lactobacillus and Clostridium leptum subgroup). Isograft, Allograft and Sham model were studied. Bacterial translocation to host organs and plasma endotoxin were determined. Alteration in gut microbiota was associated with the elevation of plasma endotoxin and a higher rate of bacterial translocation (BT) to liver in rats with acute rejection. Dynamic analysis of DGGE fingerprints showed that the gut microbiota structure of animals in the three groups was similar before the operation. But significant alterations in the composition of fecal microbiota in Allograft group were observed at 1 and 2 weeks after the OLT. The acute rejection was accompanied by the shifts of gut microbiota towards members of Bacteroides and Ruminococcus. Results from RT-qPCR indicated that Bacteroides significantly increased at 2 weeks after the OLT, whereas numbers of Bifidobacterium spp. decreased at 1 week and recovered at 2 weeks after the OLT. In summary, our data showed that rats with acute rejection after OLT exhibited significant structure shifts in the gut microbiota which dominant by overgrowth of Bacteroides and Ruminococcus, and these were associated with elevation of plasma endotoxin and higher rate of BT.

Soil bacterial community shifts associated with sugarcane straw removal

NASA Astrophysics Data System (ADS)

Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

2017-04-01

In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Reductions in fish-community contamination following lowhead dam removal linked more to shifts in food-web structure than sediment pollution.

PubMed

Davis, Robert P; Sullivan, S Mažeika P; Stefanik, Kay C

2017-12-01

Recent increases in dam removals have prompted research on ecological and geomorphic river responses, yet contaminant dynamics following dam removals are poorly understood. We investigated changes in sediment concentrations and fish-community body burdens of mercury (Hg), selenium (Se), polychlorinated biphenyls (PCB), and chlorinated pesticides before and after two lowhead dam removals in the Scioto and Olentangy Rivers (Columbus, Ohio). These changes were then related to documented shifts in fish food-web structure. Seven study reaches were surveyed from 2011 to 2015, including controls, upstream and downstream of the previous dams, and upstream restored vs. unrestored. For most contaminants, fish-community body burdens declined following dam removal and converged across study reaches by the last year of the study in both rivers. Aldrin and dieldrin body burdens in the Olentangy River declined more rapidly in the upstream-restored vs. the upstream-unrestored reach, but were indistinguishable by year three post dam removal. No upstream-downstream differences were observed in body burdens in the Olentangy River, but aldrin and dieldrin body burdens were 138 and 148% higher, respectively, in downstream reaches than in upstream reaches of the Scioto River following dam removal. The strongest relationships between trophic position and body burdens were observed with PCBs and Se in the Scioto River, and with dieldrin in the Olentangy River. Food-chain length - a key measure of trophic structure - was only weakly related to aldrin body burdens, and unrelated to other contaminants. Overall, we demonstrate that lowhead dam removal may effectively reduce ecosystem contamination, largely via shifts in fish food-web dynamics versus sediment contaminant concentrations. This study presents some of the first findings documenting ecosystem contamination following dam removal and will be useful in informing future dam removals. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

PubMed

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

Experimental soil warming at the treeline shifts fungal communities species

NASA Astrophysics Data System (ADS)

Solly, Emily; Lindahl, Björn; Dawes, Melissa; Peter, Martina; Rixen, Christian; Hagedorn, Frank

2016-04-01

In terrestrial ecosystems, fungi play a major role in decomposition processes, plant nutrient uptake and nutrient cycling. In high elevation ecosystems in Alpine and Arctic regions, the fungal community may be particularly sensitive to climate warming due to the removal of temperature limitation in the plant and soil system, faster nutrient cycling and changes in plant carbon allocation to maintain roots systems and sustain the rhizosphere. In our study, we estimated the effects of 9 years CO2 enrichment and three years of experimental soil warming on the community structure of fungal microorganisms in an alpine treeline ecosystem. In the Swiss Alps, we worked on a total of 40 plots, with c. 40-year-old Larix decidua and Pinus mugo ssp. uncinata trees (20 plots for each tree species). Half of the plots with each tree species were randomly assigned to an elevated CO2 treatment (ambient concentration +200 ppm), whereas the remaining plots received no supplementary CO2. Five individual plots for each combination of CO2 concentration and tree species were heated by an average of 4°C during the growing season with heating cables at the soil surface. At the treeline, the fungal diversity analyzed by high-throughput 454-sequencing of genetic markers, was generally low as compared to low altitude systems and mycorrhizal species made a particularly small contribution to the total fungal DNA. Soil warming led to a shift in the structure and composition of the fungal microbial community, with an increase of litter degraders and ectomycorrhizal fungi. We further observed changes in the productivity of specific fungal fruiting bodies (i.e. more Lactarius rufus sporocarps and less Hygrophorus lucorum sporocarps) during the course of the experiment, that were consistent with the 454-sequencing data. The warming effect was more pronounced in the Larix plots. These shifts were accompanied by an increased soil CO2 efflux (+40%), evidence of increased N availability and a

Habitat, topographical, and geographical components structuring shrubsteppe bird communities

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.; Leu, M.

2008-01-01

Landscapes available to birds to select for breeding locations are arrayed along multiple dimensions. Identifying the primary gradients structuring shrubsteppe bird communities in the western United States is important because widespread habitat loss and alteration are shifting the environmental template on which these birds depend. We integrated field habitat surveys, GIS coverages, and bird counts from 61 Breeding Bird Survey routes located in shrubsteppe habitats across a >800 000 km2 region to determine the gradients of habitat, topography, and geography underlying bird communities. A small set of habitat features dominated the primary environmental gradients in a canonical ordination; the 13 species in the shrubsteppe bird community were closely packed along the first two axes. Using hierarchical variance partitioning, we identified habitat as the most important pure (31% explained variation) or shared component. Topography (9%) and geography (4%) were minor components but each shared a larger contribution with habitat (habitat-topography 21%; habitat-geography 22%) in explaining the organization of the bird community. In a second tier partition of habitat structure, pure composition (% land cover) was more important (45%) than configuration (patch size and edge) (7%); the two components shared 27% of the explained variation in the bird community axes. Local (9%), community (14%), and landscape (10%) levels contributed equally. Adjacent organizational levels had a larger shared contribution (local-community 26%; community-landscape 27%) than more separated local-landscape levels (21%). Extensive conversion of shrubsteppe habitats to agriculture, exotic annual grasslands, or pinyon (Pinus spp.)-juniper (Juniperus spp.) woodlands is occurring along the primary axes of habitat structure. Because the shrubsteppe bird community was organized along short gradients dominated by habitat features, relatively small shifts in their available environment will exert a

Bacterial community shift during the startup of a full-scale oxidation ditch treating sewage.

PubMed

Chen, Yajun; Ye, Lin; Zhao, Fuzheng; Xiao, Lin; Cheng, Shupei; Zhang, Xu-Xiang

2016-10-06

Oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%~48.4%) was the most dominant bacterial phylum in the OD system but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with Flavobacterium genus of exhibited remarkable decreasing trends, while bacterial species belonging to OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of bacterial community structure and the microbial ecology during the startup of full-scale wastewater treatment bioreactor.

Anthropogenic climate change drives shift and shuffle in North Atlantic phytoplankton communities.

PubMed

Barton, Andrew D; Irwin, Andrew J; Finkel, Zoe V; Stock, Charles A

2016-03-15

Anthropogenic climate change has shifted the biogeography and phenology of many terrestrial and marine species. Marine phytoplankton communities appear sensitive to climate change, yet understanding of how individual species may respond to anthropogenic climate change remains limited. Here, using historical environmental and phytoplankton observations, we characterize the realized ecological niches for 87 North Atlantic diatom and dinoflagellate taxa and project changes in species biogeography between mean historical (1951-2000) and future (2051-2100) ocean conditions. We find that the central positions of the core range of 74% of taxa shift poleward at a median rate of 12.9 km per decade (km⋅dec(-1)), and 90% of taxa shift eastward at a median rate of 42.7 km⋅dec(-1) The poleward shift is faster than previously reported for marine taxa, and the predominance of longitudinal shifts is driven by dynamic changes in multiple environmental drivers, rather than a strictly poleward, temperature-driven redistribution of ocean habitats. A century of climate change significantly shuffles community composition by a basin-wide median value of 16%, compared with seasonal variations of 46%. The North Atlantic phytoplankton community appears poised for marked shift and shuffle, which may have broad effects on food webs and biogeochemical cycles.

Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

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

Shifts in the abundance and community structure of soil ammonia oxidizers in a wet sclerophyll forest under long-term prescribed burning.

PubMed

Long, Xi-En; Chen, Chengrong; Xu, Zhihong; He, Ji-Zheng

2014-02-01

Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles. © 2013.

Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation

PubMed Central

Vila, Jorge A.; Arnautova, Yelena A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

A server (CheShift) has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted 13Cα chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13Cα chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 Å. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed 13Cα chemical shifts are available. CheShift is available as a web server. PMID:19805131

Evidence of community structure in biomedical research grant collaborations.

PubMed

Nagarajan, Radhakrishnan; Kalinka, Alex T; Hogan, William R

2013-02-01

Recent studies have clearly demonstrated a shift towards collaborative research and team science approaches across a spectrum of disciplines. Such collaborative efforts have also been acknowledged and nurtured by popular extramurally funded programs including the Clinical Translational Science Award (CTSA) conferred by the National Institutes of Health. Since its inception, the number of CTSA awardees has steadily increased to 60 institutes across 30 states. One of the objectives of CTSA is to accelerate translation of research from bench to bedside to community and train a new genre of researchers under the translational research umbrella. Feasibility of such a translation implicitly demands multi-disciplinary collaboration and mentoring. Networks have proven to be convenient abstractions for studying research collaborations. The present study is a part of the CTSA baseline study and investigates existence of possible community-structure in Biomedical Research Grant Collaboration (BRGC) networks across data sets retrieved from the internally developed grants management system, the Automated Research Information Administrator (ARIA) at the University of Arkansas for Medical Sciences (UAMS). Fastgreedy and link-community community-structure detection algorithms were used to investigate the presence of non-overlapping and overlapping community-structure and their variation across years 2006 and 2009. A surrogate testing approach in conjunction with appropriate discriminant statistics, namely: the modularity index and the maximum partition density is proposed to investigate whether the community-structure of the BRGC networks were different from those generated by certain types of random graphs. Non-overlapping as well as overlapping community-structure detection algorithms indicated the presence of community-structure in the BRGC network. Subsequent, surrogate testing revealed that random graph models considered in the present study may not necessarily be appropriate

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Triggers and maintenance of multiple shifts in the state of a natural community

PubMed Central

Schmitt, Russell J.; Holbrook, Sally J.

2010-01-01

Ecological communities can undergo sudden and dramatic shifts between alternative persistent community states. Both ecological prediction and natural resource management rely on understanding the mechanisms that trigger such shifts and maintain each state. Differentiating between potential mechanisms is difficult, however, because shifts are often recognized only in hindsight and many occur on such large spatial scales that manipulative experiments to test their causes are difficult or impossible. Here we use an approach that focuses first on identifying changes in environmental factors that could have triggered a given state change, and second on examining whether these changes were sustained (and thus potentially maintained the new state) or transitory (explaining the shift but not its persistence). We use this approach to evaluate a community shift in which a benthic marine species of filter feeding sea cucumber (Pachythyone rubra) suddenly came to dominate subtidal rocky reefs that had previously supported high abundances of macroalgae, persisted for more than a decade, then abruptly declined. We found that a sustained period without large wave events coincided with the shift to sea cucumber dominance, but that the sea cucumbers persisted even after the end of this low wave period, indicating that different mechanisms maintained the new community. Additionally, the period of sea cucumber dominance occurred when their predators were rare, and increases in the abundance of these predators coincided with the end of sea cucumber dominance. These results underscore the complex nature of regime shifts and illustrate that focusing separately on the causes and maintenance of state change can be a productive first step for analyzing these shifts in a range of systems. PMID:20526781

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

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

Pyrosequencing-based assessment of microbial community shifts in leachate from animal carcass burial lysimeter.

PubMed

Kim, Hyun Young; Seo, Jiyoung; Kim, Tae-Hun; Shim, Bomi; Cha, Seok Mun; Yu, Seungho

2017-06-01

This study examined the use of microbial community structure as a bio-indicator of decomposition levels. High-throughput pyrosequencing technology was used to assess the shift in microbial community of leachate from animal carcass lysimeter. The leachate samples were collected monthly for one year and a total of 164,639 pyrosequencing reads were obtained and used in the taxonomic classification and operational taxonomy units (OTUs) distribution analysis based on sequence similarity. Our results show considerable changes in the phylum-level bacterial composition, suggesting that the microbial community is a sensitive parameter affected by the burial environment. The phylum classification results showed that Proteobacteria (Pseudomonas) were the most influential taxa in earlier decomposition stage whereas Firmicutes (Clostridium, Sporanaerobacter, and Peptostreptococcus) were dominant in later stage under anaerobic conditions. The result of this study can provide useful information on a time series of leachate profiles of microbial community structures and suggest patterns of microbial diversity in livestock burial sites. In addition, this result can be applicable to predict the decomposition stages under clay loam based soil conditions of animal livestock. Copyright © 2017 Elsevier B.V. All rights reserved.

Temperature-driven regime shifts in the dynamics of size-structured populations.

PubMed

Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

2011-02-01

Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

Examining shifts in zooplankton community as a response of environmental change in Lakes

NASA Astrophysics Data System (ADS)

Ghadouani, Anas; Mines, Conor; Legendre, Pierre; Yan, Norman

2014-05-01

We examined 20 years of zooplankton samples from Harp Lake for shifts in zooplankton variability following invasion by zooplankton predator Bythotrephes longimanus, using organism body size—as measured at high resolution by Laser Optical Plankton Counter (LOPC)—as the primary metric of investigation. A period of transitory high variability in the 2yr post-invasion was observed for both body size compositional variability and aggregate variability metrics, with both measures of variability shifting from low or intermediate to high variability immediately following invasion, before shifting again to intermediate variability, 2 yr post-invasion. Aggregate and compositional variability dynamics were also considered in combination over the study period, revealing that the period of transitory high variability coincided with a shift from a community-wide stasis variability pattern to one of asynchrony, before a shift back to stasis 2 yr post-invasion. These dynamics were related to changes in the significant zooplankton species within the Harp Lake community over the pre- and post- invasion periods, and are likely to be indicative of changes in the stability in the zooplankton community following invasion by Bythotrephes. The dual consideration of aggregate and compositional variability as measured by LOPC was found to provide a valuable means to assess the ecological effects of biological invasion on zooplankton communities as a whole, extending our knowledge of the effects of invasion beyond that already revealed through more traditional taxonomic investigation.

Shifting public health practice to advance health equity: recommendations from experts and community leaders.

PubMed

Knight, Erin K

2014-01-01

While the evidence base regarding the social determinants of health and their relationship to health inequities grows, the field of public health is challenged to translate this knowledge into practice changes that advance health equity. Drawing on the knowledge, beliefs, and experiences of public health experts and community leaders working to advance health equity, our objective was to develop and disseminate recommendations for changing public health practice to better address this problem. We conducted semistructured, qualitative telephone interviews (n = 25) with key informants. Interviews were recorded and transcribed, and data were coded and analyzed using both inductive and deductive methods. Member checks were used to enhance quality. A purposeful sample of key informants was selected from content experts and community leaders involved with the development of the Unnatural Causes public impact campaign. Participants represented state and local health departments, community-based organizations, national research/advocacy organizations, and academic institutions across the country. Participants distinguished between social determinants of health and their structural precursors in social and political institutions. They believed that the field of public health has an obligation to address health inequities and shifts in practice are needed that focus more attention on societal factors that underlie such inequities. According to participants, specific practice changes are difficult to identify because actions should be community specific and community driven. Recommended approaches that may be adapted to community-based needs and assets include building nontraditional partnerships, engaging in political advocacy, promoting community leadership, collecting better data on social conditions and institutional factors, and enhancing communication for health equity. Recommended shifts in practice may be facilitated by revisiting our understanding of the 3 core

Shifts of system performance and microbial community structure in a constructed wetland after exposing silver nanoparticles.

PubMed

Cao, Chong; Huang, Juan; Yan, Chunni; Liu, Jialiang; Hu, Qian; Guan, Wenzhu

2018-05-01

The increasing utilization of silver nanoparticles (Ag NPs) in industry and commerce inevitably raises its release into wastewater. In this work, effects of Ag NPs on system performance and microbial community along the way of a vertical flow constructed wetland (VFCW) were investigated, along with the removal and fate of Ag NPs within the system. Results showed that the performance of control wetland kept stable during the experimental period, and the top substrate layer (soil layer) of wetland could remove most of pollutants in the influent. The study also suggested that addition of Ag NPs did not significantly affect organic matters removal. However, adverse effects were observed on the nitrogen and phosphorus removal. Removal efficiencies of TN, NH 4 + -N and TP approximately obviously reduced by approximately 10.10%, 8.42% and 28.35% respectively in contrast to before dosing after exposing 100 μg/L Ag NPs for 94 d, while the no dosing wetland with the stable performance. It was found that Ag NPs accumulated in the upper soil layer more than in the lower soil layer, and Ag NPs could enter into the plant tissues. After continuous input of Ag NPs, removal efficiency of Ag NPs was measured as 95.72%, which showed that the CW could effectively remove Ag NPs from the wastewater. The high-throughput sequencing results revealed that Ag NPs caused the shifts in microbial community structures and changed the relative abundances of key functional bacteria, which finally resulted in a lower efficiency of biological nitrogen and phosphorus removal. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

PubMed Central

Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Jumpponen, Ari; Asiegbu, Fred O.; Heinonsalo, Jussi

2015-01-01

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics. PMID:26341215

Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

NASA Astrophysics Data System (ADS)

Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

2017-12-01

The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P < 0.05). The fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P < 0.05). The microbial biomass was positively associated with mean annual precipitation, total nitrogen and available phosphorus, and negatively associated with mean annual temperature. Our results also indicated that the variation in microbial composition was largely explained by edaphic factors, followed by climate factors. In conclusion, shrub encroachment in Inner Mongolia grasslands has significantly influenced the structure and abundance of soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

Dynamics of arbuscular mycorrhizal fungal community structure and functioning along a nitrogen enrichment gradient in an alpine meadow ecosystem.

PubMed

Jiang, Shengjing; Liu, Yongjun; Luo, Jiajia; Qin, Mingsen; Johnson, Nancy Collins; Öpik, Maarja; Vasar, Martti; Chai, Yuxing; Zhou, Xiaolong; Mao, Lin; Du, Guozhen; An, Lizhe; Feng, Huyuan

2018-03-30

Nitrogen (N) availability is increasing dramatically in many ecosystems, but the influence of elevated N on the functioning of arbuscular mycorrhizal (AM) fungi in natural ecosystems is not well understood. We measured AM fungal community structure and mycorrhizal function simultaneously across an experimental N addition gradient in an alpine meadow that is limited by N but not by phosphorus (P). AM fungal communities at both whole-plant-community (mixed roots) and single-plant-species (Elymus nutans roots) scales were described using pyro-sequencing, and the mycorrhizal functioning was quantified using a mycorrhizal-suppression treatment in the field (whole-plant-community scale) and a glasshouse inoculation experiment (single-plant-species scale). Nitrogen enrichment progressively reduced AM fungal abundance, changed AM fungal community composition, and shifted mycorrhizal functioning towards parasitism at both whole-plant-community and E. nutans scales. N-induced shifts in AM fungal community composition were tightly linked to soil N availability and/or plant species richness, whereas the shifts in mycorrhizal function were associated with the communities of specific AM fungal lineages. The observed changes in both AM fungal community structure and functioning across an N enrichment gradient highlight that N enrichment of ecosystems that are not P-limited can induce parasitic mycorrhizal functioning and influence plant community structure and ecosystem sustainability. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

PubMed

Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

2017-07-05

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

Shifts in deep-sea community structure linked to climate and food supply.

PubMed

Ruhl, Henry A; Smith, Kenneth L

2004-07-23

A major change in the community structure of the dominant epibenthic megafauna was observed at 4100 meters depth in the northeast Pacific and was synchronous to a major El Niño/La Niña event that occurred between 1997 and 1999. Photographic abundance estimates of epibenthic megafauna from 1989 to 2002 show that two taxa decreased in abundance after 1998 by 2 to 3 orders of magnitude, whereas several other species increased in abundance by 1 to 2 orders of magnitude. These faunal changes are correlated to climate fluctuations dominated by El Niño/La Niña. Megafauna even in remote marine areas appear to be affected by contemporary climatic fluctuations. Such faunal changes highlight the importance of an adequate temporal perspective in describing biodiversity, ecology, and anthropogenic impacts in deep-sea communities.

Community reorganization in the Gulf of Alaska following ocean climate regime shift

USGS Publications Warehouse

Anderson, P.J.; Piatt, John F.

1999-01-01

A shift in ocean climate during the late 1970s triggered a reorganization of community structure in the Gulf of Alaska ecosystem, as evidenced in changing catch composition on long-term (1953 to 1997) small-mesh trawl surveys. Forage species such as pandalid shrimp and capelin declined because of recruitment failure and predation, and populations have not yet recovered. Total trawl catch biomass declined >50% and remained low through the 1980s. In contrast, recruitment of high trophic-level groundfish improved during the 1980s, yielding a >250% increase in catch biomass during the 1990s. This trophic reorganization apparently had negative effects on piscivorous sea birds and marine mammals.

A comparative study of thermophilic and mesophilic anaerobic co-digestion of food waste and wheat straw: Process stability and microbial community structure shifts.

PubMed

Shi, Xuchuan; Guo, Xianglin; Zuo, Jiane; Wang, Yajiao; Zhang, Mengyu

2018-05-01

Renewable energy recovery from organic solid waste via anaerobic digestion is a promising way to provide sustainable energy supply and eliminate environmental pollution. However, poor efficiency and operational problems hinder its wide application of anaerobic digestion. The effects of two key parameters, i.e. temperature and substrate characteristics on process stability and microbial community structure were studied using two lab-scale anaerobic reactors under thermophilic and mesophilic conditions. Both the reactors were fed with food waste (FW) and wheat straw (WS). The organic loading rates (OLRs) were maintained at a constant level of 3 kg VS/(m 3 ·d). Five different FW:WS substrate ratios were utilized in different operational phases. The synergetic effects of co-digestion improved the stability and performance of the reactors. When FW was mono-digested, both reactors were unstable. The mesophilic reactor eventually failed due to volatile fatty acid accumulation. The thermophilic reactor had better performance compared to mesophilic one. The biogas production rate of the thermophilic reactor was 4.9-14.8% higher than that of mesophilic reactor throughout the experiment. The shifts in microbial community structures throughout the experiment in both thermophilic and mesophilic reactors were investigated. With increasing FW proportions, bacteria belonging to the phylum Thermotogae became predominant in the thermophilic reactor, while the phylum Bacteroidetes was predominant in the mesophilic reactor. The genus Methanosarcina was the predominant methanogen in the thermophilic reactor, while the genus Methanothrix remained predominant in the mesophilic reactor. The methanogenesis pathway shifted from acetoclastic to hydrogenotrophic when the mesophilic reactor experienced perturbations. Moreover, the population of lignocellulose-degrading microorganisms in the thermophilic reactor was higher than those in mesophilic reactor, which explained the better

Dietary and developmental shifts in butterfly-associated bacterial communities

PubMed Central

2018-01-01

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts. PMID:29892359

Biogeography and body size shuffling of aquatic salamander communities on a shifting refuge

PubMed Central

Bonett, Ronald M.; Trujano-Alvarez, Ana Lilia; Williams, Michael J.; Timpe, Elizabeth K.

2013-01-01

Freshwater habitats of coastal plains are refugia for many divergent vertebrate lineages, yet these environments are highly vulnerable to sea-level fluctuations, which suggest that resident communities have endured dynamic histories. Using the fossil record and a multi-locus nuclear phylogeny, we examine divergence times, biogeography, body size evolution and patterns of community assembly of aquatic salamanders from North American coastal plains since the Late Cretaceous. At least five salamander families occurred on the extensive Western Interior Coastal Plain (WICP), which existed from the Late Cretaceous through the Eocene. Four of these families subsequently colonized the emergent Southeastern Coastal Plain (SECP) by the Early Oligocene to Late Miocene. Three families ultimately survived and underwent extensive body size evolution in situ on the SECP. This included at least two major size reversals in recent taxa that are convergent with confamilial WICP ancestors. Dynamics of the coastal plain, major lineage extinctions and frequent extreme changes in body size have resulted in significant shuffling of the size structure of aquatic salamander communities on this shifting refuge since the Cretaceous. PMID:23466988

Soil fungal community shift evaluation as a potential cadaver decomposition indicator.

PubMed

Chimutsa, Monica; Olakanye, Ayodeji O; Thompson, Tim J U; Ralebitso-Senior, T Komang

2015-12-01

Fungi metabolise organic matter in situ and so alter both the bio-/physico-chemical properties and microbial community structure of the ecosystem. In particular, they are responsible reportedly for specific stages of decomposition. Therefore, this study aimed to extend previous bacteria-based forensic ecogenomics research by investigating soil fungal community and cadaver decomposition interactions in microcosms with garden soil (20 kg, fresh weight) and domestic pig (Sus scrofa domesticus) carcass (5 kg, leg). Soil samples were collected at depths of 0-10 cm, 10-20 cm and 20-30 cm on days 3, 28 and 77 in the absence (control -Pg) and presence (experimental +Pg) of Sus scrofa domesticus and used for total DNA extraction and nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) profiling of the 18S rRNA gene. The Shannon-Wiener (H') community diversity indices were 1.25±0.21 and 1.49±0.30 for the control and experimental microcosms, respectively, while comparable Simpson species dominance (S) values were 0.65±0.109 and 0.75±0.015. Generally, and in contrast to parallel studies of the bacterial 16S rRNA and 16S rDNA profiles, statistical analysis (t-test) of the 18S dynamics showed no mathematically significant shifts in fungal community diversity (H'; p=0.142) and dominance (S; p=0.392) during carcass decomposition, necessitating further investigations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Caribbean-wide, long-term study of seagrass beds reveals local variations, shifts in community structure and occasional collapse.

PubMed

van Tussenbroek, Brigitta I; Cortés, Jorge; Collin, Rachel; Fonseca, Ana C; Gayle, Peter M H; Guzmán, Hector M; Jácome, Gabriel E; Juman, Rahanna; Koltes, Karen H; Oxenford, Hazel A; Rodríguez-Ramirez, Alberto; Samper-Villarreal, Jimena; Smith, Struan R; Tschirky, John J; Weil, Ernesto

2014-01-01

The CARICOMP monitoring network gathered standardized data from 52 seagrass sampling stations at 22 sites (mostly Thalassia testudinum-dominated beds in reef systems) across the Wider Caribbean twice a year over the period 1993 to 2007 (and in some cases up to 2012). Wide variations in community total biomass (285 to >2000 g dry m(-2)) and annual foliar productivity of the dominant seagrass T. testudinum (<200 and >2000 g dry m(-2)) were found among sites. Solar-cycle related intra-annual variations in T. testudinum leaf productivity were detected at latitudes > 16°N. Hurricanes had little to no long-term effects on these well-developed seagrass communities, except for 1 station, where the vegetation was lost by burial below ∼1 m sand. At two sites (5 stations), the seagrass beds collapsed due to excessive grazing by turtles or sea-urchins (the latter in combination with human impact and storms). The low-cost methods of this regional-scale monitoring program were sufficient to detect long-term shifts in the communities, and fifteen (43%) out of 35 long-term monitoring stations (at 17 sites) showed trends in seagrass communities consistent with expected changes under environmental deterioration.

Caribbean-Wide, Long-Term Study of Seagrass Beds Reveals Local Variations, Shifts in Community Structure and Occasional Collapse

PubMed Central

van Tussenbroek, Brigitta I.; Cortés, Jorge; Collin, Rachel; Fonseca, Ana C.; Gayle, Peter M. H.; Guzmán, Hector M.; Jácome, Gabriel E.; Juman, Rahanna; Koltes, Karen H.; Oxenford, Hazel A.; Rodríguez-Ramirez, Alberto; Samper-Villarreal, Jimena; Smith, Struan R.; Tschirky, John J.; Weil, Ernesto

2014-01-01

The CARICOMP monitoring network gathered standardized data from 52 seagrass sampling stations at 22 sites (mostly Thalassia testudinum-dominated beds in reef systems) across the Wider Caribbean twice a year over the period 1993 to 2007 (and in some cases up to 2012). Wide variations in community total biomass (285 to >2000 g dry m−2) and annual foliar productivity of the dominant seagrass T. testudinum (<200 and >2000 g dry m−2) were found among sites. Solar-cycle related intra-annual variations in T. testudinum leaf productivity were detected at latitudes > 16°N. Hurricanes had little to no long-term effects on these well-developed seagrass communities, except for 1 station, where the vegetation was lost by burial below ∼1 m sand. At two sites (5 stations), the seagrass beds collapsed due to excessive grazing by turtles or sea-urchins (the latter in combination with human impact and storms). The low-cost methods of this regional-scale monitoring program were sufficient to detect long-term shifts in the communities, and fifteen (43%) out of 35 long-term monitoring stations (at 17 sites) showed trends in seagrass communities consistent with expected changes under environmental deterioration. PMID:24594732

Outbreaks by canopy-feeding geometrid moth cause state-dependent shifts in understorey plant communities.

PubMed

Karlsen, Stein Rune; Jepsen, Jane Uhd; Odland, Arvid; Ims, Rolf Anker; Elvebakk, Arve

2013-11-01

The increased spread of insect outbreaks is among the most severe impacts of climate warming predicted for northern boreal forest ecosystems. Compound disturbances by insect herbivores can cause sharp transitions between vegetation states with implications for ecosystem productivity and climate feedbacks. By analysing vegetation plots prior to and immediately after a severe and widespread outbreak by geometrid moths in the birch forest-tundra ecotone, we document a shift in forest understorey community composition in response to the moth outbreak. Prior to the moth outbreak, the plots divided into two oligotrophic and one eutrophic plant community. The moth outbreak caused a vegetation state shift in the two oligotrophic communities, but only minor changes in the eutrophic community. In the spatially most widespread communities, oligotrophic dwarf shrub birch forest, dominance by the allelopathic dwarf shrub Empetrum nigrum ssp. hermaphroditum, was effectively broken and replaced by a community dominated by the graminoid Avenella flexuosa, in a manner qualitatively similar to the effect of wild fires in E. nigrum communities in coniferous boreal forest further south. As dominance by E. nigrum is associated with retrogressive succession the observed vegetation state shift has widespread implications for ecosystem productivity on a regional scale. Our findings reveal that the impact of moth outbreaks on the northern boreal birch forest system is highly initial-state dependent, and that the widespread oligotrophic communities have a low resistance to such disturbances. This provides a case for the notion that climate impacts on arctic and northern boreal vegetation may take place most abruptly when conveyed by changed dynamics of irruptive herbivores.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet

PubMed Central

Peter, Hannes; Jeppesen, Erik; De Meester, Luc; Sommaruga, Ruben

2018-01-01

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes. PMID:29087379

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination.

PubMed

Jia, Shuyu; Shi, Peng; Hu, Qing; Li, Bing; Zhang, Tong; Zhang, Xu-Xiang

2015-10-20

For comprehensive insights into the effects of chlorination, a widely used disinfection technology, on bacterial community and antibiotic resistome in drinking water, this study applied high-throughput sequencing and metagenomic approaches to investigate the changing patterns of antibiotic resistance genes (ARGs) and bacterial community in a drinking water treatment and distribution system. At genus level, chlorination could effectively remove Methylophilus, Methylotenera, Limnobacter, and Polynucleobacter, while increase the relative abundance of Pseudomonas, Acidovorax, Sphingomonas, Pleomonas, and Undibacterium in the drinking water. A total of 151 ARGs within 15 types were detectable in the drinking water, and chlorination evidently increased their total relative abundance while reduced their diversity in the opportunistic bacteria (p < 0.05). Residual chlorine was identified as the key contributing factor driving the bacterial community shift and resistome alteration. As the dominant persistent ARGs in the treatment and distribution system, multidrug resistance genes (mainly encoding resistance-nodulation-cell division transportation system) and bacitracin resistance gene bacA were mainly carried by chlorine-resistant bacteria Pseudomonas and Acidovorax, which mainly contributed to the ARGs abundance increase. The strong correlation between bacterial community shift and antibiotic resistome alteration observed in this study may shed new light on the mechanism behind the chlorination effects on antibiotic resistance.

Climate change drives a shift in peatland ecosystem plant community: implications for ecosystem function and stability.

PubMed

Dieleman, Catherine M; Branfireun, Brian A; McLaughlin, James W; Lindo, Zoë

2015-01-01

The composition of a peatland plant community has considerable effect on a range of ecosystem functions. Peatland plant community structure is predicted to change under future climate change, making the quantification of the direction and magnitude of this change a research priority. We subjected intact, replicated vegetated poor fen peat monoliths to elevated temperatures, increased atmospheric carbon dioxide (CO2 ), and two water table levels in a factorial design to determine the individual and synergistic effects of climate change factors on the poor fen plant community composition. We identify three indicators of a regime shift occurring in our experimental poor fen system under climate change: nonlinear decline of Sphagnum at temperatures 8 °C above ambient conditions, concomitant increases in Carex spp. at temperatures 4 °C above ambient conditions suggesting a weakening of Sphagnum feedbacks on peat accumulation, and increased variance of the plant community composition and pore water pH through time. A temperature increase of +4 °C appeared to be a threshold for increased vascular plant abundance; however the magnitude of change was species dependent. Elevated temperature combined with elevated CO2 had a synergistic effect on large graminoid species abundance, with a 15 times increase as compared to control conditions. Community analyses suggested that the balance between dominant plant species was tipped from Sphagnum to a graminoid-dominated system by the combination of climate change factors. Our findings indicate that changes in peatland plant community composition are likely under future climate change conditions, with a demonstrated shift toward a dominance of graminoid species in poor fens. © 2014 John Wiley & Sons Ltd.

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients

PubMed Central

Liu, Jiwen; Fu, Bingbing; Yang, Hongmei; Zhao, Meixun; He, Biyan; Zhang, Xiao-Hua

2015-01-01

The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments. PMID:25713564

Quantifying relationships between bird and butterfly community shifts and environmental change.

PubMed

Debinski, Diane M; Vannimwegen, Ron E; Jakubauskas, Mark E

2006-02-01

Quantifying the manner in which ecological communities respond during a time of decreasing precipitation is a first step in understanding how they will respond to longer-term climate change. Here we coupled analysis of interannual variability in remotely sensed data with analyses of bird and butterfly community changes in montane meadow communities of the Greater Yellowstone Ecosystem. Landsat satellite imagery was used to classify these meadows into six types along a hydrological gradient. The northern portion of the ecosystem, or Gallatin region, has smaller mean patch sizes separated by ridges of mountains, whereas the southern portion of the ecosystem, or Teton region, has much larger patches within the Jackson Hole valley. Both support a similar suite of butterfly and bird species. The Gallatin region showed more overall among-year variation in the normalized difference vegetation index (NDVI) when meadow types were pooled within regions, perhaps because the patch sizes are smaller on average. Bird and butterfly communities showed significant relationships relative to meadow type and NDVI. We identified several key species that are tightly associated with specific meadow types along the hydrological gradient. Comparing taxonomic groups, fewer birds showed specific habitat affinities than butterflies, perhaps because birds are responding to differences in habitat structure among meadow types and using the landscape at a coarser scale than the butterflies. Comparing regions, the Teton region showed higher predictability of community assemblages as compared to the Gallatin region. The Gallatin region exhibited more significant temporal trends with respect to butterflies. Butterfly communities in wet meadows showed a distinctive shift along the hydrological gradient during a drought period (1997-2000). These results imply that the larger Teton meadows will show more predictable (i.e., static) species-habitat associations over the long term, but that the smaller

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community.

PubMed

Friedman, Nir; Shriker, Eran; Gold, Ben; Durman, Thomer; Zarecki, Raphy; Ruppin, Eytan; Mizrahi, Itzhak

2017-01-01

Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes. Using metabolomic analyses together with in vitro microbiology approaches and whole-genome sequencing of Methanomicrobium mobile, a key species within this group, we identified that redox potential changes with diet and is the main factor that causes these dietary induced alternations in this taxa's abundance. Our genomic analysis suggests that the redox potential effect stems from a reduced number of anti-reactive oxygen species proteins coded in this taxon's genome. Our study highlights redox potential as a pivotal factor that could serve as a sculpturing force of community assembly within anaerobic gut microbial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Leveraging disjoint communities for detecting overlapping community structure

NASA Astrophysics Data System (ADS)

Chakraborty, Tanmoy

2015-05-01

Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network. In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm.

Bacterial diversity and community structure in lettuce soil are shifted by cultivation time

NASA Astrophysics Data System (ADS)

Liu, Yiqian; Chang, Qing; Guo, Xu; Yi, Xinxin

2017-08-01

Compared with cereal production, vegetable production usually requires a greater degree of management and larger input of nutrients and irrigation, but these systems are not sustainable in the long term. This study aimed to what extent lettuce determine the bacterial community composition in the soil, during lettuce cultivation, pesticides and fertilizers were not apply to soil. Soil samples were collected from depths of 0-20cm and 20-40cm. A highthroughput sequencing approach was employed to investigate bacterial communities in lettuce-cultivated soil samples in a time-dependent manner. The dominant bacteria in the lettuce soil samples were mainly Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Firmicutes, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimo nadetes, Cyanobacteria. Proteobacteria was the most abundant phylum in the 6 soil samples. The relative abundance of Acidobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria decreased through time of lettuce cultivation, but the relative abundance of Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Nitrospirae increased over time. In the 0-20cm depth group and the 20-40cm depth soil, a similar pattern was observed that the percentage number of only shared OTUs between the early and late stage was lower than that between the early and middle stage soil, the result showed that lettuce growth can affect structure of soil bacterial communities.

Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.

PubMed

Cai, Yun; Gu, Hong; Kenney, Toby

2017-08-31

Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems. The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new). NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet.

PubMed

Peter, Hannes; Jeppesen, Erik; De Meester, Luc; Sommaruga, Ruben

2017-10-31

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.191.

Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

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

Feng, Yiquing; Roder, H.; Englander, S.W.

1990-04-10

Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences for structure change, the authors removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor calculation, when repeated using only 12 available C{sub {alpha}}H proton resonances for cytochrom c from tuna, proved to be remarkably stable.more » The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, where are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impressions one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.« less

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

PubMed

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

2009-01-01

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

Resources alter the structure and increase stochasticity in bromeliad microfauna communities.

PubMed

Petermann, Jana S; Kratina, Pavel; Marino, Nicholas A C; MacDonald, A Andrew M; Srivastava, Diane S

2015-01-01

Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down interactions (predators) and dispersal at two spatial scales in the field. We found that resource addition strongly increased the abundance and reduced the richness of microfauna communities. Community composition shifted in a predictable way towards assemblages dominated by flagellates and ciliates but with lower abundance and richness of algae and amoebae. While all functional groups responded strongly and predictably to resource addition, similarity among communities at the species level decreased, suggesting a role of stochasticity in species-level assembly processes. Dispersal limitation did not affect the communities. Since our design excluded potential priority effects we can attribute the differences in community similarity to increased demographic stochasticity of resource-enriched communities related to erratic changes in population sizes of some species. In contrast to resources, predators and environmental conditions had negligible effects on community structure. Our results demonstrate that bromeliad microfauna communities are strongly controlled by bottom-up forces. They further suggest that the relative importance of stochasticity may change with productivity and with the organizational level at which communities are examined.

Resources Alter the Structure and Increase Stochasticity in Bromeliad Microfauna Communities

PubMed Central

Petermann, Jana S.; Kratina, Pavel; Marino, Nicholas A. C.; MacDonald, A. Andrew M.; Srivastava, Diane S.

2015-01-01

Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down interactions (predators) and dispersal at two spatial scales in the field. We found that resource addition strongly increased the abundance and reduced the richness of microfauna communities. Community composition shifted in a predictable way towards assemblages dominated by flagellates and ciliates but with lower abundance and richness of algae and amoebae. While all functional groups responded strongly and predictably to resource addition, similarity among communities at the species level decreased, suggesting a role of stochasticity in species-level assembly processes. Dispersal limitation did not affect the communities. Since our design excluded potential priority effects we can attribute the differences in community similarity to increased demographic stochasticity of resource-enriched communities related to erratic changes in population sizes of some species. In contrast to resources, predators and environmental conditions had negligible effects on community structure. Our results demonstrate that bromeliad microfauna communities are strongly controlled by bottom-up forces. They further suggest that the relative importance of stochasticity may change with productivity and with the organizational level at which communities are examined. PMID:25775464

Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions.

PubMed

Cho, Kyungjin; Shin, Seung Gu; Kim, Woong; Lee, Joonyeob; Lee, Changsoo; Hwang, Seokhwan

2017-12-01

Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H 2 producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH 4 + -N] (p<0.1); this relationship suggests that ammonia was a significant parameter for bacterial selection. The bacterial niche information reported in this study can be useful to understand the ecophysiology of anaerobic digesters treating swine manure that contains high ammonia content. Copyright © 2017 Elsevier B.V. All rights reserved.

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments.

PubMed

Laverman, Anniet M; Cazier, Thibaut; Yan, Chen; Roose-Amsaleg, Céline; Petit, Fabienne; Garnier, Josette; Berthe, Thierry

2015-09-01

Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

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

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.

PubMed

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch ( Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N 2 O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand

PubMed Central

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity. PMID:28421053

Climate change effects on soil microarthropod abundance and community structure

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

Kardol, Paul; Reynolds, W. Nicholas; Norby, Richard J

2011-01-01

Long-term ecosystem responses to climate change strongly depend on how the soil subsystem and its inhabitants respond to these perturbations. Using open-top chambers, we studied the response of soil microarthropods to single and combined effects of ambient and elevated atmospheric [CO{sub 2}], ambient and elevated temperatures and changes in precipitation in constructed old-fields in Tennessee, USA. Microarthropods were assessed five years after treatments were initiated and samples were collected in both November and June. Across treatments, mites and collembola were the most dominant microarthropod groups collected. We did not detect any treatment effects on microarthropod abundance. In November, but notmore » in June, microarthropod richness, however, was affected by the climate change treatments. In November, total microarthropod richness was lower in dry than in wet treatments, and in ambient temperature treatments, richness was higher under elevated [CO{sub 2}] than under ambient [CO{sub 2}]. Differential responses of individual taxa to the climate change treatments resulted in shifts in community composition. In general, the precipitation and warming treatments explained most of the variation in community composition. Across treatments, we found that collembola abundance and richness were positively related to soil moisture content, and that negative relationships between collembola abundance and richness and soil temperature could be explained by temperature-related shifts in soil moisture content. Our data demonstrate how simultaneously acting climate change factors can affect the structure of soil microarthropod communities in old-field ecosystems. Overall, changes in soil moisture content, either as direct effect of changes in precipitation or as indirect effect of warming or elevated [CO{sub 2}], had a larger impact on microarthropod communities than did the direct effects of the warming and elevated [CO{sub 2}] treatments. Moisture-induced shifts in

Body size distributions signal a regime shift in a lake ...

EPA Pesticide Factsheets

Communities of organisms, from mammals to microorganisms, have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at multiple spatial and temporal scales. In this study, we assessed whether body size patterns serve as an indicator of a threshold between alternative regimes. Over the past 7000 years, the biological communities of Foy Lake (Montana,USA) have undergone a major regime shift owing to climate change. We used a palaeoecological record of diatom communities to estimate diatom sizes, and then analysed the discontinuous distribution of organism sizes over time. We used Bayesian classification and regression tree models to determine that all time intervals exhibited aggregations of sizes separated by gaps in the distribution and found a significant change in diatom body size distributions approximately 150 years before the identified ecosystem regime shift. We suggest that discontinuity analysis is a useful addition to the suite of tools for the detection of early warning signals of regime shifts. Communities of organisms from mammals to microorganisms have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at discrete spatial and temporal scales within ecosystems. Here, a paleoecological record of diatom community change is use

County community health associations of net voting shift in the 2016 U.S. presidential election.

PubMed

Wasfy, Jason H; Stewart, Charles; Bhambhani, Vijeta

2017-01-01

In the U.S. presidential election of 2016, substantial shift in voting patterns occurred relative to previous elections. Although this shift has been associated with both education and race, the extent to which this shift was related to public health status is unclear. To determine the extent to which county community health was associated with changes in voting between the presidential elections of 2016 and 2012. Ecological study with principal component analysis (PCA) using principal axis method to extract the components, then generalized linear regression. General community. All counties in the United States. Physically unhealthy days, mentally unhealthy days, percent food insecure, teen birth rate, primary care physician visit rate, age-adjusted mortality rate, violent crime rate, average health care costs, percent diabetic, and percent overweight or obese. The percentage of Donald Trump votes in 2016 minus percentage of Mitt Romney votes in 2012 ("net voting shift"). Complete public health data was available for 3,009 counties which were included in the analysis. The mean net voting shift was 5.4% (+/- 5.8%). Of these 3,009 counties, 2,641 (87.8%) had positive net voting shift (shifted towards Trump) and 368 counties (12.2%) had negative net voting shift (shifted away from Trump). The first principal component ("unhealthy score") accounted for 68% of the total variance in the data. The unhealthy score included all health variables except primary care physician rate, violent crime rate, and health care costs. The mean unhealthy score for counties was 0.39 (SD 0.16). Higher normalized unhealthy score was associated with positive net voting shift (22.1% shift per unit unhealthy, p < 0.0001). This association was stronger in states that switched Electoral College votes from 2012 to 2016 than in other states (5.9% per unit unhealthy, p <0.0001). Substantial association exists between a shift toward voting for Donald Trump in 2016 relative to Mitt Romney in 2012 and

Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers.

PubMed

Avrahami, Sharon; Liesack, Werner; Conrad, Ralf

2003-08-01

We investigated the effect of temperature on the activity of soil ammonia oxidizers caused by changes in the availability of ammonium and in the microbial community structure. Both short (5 days) and long (6.5, 16 and 20 weeks) incubation of an agricultural soil resulted in a decrease in ammonium concentration that was more pronounced at temperatures between 10 and 25 degrees C than at either 4 degrees C or 30-37 degrees C. Consistently, potential nitrification was higher between 10 and 25 degrees C than at either 4 degrees C or 37 degrees C. However, as long as ammonium was not limiting, release rates of N2O increased monotonously between 4 and 37 degrees C after short-term temperature adaptation, with nitrification accounting for about 35-50% of the N2O production between 4 and 25 degrees C. In order to see whether temperature may also affect the community structure of ammonia oxidizers, we studied moist soil during long incubation at low and high concentrations of commercial fertilizer. The soil was also incubated in buffered (pH 7) slurry amended with urea. Communities of ammonia oxidizers were assayed by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the alpha subunit of ammonia monooxygenase. We found that a polymerase chain reaction (PCR) system using a non-degenerated reverse primer (amoAR1) gave the best results. Community shifts occurred in all soil treatments after 16 weeks of incubation. The community shifts were obviously influenced by the different fertilizer treatments, indicating that ammonium was a selective factor for different ammonia oxidizer populations. Temperature was also a selective factor, in particular as community shifts were also observed in the soil slurries, in which ammonium concentrations and pH were better controlled. Cloning and sequencing of selected DGGE bands indicated that amoA sequences belonging to Nitrosospira cluster 1 were dominant at low temperatures (4-10 degrees C), but were absent after

Shifts in coastal Antarctic marine microbial communities during and after melt water-related surface stratification.

PubMed

Piquet, Anouk M-T; Bolhuis, Henk; Meredith, Michael P; Buma, Anita G J

2011-06-01

Antarctic coastal waters undergo major physical alterations during summer. Increased temperatures induce sea-ice melting and glacial melt water input, leading to strong stratification of the upper water column. We investigated the composition of micro-eukaryotic and bacterial communities in Ryder Bay, Antarctic Peninsula, during and after summertime melt water stratification, applying community fingerprinting (denaturing gradient gel electrophoresis) and sequencing analysis of partial 18S and 16S rRNA genes. Community fingerprinting of the eukaryotic community revealed two major patterns, coinciding with a period of melt water stratification, followed by a period characterized by regular wind-induced breakdown of surface stratification. During the first stratified period, we observed depth-related differences in eukaryotic fingerprints while differences in bacterial fingerprints were weak. Wind-induced breakdown of the melt water layer caused a shift in the eukaryotic community from an Actinocyclus sp.- to a Thalassiosira sp.-dominated community. In addition, a distinct transition in the bacterial community was found, but with a few days' delay, suggesting a response to the changes in the eukaryotic community rather than to the mixing event itself. Sequence analysis revealed a shift from an Alpha- and Gammaproteobacteria to a Cytophaga-Flavobacterium-Bacteroides-dominated community under mixed conditions. Our results show that melt water stratification and the transition to nonstabilized Antarctic surface waters may have an impact not only on micro-eukaryotic but also bacterial community composition. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence

Treesearch

Jennifer Moore-Kucera; Richard P. Dick

2008-01-01

The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research...

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

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

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and successional trajectories in plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study we sought to examine how emblematic shifts from early-successional Alnus sinuata (alder) to late successional Picea sitchensis (spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield tomore » delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early-successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate drives shifts in the relative abundance of major taxa of bacteria in alder-influenced soils, including declines in those that are enriched by alder. We found these effects to be spruce-specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Our results show that spruce leachate addition more strongly structures bacterial communities than alders (less dispersion in bacterial community beta diversity). Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.« less

Invertebrate community response to a shifting mosaic of habitat

USGS Publications Warehouse

Engle, David M.; Fuhlendorf, S.D.; Roper, A.; Leslie, David M.

2008-01-01

Grazing management has focused largely on promoting vegetation homogeneity through uniform distribution of grazing to minimize area in a pasture that is either heavily disturbed or undisturbed. An alternative management model that couples grazing and fire (i.e., patch burning) to promote heterogeneity argues that grazing and fire interact through a series of positive and negative feedbacks to cause a shifting mosaic of vegetation composition and structure across the landscape. We compared patch burning with traditional homogeneity-based management in tallgrass prairie to determine the influence of the two treatments on the aboveground invertebrate community. Patch burning resulted in a temporal flush of invertebrate biomass in patches transitional between unburned and patches burned in the current year. Total invertebrate mass was about 50% greater in these transitional patches within patch-burned pastures as compared to pastures under traditional, homogeneity-based management. Moreover, the mosaic of patches in patch-burned pastures contained a wider range of invertebrate biomass and greater abundance of some invertebrate orders than did the traditionally managed pastures. Patch burning provides habitat that meets requirements for a broad range of invertebrate species, suggesting the potential for patch burning to benefit other native animal assemblages in the food chain.

Regime Shift in Sandy Beach Microbial Communities following Deepwater Horizon Oil Spill Remediation Efforts

PubMed Central

Engel, Annette Summers; Gupta, Axita A.

2014-01-01

Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changes would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sand washing and sediment redistribution, would impact microbial ecosystem resiliency. Transects perpendicular to the shoreline were sampled from public beaches on Grand Isle, Louisiana, and Dauphin Island, Alabama, over one year. Prior to oil coming onshore, elevated levels of bacteria associated with fecal contamination were detected (e.g., Enterobacteriales and Campylobacterales). Over time, significant shifts within major phyla were identified (e.g., Proteobacteria, Firmicutes, Actinobacteria) and fecal indicator groups were replaced by taxa affiliated with open-ocean and marine systems (e.g., Oceanospirillales, Rhodospirillales, and Rhodobacterales). These new bacterial groups included putative hydrocarbon degraders, similar to those identified near the oil plume offshore. Shifts in the microbial community composition strongly correlated to more poorly sorted sediment and grain size distributional changes. Natural oceanographic processes could not account for the disrupted sediment, especially from the backshore well above the maximum high-tide levels recorded at these sites. Sand washing and tilling occurred on both open beaches from August through at least December 2010, which were mechanisms that could replace fecal indicator groups with open-ocean groups. Consequently, remediation efforts meant to return beaches to pre-spill compositions caused a regime shift that may have added potential ecosystem function, like hydrocarbon degradation, to the sediment. Future research will

Role of cyclic diguanylate in affecting microbial community shifts at different pH during the operation of simultaneous partial nitrification, anammox and denitrification process.

PubMed

Wang, Chao; Liu, Sitong; Xu, Xiaochen; Guo, Yongzhao; Yang, Fenglin; Wang, Dong

2018-05-08

The intracellular cyclic diguanylate acid (c-di-GMP) has emerged as a prominent second signal molecule that coordinates sessile-motile transition and biofilm formation in many bacteria. Herein, we study the role of c-di-GMP in affecting microbial community shifts at different pH levels during simultaneous partial nitrification, anammox and denitrification process (SNAD) in integrated fixed film activated sludge (IFAS) reactor. The results demonstrated that the contents of c-di-GMP notably decreased in suspended sludge, whereas the contents of c-di-GMP in biofilm had no significant change as pH gradually increased from 7.5 to 8.5. Most of the bacteria (Blastocatella, Brevundimonas) with flagella that have been reported to be regulated by c-di-GMP were present in suspended sludge, and the microbial community structure of suspended sludge had obvious change than biofilm. The increased alkaline pH reduced intracellular c-di-GMP content for increasing the motility of bacteria to be washed out from the reactor, causing the microbial community shifts in suspended sludge. This change would lead to the increase of nitrite-oxidizing bacteria which would inhibit anammox activity. Overall, this study provided more comprehensive information regarding the shifts of microbial community induced by c-di-GMP in SNAD-IFAS reactor. Copyright © 2018. Published by Elsevier B.V.

Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters.

PubMed

Hou, Luanfeng; Wu, Qingping; Gu, Qihui; Zhou, Qin; Zhang, Jumei

2018-07-01

Aniline has aroused general concern owing to its strong toxicity and widespread distribution in water and soil. In the present study, the bacterial community composition before and after aniline acclimation was investigated. High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the structure of the bacterial community during the aniline acclimation period. Bacillus, Lactococcus, and Enterococcus were the dominant bacteria in biologically activated carbon before acclimation. However, the proportions of Pseudomonas, Thermomonas, and Acinetobacter increased significantly and several new bacterial taxa appeared after aniline acclimation, indicating that aniline acclimation had a strong impact on the bacterial community structure of biological activated carbon samples. Strain AN-1 accounted for the highest number of colonies on incubation plates and was identified as Acinetobacter sp. according to phylogenetic analysis of the 16S ribosomal ribonucleic acid gene sequence. Strain AN-1 was able to grow on aniline at pH value 4.0-10.0 and showed high aniline-degrading ability at neutral pH.

Impact of individual interest shift on information dissemination in modular networks

NASA Astrophysics Data System (ADS)

Zhao, Narisa; Cui, Xuelian

2017-01-01

Social networks exhibit strong community structure. Many researches have been done to explore the impacts of community structure on information diffusion but few combined with human behaviors together. In this paper, we focus on how the individual interests' changing behavior impacts the dynamics of information propagation. Firstly, we propose an information dissemination model considering both the community structure and individual interest shift where social reinforcement and time decaying are taken into account. The accuracy of the model is evaluated by comparing the simulation and theoretical results. Further, the numerical results illustrate that both the community structure and the interests changing behavior have effects on the outbreak size of the information dissemination. Specially, lower modularity and higher community connection density will accelerate the speed of information propagation especially when the information maximal lifetime is shorter. In addition, the changes of individual interests in the message have a great impact on the final density of the received through increasing or decreasing the number of satisfied individuals directly. What is more, our findings suggest that when the modularity of the network is higher and the community clustering coefficient is lower individual interest shift behavior will have a heavier effect on the spread scope.

The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts

PubMed Central

Vergés, Adriana; Steinberg, Peter D.; Hay, Mark E.; Poore, Alistair G. B.; Campbell, Alexandra H.; Ballesteros, Enric; Heck, Kenneth L.; Booth, David J.; Coleman, Melinda A.; Feary, David A.; Figueira, Will; Langlois, Tim; Marzinelli, Ezequiel M.; Mizerek, Toni; Mumby, Peter J.; Nakamura, Yohei; Roughan, Moninya; van Sebille, Erik; Gupta, Alex Sen; Smale, Dan A.; Tomas, Fiona; Wernberg, Thomas; Wilson, Shaun K.

2014-01-01

Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to ‘barrens’ when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs. PMID:25009065

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Minimization of color shift generated in RGBW quad structure.

NASA Astrophysics Data System (ADS)

Kim, Hong Chul; Yun, Jae Kyeong; Baek, Heume-Il; Kim, Ki Duk; Oh, Eui Yeol; Chung, In Jae

2005-03-01

The purpose of RGBW Quad Structure Technology is to realize higher brightness than that of normal panel (RGB stripe structure) by adding white sub-pixel to existing RGB stripe structure. However, there is side effect called 'color shift' resulted from increasing brightness. This side effect degrades general color characteristics due to change of 'Hue', 'Brightness' and 'Saturation' as compared with existing RGB stripe structure. Especially, skin-tone colors show a tendency to get darker in contrast to normal panel. We"ve tried to minimize 'color shift' through use of LUT (Look Up Table) for linear arithmetic processing of input data, data bit expansion to 12-bit for minimizing arithmetic tolerance and brightness weight of white sub-pixel on each R, G, B pixel. The objective of this study is to minimize and keep Δu'v' value (we commonly use to represent a color difference), quantitative basis of color difference between RGB stripe structure and RGBW quad structure, below 0.01 level (existing 0.02 or higher) using Macbeth colorchecker that is general reference of color characteristics.

Warming and Resource Availability Shift Food Web Structure and Metabolism

PubMed Central

O'Connor, Mary I.; Piehler, Michael F.; Leech, Dina M.; Anton, Andrea; Bruno, John F.

2009-01-01

Climate change disrupts ecological systems in many ways. Many documented responses depend on species' life histories, contributing to the view that climate change effects are important but difficult to characterize generally. However, systematic variation in metabolic effects of temperature across trophic levels suggests that warming may lead to predictable shifts in food web structure and productivity. We experimentally tested the effects of warming on food web structure and productivity under two resource supply scenarios. Consistent with predictions based on universal metabolic responses to temperature, we found that warming strengthened consumer control of primary production when resources were augmented. Warming shifted food web structure and reduced total biomass despite increases in primary productivity in a marine food web. In contrast, at lower resource levels, food web production was constrained at all temperatures. These results demonstrate that small temperature changes could dramatically shift food web dynamics and provide a general, species-independent mechanism for ecological response to environmental temperature change. PMID:19707271

Shifts in microbial communities and soil nutrients along a fire chronosequence in Alaskan boreal forest

NASA Astrophysics Data System (ADS)

Treseder, K. K.; Mack, M. C.; Cross, A.

2002-12-01

Fires are important pathways of carbon loss from boreal forests, while microbial communities form equally important mechanisms for carbon accumulation between fires. We used a chronosequence in Alaska to examine shifts in microbial abundance and community composition in the several decades following severe fire, and then related these responses to soil characteristics in the same sites. The sites are located in upland forests near Delta Junction, Alaska, and represent stages at 3-, 15-, 45-, and over 100-yr following fire. Plant communities shift from herbaceous species in the youngest site, to deciduous shrubs and trees (e.g. Populus tremuloides and Salix) in the intermediate sites, to black spruce (Picea mariana) forest in the oldest site. Soil organic matter accumulated 2.8-fold over time. Potential mineralization was highest in the intermediate-aged sites, as was nitrification and standing pools of inorganic nitrogen. In contrast, inorganic phosphorus pools were highest immediately following fire, and then decreased nine-fold with age. As measured with BiologTM plates, bacterial diversity and abundance were greatest in the oldest sites. Plant roots in the intermediate-aged sites displayed higher colonization by ecto- and arbuscular mycorrhizal fungi than those in the youngest and oldest sites. Likewise, glomalin, a glycoprotein produced by arbuscular mycorrhizal fungi, was most abundant in the 14-yr old site. Glomalin is believed to contribute to the formation of water-stable aggregates in the soil. However, water stable aggregates were most abundant in the younger sites and did not follow the pattern of glomalin or arbuscular mycorrhizal abundance. Our results indicate that fire may maintain landscape-level diversity of microbial functional groups, and that carbon sequestration in microbial tissues (e.g. glomalin and fungal biomass) may be greatest in areas that have burned several decades earlier. Changes in soil structure may not be directly attributable to

Butterfly community shifts over two centuries.

PubMed

Habel, Jan Christian; Segerer, Andreas; Ulrich, Werner; Torchyk, Olena; Weisser, Wolfgang W; Schmitt, Thomas

2016-08-01

Environmental changes strongly impact the distribution of species and subsequently the composition of species assemblages. Although most community ecology studies represent temporal snap shots, long-term observations are rather rare. However, only such time series allow the identification of species composition shifts over several decades or even centuries. We analyzed changes in the species composition of a southeastern German butterfly and burnet moth community over nearly 2 centuries (1840-2013). We classified all species observed over this period according to their ecological tolerance, thereby assessing their degree of habitat specialisation. This classification was based on traits of the butterfly and burnet moth species and on their larval host plants. We collected data on temperature and precipitation for our study area over the same period. The number of species declined substantially from 1840 (117 species) to 2013 (71 species). The proportion of habitat specialists decreased, and most of these are currently endangered. In contrast, the proportion of habitat generalists increased. Species with restricted dispersal behavior and species in need of areas poor in soil nutrients had severe losses. Furthermore, our data indicated a decrease in species composition similarity between different decades over time. These data on species composition changes and the general trends of modifications may reflect effects from climate change and atmospheric nitrogen loads, as indicated by the ecological characteristics of host plant species and local changes in habitat configuration with increasing fragmentation. Our observation of major declines over time of currently threatened and protected species shows the importance of efficient conservation strategies. © 2015 Society for Conservation Biology.

Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

PubMed Central

Taniguchi, Akito; Hamasaki, Koji

2008-01-01

Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect. PMID:18177366

Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China

PubMed Central

Lv, Fenglian; Xue, Sha; Wang, Guoliang; Zhang, Chao

2017-01-01

Atmospheric nitrogen (N) deposition profoundly alters the soil microbial communities and will thus affect nutrient cycles. The effects of N availability on microbial community, however, are not clear. We used PLFA analysis to evaluate the effects of a gradient of N addition (0, 2.8, 5.6, 11.2, and 22.4 g N m-2 y-1) for three years on the rhizospheric microbial community of Pinus tabuliformis seedlings. The main factors influencing the community were quantified using structural equation modelling and redundancy analysis. At the microbial-community level, N addition increased the total phospholipid fatty acids content by increasing the dissolved organic carbon (DOC) and root biomass. Increases in soil microbial biomass carbon and N, however, was attributed to the increased DOC, N content and decreased pH. At the microbial-groups level, Fungal, arbuscular mycorrhizal fungal (AMF), gram-positive bacterial (GP) abundances and the GP:GN ratio first increased and then decreased with N addition. Nitrogen addition increased the abundances of bacteria, fungi, and actinomycetes mainly by increasing the DOC content and decreasing root biomass. Additionally, the decrease of pH and ammonium N caused by N addition increased the fungal abundances and reduced actinomycete abundances, respectively. Nitrogen addition shifted the rhizospheric microbial community mainly by altering the DOC content and root biomass. The current rate of N deposition (2.5 g N m-2 y-1) benefits plant growth and increases the abundances of fungi, arbuscular mycorrhizal fungi, GP, actinomycetes and the GP:GN ratio. PMID:28234932

Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

PubMed

Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

2013-10-01

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

Ectomycorrhizal fungal diversity and community structure associated with cork oak in different landscapes.

PubMed

Reis, Francisca; Valdiviesso, Teresa; Varela, Carolina; Tavares, Rui M; Baptista, Paula; Lino-Neto, Teresa

2018-05-01

Cork oak (Quercus suber L.) forests play an important ecological and economic role. Ectomycorrhizal fungi (ECMF) are key components for the sustainability and functioning of these ecosystems. The community structure and composition of ECMF associated with Q. suber in different landscapes of distinct Mediterranean bioclimate regions have not previously been compared. In this work, soil samples from cork oak forests residing in different bioclimates (arid, semi-arid, sub-humid, and humid) were collected and surveyed for ectomycorrhizal (ECM) root tips. A global analysis performed on 3565 ECM root tips revealed that the ECMF community is highly enriched in Russula, Tomentella, and Cenoccocum, which correspond to the ECMF genera that mainly contribute to community differences. The ECMF communities from the rainiest and the driest cork oak forests were distinct, with soils from the rainiest climates being more heterogeneous than those from the driest climates. The analyses of several abiotic factors on the ECMF communities revealed that bioclimate, precipitation, soil texture, and forest management strongly influenced ECMF structure. Shifts in ECMF with different hyphal exploration types were also detected among forests, with precipitation, forest system, and soil texture being the main drivers controlling their composition. Understanding the effects of environmental factors on the structuring of ECM communities could be the first step for promoting the sustainability of this threatened ecosystem.

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

2008-01-01

A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

Dynamic functional connectivity using state-based dynamic community structure: method and application to opioid analgesia.

PubMed

Robinson, Lucy F; Atlas, Lauren Y; Wager, Tor D

2015-03-01

We present a new method, State-based Dynamic Community Structure, that detects time-dependent community structure in networks of brain regions. Most analyses of functional connectivity assume that network behavior is static in time, or differs between task conditions with known timing. Our goal is to determine whether brain network topology remains stationary over time, or if changes in network organization occur at unknown time points. Changes in network organization may be related to shifts in neurological state, such as those associated with learning, drug uptake or experimental conditions. Using a hidden Markov stochastic blockmodel, we define a time-dependent community structure. We apply this approach to data from a functional magnetic resonance imaging experiment examining how contextual factors influence drug-induced analgesia. Results reveal that networks involved in pain, working memory, and emotion show distinct profiles of time-varying connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Shifts in the community structure and activity of anaerobic ammonium oxidation bacteria along an estuarine salinity gradient

NASA Astrophysics Data System (ADS)

Zheng, Yanling; Jiang, Xiaofen; Hou, Lijun; Liu, Min; Lin, Xianbiao; Gao, Juan; Li, Xiaofei; Yin, Guoyu; Yu, Chendi; Wang, Rong

2016-06-01

Anaerobic ammonium oxidation (anammox) is a major microbial pathway for nitrogen (N) removal in estuarine and coastal environments. However, understanding of anammox bacterial dynamics and associations with anammox activity remains scarce along estuarine salinity gradient. In this study, the diversity, abundance, and activity of anammox bacteria, and their potential contributions to total N2 production in the sediments along the salinity gradient (0.1-33.8) of the Yangtze estuarine and coastal zone, were studied using 16S rRNA gene clone library, quantitative polymerase chain reaction assay, and isotope-tracing technique. Phylogenetic analysis showed a significant change in anammox bacterial community structure along the salinity gradient (P < 0.01), with the dominant genus shifting from Brocadia in the freshwater region to Scalindua in the open ocean. Anammox bacterial abundance ranged from 3.67 × 105 to 8.22 × 107 copies 16S rRNA gene g-1 and related significantly with salinity (P < 0.05). The anammox activity varied between 0.08 and 6.46 nmol N g-1 h-1 and related closely with anammox bacterial abundance (P < 0.01). Contributions of anammox activity to total N loss were highly variable along the salinity gradient, ranging from 5 to 77% and were significantly negatively correlated with salinity (P < 0.01). Sediment organic matter was also recognized as an important factor in controlling the relative role of anammox to total N2 production in the Yangtze estuarine and coastal zone. Overall, our data demonstrated a biogeographical distribution of anammox bacterial diversity, abundance, and activity along the estuarine salinity gradient and suggested that salinity is a major environmental control on anammox process in the estuarine and coastal ecosystems.

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

PubMed

Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

2017-07-01

Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

Mechanisms shaping size structure and functional diversity of phytoplankton communities in the ocean

PubMed Central

Acevedo-Trejos, Esteban; Brandt, Gunnar; Bruggeman, Jorn; Merico, Agostino

2015-01-01

The factors regulating phytoplankton community composition play a crucial role in structuring aquatic food webs. However, consensus is still lacking about the mechanisms underlying the observed biogeographical differences in cell size composition of phytoplankton communities. Here we use a trait-based model to disentangle these mechanisms in two contrasting regions of the Atlantic Ocean. In our model, the phytoplankton community can self-assemble based on a trade-off emerging from relationships between cell size and (1) nutrient uptake, (2) zooplankton grazing, and (3) phytoplankton sinking. Grazing ‘pushes’ the community towards larger cell sizes, whereas nutrient uptake and sinking ‘pull’ the community towards smaller cell sizes. We find that the stable environmental conditions of the tropics strongly balance these forces leading to persistently small cell sizes and reduced size diversity. In contrast, the seasonality of the temperate region causes the community to regularly reorganize via shifts in species composition and to exhibit, on average, bigger cell sizes and higher size diversity than in the tropics. Our results raise the importance of environmental variability as a key structuring mechanism of plankton communities in the ocean and call for a reassessment of the current understanding of phytoplankton diversity patterns across latitudinal gradients. PMID:25747280

Coral–algal phase shifts alter fish communities and reduce fisheries production

PubMed Central

Ainsworth, Cameron H; Mumby, Peter J

2015-01-01

Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One set of simulations represents extreme scenarios, including 100% loss of coral. In this experiment, ecosystem changes are driven by coral loss itself and a degree of habitat dependency by reef fish is assumed. An alternative simulation is presented without assumed habitat dependency, where changes to the ecosystem are driven by historical observations of reef fish communities when coral is lost. The coral–algal phase shift results in reduced biodiversity and ecosystem maturity. Relative increases in the biomass of small-bodied fish species mean higher productivity on reefs overall, but much reduced landings of traditionally targeted species. PMID:24953835

Phylum level change in the cecal and fecal gut communities of rats fed diets containing different fermentable substrates supports a role for nitrogen as a factor contributing to community structure.

PubMed

Kalmokoff, Martin; Franklin, Jeff; Petronella, Nicholas; Green, Judy; Brooks, Stephen P J

2015-05-06

Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility) towards the Bacteroidetes in feces (e.g., Bacteroidales transposons). We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut.

Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta

PubMed Central

Farruggia, Mary Jade; Schreier, Brian; Sommer, Ted

2017-01-01

Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta’s pelagic food web may have been a key driver of change. PMID:28118393

Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta.

PubMed

Mahardja, Brian; Farruggia, Mary Jade; Schreier, Brian; Sommer, Ted

2017-01-01

Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta's pelagic food web may have been a key driver of change.

County community health associations of net voting shift in the 2016 U.S. presidential election

PubMed Central

Stewart, Charles; Bhambhani, Vijeta

2017-01-01

Importance In the U.S. presidential election of 2016, substantial shift in voting patterns occurred relative to previous elections. Although this shift has been associated with both education and race, the extent to which this shift was related to public health status is unclear. Objective To determine the extent to which county community health was associated with changes in voting between the presidential elections of 2016 and 2012. Design Ecological study with principal component analysis (PCA) using principal axis method to extract the components, then generalized linear regression. Setting General community. Participants All counties in the United States. Exposures Physically unhealthy days, mentally unhealthy days, percent food insecure, teen birth rate, primary care physician visit rate, age-adjusted mortality rate, violent crime rate, average health care costs, percent diabetic, and percent overweight or obese. Main outcome The percentage of Donald Trump votes in 2016 minus percentage of Mitt Romney votes in 2012 (“net voting shift”). Results Complete public health data was available for 3,009 counties which were included in the analysis. The mean net voting shift was 5.4% (+/- 5.8%). Of these 3,009 counties, 2,641 (87.8%) had positive net voting shift (shifted towards Trump) and 368 counties (12.2%) had negative net voting shift (shifted away from Trump). The first principal component (“unhealthy score”) accounted for 68% of the total variance in the data. The unhealthy score included all health variables except primary care physician rate, violent crime rate, and health care costs. The mean unhealthy score for counties was 0.39 (SD 0.16). Higher normalized unhealthy score was associated with positive net voting shift (22.1% shift per unit unhealthy, p < 0.0001). This association was stronger in states that switched Electoral College votes from 2012 to 2016 than in other states (5.9% per unit unhealthy, p <0.0001). Conclusions and relevance

Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

PubMed Central

Cárdenas, Anny; Rodriguez-R, Luis M; Pizarro, Valeria; Cadavid, Luis F; Arévalo-Ferro, Catalina

2012-01-01

Coral reefs are deteriorating at an alarming rate mainly as a consequence of the emergence of coral diseases. The white plague disease (WPD) is the most prevalent coral disease in the southwestern Caribbean, affecting dozens of coral species. However, the identification of a single causal agent has proved problematic. This suggests more complex etiological scenarios involving alterations in the dynamic interaction between environmental factors, the coral immune system and the symbiotic microbial communities. Here we compare the microbiome of healthy and WPD-affected corals from the two reef-building species Diploria strigosa and Siderastrea siderea collected at the Tayrona National Park in the Caribbean of Colombia. Microbiomes were analyzed by combining culture-dependent methods and pyrosequencing of 16S ribosomal DNA (rDNA) V5-V6 hypervariable regions. A total of 20 410 classifiable 16S rDNA sequences reads were obtained including all samples. No significant differences in operational taxonomic unit diversity were found between healthy and affected tissues; however, a significant increase of Alphaproteobacteria and a concomitant decrease in the Beta- and Gammaproteobacteria was observed in WPD-affected corals of both species. Significant shifts were also observed in the orders Rhizobiales, Caulobacteriales, Burkholderiales, Rhodobacterales, Aleteromonadales and Xanthomonadales, although they were not consistent between the two coral species. These shifts in the microbiome structure of WPD-affected corals suggest a loss of community-mediated growth control mechanisms on bacterial populations specific for each holobiont system. PMID:21955993

The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts.

PubMed

Vergés, Adriana; Steinberg, Peter D; Hay, Mark E; Poore, Alistair G B; Campbell, Alexandra H; Ballesteros, Enric; Heck, Kenneth L; Booth, David J; Coleman, Melinda A; Feary, David A; Figueira, Will; Langlois, Tim; Marzinelli, Ezequiel M; Mizerek, Toni; Mumby, Peter J; Nakamura, Yohei; Roughan, Moninya; van Sebille, Erik; Gupta, Alex Sen; Smale, Dan A; Tomas, Fiona; Wernberg, Thomas; Wilson, Shaun K

2014-08-22

Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to 'barrens' when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

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

In situ permafrost thaw due to climate change drives holistic microbial community shifts with implications for methane cycling

NASA Astrophysics Data System (ADS)

Mondav, Rhiannon; McCalley, Carmody; Hodgkins, Suzanne; Rich, Virginia; Frolking, Steve; Saleska, Scott; Barnes, Andrew; Chanton, Jeff; Crill, Patrick

2014-05-01

Thawing permafrost is a potentially significant source of radiative forcing feedback due to increased emissions of methane, a biogenic greenhouse gas (GHG). This study investigated changes in the microbial community along a permafrost thaw gradient at Stordalen Mire, Sweden using 16S rRNA gene amplicon and metagenomic methods. In situ measurements of geochemical parameters, including CH4 and C isotopes, enabled linkage of community dynamics to significant shifts in C balance. The thaw gradient ranged from intact at a palsa (low productivity and GHG emissions), through partially thawed in a bog (high productivity, low GHG emissions) to a completely thawed fen (high productivity and GHG emissions). Microbial assemblages in both the palsa and fen were highly diverse (in both richness and evenness), consistent with climax communities. The microbial community in the bog had distinctly lower diversity, characteristic of ecosystem disturbance. The palsa community was dominated by Acidobacteria and Proteobacteria, as is typical of a range of soils including permafrost. Methanogens dominated both the bog and fen and were most abundant within the zone of water table fluctuation. Inferring methanogens' production pathway from phylogeny showed a shift from mostly hydrogenotrophic methanogens in the bog towards acetotrophic methanogens in the fen. This corroborated porewater and flux emitted CH4 and CO2 carbon isotopic 13C signatures of CH4 and CO2. The fen, where the highest CH4 flux was recorded, was significantly richer in methanogenic archaea. A novel archaea, Candidatus Methanoflorens stordalenmirensis, was present at up to 70% relative abundance in the bog, enabling recovery of a population genome. The genome (and associated metaproteome) of 'M. stordalenmirensis' indicates that hydrogenotrophic methane production is its main energy conservation pathway. 'Methanoflorens' may be an indicator species of permafrost thaw, it is globally ubiquitous, and appears a major

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples.

PubMed

La Cono, Violetta; Smedile, Francesco; La Spada, Gina; Arcadi, Erika; Genovese, Maria; Ruggeri, Gioacchino; Genovese, Lucrezia; Giuliano, Laura; Yakimov, Michail M

2015-06-01

Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community.

PubMed

Zaghmouri, Imen; Michotey, Valerie D; Armougom, Fabrice; Guasco, Sophie; Bonin, Patricia C

2018-05-01

The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera. Copyright © 2018 Elsevier Ltd. All rights reserved.

Iranian Critical ELT: A Belated but Growing Intellectual Shift in Iranian ELT Community

ERIC Educational Resources Information Center

Aghagolzadeh, Ferdows; Davari, Hossein

2014-01-01

Reviewing and discussing the development of critical studies in the field of applied linguistics in general and English language teaching (ELT) in particular in Iran, this paper attempts to highlight the main contributions in this field. Introducing a new growing critical-oriented shift in Iranian ELT community as the one which has been mostly…

Epidemic Wave Dynamics Attributable to Urban Community Structure: A Theoretical Characterization of Disease Transmission in a Large Network

PubMed Central

Eggo, Rosalind M; Lenczner, Michael

2015-01-01

Background Multiple waves of transmission during infectious disease epidemics represent a major public health challenge, but the ecological and behavioral drivers of epidemic resurgence are poorly understood. In theory, community structure—aggregation into highly intraconnected and loosely interconnected social groups—within human populations may lead to punctuated outbreaks as diseases progress from one community to the next. However, this explanation has been largely overlooked in favor of temporal shifts in environmental conditions and human behavior and because of the difficulties associated with estimating large-scale contact patterns. Objective The aim was to characterize naturally arising patterns of human contact that are capable of producing simulated epidemics with multiple wave structures. Methods We used an extensive dataset of proximal physical contacts between users of a public Wi-Fi Internet system to evaluate the epidemiological implications of an empirical urban contact network. We characterized the modularity (community structure) of the network and then estimated epidemic dynamics under a percolation-based model of infectious disease spread on the network. We classified simulated epidemics as multiwave using a novel metric and we identified network structures that were critical to the network’s ability to produce multiwave epidemics. Results We identified robust community structure in a large, empirical urban contact network from which multiwave epidemics may emerge naturally. This pattern was fueled by a special kind of insularity in which locally popular individuals were not the ones forging contacts with more distant social groups. Conclusions Our results suggest that ordinary contact patterns can produce multiwave epidemics at the scale of a single urban area without the temporal shifts that are usually assumed to be responsible. Understanding the role of community structure in epidemic dynamics allows officials to anticipate epidemic

The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure.

PubMed

Louati, Hela; Said, Olfa Ben; Soltani, Amel; Got, Patrice; Mahmoudi, Ezzeddine; Cravo-Laureau, Cristiana; Duran, Robert; Aissa, Patricia; Pringault, Olivier

2013-11-01

Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

PubMed Central

Sheik, Cody S.; Stevenson, Emily I.; Den Uyl, Paul A.; Arendt, Carli A.; Aciego, Sarah M.; Dick, Gregory J.

2015-01-01

Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time. PMID:26042114

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

PubMed Central

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

2013-01-01

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

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure

PubMed Central

Kalmokoff, Martin; Franklin, Jeff; Petronella, Nicholas; Green, Judy; Brooks, Stephen P.J.

2015-01-01

Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility) towards the Bacteroidetes in feces (e.g., Bacteroidales transposons). We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut. PMID:25954902

Benthic community structure, diversity, and productivity in the shallow Barents Sea bank (Svalbard Bank).

PubMed

Kędra, Monika; Renaud, Paul E; Andrade, Hector; Goszczko, Ilona; Ambrose, William G

2013-01-01

The Barents Sea is among the most productive areas in the world oceans, and its shallow banks exhibit particularly high rates of primary productivity reaching over 300 g C m -2 year -1 . Our study focused on the Svalbard Bank, an important feeding area for fishes and whales. In order to investigate how benthic community structure and benthic secondary production vary across environmental gradients and through time, we sampled across the bank and compared results with a similar study conducted 85 years ago. Considerable variability in community structure and function across bank corresponded with differences in the physical structure of the habitat, including currents, sedimentation regimes and sediment type, and overlying water masses. Despite an intensive scallop fishery and climatic shifts that have taken place since the last survey in the 1920s, benthic community structure was very similar to that from the previous survey, suggesting strong system resilience. Primary and secondary production over shallow banks plays a large role in the Barents Sea and may act as a carbon subsidy to surrounding fish populations, of which many are of commercial importance.

Bacterial Community Structure Shifted by Geosmin in Granular Activated Carbon System of Water Treatment Plants.

PubMed

Pham, Ngoc Dung; Lee, Eun-Hee; Chae, Seon-Ha; Cho, Yongdeok; Shin, Hyejin; Son, Ahjeong

2016-01-01

We investigated the relation between the presence of geosmin in water and the bacterial community structure within the granular activated carbon (GAC) system of water treatment plants in South Korea. GAC samples were collected in May and August of 2014 at three water treatment plants (Sungnam, Koyang, and Yeoncho in Korea). Dissolved organic carbon and geosmin were analyzed before and after GAC treatment. Geosmin was found in raw water from Sungnam and Koyang water treatment plants but not in that from Yeoncho water treatment plant. Interestingly, but not surprisingly, the 16S rRNA clone library indicated that the bacterial communities from the Sungnam and Koyang GAC systems were closely related to geosmin-degrading bacteria. Based on the phylogenetic tree and multidimensional scaling plot, bacterial clones from GAC under the influence of geosmin were clustered with Variovorax paradoxus strain DB 9b and Comamonas sp. DB mg. In other words, the presence of geosmin in water might have inevitably contributed to the growth of geosmin degraders within the respective GAC system.

Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event.

PubMed

García-Sais, Jorge R; Williams, Stacey M; Amirrezvani, Ali

2017-01-01

This work analyzes the mortality, recovery, and shifts in the composition of scleractinian corals from Puerto Rico one decade after the 2005 regional coral bleaching event. Temporal and spatial patterns of coral community structure were examined using a stratified, non-random sampling approach based on five permanent transects per reef at 16 reef stations. A negative correlation between percent coral cover loss and light attenuation coefficient (Kd 490 ) was observed, suggesting that light attenuation, as influenced by water turbidity and depth, played a major role in coral protection during the bleaching event ("sunblock effect"). Responses of coral assemblages varied after the bleaching event, including shifts of cover from massive corals ( Orbicella spp.) to opportunistic ( Porites astreoides ) and branching corals ( Madracis auretenra , P. porites ) and/or turf algae; partial recovery of reef substrate cover by O. annularis complex; and no measurable changes in coral assemblages before and after the event.

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

Changes in methane emission and microbial community structure in a Phragmites australis-expanding tidal marsh of a temperature region

NASA Astrophysics Data System (ADS)

Kim, J.; Lee, J.; Kang, H.

2017-12-01

Phragmites australis is one of the representative vegetation of coastal wetlands which is distributed in North America, East Asia and European Countries. In North America, P. australis has invaded large areas of coastal wetlands, which causes various ecological problems such as increases in methane emission and reduction in biodiversity. In South Korea, P. australis is rapidly expanded in tidal marshes in Suncheon Bay. The expansion of P. australis enhanced methane emission by increasing dissolved organic carbon and soil moisture, and changing in relative abundances of methanogen, methanotroph, and sulfate reducing bacteria. Microbial community structure might be also shifted and affect methane cycle, but accurate observation on microbial community structure has not been fully illustrated yet. Therefore, we tried to monitor the changing microbial community structure due to P. australis expansion by using Next Generation Sequencing (NGS). NGS results showed that microbial community was substantially changed with the expansion. We also observed seasonal variations and chronosequence of microbial community structures along the expansion of P. australis, which showed distinctive changing patterns. P. australis expansion substantially affected microbial community structure in tidal marsh which may play an important role in methane cycle in tidal marshes.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

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

NASA Astrophysics Data System (ADS)

Sibert, E. C.

2017-12-01

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

Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments.

PubMed

Canion, Andy; Overholt, Will A; Kostka, Joel E; Huettel, Markus; Lavik, Gaute; Kuypers, Marcel M M

2014-10-01

The temperature dependency of denitrification and anaerobic ammonium oxidation (anammox) rates from Arctic fjord sediments was investigated in a temperature gradient block incubator for temperatures ranging from -1 to 40°C. Community structure in intact sediments and slurry incubations was determined using Illumina SSU rRNA gene sequencing. The optimal temperature (Topt ) for denitrification was 25-27°C, whereas anammox rates were optimal at 12-17°C. Both denitrification and anammox exhibited temperature responses consistent with a psychrophilic community, but anammox bacteria may be more specialized for psychrophilic activity. Long-term (1-2 months) warming experiments indicated that temperature increases of 5-10°C above in situ had little effect on the microbial community structure or the temperature response of denitrification and anammox. Increases of 25°C shifted denitrification temperature responses to mesophilic with concurrent community shifts, and anammox activity was eliminated above 25°C. Additions of low molecular weight organic substrates (acetate and lactate) caused increases in denitrification rates, corroborating the hypothesis that the supply of organic substrates is a more dominant control of respiration rates than low temperature. These results suggest that climate-related changes in sinking particulate flux will likely alter rates of N removal more rapidly than warming. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Community-level consequences of cannibalism.

PubMed

Ohlberger, Jan; Langangen, Oystein; Stenseth, Nils C; Vøllestad, L Asbjørn

2012-12-01

Ecological interactions determine the structure and dynamics of communities and their responses to the environment. Understanding the community-level effects of ecological interactions, such as intra- and interspecifc competition, predation, and cannibalism, is therefore central to ecological theory and ecosystem management. Here, we investigate the community-level consequences of cannibalism in populations with density-dependent maturation and reproduction. We model a stage-structured consumer population with an ontogenetic diet shift to analyze how cannibalism alters the conditions for the invasion and persistence of stage-specific predators and competitors. Our results demonstrate that cannibalistic interactions can facilitate coexistence with other species at both trophic levels. This effect of cannibalism critically depends on the food dependence of the demographic processes. The underlying mechanism is a cannibalism-induced shift in the biomass distribution between the consumer life stages. These findings suggest that cannibalism may alter the structure of ecological communities through its effects on species coexistence.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources.

PubMed

Wan, Rui; Yang, Yuyin; Sun, Weimin; Wang, Zhao; Xie, Shuguang

2014-02-01

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

Sensitivity of coral recruitment to subtle shifts in early community succession.

PubMed

Doropoulos, Christopher; Roff, George; Visser, Mart-Simone; Mumby, Peter J

2017-02-01

Community succession following disturbance depends on positive and negative interactions, the strength of which change along environmental gradients. To investigate how early succession affects coral reef recovery, we conducted an 18-month experiment in Palau, using recruitment tiles and herbivore exclusion cages. One set of reefs has higher wave exposure and had previously undergone a phase shift to macroalgae following a major typhoon, whereas the other set of reefs have lower wave exposure and did not undergo a macroalgal phase shift. Similar successional trajectories were observed at all sites when herbivores were excluded: turf algae dominated early succession, followed by shifts to foliose macroalgae and heterotrophic invertebrates. However, trajectories differed in the presence of herbivores. At low wave exposure reefs, herbivores promoted coralline algae and limited turf and encrusting fleshy algae in crevice microhabitats, facilitating optimal coral recruitment. Under medium wave exposure, relatively higher but still low coverage of turf and encrusting fleshy algae (15-25%) found in crevice microhabitats inhibited coral recruitment, persisting throughout multiple recruitment events. Our results indicate that altered interaction strength in different wave environments following disturbance can drive subtle changes in early succession that cascade to alter secondary succession to coral recruitment and system recovery. © 2016 by the Ecological Society of America.

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.

Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries

PubMed Central

Kerrigan, Elizabeth A.; Irwin, Andrew J.

2015-01-01

Climate change over the last two centuries has been associated with significant shifts in diatom community structure in lakes from the high arctic to temperate latitudes. To test the hypotheses that recent climate warming selects for species of smaller size within communities and a decrease in the average size of species within populations, we quantified the size of individual diatom valves from 10 depths in a sediment core covering the last ∼200 years from a pristine subarctic lake. Over the last ∼200 years, changes in the relative abundance of species of different average size and changes in the average valve size of populations of species contribute equally to the changes in community size structure, but are often opposite in sign, compensating for one another and moderating temporal changes in community size structure. In the surface sediments that correspond to the recent decades when air temperatures have warmed, the mean size of valves in the diatom community has significantly decreased due to an increase in the proportion of smaller-sized planktonic diatom species. PMID:26157637

Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event

PubMed Central

Amirrezvani, Ali

2017-01-01

This work analyzes the mortality, recovery, and shifts in the composition of scleractinian corals from Puerto Rico one decade after the 2005 regional coral bleaching event. Temporal and spatial patterns of coral community structure were examined using a stratified, non-random sampling approach based on five permanent transects per reef at 16 reef stations. A negative correlation between percent coral cover loss and light attenuation coefficient (Kd490) was observed, suggesting that light attenuation, as influenced by water turbidity and depth, played a major role in coral protection during the bleaching event (“sunblock effect”). Responses of coral assemblages varied after the bleaching event, including shifts of cover from massive corals (Orbicella spp.) to opportunistic (Porites astreoides) and branching corals (Madracis auretenra, P. porites) and/or turf algae; partial recovery of reef substrate cover by O. annularis complex; and no measurable changes in coral assemblages before and after the event. PMID:28761791

Epidemic spreading on complex networks with community structures

PubMed Central

Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

Body size distributions signal a regime shift in a lake ecosystem

USGS Publications Warehouse

Spanbauer, Trisha; Allen, Craig R.; Angeler, David G.; Eason, Tarsha; Fritz, Sherilyn C.; Garmestani, Ahjond S.; Nash, Kirsty L.; Stone, Jeffery R.; Stow, Craig A.; Sundstrom, Shana M.

2016-01-01

Communities of organisms, from mammals to microorganisms, have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at multiple spatial and temporal scales. In this study, we assessed whether body size patterns serve as an indicator of a threshold between alternative regimes. Over the past 7000 years, the biological communities of Foy Lake (Montana, USA) have undergone a major regime shift owing to climate change. We used a palaeoecological record of diatom communities to estimate diatom sizes, and then analysed the discontinuous distribution of organism sizes over time. We used Bayesian classification and regression tree models to determine that all time intervals exhibited aggregations of sizes separated by gaps in the distribution and found a significant change in diatom body size distributions approximately 150 years before the identified ecosystem regime shift. We suggest that discontinuity analysis is a useful addition to the suite of tools for the detection of early warning signals of regime shifts.

Changes in the community structure of free-living heterotrophic bacteria in the open tropical Pacific Ocean in response to microalgal lysate-derived dissolved organic matter.

PubMed

Tada, Yuya; Suzuki, Koji

2016-07-01

Dissolved organic matter derived from phytoplankton (DOMP) can affect the bacterial biomass and community structure in aquatic ecosystems. Here, we examined the community response of free-living heterotrophic bacteria, with respect to cellular nucleic acid levels, to the DOMP lysates derived from three phytoplankton strains in the open tropical Pacific. The free amino acid (FAA) composition of each DOMP lysate differed among the microalgal strains. Terminal restriction fragment-length polymorphism analyses with 16S rRNA genes revealed that the community shifts of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria varied significantly with the different DOMP lysate treatments. Furthermore, the FAA composition in DOMP lysates significantly affected the bacterial community shifts in HNA and LNA. Similarity percentage analysis using 16S rRNA gene deep-sequencing revealed that the DOMP lysates from the pelagophyte Pelagomonas calceolata caused relatively large community shifts with Alcaligenes predominating in the HNA fraction. In contrast, the DOMP lysate from the diatom Thalassiosira oceanica induced a community shift in the LNA fraction with a predominance of uncultured Actinobacteria Thus, the data indicate that the DOMP lysates from different microalgae constitute a primary factor altering the dominant bacterial groups in the open ocean. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

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

PubMed

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

2011-10-01

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

Microalgae community shifts during the biogas upgrading in an alkaline open photobioreactor.

PubMed

Granada-Moreno, C I; Aburto-Medina, A; de Los Cobos Vasconcelos, D; González-Sánchez, A

2017-10-01

To achieve the functional specialization of a microalgae community through operational tuning of an open photobioreactor used for biogas upgrading under alkaline conditions. An open photobioreactor was inoculated with an indigenous microalgae sample from the Texcoco Soda Lake. A microalgae community was adapted to fix CO 2 from synthetic biogas through different culture conditions reaching a maximum of 220 mg CO 2  l -1 per day. Picochlorum sp. and Scenedesmus sp. were identified as the prominent microalgae genera by molecular fingerprinting (partial sequencing of 16S rRNA and 18S rRNA genes) but only the first was detected by microscopy screening. Changes in the microalgae community profile were monitored by a range-weighted richness index, reaching the lowest value when biogas was upgraded. A robust microalgae community in the open photobioreactor was obtained after different culture conditions. The specialization of microalgae community for CO 2 fixation under H 2 S presence was driven by biogas upgrading conditions. The alkaline conditions enhance the CO 2 absorption from biogas and could optimize specialized microalgae communities in the open photobioreactor. Denaturing gradient gel electrophoresis fingerprinting and richness index comparison are useful methods for the evaluation of microalgae community shifts and photosynthetic activity performance, particularly in systems intended for CO 2 removal from biogas where the CO 2 assimilation potential can be related to the microbial richness. © 2017 The Society for Applied Microbiology.

Fine Structure of Tibetan Kefir Grains and Their Yeast Distribution, Diversity, and Shift

PubMed Central

Lu, Man; Wang, Xingxing; Sun, Guowei; Qin, Bing; Xiao, Jinzhou; Yan, Shuling; Pan, Yingjie; Wang, Yongjie

2014-01-01

Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species – Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S

Competition and facilitation structure plant communities under nurse tree canopies in extremely stressful environments.

PubMed

Al-Namazi, Ali A; El-Bana, Magdy I; Bonser, Stephen P

2017-04-01

Nurse plant facilitation in stressful environments can produce an environment with relatively low stress under its canopy. These nurse plants may produce the conditions promoting intense competition between coexisting species under the canopy, and canopies may establish stress gradients, where stress increases toward the edge of the canopy. Competition and facilitation on these stress gradients may control species distributions in the communities under canopies. We tested the following predictions: (1) interactions between understory species shift from competition to facilitation in habitats experiencing increasing stress from the center to the edge of canopy of a nurse plant, and (2) species distributions in understory communities are controlled by competitive interactions at the center of canopy, and facilitation at the edge of the canopy. We tested these predictions using a neighbor removal experiment under nurse trees growing in arid environments. Established individuals of each of four of the most common herbaceous species in the understory were used in the experiment. Two species were more frequent in the center of the canopy, and two species were more frequent at the edge of the canopy. Established individuals of each species were subjected to neighbor removal or control treatments in both canopy center and edge habitats. We found a shift from competitive to facilitative interactions from the center to the edge of the canopy. The shift in the effect of neighbors on the target species can help to explain species distributions in these canopies. Canopy-dominant species only perform well in the presence of neighbors in the edge microhabitat. Competition from canopy-dominant species can also limit the performance of edge-dominant species in the canopy microhabitat. The shift from competition to facilitation under nurse plant canopies can structure the understory communities in extremely stressful environments.

Influence of a breakwater on nearby rocky intertidal community structure.

PubMed

Martins, Gustavo M; Amaral, André F; Wallenstein, Francisco M; Neto, Ana I

2009-01-01

It is widely recognised that coastal-defence structures generally affect the structure of the assemblages they support, yet their impact on adjacent systems has been largely ignored. Breakwaters modify the nearby physical environment (e.g. wave action) suggesting a local impact on biological parameters. In the present study, an ACI (After-Control-Impact) design was used to test the general hypothesis that the artificial sheltering of an exposed coast has a strong effect on the structure and functioning of adjacent systems. The effects of a reduction in hydrodynamics were clear for a number of taxa and included the replacement of barnacles, limpets and frondose algae by an increasing cover of ephemeral algae. These effects were evident both at early and late successional stages. Results suggest that the artificial sheltering of naturally exposed coasts can have a strong impact promoting a shift from consumer- to producer-dominated communities, which has important ecological and energetic consequences for the ecosystem.

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

PubMed Central

Mitchell, Jeffrey; Scow, Kate

2018-01-01

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0–5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals–organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

PubMed Central

2012-01-01

Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

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

Wei, H.; Tucker, M. P.; Baker, J. O.

2012-04-01

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as amore » model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.« less

Differences between the bacterial community structures of first- and multi-year Arctic sea ice in the Lincoln Sea.

NASA Astrophysics Data System (ADS)

Hatam, I.; Beckers, J. F.; Haas, C.; Lanoil, B. D.

2014-12-01

The Arctic sea ice composition is shifting from predominantly thick perennial ice (multiyear ice -MYI) to thinner, seasonal ice (first year ice -FYI). The effects of the shift on the Arctic ecosystem and macro-organisms of the Arctic Ocean have been the focus of many studies and have also been extensively debated in the public domain. The effect of this shift on the microbial constituents of the Arctic sea ice has been grossly understudied, although it is a vast habitat for a microbial community that plays a key role in the biogeochemical cycles and energy flux of the Arctic Ocean. MYI and FYI differ in many chemical and physical attributes (e.g. bulk salinity, brine volume, thickness and age), therefore comparing and contrasting the structure and composition of microbial communities from both ice types will be crucial to our understanding of the challenges that the Arctic Ocean ecosystem faces as MYI cover continues to decline. Here, we contend that due to the differences in abiotic conditions, differences in bacterial community structure will be greater between samples from different ice types than within samples from the same ice type. We also argue that since FYI is younger, its community structure will be closer to that of the surface sea water (SW). To test this hypotheses, we extracted DNA and used high throughput sequencing to sequence V1-V3 regions of the bacterial 16s rRNA gene from 10 sea ice samples (5 for each ice type) and 4 surface sea water (SW) collected off the shore of Northern Ellesmere Island, NU, CAN, during the month of May from 2010-2012. Our results showed that observed richness was higher in FYI than MYI. FYI and MYI shared 26% and 36% of their observed richness respectively. While FYI shared 23% of its observed richness with SW, MYI only shared 17%. Both ice types showed similar levels of endemism (61% of the observed richness). This high level of endemism results in the grouping of microbial communities from MYI, FYI, and SW to three

The annual planktonic protist community structure in an ice-free high Arctic fjord (Adventfjorden, West Spitsbergen)

NASA Astrophysics Data System (ADS)

Kubiszyn, A. M.; Wiktor, J. M.; Wiktor, J. M.; Griffiths, C.; Kristiansen, S.; Gabrielsen, T. M.

2017-05-01

We investigated the size and trophic structure of the annual planktonic protist community structure in the ice-free Adventfjorden in relation to environmental factors. Our high-resolution (weekly to monthly) study was conducted in 2012, when warm Atlantic water was advected into the fjord in winter and summer. We observed a distinct seasonality in the protist communities. The winter protist community was characterised by extremely low levels of protist abundance and biomass (primarily Dinophyceae, Ciliophora and Bacillariophyceae) in a homogenous water column. In the second half of April, the total protist abundance and biomass rapidly increased, thus initiating the spring bloom in a still well-mixed water column. The spring bloom was initially dominated by the prymnesiophyte Phaeocystis pouchetii and Bacillariophyceae (primarily from the genera Thalassiosira, Fragilariopsis and Chaetoceros) and was later strictly dominated by Phaeocystis colonies. When the bloom terminated in mid-June, the community shifted towards flagellates (Dinophyceae, Ciliophora, Cryptophyceae and nanoflagellates 3-7 μm in size) in a stratified, nutrient-depleted water column. Decreases in the light intensity decreased the protist abundance and biomass, and the fall community (Dinophyceae, Cryptophyceae and Bacillariophyceae) was followed by the winter community.

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

NASA Astrophysics Data System (ADS)

Ricketts, Michael P.; Poretsky, Rachel S.; Welker, Jeffrey M.; Gonzalez-Meler, Miquel A.

2016-09-01

Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow ˜ 100 % and intermediate snow ˜ 50 % increased snowpack relative to the control, and low snow ˜ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Afforestation alters community structure of soil fungi.

PubMed

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Retreat from Alma Ata? The WHO's report on Task Shifting to community health workers for AIDS care in poor countries.

PubMed

Campbell, C; Scott, K

2011-01-01

This paper examines the potential of community health worker (CHW) programmes, as proposed by the 2008 World Health Organisation (WHO) document Task Shifting to tackle health worker shortages, to contribute to HIV/AIDS prevention and treatment and various Millennium Development Goals in low-income countries. It examines the WHO proposal through a literature review of factors that have facilitated the success of previous CHW experiences. The WHO has taken account of five key lessons learnt from past CHW programmes (the need for strong management, appropriate selection, suitable training, adequate retention structures and good relationships with other healthcare workers). It has, however, neglected to emphasise the importance of a sixth lesson, the 'community embeddedness' of CHWs, found to be of critical importance to the success of past CHW programmes. We have no doubt that the WHO plans will increase the number of workers able to perform medically oriented tasks. However, we argue that without community embeddedness, CHWs will be unable to successfully perform the socially oriented tasks assigned to them by the WHO, such as health education and counselling. We locate the WHO's neglect of community embeddedness within the context of a broader global public health trend away from community-focused primary healthcare towards biomedically focused selective healthcare.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

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

PubMed

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

2017-07-01

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

Tripartite community structure in social bookmarking data

NASA Astrophysics Data System (ADS)

Neubauer, Nicolas; Obermayer, Klaus

2011-12-01

Community detection is a branch of network analysis concerned with identifying strongly connected subnetworks. Social bookmarking sites aggregate datasets of often hundreds of millions of triples (document, user, and tag), which, when interpreted as edges of a graph, give rise to special networks called 3-partite, 3-uniform hypergraphs. We identify challenges and opportunities of generalizing community detection and in particular modularity optimization to these structures. Two methods for community detection are introduced that preserve the hypergraph's special structure to different degrees. Their performance is compared on synthetic datasets, showing the benefits of structure preservation. Furthermore, a tool for interactive exploration of the community detection results is introduced and applied to examples from real datasets. We find additional evidence for the importance of structure preservation and, more generally, demonstrate how tripartite community detection can help understand the structure of social bookmarking data.

Effects of contaminated dredge spoils on wetland plant communities: A literature review

USGS Publications Warehouse

Stewart, Paul M.; Garza, Eric L.; Butcher, Jason T.; Simon, Thomas P.

2003-01-01

Contaminated dredge spoil is a national concern due to its scope and effects on biota, water quality, and the physical environment. This literature review discusses the effects of contaminated dredge spoils on wetland plant communities. Plant communities naturally shift over time with changing environmental conditions. Addition of toxins and nutrients and changes in hydrology may influence plant community structure. The storage and disposal of nutrient and metal contaminated dredge spoils may cause shifts in nearby plant communities. Shifts in species composition and diversity may not be observed for decades after nutrient enrichment, causing any disturbance to remain undetected. Plant community shifts often have great amounts of inertia and are difficult to reverse.

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem.

PubMed

Brown, Shawn P; Callaham, Mac A; Oliver, Alena K; Jumpponen, Ari

2013-12-01

Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000 + reads per sample after subsampling) indicate that frequent fires (3-year fire interval) shift soil fungus communities, whereas infrequent fires (6-year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals, whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that (1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; (2) frequent prescribed fires elicit a shift in soil fungal communities; and (3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Seasonality and vertical structure of microbial communities in an ocean gyre.

PubMed

Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A; Donatz, Michael G; Burton, Robert M; Carlson, Craig A; Giovannoni, Stephen J

2009-10-01

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

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

Yang, Sihang; Zhang, Yuguang; Cong, Jing

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE PAGES

Yang, Sihang; Zhang, Yuguang; Cong, Jing; ...

2017-02-10

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Influence of phosphorus availability on the community structure and physiology of cultured biofilms.

PubMed

Li, Shuangshuang; Wang, Chun; Qin, Hongjie; Li, Yinxia; Zheng, Jiaoli; Peng, Chengrong; Li, Dunhai

2016-04-01

Biofilms have important effects on nutrient cycling in aquatic ecosystems. However, publications about the community structure and functions under laboratory conditions are rare. This study focused on the developmental and physiological properties of cultured biofilms under various phosphorus concentrations performed in a closely controlled continuous flow incubator. The results showed that the biomass (Chl a) and photosynthesis of algae were inhibited under P-limitation conditions, while the phosphatase activity and P assimilation rate were promoted. The algal community structure of biofilms was more likely related to the colonization stage than with the phosphorus availability. Cyanobacteria were more competitive than other algae in biofilms, particularly when cultured under low P levels. A dominance shift occurred from non-filamentous algae in the early stage to filamentous algae in the mid and late stages under P concentrations of 0.01, 0.1 and 0.6 mg/L. However, the total N content, dry weight biomass and bacterial community structure of biofilms were unaffected by phosphorus availability. This may be attributed to the low respiration rate, high accumulation of extracellular polymeric substances and high alkaline phosphatase activity in biofilms when phosphorus availability was low. The bacterial community structure differed over time, while there was little difference between the four treatments, which indicated that it was mainly affected by the colonization stage of the biofilms rather than the phosphorus availability. Altogether, these results suggested that the development of biofilms was influenced by the phosphorus availability and/or the colonization stage and hence determined the role that biofilms play in the overlying water. Copyright © 2015. Published by Elsevier B.V.

Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment.

PubMed

Wang, Zhao; Yang, Yuyin; He, Tao; Xie, Shuguang

2015-04-01

Biodegradation by autochthonous microbial community is an important way to clean up nonylphenol (NP) from contaminated river sediment. Knowledge of sediment microbial community can aid in our understanding of biological processes related to NP degradation. However, the change in sediment microbial community associated with NP biodegradation remains unclear. The present study investigated the shift in bacterial community structure and NP-degrading gene abundance in response to NP attenuation in river sediment. Sediment microcosms with different levels of 4-NP (0, 100, or 300 μg/g) were constructed. A nearly complete attenuation of NP occurred in the microcosm with 100 μg/g NP after 9 days' incubation, while a residual NP rate of 8.1 % was observed in the microcosm with 300 μg/g NP after 22 days' incubation. Illumina MiSeq sequencing analysis indicated that Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes predominated in NP-degrading river sediment. Sediment bacterial community structure varied significantly during NP biodegradation and subsequent incubation, which was affected by the level of added NP. The n-alkane biodegradation (alkB) gene abundance showed a significant variation in each NP-amended microcosm (100 or 300 μg/g), while a significant increase in the single component monooxygenase (sMO) gene abundance only occurred in the microcosm spiked with 300 μg/g NP. This study can provide some new insights toward NP-degrading microbial ecology in the environment.

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure.

PubMed

Hill, Richard; Saetnan, Eli R; Scullion, John; Gwynn-Jones, Dylan; Ostle, Nick; Edwards, Arwyn

2016-06-01

Microbial responses to Arctic climate change could radically alter the stability of major stores of soil carbon. However, the sensitivity of plot-scale experiments simulating climate change effects on Arctic heathland soils to potential confounding effects of spatial and temporal changes in soil microbial communities is unknown. Here, the variation in heathland soil bacterial communities at two survey sites in Sweden between spring and summer 2013 and at scales between 0-1 m and, 1-100 m and between sites (> 100 m) were investigated in parallel using 16S rRNA gene T-RFLP and amplicon sequencing. T-RFLP did not reveal spatial structuring of communities at scales < 100 m in any site or season. However, temporal changes were striking. Amplicon sequencing corroborated shifts from r- to K-selected taxon-dominated communities, influencing in silico predictions of functional potential. Network analyses reveal temporal keystone taxa, with a spring betaproteobacterial sub-network centred upon a Burkholderia operational taxonomic unit (OTU) and a reconfiguration to a summer sub-network centred upon an alphaproteobacterial OTU. Although spatial structuring effects may not confound comparison between plot-scale treatments, temporal change is a significant influence. Moreover, the prominence of two temporally exclusive keystone taxa suggests that the stability of Arctic heathland soil bacterial communities could be disproportionally influenced by seasonal perturbations affecting individual taxa. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

History of adaptation determines short-term shifts in performance and community structure of hydrogen-producing microbial communities degrading wheat straw.

PubMed

Valdez-Vazquez, Idania; Morales, Ana L; Escalante, Ana E

2017-11-01

This study addresses the question of ecological interest for the determination of structure and diversity of microbial communities that degrade lignocellulosic biomasses to produce biofuels. Two microbial consortia with different history, native of wheat straw (NWS) and from a methanogenic digester (MD) fed with cow manure, were contrasted in terms of hydrogen performance, substrate disintegration and microbial diversity. NWS outperformed the hydrogen production rate of MD. Microscopic images revealed that NWS acted on the cuticle and epidermis, generating cellulose strands with high crystallinity, while MD degraded deeper layers, equally affecting all polysaccharides. The bacterial composition markedly differed according to the inocula origin. NWS almost solely comprised hydrogen producers of the phyla Firmicutes and Proteobacteria, with 38% members of Enterococcus. After hydrogen fermentation, NWS comprised 8% Syntrophococcus, an acetogen that cleaves aryl ethers of constituent groups on the aromatic components of lignin. Conversely, MD comprised thirteen phyla, primarily including Firmicutes with H 2 -producing members, and Bacteroidetes with non-H 2 -producing members, which reduced the hydrogen performance. Overall, the results of this study provide clear evidence that the history of adaptation of NWS enhanced the hydrogen performance from untreated wheat straw. Further, native wheat straw communities have the potential to refine cellulose fibers and produce biofuels simultaneously. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Hyperfine structure and isotope shift analysis of singly ionized titanium

NASA Astrophysics Data System (ADS)

Bouazza, Safa

2013-04-01

The even-parity low configuration system of Ti II has been considered on the basis of the experimental data found in the literature, and its fine structure has been reanalyzed by simultaneous parameterization of one- and two-body interactions for the model space (3d + 4s)3. Furthermore, the main one-electron hyperfine structure parameters for these configurations have been evaluated. For instance, for 3d24s1, a_{3{\\rm{d}}}^{01} = - {\\rm{63}}.{\\rm{2}}\\left( {{\\rm{3}}.{\\rm{1}}} \\right)\\,{\\rm{MHz}} and a_{4{\\rm{s}}}^{10} = - {\\rm{984}}.{\\rm{1}}\\left( {{\\rm{7}}.{\\rm{1}}} \\right)\\,{\\rm{MHz}} . Field shifts (FS) and specific mass shifts (SMS) of the main Ti II configurations are deduced by means of ab initio estimates combined with a small quantity of experimental isotope shift data available in the literature: FS(3d3) = -63.3 MHz, FS(3d24p1) = -49.7 MHz, FS(3d14s2) = 98.2 MHz, FS(4s24P1) = 163.4 MHz and SMS(3d3) = 1453.3 MHz, SMS(3d14s2) = -2179.7 MHz, …, referred to 3d24s1 for the pair Ti46-Ti48.

Community structure of zooplankton in the main entrance of Bahía Magdalena, México during 1996.

PubMed

Gómez-Gutiérrez, J; Palomares-García, R; Hernández-Trujillo, S; Carballido-Carranza, A

2001-06-01

The zooplankton community structure, including copepods, euphausiids, chaetognaths, and decapod larvae, was monitored during six circadian cycles using Bongo net (500 microns mesh net) samples from Bahía Magdalena, on the southwest coast of Baja California, México. Samples were obtained during three oceanographic surveys (March, July, and December 1996) to describe the changes in the zooplankton community structure throughout the main mouth of Bahía Magdalena. The zooplankton community structure showed strong changes with a close relation to environmental conditions. During March, a well-mixed water column with low temperature and salinity indicated an influence of the California Current water and local upwelling processes. During July, temperature increased and a wide salinity range was recorded. The stratification of the water column was intense during summer, enhancing the thermocline. The highest temperatures and salinity were recorded in December, related to the presence of the Costa Rica Coastal Current (CRCC). The thermocline deepened as water temperature increased. A typical temperate community structure with low specific richness dominated by Calanus pacificus, Nyctiphanes simplex, and Acartia clausi and high zooplankton biomass (average 9.3 and 5.5 ml 1000 m-3 respectively) during March and July shifted to a more complex tropical community structure with a low zooplankton biomass in December (average 0.37 ml 1000 m-3). The mouth of Bahía Magdalena has a vigorous exchange of water caused by tidal currents. The zooplankton community structure was not significantly different between the central part of Bahía Magdalena and the continental shelf outside the bay for all months. The results suggest a more dynamic inside-outside interaction of zooplankton assemblages than first thought.

Investigating brain community structure abnormalities in bipolar disorder using path length associated community estimation.

PubMed

Gadelkarim, Johnson J; Ajilore, Olusola; Schonfeld, Dan; Zhan, Liang; Thompson, Paul M; Feusner, Jamie D; Kumar, Anand; Altshuler, Lori L; Leow, Alex D

2014-05-01

In this article, we present path length associated community estimation (PLACE), a comprehensive framework for studying node-level community structure. Instead of the well-known Q modularity metric, PLACE utilizes a novel metric, Ψ(PL), which measures the difference between intercommunity versus intracommunity path lengths. We compared community structures in human healthy brain networks generated using these two metrics and argued that Ψ(PL) may have theoretical advantages. PLACE consists of the following: (1) extracting community structure using top-down hierarchical binary trees, where a branch at each bifurcation denotes a collection of nodes that form a community at that level, (2) constructing and assessing mean group community structure, and (3) detecting node-level changes in community between groups. We applied PLACE and investigated the structural brain networks obtained from a sample of 25 euthymic bipolar I subjects versus 25 gender- and age-matched healthy controls. Results showed community structural differences in posterior default mode network regions, with the bipolar group exhibiting left-right decoupling. Copyright © 2013 Wiley Periodicals, Inc.

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures.

PubMed

Gu, Ganyu; Ottesen, Andrea; Bolten, Samantha; Ramachandran, Padmini; Reed, Elizabeth; Rideout, Steve; Luo, Yaguang; Patel, Jitendra; Brown, Eric; Nou, Xiangwu

2018-08-01

Fresh produce, like spinach, harbors diverse bacterial populations, including spoilage and potentially pathogenic bacteria. This study examined the effects of produce washing in chlorinated water and subsequent storage on the microbiota of spinach. Baby spinach leaves from a commercial fresh-cut produce processor were assessed before and after washing in chlorinated water, and then after one week's storage at 4, 10, and 15 °C. Microbial communities on spinach were analyzed by non-selective plating, qPCR, and 16S rDNA amplicon sequencing. Bacterial populations on spinach, averaging 6.12 ± 0.61 log CFU/g, were reduced by 1.33 ± 0.57 log after washing. However, populations increased by 1.77-3.24 log after storage, with larger increases occurring at higher temperature (15 > 10 > 4 °C). The predominant phylum identified on unwashed spinach leaves was Proteobacteria; dominant genera were Pseudomonas and Sphingomonas. Bacterial communities shifted significantly after chlorine washing and storage. Several Proteobacteria species, such as Stenotrophomonas sp. and Erwinia sp., were relatively tolerant of chlorine treatment, while species of Flavobacterium and Pedobacter (phylum Bacteroidetes) grew rapidly during storage, especially at abusive temperatures. Cupriavidus sp. and Ralstonia sp. showed significant increases after washing. After storage, microbial communities on spinach appeared to shift back toward the pre-washing distributions. Copyright © 2018. Published by Elsevier Ltd.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

PubMed

Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

2018-05-01

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

Tipping Points in Resource Abundance Drive Irreversible Changes in Community Structure.

PubMed

Haney, Seth D; Siepielski, Adam M

2018-05-01

Global climate change has made what were seemingly extraordinary environmental conditions, such as prolonged droughts, commonplace. One consequence of extreme environmental change is concomitant changes in resource abundance. How will such extreme resource changes impact biodiversity? We developed a trait-based consumer-resource model to examine how resource abundance affects the potential for adaptive evolution and coexistence among competitors. We found that moderate changes in resource abundance have little effect on trait evolution. However, when resource scarcities were sufficiently extreme, a critical transition-a tipping point-occurred, which caused consumer traits to diverge and restructured the community in a way that outlasted the scarcity. Therefore, even though traits can evolve in response to minor resource fluctuations, large environmental shifts may be necessary for producing long-lasting impacts on community structure. These results may also help to illuminate patterns of stasis frequently observed in nature, despite the considerable evidence demonstrating rapid evolutionary change.

The effects of top-down versus bottom-up control on benthic coral reef community structure.

PubMed

Smith, Jennifer E; Hunter, Cynthia L; Smith, Celia M

2010-06-01

While climate change and associated increases in sea surface temperature and ocean acidification, are among the most important global stressors to coral reefs, overfishing and nutrient pollution are among the most significant local threats. Here we examined the independent and interactive effects of reduced grazing pressure and nutrient enrichment using settlement tiles on a coral-dominated reef via long-term manipulative experimentation. We found that unique assemblages developed in each treatment combination confirming that both nutrients and herbivores are important drivers of reef community structure. When herbivores were removed, fleshy algae dominated, while crustose coralline algae (CCA) and coral were more abundant when herbivores were present. The effects of fertilization varied depending on herbivore treatment; without herbivores fleshy algae increased in abundance and with herbivores, CCA increased. Coral recruits only persisted in treatments exposed to grazers. Herbivore removal resulted in rapid changes in community structure while there was a lag in response to fertilization. Lastly, re-exposure of communities to natural herbivore populations caused reversals in benthic community trajectories but the effects of fertilization remained for at least 2 months. These results suggest that increasing herbivore populations on degraded reefs may be an effective strategy for restoring ecosystem structure and function and in reversing coral-algal phase-shifts but that this strategy may be most effective in the absence of other confounding disturbances such as nutrient pollution.

Groundwater geochemistry and microbial community structure in the aquifer transition from volcanic to alluvial areas.

PubMed

Amalfitano, S; Del Bon, A; Zoppini, A; Ghergo, S; Fazi, S; Parrone, D; Casella, P; Stano, F; Preziosi, E

2014-11-15

Groundwaters may act as sinks or sources of organic and inorganic solutes, depending on the relative magnitude of biochemical mobilizing processes and groundwater-surface water exchanges. The objective of this study was to link the lithological and hydrogeological gradients to the aquatic microbial community structure in the transition from aquifer recharge (volcanic formations) to discharge areas (alluvial deposits). A field-scale analysis was performed along a water table aquifer in which volcanic products decreased in thickness and areal extension, while alluvial deposits became increasingly important. We measured the main groundwater physical parameters and the concentrations of major and trace elements. In addition, the microbial community structure was assessed by estimating the occurrence of total coliforms and Escherichia coli, the prokaryotic abundance, the cytometric and phylogenetic community composition. The overall biogeochemical asset differed along the aquifer flow path. The concentration of total and live prokaryotic cells significantly increased in alluvial waters, together with the percentages of Beta- and Delta-Proteobacteria. The microbial propagation over a theoretical groundwater travel time allowed for the identification of microbial groups shifting significantly in the transition between the two different hydrogeochemical facies. The microbial community structure was intimately associated with geochemical changes, thus it should be further considered in view of a better understanding of groundwater ecology and sustainable management strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Perceptions of health stakeholders on task shifting and motivation of community health workers in different socio demographic contexts in Kenya (nomadic, peri-urban and rural agrarian).

PubMed

Ochieng, Beverly; Akunja, Edith; Edwards, Nancy; Mombo, Diana; Marende, Leah; Kaseje, Dan C O

2014-01-01

The shortage of health professionals in low income countries is recognized as a crisis. Community health workers are part of a "task-shift" strategy to address this crisis. Task shifting in this paper refers to the delegation of tasks from health professionals to lay, trained volunteers. In Kenya, there is a debate as to whether these volunteers should be compensated, and what motivation strategies would be effective in different socio-demographic contexts, based type of tasks shifted. The purpose of this study was to find out, from stakeholders' perspectives, the type of tasks to be shifted to community health workers and the appropriate strategies to motivate and retain them. This was an analytical comparative study employing qualitative methods: key informant interviews with health policy makers, managers, and service providers, and focus group discussions with community health workers and service consumers, to explore their perspectives on tasks to be shifted and appropriate motivation strategies. The study found that there were tasks to be shifted and motivation strategies that were common to all three contexts. Common tasks were promotive, preventive, and simple curative services. Common motivation strategies were supportive supervision, means of identification, equitable allocation of resources, training, compensation, recognition, and evidence based community dialogue. The study concluded that inclusion of curative tasks for community health workers, particularly in nomadic contexts, is inevitable but raises the need for accreditation of their training and regulation of their tasks.

Triclosan alterations of estuarine phytoplankton community structure.

PubMed

Pinckney, James L; Thompson, Laura; Hylton, Sarah

2017-06-15

Antimicrobial additives in pharmaceutical and personal care products are a major environmental concern due to their potential ecological impacts on aquatic ecosystems. Triclosan (TCS) has been used as an antiseptic, disinfectant, and preservative in various media. The sublethal and lethal effects of TCS on estuarine phytoplankton community composition were investigated using bioassays of natural phytoplankton communities to measure phytoplankton responses to different concentrations of TCS ranging from 1 to 200μgl -1 . The EC 50 (the concentration of an inhibitor where the growth is reduced by half) for phytoplankton groups (diatoms, chlorophytes, cryptophytes) examined in this ranged from 10.7 to 113.8μg TCS l -1 . Exposures resulted in major shifts in phytoplankton community composition at concentrations as low as 1.0μg TCS l -1 . This study demonstrates estuarine ecosystem sensitivity to TCS exposure and highlights potential alterations in phytoplankton community composition at what are typically environmental concentrations of TCS in urbanized estuaries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater.

PubMed

LaPara, Timothy M; Klatt, Christian G; Chen, Ruoyu

2006-02-10

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.

ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

EPA Science Inventory

Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

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.

Epidemics in adaptive networks with community structure

NASA Astrophysics Data System (ADS)

Shaw, Leah; Tunc, Ilker

2010-03-01

Models for epidemic spread on static social networks do not account for changes in individuals' social interactions. Recent studies of adaptive networks have modeled avoidance behavior, as non-infected individuals try to avoid contact with infectives. Such models have not generally included realistic social structure. Here we study epidemic spread on an adaptive network with community structure. We model the effect of heterogeneous communities on infection levels and epidemic extinction. We also show how an epidemic can alter the community structure.

Cluster structure and Coulomb shift in two-center mirror systems

NASA Astrophysics Data System (ADS)

Nakao, M.; Umehara, H.; Sonoda, S.; Ebata, S.; Ito, M.

2017-11-01

The α + 14C elastic scattering and the nuclear structure of its compound systems, 18O = α + 14C, are analyzed on the basis of the semi-microscopic model. The α + 14C interaction potential is constructed from the double folding (DF) model with the effective nucleon-nucleon interaction of the density-dependent Michigan 3-range Yukawa. The DF potential is applied to the α+14C elastic scattering in the energy range of Eα/Aα = 5.5 8.8 MeV, and the observed differential cross sections are reasonably reproduced. The energy spectra of 18O are calculated by employing the orthogonality condition model (OCM) plus the absorbing boundary condition (ABC). The OCM + ABC calculation predicts the formation of the 0+ resonance around E = 3MeV with respect to the α threshold, which seems to correspond to the resonance identified in the recent experiment. We also apply the OCM + ABC calculation to the mirror system, such as 18Ne = α+14O, and the Coulomb shift of 18O - 18Ne is evaluated. We have found that the Coulomb shift is clearly reduced in the excited 0+ state due to the development of the α cluster structure. This result strongly supports that the Coulomb shift is a candidate of new probe to identify the clustering phenomena.

Community structure in networks

NASA Astrophysics Data System (ADS)

Newman, Mark

2004-03-01

Many networked systems, including physical, biological, social, and technological networks, appear to contain ``communities'' -- groups of nodes within which connections are dense, but between which they are sparser. The ability to find such communities in an automated fashion could be of considerable use. Communities in a web graph for instance might correspond to sets of web sites dealing with related topics, while communities in a biochemical network or an electronic circuit might correspond to functional units of some kind. We present a number of new methods for community discovery, including methods based on ``betweenness'' measures and methods based on modularity optimization. We also give examples of applications of these methods to both computer-generated and real-world network data, and show how our techniques can be used to shed light on the sometimes dauntingly complex structure of networked systems.

Response of bird community structure to habitat management in piñon-juniper woodland-sagebrush ecotones

USGS Publications Warehouse

Knick, Steven T.; Hanser, Steven E.; Grace, James B.; Hollenbeck, Jeff P.; Leu, Matthias

2017-01-01

Piñon (Pinus spp.) and juniper (Juniperus spp.) woodlands have been expanding their range across the intermountain western United States into landscapes dominated by sagebrush (Artemisia spp.) shrublands. Management actions using prescribed fire and mechanical cutting to reduce woodland cover and control expansion provided opportunities to understand how environmental structure and changes due to these treatments influence bird communities in piñon-juniper systems. We surveyed 43 species of birds and measured vegetation for 1–3 years prior to treatment and 6–7 years post-treatment at 13 locations across Oregon, California, Idaho, Nevada, and Utah. We used structural equation modeling to develop and statistically test our conceptual model that the current bird assembly at a site is structured primarily by the previous bird community with additional drivers from current and surrounding habitat conditions as well as external regional bird dynamics. Treatment reduced woodland cover by >5% at 80 of 378 survey sites. However, habitat change achieved by treatment was highly variable because actual disturbance differed widely in extent and intensity. Biological inertia in the bird community was the strongest single driver; 72% of the variation in the bird assemblage was explained by the community that existed seven years earlier. Greater net reduction in woodlands resulted in slight shifts in the bird community to one having ecotone or shrubland affinities. However, the overall influence of woodland changes from treatment were relatively small and were buffered by other extrinsic factors. Regional bird dynamics did not significantly influence the structure of local bird communities at our sites. Our results suggest that bird communities in piñon-juniper woodlands can be highly stable when management treatments are conducted in areas with more advanced woodland development and at the level of disturbance measured in our study.

Shifts in an invasive rodent community favoring black rats (Rattus rattus) following restoration of native forest

USGS Publications Warehouse

Shiels, Aaron B.; Medeiros, Arthur C.; von Allmen, Erica I.

2017-01-01

One potential, unintended ecological consequence accompanying forest restoration is a shift in invasive animal populations, potentially impacting conservation targets. Eighteen years after initial restoration (ungulate exclusion, invasive plant control, and out planting native species) at a 4 ha site on Maui, Hawai'i, we compared invasive rodent communities in a restored native dry forest and adjacent non-native grassland. Quarterly for 1 year, we trapped rodents on three replicate transects (107 rodent traps) in each habitat type for three consecutive nights. While repeated trapping may have reduced the rat (Black rat, Rattus rattus) population in the forest, it did not appear to reduce the mouse (House mouse, Mus musculus) population in the grassland. In unrestored grassland, mouse captures outnumbered rat captures 220:1, with mice averaging 54.9 indiv./night versus rats averaging 0.25 indiv./night. In contrast, in restored native forest, rat captures outnumbered mouse captures by nearly 5:1, averaging 9.0 indiv./night versus 1.9 indiv./night for mice. Therefore, relatively recent native forest restoration increased Black rat abundance and also increased their total biomass in the restored ecosystem 36-fold while reducing House mouse biomass 35-fold. Such a community shift is worrisome because Black rats pose a much greater threat than do mice to native birds and plants, perhaps especially to large-seeded tree species. Land managers should be aware that forest restoration (i.e. converting grassland to native forest) can invoke shifts in invasive rodent populations, potentially favoring Black rats. Without intervention, this shift may pose risks for intended conservation targets and modify future forest restoration trajectories.

Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

PubMed

Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

2015-10-30

The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.

Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India.

PubMed

Patel, Vilas; Munot, Hitendra; Shouche, Yogesh S; Madamwar, Datta

2014-06-01

Bacterial community structure was analyzed from coastal water of Alang-Sosiya ship breaking yard (ASSBY), world's largest ship breaking yard, near Bhavnagar, using 16S rRNA gene sequencing (cultured dependent and culture independent). In clone libraries, total 2324 clones were retrieved from seven samples (coastal water of ASSBY for three seasons along with one pristine coastal water) which were grouped in 525 operational taxonomic units. Proteobacteria was found to be dominant in all samples. In pristine samples, Gammaproteobacteria was found to be dominant, whereas in polluted samples dominancy of Gammaproteobacteria has shifted to Betaproteobacteria and Epsilonproteobacteria. Richness and diversity indices also indicated that bacterial community in pristine sample was the most diverse followed by summer, monsoon and winter samples. To the best of knowledge, this is the first study describing bacterial community structure from coastal water of ASSBY, and it suggests that seasonal fluctuation and anthropogenic pollutions alters the bacterial community structure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems.

PubMed

Zhang, Li-Mei; Duff, Aoife M; Smith, Cindy J

2018-04-24

Terrestrial-marine boundaries are significant sites of biogeochemical activity with delineated gradients from land to sea. While niche differentiation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) driven by pH and nitrogen is well known, the patterns and environmental drivers of AOA and AOB community structure and activity across soil-sediment boundaries have not yet been determined. In this study, nitrification potential rate, community composition and transcriptional activity of AOA and AOB in soil, soil/sediment interface and sediments of two coastal Bays were characterized using a combination of field investigations and microcosm incubations. At DNA level, amoA gene abundances of AOA were significantly greater than AOB in soil, while in sediments AOB were significantly more abundant than AOA, but at the soil/sediment interface there were equal numbers of AOA and AOB amoA genes. Microcosm incubations provided further evidence, through qPCR and DGGE-sequencing analysis of amoA transcripts, that AOA were active in soil, AOB in sediment and both AOA and AOB were active at the soil/sediment interface. The AOA and AOB community composition shifted across the coastal soil-interface-sediment gradient with salinity and pH identified as major environmental drivers. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Linking microbial community structure to function in representative simulated systems.

PubMed

Marcus, Ian M; Wilder, Hailey A; Quazi, Shanin J; Walker, Sharon L

2013-04-01

Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present.

Linking Microbial Community Structure to Function in Representative Simulated Systems

PubMed Central

Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

2013-01-01

Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

PubMed Central

Wafula, Denis; White, John R.; Canion, Andy; Jagoe, Charles; Pathak, Ashish

2015-01-01

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nir

Warming and Elevated CO2 Interact to Drive Rapid Shifts in Marine Community Production.

PubMed

Sorte, Cascade J B; Bracken, Matthew E S

2015-01-01

Predicting the outcome of future climate change requires an understanding of how alterations in multiple environmental factors manifest in natural communities and affect ecosystem functioning. We conducted an in situ, fully factorial field manipulation of CO2 and temperature on a rocky shoreline in southeastern Alaska, USA. Warming strongly impacted functioning of tide pool systems within one month, with the rate of net community production (NCP) more than doubling in warmed pools under ambient CO2 levels relative to initial NCP values. However, in pools with added CO2, NCP was unaffected by warming. Productivity responses paralleled changes in the carbon-to-nitrogen ratio of a red alga, the most abundant primary producer species in the system, highlighting the direct link between physiology and ecosystem functioning. These observed changes in algal physiology and community productivity in response to our manipulations indicate the potential for natural systems to shift rapidly in response to changing climatic conditions and for multiple environmental factors to act antagonistically.

Warming and Elevated CO2 Interact to Drive Rapid Shifts in Marine Community Production

PubMed Central

Sorte, Cascade J. B.; Bracken, Matthew E. S.

2015-01-01

Predicting the outcome of future climate change requires an understanding of how alterations in multiple environmental factors manifest in natural communities and affect ecosystem functioning. We conducted an in situ, fully factorial field manipulation of CO2 and temperature on a rocky shoreline in southeastern Alaska, USA. Warming strongly impacted functioning of tide pool systems within one month, with the rate of net community production (NCP) more than doubling in warmed pools under ambient CO2 levels relative to initial NCP values. However, in pools with added CO2, NCP was unaffected by warming. Productivity responses paralleled changes in the carbon-to-nitrogen ratio of a red alga, the most abundant primary producer species in the system, highlighting the direct link between physiology and ecosystem functioning. These observed changes in algal physiology and community productivity in response to our manipulations indicate the potential for natural systems to shift rapidly in response to changing climatic conditions and for multiple environmental factors to act antagonistically. PMID:26714167

The Underlying Social Dynamics of Paradigm Shifts.

PubMed

Rodriguez-Sickert, Carlos; Cosmelli, Diego; Claro, Francisco; Fuentes, Miguel Angel

2015-01-01

We develop here a multi-agent model of the creation of knowledge (scientific progress or technological evolution) within a community of researchers devoted to such endeavors. In the proposed model, agents learn in a physical-technological landscape, and weight is attached to both individual search and social influence. We find that the combination of these two forces together with random experimentation can account for both i) marginal change, that is, periods of normal science or refinements on the performance of a given technology (and in which the community stays in the neighborhood of the current paradigm); and ii) radical change, which takes the form of scientific paradigm shifts (or discontinuities in the structure of performance of a technology) that is observed as a swift migration of the knowledge community towards the new and superior paradigm. The efficiency of the search process is heavily dependent on the weight that agents posit on social influence. The occurrence of a paradigm shift becomes more likely when each member of the community attaches a small but positive weight to the experience of his/her peers. For this parameter region, nevertheless, a conservative force is exerted by the representatives of the current paradigm. However, social influence is not strong enough to seriously hamper individual discovery, and can act so as to empower successful individual pioneers who have conquered the new and superior paradigm.

The Underlying Social Dynamics of Paradigm Shifts

PubMed Central

Claro, Francisco; Fuentes, Miguel Angel

2015-01-01

We develop here a multi-agent model of the creation of knowledge (scientific progress or technological evolution) within a community of researchers devoted to such endeavors. In the proposed model, agents learn in a physical-technological landscape, and weight is attached to both individual search and social influence. We find that the combination of these two forces together with random experimentation can account for both i) marginal change, that is, periods of normal science or refinements on the performance of a given technology (and in which the community stays in the neighborhood of the current paradigm); and ii) radical change, which takes the form of scientific paradigm shifts (or discontinuities in the structure of performance of a technology) that is observed as a swift migration of the knowledge community towards the new and superior paradigm. The efficiency of the search process is heavily dependent on the weight that agents posit on social influence. The occurrence of a paradigm shift becomes more likely when each member of the community attaches a small but positive weight to the experience of his/her peers. For this parameter region, nevertheless, a conservative force is exerted by the representatives of the current paradigm. However, social influence is not strong enough to seriously hamper individual discovery, and can act so as to empower successful individual pioneers who have conquered the new and superior paradigm. PMID:26418255

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

NASA Astrophysics Data System (ADS)

Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

2017-12-01

New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem.

PubMed

Rodríguez-Caballero, G; Caravaca, F; Fernández-González, A J; Alguacil, M M; Fernández-López, M; Roldán, A

2017-04-15

The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of phytoplankton distribution and community structure in the German Bight with respect to the different size classes

NASA Astrophysics Data System (ADS)

Wollschläger, Jochen; Wiltshire, Karen Helen; Petersen, Wilhelm; Metfies, Katja

2015-05-01

Investigation of phytoplankton biodiversity, ecology, and biogeography is crucial for understanding marine ecosystems. Research is often carried out on the basis of microscopic observations, but due to the limitations of this approach regarding detection and identification of picophytoplankton (0.2-2 μm) and nanophytoplankton (2-20 μm), these investigations are mainly focused on the microphytoplankton (20-200 μm). In the last decades, various methods based on optical and molecular biological approaches have evolved which enable a more rapid and convenient analysis of phytoplankton samples and a more detailed assessment of small phytoplankton. In this study, a selection of these methods (in situ fluorescence, flow cytometry, genetic fingerprinting, and DNA microarray) was placed in complement to light microscopy and HPLC-based pigment analysis to investigate both biomass distribution and community structure of phytoplankton. As far as possible, the size classes were analyzed separately. Investigations were carried out on six cruises in the German Bight in 2010 and 2011 to analyze both spatial and seasonal variability. Microphytoplankton was identified as the major contributor to biomass in all seasons, followed by the nanophytoplankton. Generally, biomass distribution was patchy, but the overall contribution of small phytoplankton was higher in offshore areas and also in areas exhibiting higher turbidity. Regarding temporal development of the community, differences between the small phytoplankton community and the microphytoplankton were found. The latter exhibited a seasonal pattern regarding number of taxa present, alpha- and beta-diversity, and community structure, while for the nano- and especially the picophytoplankton, a general shift in the community between both years was observable without seasonality. Although the reason for this shift remains unclear, the results imply a different response of large and small phytoplankton to environmental influences.

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

Microbial Community Shifts due to Hydrofracking: Observations from Field-Scale Observations and Laboratory-Scale Incubations

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Ansari, M.; Hartsock, A.; Lui, S.; Lenhart, J.

2012-12-01

The use of fluids containing chemicals and variable water sources during the hydrofracking of unconventional shale is the source of considerable controversy due to perceived risks from altered subsurface biogeochemistry and the potential for contaminating potable water supplies. Rapid shifts in subsurface biogeochemistry are often driven by available macronutrients combined with the abundance and metabolic condition of the subsurface microbiota. While the depth that fracturing occurs in the Marcellus formation is reasonably deep to pose little risk to groundwater supplies, no published studies have systematically characterized the indigenous microbial population and how this community is altered through variable fluid management practices (e.g., chemical composition, source water makeup). In addition, limited information is available on how shallower microbial communities and geochemical conditions might be affected through the accidental release of these fluids to groundwater aquifers. Our measurements indicate field-applied and laboratory-generated fracking fluids contain levels of organic carbon greater than 300 mg/l and nitrogen concentrations greater than 80 mg/l that may differentially stimulate microbial growth in subsurface formations. In contrast to certain inorganic constituents (e.g., chloride) which increase in concentration through the flowback period; dissolved organic carbon levels decrease with time after the fracturing process through multiple attenuation processes (dilution, sorption, microbial utilization). Pyrosequencing data of the 16S rRNA gene indicate a shift from a more diverse source water microbial community to a less diverse community typical of a brine formation as time after fracturing increases. The introduction of varying percentages of a laboratory-generated fracking fluid to microcosm bottles containing groundwater and aquifer media stimulated biogeochemical changes similar to the introduction of landfill leachate, another

Performance and sleepiness in nurses working 12-h day shifts or night shifts in a community hospital.

PubMed

Wilson, Marian; Permito, Regan; English, Ashley; Albritton, Sandra; Coogle, Carlana; Van Dongen, Hans P A

2017-10-05

Hospitals are around-the-clock operations and nurses are required to care for patients night and day. The nursing shortage and desire for a more balanced work-to-home life has popularized 12-h shifts for nurses. The present study investigated sleep/wake cycles and fatigue levels in 22 nurses working 12-h shifts, comparing day versus night shifts. Nurses (11day shift and 11 night shift) were recruited from a suburban acute-care medical center. Participants wore a wrist activity monitor and kept a diary to track their sleep/wake cycles for 2 weeks. They also completed a fatigue test battery, which included the Psychomotor Vigilance Test (PVT) and the Karolinska Sleepiness Scale (KSS), at the beginning, middle and end of 4 duty shifts. Daily sleep duration was 7.1h on average. No overall difference in mean daily sleep duration was found between nurses working day shifts versus night shifts. Objective performance on the PVT remained relatively good and stable at the start, middle, and end of duty shifts in day shift workers, but gradually degraded across duty time in night shift workers. Compared to day shift workers, night shift workers also exhibited more performance variability among measurement days and between participants at each testing time point. The same pattern was observed for subjective sleepiness on the KSS. However, congruence between objective and subjective measures of fatigue was poor. Our findings suggest a need for organizations to evaluate practices and policies to mitigate the inevitable fatigue that occurs during long night shifts, in order to improve patient and healthcare worker safety. Examination of alternative shift lengths or sanctioned workplace napping may be strategies to consider. Copyright © 2017 Elsevier Ltd. All rights reserved.

Combining Population Structure with Historic Abitoic Processes to Better Understand Species and Community Range Shifts in Response to Climate Change

NASA Astrophysics Data System (ADS)

Graham, N. M.

2015-12-01

The evolution and speciation of plants is directly tied to the environment as the constrained stages of dispersal creates strong genetic differentiation among populations. This can result in differing genetic patterns between nuclear and chloroplast loci, where genes are inherited differently and dispersed via separate vectors. By developing distribution models based on genetic patterns found within a species, it is possible to begin understanding the influence of historic geomorphic and/or climatic processes on population evolution. If genetic patterns of the current range correlate with specific patterns of climate variability within the Pleistocene, it is possible that future shifts in species distribution in response to climate change can be more accurately modelled due to the historic signature that is found within inherited genes. Preliminary genetic analyses of Linanthus dichotomus, an annual herb distributed across California, suggests that the current taxonomic treatment does not accurately depict how this species is evolving. Genetic patterns of chloroplast genes suggest that populations are more correlated with biogeography than what the current nomenclature states. Additionally, chloroplast and nuclear genes show discrepancies in the dispersal across the landscape, suggesting pollinator driven gene flow overcoming seed dispersal boundaries. By comparing discrepancies between pollinator and seed induced gene flow we may be able to gain insight into historical pollinator communities within the Pleistocene. This information can then be applied to projected climate models to more accurately understand how species and/or communities will respond to a changing environment.

Effects of pond management on biodiversity patterns and community structure of zooplankton in urban environments.

PubMed

Suski, Jamie G; Swan, Christopher M; Salice, Christopher J; Wahl, Charles F

2018-04-01

As urban areas continue expanding, major cities become connected forming megacities. Urban encroachment into natural areas transforms the landscape into a built environment with heterogeneously distributed patches of novel habitat. Community structure within novel habitats is influenced by anthropogenic factors including fragmentation and species interactions. Alterations in complex biodiversity patterns may be used to assess how urban stressors impact community assemblages which, ultimately, may inform sustainable management decisions. To manage algal blooms, Aquashade® is applied directly to ponds. We investigated the effects of Aquashade®, nutrient loading and dispersal on local species diversity and compositional turnover of zooplankton communities from suburban ponds in Columbia, MD, USA using a mesocosm approach. We found that Aquashade® acted as an environmental filter by increasing local species diversity and decreasing compositional turnover. This ultimately could have an overall homogenizing effect on the regional species pool (or γ-diversity). The same pattern was observed in mesocosms that received simulated dispersal events of zooplankton. Nutrients, overall, increased autotrophic biomass and while Aquashade® had no effect on autotrophic biomass, the interaction of nutrients and Aquashade® similarly caused a homogenization of the zooplankton community. Additionally, there was an overall increase in cladoceran ephippia in mesocosms receiving Aquashade® compared to those not, suggesting there is a 'trigger' switching cladocerans from parthenogenic to sexual reproduction. Taken together, our results show the application of Aquashade®, nutrient loading and dispersal shift biodiversity patterns in urban zooplankton communities. We hypothesize these shifts originate at the resource level through alterations in the phytoplankton community either through composition or nutritive value in ponds receiving Aquashade®. Our study illustrates the importance

Similarity between community structures of different online social networks and its impact on underlying community detection

NASA Astrophysics Data System (ADS)

Fan, W.; Yeung, K. H.

2015-03-01

As social networking services are popular, many people may register in more than one online social network. In this paper we study a set of users who have accounts of three online social networks: namely Foursquare, Facebook and Twitter. Community structure of this set of users may be reflected in these three online social networks. Therefore, high correlation between these reflections and the underlying community structure may be observed. In this work, community structures are detected in all three online social networks. Also, we investigate the similarity level of community structures across different networks. It is found that they show strong correlation with each other. The similarity between different networks may be helpful to find a community structure close to the underlying one. To verify this, we propose a method to increase the weights of some connections in networks. With this method, new networks are generated to assist community detection. By doing this, value of modularity can be improved and the new community structure match network's natural structure better. In this paper we also show that the detected community structures of online social networks are correlated with users' locations which are identified on Foursquare. This information may also be useful for underlying community detection.

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant

Typology of State-Level Community College Governance Structures

ERIC Educational Resources Information Center

Fletcher, Jeffrey A.; Friedel, Janice Nahra

2017-01-01

Despite having a well-documented history about community colleges across the United States, relatively few discussions have covered state-level governance structures. To understand the typology of state community college governance structures, it must first be recognized that community college governance is characterized as a complex web of…

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.

Estimating carnivore community structures

PubMed Central

Jiménez, José; Nuñez-Arjona, Juan Carlos; Rueda, Carmen; González, Luis Mariano; García-Domínguez, Francisco; Muñoz-Igualada, Jaime; López-Bao, José Vicente

2017-01-01

Obtaining reliable estimates of the structure of carnivore communities is of paramount importance because of their ecological roles, ecosystem services and impact on biodiversity conservation, but they are still scarce. This information is key for carnivore management: to build support for and acceptance of management decisions and policies it is crucial that those decisions are based on robust and high quality information. Here, we combined camera and live-trapping surveys, as well as telemetry data, with spatially-explicit Bayesian models to show the usefulness of an integrated multi-method and multi-model approach to monitor carnivore community structures. Our methods account for imperfect detection and effectively deal with species with non-recognizable individuals. In our Mediterranean study system, the terrestrial carnivore community was dominated by red foxes (0.410 individuals/km2); Egyptian mongooses, feral cats and stone martens were similarly abundant (0.252, 0.249 and 0.240 individuals/km2, respectively), whereas badgers and common genets were the least common (0.130 and 0.087 individuals/km2, respectively). The precision of density estimates improved by incorporating multiple covariates, device operation, and accounting for the removal of individuals. The approach presented here has substantial implications for decision-making since it allows, for instance, the evaluation, in a standard and comparable way, of community responses to interventions. PMID:28120871

Strong shift in the diazotrophic endophytic bacterial community inhabiting rice (Oryza sativa) plants after flooding.

PubMed

Ferrando, Lucía; Fernández Scavino, Ana

2015-09-01

Flooding impacts soil microbial communities, but its effect on endophytic communities has rarely been explored. This work addresses the effect of flooding on the abundance and diversity of endophytic diazotrophic communities on rice plants established in a greenhouse experiment. The nifH gene was significantly more abundant in roots after flooding, whereas the nifH gene copy numbers in leaves were unaffected and remained low. The PCA (principal component analysis) of T-RFLP (terminal restriction fragment length polymorphism) profiles indicated that root communities of replicate plots were more similar and diverse after flooding than before flooding. The nifH libraries obtained by cloning and 454 pyrosequencing consistently showed a remarkable shift in the diazotrophic community composition after flooding. Gammaproteobacteria (66-98%), mainly of the genus Stenotrophomonas, prevailed in roots before flooding, whereas Betaproteobacteria was the dominant class (26-34%) after flooding. A wide variety of aerotolerant and anaerobic diazotrophic bacteria (e.g. Dechloromonas, Rhodopseudomonas, Desulfovibrio, Geobacter, Chlorobium, Spirochaeta, Selenomonas and Dehalobacter) with diverse metabolic traits were retrieved from flooded rice roots. These findings suggest that endophytic communities could be significantly impacted by changes in plant-soil conditions derived from flooding during rice cropping. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter

USGS Publications Warehouse

Findlay, S.E.G.; Sinsabaugh, R. L.; Sobczak, W.V.; Hoostal, M.

2003-01-01

Hyporheic sediment bacterial communities were exposed to dissolved organic matter (DOM) from a variety of sources to assess the interdependence of bacterial metabolism and community composition. Experiments ranged from small-scale core perfusions with defined compounds (glucose, bovine serum albumin) to mesocosms receiving natural leaf leachate or water from different streams. Response variables included bacterial production, oxygen consumption, extracellular enzyme activity, and community similarity as manifest by changes in banding patterns of randomly amplified polymorphic DNA (RAPD). All DOM manipulations generated responses in at least one metabolic variable. Additions of both labile and recalcitrant materials increased either oxygen consumption, production, or both depending on background DOM. Enzyme activities were affected by both types of carbon addition with largest effects from the labile mixture. Cluster analysis of RAPD data showed strong divergence of communities exposed to labile versus recalcitrant DOM. Additions of leaf leachate to mesocosms representing hyporheic flow-paths caused increases in oxygen consumption and some enzyme activities with weaker effects on production. Community structure yeas strongly affected; samples from the leachate-amended mesocosms clustered separately from the control samples. In mesocosms receiving water from streams ranging in DOC (0.5-4.5 mg L-1), there were significant differences in bacterial growth, oxygen consumption, and enzyme activities. RAPD analysis showed strongest clustering of samples by stream type with more subtle effects of position along the flowpaths. Responses in community metabolism were always accompanied by shifts in community composition, suggesting carbon supply affects both functional and structural attributes of hyporheic bacterial communities.

Community Attachment and Satisfaction: The Role of a Community's Social Network Structure

ERIC Educational Resources Information Center

Crowe, Jessica

2010-01-01

This paper links the micro and macro levels of analysis by examining how different aspects of community sentiment are affected by one's personal ties to the community compared with the organizational network structure of the community. Using data collected from residents of six communities in Washington State, network analysis combined with…

The solution structure of Ln (DOTP) 5- complexxes. A comparison of lanthanide-induced paramagnetic shifts with the MMX energy-minimized structure

NASA Astrophysics Data System (ADS)

Geraldes, Carlos F. G. C.; Sherry, A. Dean; Kiefer, Garry E.

Complexes between the trivalent lanthanide ions and the macrocyclic chelate 1,4,7,10-tetraazacyclododecane- N,N',N″,N‴-tetra(methylene phosphonate) (DOTP) have been examined by high-resolution NMR spectroscopy. The proton spectra of the diamagnetic La(DOTP) 5- and Lu(DOTP) 5- complexes provide evidence for very rigid chelate structures with the ethylenediamine-containing chelate rings essentially locked into a single conformation at room temperature. The activation energy for ethylenediamine chelate ring interconversions in these complexes is approximately 100 kJ mol -1, considerably higher than that reported previously for the corresponding Ln(DOTA) - complexes (DOTA is the tetraacetate analog of DOTP). Lanthanide-induced shifts are reported for all 1H, 13C, and 31P nuclei in 11 Ln(DOTP) 5- complexes. The proton spectra of these complexes display unusually large lanthanide-induced shifts, one showing a spectrum in which the 1H resonances span 900 ppm. The contact and pseudocontact contributions to these shifts were separated using Reilley's temperature-independent method and the resulting pseudocontact lanthanide-induced NMR shifts were in excellent agreement with those calculated for a structure derived using MMX molecular modeling methods. The pseudocontact shifts provide evidence for Ln (DOTP) 5- chelates which have virtually identical structures along the lanthanide series, with the possible exception of Tm(DOTP) 5-.

Social significance of community structure: Statistical view

NASA Astrophysics Data System (ADS)

Li, Hui-Jia; Daniels, Jasmine J.

2015-01-01

Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a framework to analyze the significance of a social community. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of the nodes and their corresponding leaders. Then, using a log-likelihood score, the tightness of the community can be derived. Based on the distribution of community tightness, we establish a connection between p -value theory and network analysis, and then we obtain a significance measure of statistical form . Finally, the framework is applied to both benchmark networks and real social networks. Experimental results show that our work can be used in many fields, such as determining the optimal number of communities, analyzing the social significance of a given community, comparing the performance among various algorithms, etc.

An ex-post evaluation approach to assess the impacts of accomplished urban structure shift on landscape connectivity.

PubMed

Huang, Junlong; He, Jianhua; Liu, Dianfeng; Li, Chun; Qian, Jing

2018-05-01

Many studies have been conducted to evaluate the effects of different urban structures on landscape connectivity, and most of them rely on the comparison approach or ex-ante scenario analysis. However, we still lack an ex-post method to capture the consequences of accomplished urban structure shift (from monocentric to polycentric), which is guided by the land use planning. To fill this gap, we develop an ex-post evaluation approach which integrates counterfactual analysis and landscape graphs. Counterfactual analysis is combined with cellular automata simulation model, to uncover what the city might look like, if it had continued to expand in a monocentric structure; and the landscape graphs enable us to reveal the possible landscape connectivity in actual and counterfactual scenarios. We select Nanjing city as the study area and 4 target species, to delve into the varying impacts of the urban structure shift on different taxonomic groups. Our case study demonstrates that: (1) the impact of urban structure shift is more relevant to the long disperser; (2) the actual landscape (polycentric) would facilitate the bird's dispersal, while (3) forest mammals have higher connectivity in the counterfactual scenario (monocentric), and the possible reasons are discussed. Finally, we demonstrate that the urban structure shift might not necessarily cause the connectivity decline, on condition that the key connectivity providers are identified by integrating ecological network analysis into the land use planning, and well preserved in the shift. Copyright © 2017 Elsevier B.V. All rights reserved.

MOLECULAR CHARACTERIZATION OF MICROBIAL COMMUNITIES IN A JP-4 FUEL CONTAMINATED SOIL

EPA Science Inventory

In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and satur...

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.

PubMed

Mallon, C A; Le Roux, X; van Doorn, G S; Dini-Andreote, F; Poly, F; Salles, J F

2018-03-01

Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.

Dynamics and control of diseases in networks with community structure.

PubMed

Salathé, Marcel; Jones, James H

2010-04-08

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

Emergence of structured communities through evolutionary dynamics.

PubMed

Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploring Community-Engaged Scholarship as an Intervention to Change and Improve Communities

ERIC Educational Resources Information Center

Watson-Thompson, Jomella

2015-01-01

For most colleges and universities, community-engaged scholarship (CES) is a value that supports the public mission of academic institutions. However, shifting CES from a core value to a guiding principle requires demonstrable support and structural modifications to academic practices and policies. Through this reflective paper, I will propose…

Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

PubMed

Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

2013-06-01

The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate.

PubMed

Beall, B F N; Twiss, M R; Smith, D E; Oyserman, B O; Rozmarynowycz, M J; Binding, C E; Bourbonniere, R A; Bullerjahn, G S; Palmer, M E; Reavie, E D; Waters, Lcdr M K; Woityra, Lcdr W C; McKay, R M L

2016-06-01

Mid-winter limnological surveys of Lake Erie captured extremes in ice extent ranging from expansive ice cover in 2010 and 2011 to nearly ice-free waters in 2012. Consistent with a warming climate, ice cover on the Great Lakes is in decline, thus the ice-free condition encountered may foreshadow the lakes future winter state. Here, we show that pronounced changes in annual ice cover are accompanied by equally important shifts in phytoplankton and bacterial community structure. Expansive ice cover supported phytoplankton blooms of filamentous diatoms. By comparison, ice free conditions promoted the growth of smaller sized cells that attained lower total biomass. We propose that isothermal mixing and elevated turbidity in the absence of ice cover resulted in light limitation of the phytoplankton during winter. Additional insights into microbial community dynamics were gleaned from short 16S rRNA tag (Itag) Illumina sequencing. UniFrac analysis of Itag sequences showed clear separation of microbial communities related to presence or absence of ice cover. Whereas the ecological implications of the changing bacterial community are unclear at this time, it is likely that the observed shift from a phytoplankton community dominated by filamentous diatoms to smaller cells will have far reaching ecosystem effects including food web disruptions. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial community and nitrogen cycling shift with snowmelt in high-elevation barren soils of Mount Rainier National Park

NASA Astrophysics Data System (ADS)

Simpson, A.; Zabowski, D.

2015-12-01

Climate change and nutrient deposition have the potential to accelerate soil formation in high-elevation sediments recently exposed by glacier or snow melt. This process has implications not only for ecosystem formation on Earth but for the formation of Earth-like ecosystems on other planets and icy moons. Research into microbial communities shifting from subnival to mesotrophic conditions has mainly focused on changes on respiration and biomass, and is generally limited to one or two well-studied geographical locations. In particular, more information is needed on microbial shifts in snow-covered volcanic sediments, which may prove the closest analog to the most 'habitable' non-terrestrial environments for Earth microorganisms. We sampled in volcanic soil and sediment along gradients of elevation and snowmelt - dry soil, moist soil next to snowpack, and soil underneath snowpack - at the Muir Snowfields at Mount Rainier National Park, in order to investigate changes in carbon and nitrogen compounds, microbial diversity and gene expression. Initial results show a decrease in available ammonium and increase in microbial biomass carbon in exposed sediment with increasing soil moisture, and a sharp decrease in microbial C:N ratios after snowmelt and drying. Available/labile organic carbon and organic nitrogen decrease strongly with elevation, while microbial biomass carbon and nitrogen and mineral nitrogen compounds show no change with elevation. Though gene expression data is needed for confirmation, we hypothesize that these snowfields receive strong wind-borne deposits of carbon and nitrogen but that chemoautotrophic communities under semi-permanent snowpack do not shift to more mesotrophic communities until after exposed sediment has already begun to desiccate, limiting soil formation.

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure.

PubMed

Han, Ziming; Deng, Mingwen; Yuan, Anqi; Wang, Jiahui; Li, Hao; Ma, Jincai

2018-06-01

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities. Copyright © 2017 Elsevier B.V. All rights reserved.

Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA.

PubMed

Wu, Shijin; Li, Yuan; Wang, Penghua; Zhong, Li; Qiu, Lequan; Chen, Jianmeng

2016-04-01

The environmental risk of fluoride and chloride pollution is pronounced in soils adjacent to solar photovoltaic sites. The elevated levels of fluoride and chloride in these soils have had significant impacts on the population size and overall biological activity of the soil microbial communities. The microbial community also plays an essential role in remediation of these soils. Questions remain as to how the fluoride and chloride contamination and subsequent remediation at these sites have impacted the population structure of the soil microbial communities. We analyzed the microbial communities in soils collected from close to a solar photovoltaic enterprise by pyrosequencing of the 16S rRNA tag. In addition, we used multivariate statistics to identity the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa and sharing significant correlations with different degrees of fluoride and chloride contamination. The contaminated soils harbored abundant bacteria that were probably resistant to the high acidity, high fluoride and chloride concentration, and high osmotic pressure environment. The dominant genera were Sphingomonas, Subgroup_6_norank, Clostridium sensu stricto, Nitrospira, Rhizomicrobium, and Acidithiobacillus. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.

Shifted energy fluxes, increased Bowen ratios, and reduced thaw depths linked with drainage-induced changes in permafrost ecosystem structure

NASA Astrophysics Data System (ADS)

Göckede, Mathias; Kittler, Fanny; Kwon, Min Jung; Burjack, Ina; Heimann, Martin; Kolle, Olaf; Zimov, Nikita; Zimov, Sergey

2017-12-01

Hydrologic conditions are a key factor in Arctic ecosystems, with strong influences on ecosystem structure and related effects on biogeophysical and biogeochemical processes. With systematic changes in water availability expected for large parts of the northern high-latitude region in the coming centuries, knowledge on shifts in ecosystem functionality triggered by altered water levels is crucial for reducing uncertainties in climate change predictions. Here, we present findings from paired ecosystem observations in northeast Siberia comprising a drained and a control site. At the drainage site, the water table has been artificially lowered by up to 30 cm in summer for more than a decade. This sustained primary disturbance in hydrologic conditions has triggered a suite of secondary shifts in ecosystem properties, including vegetation community structure, snow cover dynamics, and radiation budget, all of which influence the net effects of drainage. Reduced thermal conductivity in dry organic soils was identified as the dominating drainage effect on energy budget and soil thermal regime. Through this effect, reduced heat transfer into deeper soil layers leads to shallower thaw depths, initially leading to a stabilization of organic permafrost soils, while the long-term effects on permafrost temperature trends still need to be assessed. At the same time, more energy is transferred back into the atmosphere as sensible heat in the drained area, which may trigger a warming of the lower atmospheric surface layer.

Cascading failures in complex networks with community structure

NASA Astrophysics Data System (ADS)

Lin, Guoqiang; di, Zengru; Fan, Ying

2014-12-01

Much empirical evidence shows that when attacked with cascading failures, scale-free or even random networks tend to collapse more extensively when the initially deleted node has higher betweenness. Meanwhile, in networks with strong community structure, high-betweenness nodes tend to be bridge nodes that link different communities, and the removal of such nodes will reduce only the connections among communities, leaving the networks fairly stable. Understanding what will affect cascading failures and how to protect or attack networks with strong community structure is therefore of interest. In this paper, we have constructed scale-free Community Networks (SFCN) and Random Community Networks (RCN). We applied these networks, along with the Lancichinett-Fortunato-Radicchi (LFR) benchmark, to the cascading-failure scenario to explore their vulnerability to attack and the relationship between cascading failures and the degree distribution and community structure of a network. The numerical results show that when the networks are of a power-law distribution, a stronger community structure will result in the failure of fewer nodes. In addition, the initial removal of the node with the highest betweenness will not lead to the worst cascading, i.e. the largest avalanche size. The Betweenness Overflow (BOF), an index that we developed, is an effective indicator of this tendency. The RCN, however, display a different result. In addition, the avalanche size of each node can be adopted as an index to evaluate the importance of the node.

Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

PubMed

Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

2017-03-07

Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

A critical review on the interaction of substrate nutrient balance and microbial community structure and function in anaerobic co-digestion.

PubMed

Xu, Rong; Zhang, Kai; Liu, Pu; Khan, Aman; Xiong, Jian; Tian, Fake; Li, Xiangkai

2018-01-01

Anaerobic co-digestion generally results in a higher yield of biogas than mono-digestion, hence co-digestion has become a topic of general interest in recent studies of anaerobic digestion. Compared with mono-digestion, co-digestion utilizes multiple substrates. The balance of substrate nutrient in co-digestion comprises better adjustments of C/N ratio, pH, moisture, trace elements, and dilution of toxic substances. All of these changes could result in positive shifts in microbial community structure and function in the digestion processes and consequent augmentation of biogas production. Nevertheless, there have been few reviews on the interaction of nutrient and microbial community in co-digestions. The objective of this review is to investigate recent achievements and perspectives on the interaction of substrate nutrient balance and microbial community structure and function. This may provide valuable information on the optimization of combinations of substrates and prediction of bioreactor performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

Shifts in Plant Community Assembly Processes across Growth Forms along a Habitat Severity Gradient: A Test of the Plant Functional Trait Approach.

PubMed

Xu, Jinshi; Chai, Yongfu; Wang, Mao; Dang, Han; Guo, Yaoxin; Chen, Yu; Zhang, Chenguang; Li, Ting; Zhang, Lixia; Yue, Ming

2018-01-01

Species respond to changes in their environments. A core goal in ecology is to understand the process of plant community assembly in response to a changing climate. Examining the performance of functional traits and trait-based assembly patterns across species among different growth forms is a useful way to explore the assembly process. In this study, we constructed a habitat severity gradient including several environment factors along a 2300 m wide elevational range at Taibai Mountain, central China. Then we assessed the shift on functional trait values and community assembly patterns along this gradient across species among different growth forms. We found that (1) although habitat-severity values closely covaried with elevation in this study, an examined communities along a habitat severity gradient might reveal community dynamics and species responses under future climate change. (2) the occurrence of trait values along the habitat severity gradient across different growth forms were similar, whereas the assembly pattern of herbaceous species was inconsistent with the community and woody species. (3) the trait-trait relationships of herbaceous species were dissimilar to those of the community and woody species. These results suggest that (1) community would re-assemble along habitat severity gradient through environmental filtering, regardless of any growth forms and that (2) different growth forms' species exhibiting similar trait values' shift but different trait-trait relationship by different trait combinations.

Finding community structure in very large networks

NASA Astrophysics Data System (ADS)

Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher

2004-12-01

The discovery and analysis of community structure in networks is a topic of considerable recent interest within the physics community, but most methods proposed so far are unsuitable for very large networks because of their computational cost. Here we present a hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O(mdlogn) where d is the depth of the dendrogram describing the community structure. Many real-world networks are sparse and hierarchical, with mtilde n and dtilde logn , in which case our algorithm runs in essentially linear time, O(nlog2n) . As an example of the application of this algorithm we use it to analyze a network of items for sale on the web site of a large on-line retailer, items in the network being linked if they are frequently purchased by the same buyer. The network has more than 400 000 vertices and 2×106 edges. We show that our algorithm can extract meaningful communities from this network, revealing large-scale patterns present in the purchasing habits of customers.

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.

Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

PubMed

Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

2016-08-01

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

Perceptions of health stakeholders on task shifting and motivation of community health workers in different socio demographic contexts in Kenya (nomadic, peri-urban and rural agrarian)

PubMed Central

2014-01-01

Background The shortage of health professionals in low income countries is recognized as a crisis. Community health workers are part of a “task-shift” strategy to address this crisis. Task shifting in this paper refers to the delegation of tasks from health professionals to lay, trained volunteers. In Kenya, there is a debate as to whether these volunteers should be compensated, and what motivation strategies would be effective in different socio-demographic contexts, based type of tasks shifted. The purpose of this study was to find out, from stakeholders’ perspectives, the type of tasks to be shifted to community health workers and the appropriate strategies to motivate and retain them. Methods This was an analytical comparative study employing qualitative methods: key informant interviews with health policy makers, managers, and service providers, and focus group discussions with community health workers and service consumers, to explore their perspectives on tasks to be shifted and appropriate motivation strategies. Results The study found that there were tasks to be shifted and motivation strategies that were common to all three contexts. Common tasks were promotive, preventive, and simple curative services. Common motivation strategies were supportive supervision, means of identification, equitable allocation of resources, training, compensation, recognition, and evidence based community dialogue. Further, in the nomadic and peri-urban sites, community health workers had assumed curative services beyond the range provided for in the Kenyan task shifting policy. This was explained to be influenced by lack of access to care due to distance to health facilities, population movement, and scarcity of health providers in the nomadic setting and the harsh economic realities in peri-urban set up. Therefore, their motivation strategies included training on curative skills, technical support, and resources for curative care. Data collection was viewed as an

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

PubMed Central

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

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

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

PubMed

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

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

Ecological and Evolutionary Effects of Stickleback on Community Structure

PubMed Central

Des Roches, Simone; Shurin, Jonathan B.; Schluter, Dolph; Harmon, Luke J.

2013-01-01

Species’ ecology and evolution can have strong effects on communities. Both may change concurrently when species colonize a new ecosystem. We know little, however, about the combined effects of ecological and evolutionary change on community structure. We simultaneously examined the effects of top-predator ecology and evolution on freshwater community parameters using recently evolved generalist and specialist ecotypes of three-spine stickleback (Gasterosteus aculeatus). We used a mesocosm experiment to directly examine the effects of ecological (fish presence and density) and evolutionary (phenotypic diversity and specialization) factors on community structure at lower trophic levels. We evaluated zooplankton biomass and composition, periphyton and phytoplankton chlorophyll-a concentration, and net primary production among treatments containing different densities and diversities of stickleback. Our results showed that both ecological and evolutionary differences in the top-predator affect different aspects of community structure and composition. Community structure, specifically the abundance of organisms at each trophic level, was affected by stickleback presence and density, whereas composition of zooplankton was influenced by stickleback diversity and specialization. Primary productivity, in terms of chlorophyll-a concentration and net primary production was affected by ecological but not evolutionary factors. Our results stress the importance of concurrently evaluating both changes in density and phenotypic diversity on the structure and composition of communities. PMID:23573203

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Climate extremes drive changes in functional community structure.

PubMed

Boucek, Ross E; Rehage, Jennifer S

2014-06-01

The response of communities to climate extremes can be quite variable. Much of this variation has been attributed to differences in community-specific functional trait diversity, as well as community composition. Yet, few if any studies have explicitly tested the response of the functional trait structure of communities following climate extremes (CEs). Recently in South Florida, two independent, but sequential potential CEs took place, a 2010 cold front, followed by a 2011 drought, both of which had profound impacts on a subtropical estuarine fish community. These CEs provided an opportunity to test whether the structure of South Florida fish communities following each extreme was a result of species-specific differences in functional traits. From historical temperature (1927-2012) and freshwater inflows records into the estuary (1955-2012), we determined that the cold front was a statistically extreme disturbance, while the drought was not, but rather a decadal rare disturbance. The two disturbances predictably affected different parts of functional community structure and thus different component species. The cold front virtually eliminated tropical species, including large-bodied snook, mojarra species, nonnative cichlids, and striped mullet, while having little affect on temperate fishes. Likewise, the drought severely impacted freshwater fishes including Florida gar, bowfin, and two centrarchids, with little effect on euryhaline species. Our findings illustrate the ability of this approach to predict and detect both the filtering effects of different types of disturbances and the implications of the resulting changes in community structure. Further, we highlight the value of this approach to developing predictive frameworks for better understanding community responses to global change. © 2014 John Wiley & Sons Ltd.

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

PubMed Central

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs.

PubMed

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.

PubMed

Li, Bing; Wu, Wei-Min; Watson, David B; Cardenas, Erick; Chao, Yuanqing; Phillips, D H; Mehlhorn, Tonia; Lowe, Kenneth; Kelly, Shelly D; Li, Pengsong; Tao, Huchun; Tiedje, James M; Criddle, Craig S; Zhang, Tong

2018-05-01

network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites. Copyright © 2018 American Society for Microbiology.

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community

The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities

PubMed Central

Clark, Graeme F.; Stark, Jonathan S.; Palmer, Anne S.; Riddle, Martin J.; Johnston, Emma L.

2017-01-01

On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics. PMID:28076438

The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities.

PubMed

Clark, Graeme F; Stark, Jonathan S; Palmer, Anne S; Riddle, Martin J; Johnston, Emma L

2017-01-01

On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics.

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem

PubMed Central

Waghmode, Tatoba R.; Chen, Shuaimin; Li, Jiazhen; Sun, Ruibo; Liu, Binbin; Hu, Chunsheng

2018-01-01

Soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, the response of the soil nitrifier and denitrifier communities to climate warming is poorly understood. A long-term field warming experiment has been conducted for 8 years at Luancheng Experimental Farm Station on the North China Plain; we used this field to examine how soil microbial community structure, nitrifier, and denitrifier abundance respond to warming under regular irrigation (RI) and high irrigation (HI) at different soil depths (0–5, 5–10, and 10–20 cm). Nitrifier, denitrifier, and the total bacterial abundance were assessed by quantitative polymerase chain reaction of the functional genes and 16S rRNA gene, respectively. Bacterial community structure was studied through high throughput sequencing of the 16S rRNA gene. Under RI, warming significantly (P < 0.05) increased the potential nitrification rate and nitrate concentration and decreased the soil moisture. In most of the samples, warming increased the ammonia-oxidizing bacteria abundance but decreased the ammonia-oxidizing archaea (AOA) and denitrifier (nirK, nirS, and nosZ genes) abundance. Under HI, there was a highly increased AOA and 16S rRNA gene abundance and a slightly higher denitrifier abundance compared with RI. Warming decreased the bacterial diversity and species richness, and the microbial community structure differed greatly between the warmed and control plots. The decrease in bacterial diversity was higher in RI than HI and at the 0–5 cm depths than at the 5–10 and 10–20 cm soil depths. Warming led to an increase in the relative abundance of Actinobacteria, Bacteroidetes, and TM7 but a decrease in Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Nitrospira, and Planctomycetes. The greater shift in microbial community structure was observed only in RI at the 0–5 cm soil depth. This study provides new insight into our understanding of the nitrifier and denitrifier

Timing of sea ice retreat can alter phytoplankton community structure in the western Arctic Ocean

NASA Astrophysics Data System (ADS)

Fujiwara, A.; Hirawake, T.; Suzuki, K.; Imai, I.; Saitoh, S.-I.

2014-04-01

This study assesses the response of phytoplankton assemblages to recent climate change, especially with regard to the shrinking of sea ice in the northern Chukchi Sea of the western Arctic Ocean. Distribution patterns of phytoplankton groups in the late summers of 2008-2010 were analysed based on HPLC pigment signatures and, the following four major algal groups were inferred via multiple regression and cluster analyses: prasinophytes, diatoms, haptophytes and dinoflagellates. A remarkable interannual difference in the distribution pattern of the groups was found in the northern basin area. Haptophytes dominated and dispersed widely in warm surface waters in 2008, whereas prasinophytes dominated in cold water in 2009 and 2010. A difference in the onset date of sea ice retreat was evident among years-the sea ice retreat in 2008 was 1-2 months earlier than in 2009 and 2010. The spatial distribution of early sea ice retreat matched the areas in which a shift in algal community composition was observed. Steel-Dwass's multiple comparison tests were used to assess the physical, chemical and biological parameters of the four clusters. We found a statistically significant difference in temperature between the haptophyte-dominated cluster and the other clusters, suggesting that the change in the phytoplankton communities was related to the earlier sea ice retreat in 2008 and the corollary increase in sea surface temperatures. Longer periods of open water during the summer, which are expected in the future, may affect food webs and biogeochemical cycles in the western Arctic due to shifts in phytoplankton community structure.

Timing of sea ice retreat can alter phytoplankton community structure in the western Arctic Ocean

NASA Astrophysics Data System (ADS)

name prefix surname suffix, given; Fujiwara, A.; Hirawake, T.; Suzuki, K.; Imai, I.; Saitoh, S.-I.

2013-09-01

This study assesses the response of phytoplankton assemblages to recent climate change, especially with regard to the shrinking of sea ice in the northern Chukchi Sea of the western Arctic Ocean. Distribution patterns of phytoplankton groups in the late summers of 2008-2010 were analyzed based on HPLC pigment signatures and, the following four major algal groups were inferred via multiple regression and cluster analyses: prasinophytes, diatoms, haptophytes and dinoflagellates. A remarkable interannual difference in the distribution pattern of the groups was found in the northern basin area. Haptophytes dominated and dispersed widely in warm surface waters in 2008, whereas prasinophytes dominated in cold water in 2009 and 2010. A difference in the onset date of sea ice retreat was evident among years - the sea ice retreat in 2008 was 1-2 months earlier than in 2009 and 2010. The spatial distribution of early sea ice retreat matched the areas in which a shift in algal community composition was observed. Steel-Dwass's multiple comparison tests were used to assess the physical, chemical and biological parameters of the four clusters. We found a statistically significant difference in temperature between the haptophyte-dominated cluster and the other clusters, suggesting that the change in the phytoplankton communities was related to the earlier sea ice retreat in 2008 and the corollary increase in sea surface temperatures. Longer periods of open water during the summer, which are expected in the future, may affect food webs and biogeochemical cycles in the western Arctic due to shifts in phytoplankton community structure.

Predicting climate-driven regime shifts versus rebound potential in coral reefs.

PubMed

Graham, Nicholas A J; Jennings, Simon; MacNeil, M Aaron; Mouillot, David; Wilson, Shaun K

2015-02-05

Climate-induced coral bleaching is among the greatest current threats to coral reefs, causing widespread loss of live coral cover. Conditions under which reefs bounce back from bleaching events or shift from coral to algal dominance are unknown, making it difficult to predict and plan for differing reef responses under climate change. Here we document and predict long-term reef responses to a major climate-induced coral bleaching event that caused unprecedented region-wide mortality of Indo-Pacific corals. Following loss of >90% live coral cover, 12 of 21 reefs recovered towards pre-disturbance live coral states, while nine reefs underwent regime shifts to fleshy macroalgae. Functional diversity of associated reef fish communities shifted substantially following bleaching, returning towards pre-disturbance structure on recovering reefs, while becoming progressively altered on regime shifting reefs. We identified threshold values for a range of factors that accurately predicted ecosystem response to the bleaching event. Recovery was favoured when reefs were structurally complex and in deeper water, when density of juvenile corals and herbivorous fishes was relatively high and when nutrient loads were low. Whether reefs were inside no-take marine reserves had no bearing on ecosystem trajectory. Although conditions governing regime shift or recovery dynamics were diverse, pre-disturbance quantification of simple factors such as structural complexity and water depth accurately predicted ecosystem trajectories. These findings foreshadow the likely divergent but predictable outcomes for reef ecosystems in response to climate change, thus guiding improved management and adaptation.

Climate change and physical disturbance cause similar community shifts in biological soil crusts

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

Ferrenberg, Scott; Reed, Sasha C.; Belnap, Jayne

In biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface— fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover are present.Though there has been long-standing concern over impacts of physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, in this paper we examined the effects of 10 y of experimental warming and altered precipitation (in full-factorial design) on biocrustmore » communities and compared the effects of altered climate with those of long-term physical disturbance (>10 y of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increases in cyanobacteria cover, with more variable effects on lichens. Although the pace of community change varied significantly among treatments, these results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. Finally, this is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed as treatments in our study.« less

Climate change and physical disturbance cause similar community shifts in biological soil crusts.

PubMed

Ferrenberg, Scott; Reed, Sasha C; Belnap, Jayne

2015-09-29

Biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface—are fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover. Although there has been long-standing concern over impacts of physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, we examined the effects of 10 y of experimental warming and altered precipitation (in full-factorial design) on biocrust communities and compared the effects of altered climate with those of long-term physical disturbance (>10 y of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increases in cyanobacteria cover, with more variable effects on lichens. Although the pace of community change varied significantly among treatments, our results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. This is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed as treatments in our study.

Climate change and physical disturbance cause similar community shifts in biological soil crusts

DOE PAGES

Ferrenberg, Scott; Reed, Sasha C.; Belnap, Jayne

2015-09-14

In biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface— fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover are present.Though there has been long-standing concern over impacts of physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, in this paper we examined the effects of 10 y of experimental warming and altered precipitation (in full-factorial design) on biocrustmore » communities and compared the effects of altered climate with those of long-term physical disturbance (>10 y of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increases in cyanobacteria cover, with more variable effects on lichens. Although the pace of community change varied significantly among treatments, these results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. Finally, this is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed as treatments in our study.« less

Climate change and physical disturbance cause similar community shifts in biological soil crusts

USGS Publications Warehouse

Ferrenberg, Scott; Reed, Sasha C.; Belnap, Jayne

2015-01-01

Biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface—are fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover. While there has been long-standing concern over impacts of 5 physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is also increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, USA, we examined the effects of 10 years of experimental warming and altered precipitation (in full-factorial design) on biocrust communities, and compared the effects of altered climate with those of long-term physical 10 disturbance (>10 years of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increased cyanobacteria cover, with more variable effects 15 on lichens. While the pace of community change varied significantly among treatments, our results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. This is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed by the climate treatments used in our study.

Variations in the Summer Phytoplankton Community Structure in Atlantic sub-Arctic and Arctic Waters

NASA Astrophysics Data System (ADS)

Small, A.; Hughes, C.; Bouman, H. A.

2016-02-01

Shifts in phytoplankton community structure serve not only as indicators of environmental change but also have implications for food-web interactions and biogeochemical cycles. The community structure of marine phytoplankton in sub-Arctic and Arctic waters was examined using 159 samples collected in the summer of 2013 along a latitudinal gradient spanning from 61.1 to 83.1 degrees N along the east coast of Greenland. Accessory pigment concentrations were used to infer information about the phytoplankton taxa present using CHEMTAX (CHEMical TAXonomy), an iterative MATLAB subroutine. The main algal classes found within the study region were diatoms, dinoflagellates, haptophytes, chlorophytes, cryptophytes and prasinophytes. Diatoms were present at nearly all stations and depths and were large contributors to the total pigment biomass for both ice and open water stations. Deeper samples were mainly dominated by diatoms and haptophytes. Surface sample communities were characterised by mixed assemblages, including dinoflagellates and chlorophytes although diatoms and haptophytes still comprised a significant portion of the pigment biomass. The differences in community structure were investigated in relation to the environmental conditions through multivariate statistical analysis (cluster and principle component analyses) in order to understand the factors influencing the spatial distribution of the various algal classes. Diagnostic pigment indices were also used to calculate the concentration of Chl-a attributed to three size classes (picophytoplankton 0.2-2µm, nanophytoplankton 2-20µm and microphytoplankton >20µm). These data were compared to a similar dataset from the same cruise where size fractionated Chl-a was separated by sequential filtration and quantified by fluorometric analysis. Size-fractionated Chl-a as measured directly by sequential filtration suggested a primarily mixed community across the study region. In contrast pigment based analysis suggested a

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.

PubMed

Knelman, Joseph E; Graham, Emily B; Prevéy, Janet S; Robeson, Michael S; Kelly, Patrick; Hood, Eran; Schmidt, Steve K

2018-01-01

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

PubMed Central

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.; Robeson, Michael S.; Kelly, Patrick; Hood, Eran; Schmidt, Steve K.

2018-01-01

Past research demonstrating the importance plant–microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant–microbe interactions with late-successional plants and interspecific plant interactions more generally. PMID:29467741

Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

USGS Publications Warehouse

Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

1999-01-01

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65

Pyrosequencing reveals the microbial communities in the Red Sea sponge Carteriospongia foliascens and their impressive shifts in abnormal tissues.

PubMed

Gao, Zhao-Ming; Wang, Yong; Lee, On On; Tian, Ren-Mao; Wong, Yue Him; Bougouffa, Salim; Batang, Zenon; Al-Suwailem, Abdulaziz; Lafi, Feras F; Bajic, Vladimir B; Qian, Pei-Yuan

2014-10-01

Abnormality and disease in sponges have been widely reported, yet how sponge-associated microbes respond correspondingly remains inconclusive. Here, individuals of the sponge Carteriospongia foliascens under abnormal status were collected from the Rabigh Bay along the Red Sea coast. Microbial communities in both healthy and abnormal sponge tissues and adjacent seawater were compared to check the influences of these abnormalities on sponge-associated microbes. In healthy tissues, we revealed low microbial diversity with less than 100 operational taxonomic units (OTUs) per sample. Cyanobacteria, affiliated mainly with the sponge-specific species "Candidatus Synechococcus spongiarum," were the dominant bacteria, followed by Bacteroidetes and Proteobacteria. Intraspecies dynamics of microbial communities in healthy tissues were observed among sponge individuals, and potential anoxygenic phototrophic bacteria were found. In comparison with healthy tissues and the adjacent seawater, abnormal tissues showed dramatic increase in microbial diversity and decrease in the abundance of sponge-specific microbial clusters. The dominated cyanobacterial species Candidatus Synechococcus spongiarum decreased and shifted to unspecific cyanobacterial clades. OTUs that showed high similarity to sequences derived from diseased corals, such as Leptolyngbya sp., were found to be abundant in abnormal tissues. Heterotrophic Planctomycetes were also specifically enriched in abnormal tissues. Overall, we revealed the microbial communities of the cyanobacteria-rich sponge, C. foliascens, and their impressive shifts under abnormality.

Shifts in Nitrification Kinetics and Microbial Community during Bioaugmentation of Activated Sludge with Nitrifiers Enriched on Sludge Reject Water

PubMed Central

Yu, Lifang; Peng, Dangcong; Pan, Ruiling

2012-01-01

This study used two laboratory-scale sequencing batch reactors (SBRs) to evaluate the shifts in nitrification kinetics and microbial communities of an activated sludge sewage treatment system (main stream) during bioaugmentation with nitrifiers cultivated on real sludge reject water (side stream). Although bioaugmentation exerted a strong influence on the microbial community and the nitrification kinetics in the main stream, there was 58% of maximum ammonia uptake rate (AUR) and 80% of maximum nitrite uptake rate (NUR) loss of the seed source after bioaugmentation. In addition, nitrite accumulation occurred during bioaugmentation due to the unequal and asynchronous increase of the AUR (from 2.88 to 13.36 mg N/L·h) and NUR (from 0.76 to 4.34 mg N/L·h). FISH results showed that ammonia oxidizing bacteria (AOB) was inclined to be washed out with effluent in contrast to nitrite oxidizing bacteria (NOB), and Nitrosococcus mobilis lineage was the dominant AOB, while the dominant NOB in the main stream gradually transferred from Nitrospira to Nitrobacter. Nitrospina and Nitrococcus which existed in the seed source could not be detected in the main stream. It can be inferred that nitrite accumulation occurred due to the mismatch of NOB structure but washed out with effluent. PMID:23091354

Eukaryotic Community Shift in Response to Organic Loading Rate of an Aerobic Trickling Filter (Down-Flow Hanging Sponge Reactor) Treating Domestic Sewage.

PubMed

Miyaoka, Yuma; Hatamoto, Masashi; Yamaguchi, Takashi; Syutsubo, Kazuaki

2017-05-01

In this study, changes in eukaryotic community structure and water quality were investigated in an aerobic trickling filter (down-flow hanging sponge, DHS) treating domestic sewage under different organic loading rates (OLRs). The OLR clearly influenced both sponge pore water quality and relative flagellates and ciliates (free-swimming, carnivorous, crawling, and stalked protozoa) abundances in the retained sludge. Immediately after the OLR was increased from 1.05 to 1.97 kg chemical oxygen demand (COD) m -3  day -1 , COD and NH 4 + -N treatment efficiencies both deteriorated, and relative flagellates and ciliates abundances then increased from 2-8 % to 51-65 % total cells in the middle-bottom part of the DHS reactor. In a continuous operation at a stable OLR (2.01 kg COD m -3  day -1 ), effluent water quality improved, and relative flagellates and ciliates abundances decreased to 15-46 % total cells in the middle-bottom part of the DHS reactor. This result may indicate that flagellates and ciliates preferentially graze on dispersed bacteria, thus, stabilizing effluent water quality. Additionally, to investigate eukaryotic community structure, clone libraries based on the 18S ribosomal ribonucleic acid (rRNA) gene of the retained sludge were constructed. The predominant group was Nucletmycea phylotypes, representing approximately 29-56 % total clones. Furthermore, a large proportion of the clones had <97 % sequence identity in the NCBI database. This result indicates that phylogenetically unknown eukaryotes were present in the DHS reactor. These results provide insights into eukaryotic community shift in the DHS reactor treating domestic sewage.

Modelling Vulnerability and Range Shifts in Ant Communities Responding to Future Global Warming in Temperate Forests.

PubMed

Kwon, Tae-Sung; Li, Fengqing; Kim, Sung-Soo; Chun, Jung Hwa; Park, Young-Seuk

2016-01-01

Global warming is likely leading to species' distributional shifts, resulting in changes in local community compositions and diversity patterns. In this study, we applied species distribution models to evaluate the potential impacts of temperature increase on ant communities in Korean temperate forests, by testing hypotheses that 1) the risk of extinction of forest ant species would increase over time, and 2) the changes in species distribution ranges could drive upward movements of ant communities and further alter patterns of species richness. We sampled ant communities at 335 evenly distributed sites across South Korea and modelled the future distribution range for each species using generalized additive models. To account for spatial autocorrelation, autocovariate regressions were conducted prior to generalized additive models. Among 29 common ant species, 12 species were estimated to shrink their suitable geographic areas, whereas five species would benefit from future global warming. Species richness was highest at low altitudes in the current period, and it was projected to be highest at the mid-altitudes in the 2080s, resulting in an upward movement of 4.9 m yr-1. This altered the altitudinal pattern of species richness from a monotonic-decrease curve (common in temperate regions) to a bell-shaped curve (common in tropical regions). Overall, ant communities in temperate forests are vulnerable to the on-going global warming and their altitudinal movements are similar to other faunal communities.

Information transfer in community structured multiplex networks

NASA Astrophysics Data System (ADS)

Solé Ribalta, Albert; Granell, Clara; Gómez, Sergio; Arenas, Alex

2015-08-01

The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

Network community structure and loop coefficient method

NASA Astrophysics Data System (ADS)

Vragović, I.; Louis, E.

2006-07-01

A modular structure, in which groups of tightly connected nodes could be resolved as separate entities, is a property that can be found in many complex networks. In this paper, we propose a algorithm for identifying communities in networks. It is based on a local measure, so-called loop coefficient that is a generalization of the clustering coefficient. Nodes with a large loop coefficient tend to be core inner community nodes, while other vertices are usually peripheral sites at the borders of communities. Our method gives satisfactory results for both artificial and real-world graphs, if they have a relatively pronounced modular structure. This type of algorithm could open a way of interpreting the role of nodes in communities in terms of the local loop coefficient, and could be used as a complement to other methods.

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture.

PubMed

Castro-Gutiérrez, Víctor; Masís-Mora, Mario; Carazo-Rojas, Elizabeth; Mora-López, Marielos; Rodríguez-Rodríguez, Carlos E

2018-04-01

An experimental study evaluating the effect of bioaugmentation and antibiotic (oxytetracycline) application on pesticide degradation and microbial community structure of a biomixture used in a biopurification system (BPR) was conducted. The bioaugmentation employed a carbofuran-degrading bacterial consortium. The non-bioaugmented biomixture showed excellent performance for removal of atrazine (t 1/2 : 9.9 days), carbendazim (t 1/2 : 3.0 days), carbofuran (t 1/2 : 2.8 days), and metalaxyl (t 1/2 : 2.7 days). Neither the addition of oxytetracycline nor bioaugmentation affected the efficiency of pesticide removal or microbial community (bacterial and fungal) structure, as determined by DGGE analysis. Instead, biomixture aging was mainly responsible for microbial population shifts. Even though the bioaugmentation did not enhance the biomixtures' performance, this matrix showed a high capability to sustain initial stresses related to antibiotic addition; therefore, simultaneous elimination of this particular mixture of pesticides together with oxytetracycline residues is not discouraged.

L2-Proficiency-Dependent Laterality Shift in Structural Connectivity of Brain Language Pathways.

PubMed

Xiang, Huadong; van Leeuwen, Tessa Marije; Dediu, Dan; Roberts, Leah; Norris, David G; Hagoort, Peter

2015-08-01

Diffusion tensor imaging (DTI) and a longitudinal language learning approach were applied to investigate the relationship between the achieved second language (L2) proficiency during L2 learning and the reorganization of structural connectivity between core language areas. Language proficiency tests and DTI scans were obtained from German students before and after they completed an intensive 6-week course of the Dutch language. In the initial learning stage, with increasing L2 proficiency, the hemispheric dominance of the Brodmann area (BA) 6-temporal pathway (mainly along the arcuate fasciculus) shifted from the left to the right hemisphere. With further increased proficiency, however, lateralization dominance was again found in the left BA6-temporal pathway. This result is consistent with reports in the literature that imply a stronger involvement of the right hemisphere in L2 processing especially for less proficient L2 speakers. This is the first time that an L2 proficiency-dependent laterality shift in the structural connectivity of language pathways during L2 acquisition has been observed to shift from left to right and back to left hemisphere dominance with increasing L2 proficiency. The authors additionally find that changes in fractional anisotropy values after the course are related to the time elapsed between the two scans. The results suggest that structural connectivity in (at least part of) the perisylvian language network may be subject to fast dynamic changes following language learning.

Evidence for the functional significance of diazotroph community structure in soil.

PubMed

Hsu, Shi-Fang; Buckley, Daniel H

2009-01-01

Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

Size really does matter: effects of filter fractionation on microbial community structure in a model oxygen minimum zone.

NASA Astrophysics Data System (ADS)

Torres Beltran, M.

2016-02-01

The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 "Microbial Community Responses to Ocean Deoxygenation" workshop held in Vancouver, British Columbia in July 2014 had the primary objective of kick-starting the establishment of a minimal core of technologies, techniques and standard operating procedures (SOPs) to enable compatible process rate and multi-molecular data (DNA, RNA and protein) collection in marine oxygen minimum zones (OMZs) and other oxygen starved waters. Experimental activities conducted in Saanich Inlet, a seasonally anoxic fjord on Vancouver Island British Columbia, were designed to compare and cross-calibrate in situ sampling devices (McLane PPS system) with conventional bottle sampling and incubation methods. Bottle effects on microbial community composition, and activity were tested using different filter combinations and sample volumes to compare PPS/IPS (0.4 µm) versus Sterivex (0.22 µm) filtration methods with and without prefilters (2.7 µm). Resulting biomass was processed for small subunit ribosomal RNA gene sequencing across all three domains of life on the 454 platform followed by downstream community structure analyses. Significant community shifts occurred within and between filter fractions for in situ versus on-ship processed samples. For instance, the relative abundance of several bacterial phyla including Bacteroidetes, Delta and Gammaproteobacteria decreased five-fold on-ship when compared to in situ filtration. Similarly, experimental mesocosms showed similar community structure and activity to in situ filtered samples indicating the need to cross-calibrate incubations to constrain bottle effects. In addition, alpha and beta diversity significantly changed as function of filter size and volume, as well as the operational taxonomic units identified using indicator species analysis for each filter size. Our results provide statistical support that microbial community structure is systematically biased

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Natural acidification changes the timing and rate of succession, alters community structure, and increases homogeneity in marine biofouling communities.

PubMed

Brown, Norah E M; Milazzo, Marco; Rastrick, Samuel P S; Hall-Spencer, Jason M; Therriault, Thomas W; Harley, Christopher D G

2018-01-01

Ocean acidification may have far-reaching consequences for marine community and ecosystem dynamics, but its full impacts remain poorly understood due to the difficulty of manipulating pCO 2 at the ecosystem level to mimic realistic fluctuations that occur on a number of different timescales. It is especially unclear how quickly communities at various stages of development respond to intermediate-scale pCO 2 change and, if high pCO 2 is relieved mid-succession, whether past acidification effects persist, are reversed by alleviation of pCO 2 stress, or are worsened by departures from prior high pCO 2 conditions to which organisms had acclimatized. Here, we used reciprocal transplant experiments along a shallow water volcanic pCO 2 gradient to assess the importance of the timing and duration of high pCO 2 exposure (i.e., discrete events at different stages of successional development vs. continuous exposure) on patterns of colonization and succession in a benthic fouling community. We show that succession at the acidified site was initially delayed (less community change by 8 weeks) but then caught up over the next 4 weeks. These changes in succession led to homogenization of communities maintained in or transplanted to acidified conditions, and altered community structure in ways that reflected both short- and longer-term acidification history. These community shifts are likely a result of interspecific variability in response to increased pCO 2 and changes in species interactions. High pCO 2 altered biofilm development, allowing serpulids to do best at the acidified site by the end of the experiment, although early (pretransplant) negative effects of pCO 2 on recruitment of these worms were still detectable. The ascidians Diplosoma sp. and Botryllus sp. settled later and were more tolerant to acidification. Overall, transient and persistent acidification-driven changes in the biofouling community, via both past and more recent exposure, could have important

Community structural characteristics and the adoption of fluoridation.

PubMed Central

Smith, R A

1981-01-01

A study of community structural characteristics associated with fluoridation outcomes was conducted in 47 communities. A three-part outcome distinction was utilized: communities never having publicly considered the fluoridation issue, those rejecting it, and those accepting it. The independent variables reflect the complexity of the community social and economic structure, social integration, and the centralization of authority. Results of mean comparisons show statistically significant differences between the three outcome types on the independent variables. A series of discriminant analyses provides furtheor evidence of how the independent variables are associated with each outcome type. Non-considering communities are shown to be low in complexity, and high in social integration and the centralization of governmental authority. Rejecters are shown to be high in complexity, but low in social integration and centralized authority. Adopters are relatively high on all three sets of variables. Theretical reasoning is provided to support the hypothesis and why these results are expected. The utility of these results and structural explanations in general are discussed, especially for public/environmental health planning and political activities. PMID:7258427

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

PubMed Central

Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

1999-01-01

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the

Shifts in community size structure drive temperature invariance of secondary production in a stream-warming experiment.

PubMed

Nelson, Daniel; Benstead, Jonathan P; Huryn, Alexander D; Cross, Wyatt F; Hood, James M; Johnson, Philip W; Junker, James R; Gíslason, Gísli M; Ólafsson, Jón S

2017-07-01

A central question at the interface of food-web and climate change research is how secondary production, or the formation of heterotroph biomass over time, will respond to rising temperatures. The metabolic theory of ecology (MTE) hypothesizes the temperature-invariance of secondary production, driven by matched and opposed forces that reduce biomass of heterotrophs while increasing their biomass turnover rate (production : biomass, or P:B) with warming. To test this prediction at the whole community level, we used a geothermal heat exchanger to experimentally warm a stream in southwest Iceland by 3.8°C for two years. We quantified invertebrate community biomass, production, and P : B in the experimental stream and a reference stream for one year prior to warming and two years during warming. As predicted, warming had a neutral effect on community production, but this result was not driven by opposing effects on community biomass and P:B. Instead, warming had a positive effect on both the biomass and production of larger-bodied, slower-growing taxa (e.g., larval black flies, dipteran predators, snails) and a negative effect on small-bodied taxa with relatively high growth rates (e.g., ostracods, larval chironomids). We attribute these divergent responses to differences in thermal preference between small- vs. large-bodied taxa. Although metabolic demand vs. resource supply must ultimately constrain community production, our results highlight the potential for idiosyncratic community responses to warming, driven by variation in thermal preference and body size within regional species pools. © 2017 by the Ecological Society of America.

Influence of ocean acidification on plankton community structure during a winter-to-summer succession: An imaging approach indicates that copepods can benefit from elevated CO2 via indirect food web effects

PubMed Central

Taucher, Jan; Haunost, Mathias; Boxhammer, Tim; Bach, Lennart T.; Algueró-Muñiz, María; Riebesell, Ulf

2017-01-01

Plankton communities play a key role in the marine food web and are expected to be highly sensitive to ongoing environmental change. Oceanic uptake of anthropogenic carbon dioxide (CO2) causes pronounced shifts in marine carbonate chemistry and a decrease in seawater pH. These changes–summarized by the term ocean acidification (OA)–can significantly affect the physiology of planktonic organisms. However, studies on the response of entire plankton communities to OA, which also include indirect effects via food-web interactions, are still relatively rare. Thus, it is presently unclear how OA could affect the functioning of entire ecosystems and biogeochemical element cycles. In this study, we report from a long-term in situ mesocosm experiment, where we investigated the response of natural plankton communities in temperate waters (Gullmarfjord, Sweden) to elevated CO2 concentrations and OA as expected for the end of the century (~760 μatm pCO2). Based on a plankton-imaging approach, we examined size structure, community composition and food web characteristics of the whole plankton assemblage, ranging from picoplankton to mesozooplankton, during an entire winter-to-summer succession. The plankton imaging system revealed pronounced temporal changes in the size structure of the copepod community over the course of the plankton bloom. The observed shift towards smaller individuals resulted in an overall decrease of copepod biomass by 25%, despite increasing numerical abundances. Furthermore, we observed distinct effects of elevated CO2 on biomass and size structure of the entire plankton community. Notably, the biomass of copepods, dominated by Pseudocalanus acuspes, displayed a tendency towards elevated biomass by up to 30–40% under simulated ocean acidification. This effect was significant for certain copepod size classes and was most likely driven by CO2-stimulated responses of primary producers and a complex interplay of trophic interactions that allowed this

Virality Prediction and Community Structure in Social Networks

NASA Astrophysics Data System (ADS)

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-08-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications.

Virality Prediction and Community Structure in Social Networks

PubMed Central

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-01-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications. PMID:23982106

Virality prediction and community structure in social networks.

PubMed

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-01-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications.

The synergetic effects of turbulence and turbidity on the zooplankton community structure in large, shallow Lake Taihu.

PubMed

Zhou, Jian; Qin, Boqiang; Han, Xiaoxia

2018-01-01

Climate change is predicted to influence the heat budget of aquatic ecosystems and, in turn, affect the stability of the water column leading to increased turbulence coupled with enhanced turbidity. However, the synergetic effects of turbulence and turbidity on zooplankton community structure remain to be understood in large, shallow lakes. To determine the possible synergetic effects of these factors on zooplankton communities, a 15-day mesocosm experiment was carried out and tested under four turbulence and turbidity regimes namely control (ɛ = 0, 7.6 ± 4.2 NTU), low (ɛ = 6.01 × 10 -8  m 2  s -3 , 19.4 ± 8.6 NTU), medium (ɛ = 2.95 × 10 -5  m 2  s -3 , 55.2 ± 14.4 NTU), and high (ɛ = 2.39 × 10 -4  m 2  s -3 , 741.6 ± 105.2 NTU) conditions, which were comparable to the natural conditions in Lake Taihu. Results clearly showed the negative effects of turbulence and turbidity on zooplankton survival, which also differed among taxa. Specifically, increased turbulence and turbidity levels influenced the competition among zooplankton species, which resulted to the shift from being large body crustacean-dominated (copepods and cladocerans) to rotifer-dominated community after 3 days. The shift could be associated with the decrease in vulnerability of crustaceans in such environments. Our findings suggested that changes in the level of both turbidity and turbulence in natural aquatic systems would have significant repercussions on the zooplankton communities, which could contribute to the better understanding of community and food web dynamics in lake ecosystems exposed to natural mixing/disturbances.

Lamb shifts and hyperfine structure in 6Li+ and 7Li+: Theory and experiment

NASA Astrophysics Data System (ADS)

Riis, E.; Sinclair, A. G.; Poulsen, O.; Drake, G. W. F.; Rowley, W. R. C.; Levick, A. P.

1994-01-01

High-precision laser-resonance measurements accurate to +/-0.5 MHz or better are reported for transitions among the 1s2s 3S1-1s2p 3PJ hyperfine manifolds for each of J=0, 1, and 2 in both 6Li+ and 7Li+. A detailed analysis of hyperfine structure is performed for both the S and P states, using newly calculated values for the magnetic dipole and electric quadrupole coupling constants, and the hyperfine shifts subtracted from the measurements. The resulting transition frequencies are then analyzed on three different levels. First, the isotope shifts in the fine-structure splittings are calculated from the relativistic reduced mass and recoil terms in the Breit interaction, and compared with experiment at the +/-0.5-MHz level of accuracy. This comparison is particularly significant because J-independent theoretical uncertainties reduce through cancellation to the +/-0.01-MHz level. Second, the isotope shifts in the full transition frequencies are used to deduce the difference in rms nuclear radii. The result is Rrms(6Li)-Rrms(7Li)=0.15+/-0.01 fm, in agreement with nuclear scattering data, but with substantially improved accuracy. Third, high-precision calculations of the low-order non-QED contributions to the transition frequencies are subtracted from the measurements to obtain the residual QED shifts. The isotope-averaged and spin-averaged effective shift for 7Li+ is 37 429.40+/-0.39 MHz, with an additional uncertainty of +/-1.5 MHz due to finite nuclear size corrections. The accuracy of 11 parts per million is the best two-electron Lamb shift measurement in the literature, and is comparable to the accuracies achieved in hydrogen. Theoretical contributions to the two-electron Lamb shift are discussed, including terms of order (αZ)4 recently obtained by Chen, Cheng, and Johnson [Phys. Rev. A 47, 3692 (1993)], and the results used to extract a QED shift for the 2 3S1 state. The result of 30 254+/-12 MHz is shown to be in good accord with theory (30 250+/-30 MHz) when

Distributed network management in the flat structured mobile communities

NASA Astrophysics Data System (ADS)

Balandina, Elena

2005-10-01

Delivering proper management into the flat structured mobile communities is crucial for improving users experience and increase applications diversity in mobile networks. The available P2P applications do application-centric management, but it cannot replace network-wide management, especially when a number of different applications are used simultaneously in the network. The network-wide management is the key element required for a smooth transition from standalone P2P applications to the self-organizing mobile communities that maintain various services with quality and security guaranties. The classical centralized network management solutions are not applicable in the flat structured mobile communities due to the decentralized nature and high mobility of the underlying networks. Also the basic network management tasks have to be revised taking into account specialties of the flat structured mobile communities. The network performance management becomes more dependent on the current nodes' context, which also requires extension of the configuration management functionality. The fault management has to take into account high mobility of the network nodes. The performance and accounting managements are mainly targeted in maintain an efficient and fair access to the resources within the community, however they also allow unbalanced resource use of the nodes that explicitly permit it, e.g. as a voluntary donation to the community or due to the profession (commercial) reasons. The security management must implement the new trust models, which are based on the community feedback, professional authorization, and a mix of both. For fulfilling these and another specialties of the flat structured mobile communities, a new network management solution is demanded. The paper presents a distributed network management solution for flat structured mobile communities. Also the paper points out possible network management roles for the different parties (e.g. operators, service

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

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

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

Experimental sulfate amendment alters peatland bacterial community structure.

PubMed

Strickman, R J S; Fulthorpe, R R; Coleman Wasik, J K; Engstrom, D R; Mitchell, C P J

2016-10-01

As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group. Copyright © 2016 Elsevier B.V. All rights reserved.

Response of the microbial community structure of biofilms to ferric iron in microbial fuel cells.

PubMed

Liu, Qian; Yang, Yang; Mei, Xiaoxue; Liu, Bingfeng; Chen, Chuan; Xing, Defeng

2018-08-01

Ferric iron can affect the current generation of microbial electrochemical system (MES); however, how it influences microbial biofilm formation and metabolic activity has not been reported. Here, we describe the response of microbial electrode biofilm communities to insoluble ferric iron (Fe 3+ ) at different concentrations in microbial fuel cells (MFCs). Insoluble ferric iron (200μM) improved electrochemical activity of the MFCs microbial biofilms during start-up and resulted in a higher maximum power density of 0.95W/m 2 , compared with the control (0.76W/m 2 ), 500μM Fe 3+ (0.83W/m 2 ), 1000μM Fe 3+ (0.73W/m 2 ), and 2000μM Fe 3+ (0.59W/m 2 ) treatments. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that the predominant populations in the anode biofilms of the MFCs belonged to Geobacter, with relative abundance of 66-75%. Microbial cathode biofilm communities were more susceptible to Fe 3+ , as an obvious shift in the cathode biofilm community structures occurred as Fe 3+ concentration was increased. The most predominant populations in the MFC cathode biofilms without Fe 3+ and with 200μM Fe 3+ were affiliated with Thauera (46% and 35%), whereas no absolutely predominant populations were present in the MFC cathode biofilm with 1000μM Fe 3+ . The results demonstrate that a low concentration of Fe 3+ facilitated the power output of MFCs and shaped community structures of the electrode biofilm. Copyright © 2018 Elsevier B.V. All rights reserved.

A new hierarchical method to find community structure in networks

NASA Astrophysics Data System (ADS)

Saoud, Bilal; Moussaoui, Abdelouahab

2018-04-01

Community structure is very important to understand a network which represents a context. Many community detection methods have been proposed like hierarchical methods. In our study, we propose a new hierarchical method for community detection in networks based on genetic algorithm. In this method we use genetic algorithm to split a network into two networks which maximize the modularity. Each new network represents a cluster (community). Then we repeat the splitting process until we get one node at each cluster. We use the modularity function to measure the strength of the community structure found by our method, which gives us an objective metric for choosing the number of communities into which a network should be divided. We demonstrate that our method are highly effective at discovering community structure in both computer-generated and real-world network data.

Benthic macroinvertebrate community structure in 20 streams of varying pH and humic content.

PubMed

Kullberg, A

1992-01-01

The structure of stream benthic macroinvertebrate communities in relation to pH and humic content was studied in 20 second and third-order forest streams in southern Sweden. Streams varied in pH from 4.2 to 8.0, and in humic content from a colour of 5 to 1200 mg Pt litre(-1). There was a positive relationship between pH and species richness, with a discontinuity occurring at pH approximately 5.7. At pH > 5.7, species richness decreased with increasing colour. At pH < 5.7 there was a positive correlation between species richness and humic concentration up to a colour of about 200-300 mg Pt litre(-1). this may be explained by high concentrations, 0.4-0.9 mg litre(-1), of labile monomeric Al occurring in the low coloured acid streams. In streams with a colour > 200 mg Pt litre(-1) labile monomeric Al was less than 0.2 mg litre(-1). There was no significant change in species richness above this threshold, but a shift in species composition towards a dominance of Plecoptera and Chironomidae. This threshold model seems to explain the observed differences in stream benthic community structure better than a simple linear relationship with pH or humic content.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

PubMed Central

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-01-01

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

PubMed

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Bioaugmentation of Hydrogenispora ethanolica LX-B affects hydrogen production through altering indigenous bacterial community structure.

PubMed

Yang, Zhiman; Guo, Rongbo; Shi, Xiaoshuang; He, Shuai; Wang, Lin; Dai, Meng; Qiu, Yanling; Dang, Xiaoxiao

2016-07-01

Bioaugmentation can facilitate hydrogen production from complex organic substrates, but it still is unknown how indigenous microbial communities respond to the added bacteria. Here, using a Hydrogenispora ethanolica LX-B (named as LX-B) bioaugmentation experiments, the distribution of metabolites and the responses of indigenous bacterial communities were investigated via batch cultivation (BC) and repeated batch cultivation (RBC). In BC the LX-B/sludge ratio of 0.12 achieved substantial high hydrogen yield, which was over twice that of control. In RBC one-time bioaugmentation and repeated batch bioaugmentation of LX-B resulted in the hydrogen yield that was average 1.2-fold and 0.8-fold higher than that in control, respectively. This improved hydrogen production performance mainly benefited from a shift in composition of the indigenous bacterial community caused by LX-B bioaugmentation. The findings represented an important step in understanding the relationship between bioaugmentation, a shift in bacterial communities, and altered bioreactor performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Locating Structural Centers: A Density-Based Clustering Method for Community Detection

PubMed Central

Liu, Gongshen; Li, Jianhua; Nees, Jan P.

2017-01-01

Uncovering underlying community structures in complex networks has received considerable attention because of its importance in understanding structural attributes and group characteristics of networks. The algorithmic identification of such structures is a significant challenge. Local expanding methods have proven to be efficient and effective in community detection, but most methods are sensitive to initial seeds and built-in parameters. In this paper, we present a local expansion method by density-based clustering, which aims to uncover the intrinsic network communities by locating the structural centers of communities based on a proposed structural centrality. The structural centrality takes into account local density of nodes and relative distance between nodes. The proposed algorithm expands a community from the structural center to the border with a single local search procedure. The local expanding procedure follows a heuristic strategy as allowing it to find complete community structures. Moreover, it can identify different node roles (cores and outliers) in communities by defining a border region. The experiments involve both on real-world and artificial networks, and give a comparison view to evaluate the proposed method. The result of these experiments shows that the proposed method performs more efficiently with a comparative clustering performance than current state of the art methods. PMID:28046030

Optimal community structure for social contagions

NASA Astrophysics Data System (ADS)

Su, Zhen; Wang, Wei; Li, Lixiang; Stanley, H. Eugene; Braunstein, Lidia A.

2018-05-01

Community structure is an important factor in the behavior of real-world networks because it strongly affects the stability and thus the phase transition order of the spreading dynamics. We here propose a reversible social contagion model of community networks that includes the factor of social reinforcement. In our model an individual adopts a social contagion when the number of received units of information exceeds its adoption threshold. We use mean-field approximation to describe our proposed model, and the results agree with numerical simulations. The numerical simulations and theoretical analyses both indicate that there is a first-order phase transition in the spreading dynamics, and that a hysteresis loop emerges in the system when there is a variety of initially adopted seeds. We find an optimal community structure that maximizes spreading dynamics. We also find a rich phase diagram with a triple point that separates the no-diffusion phase from the two diffusion phases.

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time

PubMed Central

Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

2016-01-01

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil. PMID:27187071

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

PubMed

Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

2016-01-01

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

Latitudinal trends and temporal shifts in the catch composition of bottom trawls conducted on the eastern Bering Sea shelf

NASA Astrophysics Data System (ADS)

Stevenson, Duane E.; Lauth, Robert R.

2012-06-01

Latitudinal species diversity gradients are well known in both terrestrial and aquatic ecosystems throughout the world. However, trends in relative abundance and other shifts in community structure with latitude, which can be more sensitive to environmental shifts such as climate change, have received less attention. Here we investigate latitudinal trends in the seafloor community of the eastern Bering Sea using catches of fishes and epibenthic invertebrates in bottom trawl surveys conducted from 1982 to 2010. Our results indicate that the overall biomass of the epibenthic community declines with increasing latitude in the eastern Bering Sea. This latitudinal trend is primarily driven by declining fish catches in the northern Bering Sea, which in turn reflects changes in the structure of the fish community. The fish fauna in northern latitudes is increasingly dominated by gadids, though the species composition of the gadid fauna also changes with latitude, with smaller species becoming more common in the north. The biomass of the invertebrate megafauna remains relatively consistent throughout the eastern Bering Sea, but invertebrates make up a larger proportion of the catch in bottom trawls conducted at higher latitudes. The epibenthic invertebrate megafauna in the eastern Bering Sea is composed primarily of sea stars (Asteriidae) and oregoniid crabs (Chionoecetes and Hyas), though no clear latitudinal trends in the invertebrate community are evident. Limited trawl data from the eastern Chukchi Sea indicate that the fish community farther north is even more heavily dominated by gadids, and the epibenthic invertebrate community is dominated by asteriid sea stars. Temperature data from bottom trawl surveys in the southeastern Bering Sea over the past decade indicate that there was a distinct temperature shift around 2005, and the relatively warm years of 2001-2005 were followed by five relatively cold years. This shift in the summer temperature regime of the Bering

Seasonal changes in community composition and trophic structure of fish populations of five salt marshes along the Essex coastline, United Kingdom

NASA Astrophysics Data System (ADS)

Green, Benjamin C.; Smith, David J.; Earley, Sarah E.; Hepburn, Leanne J.; Underwood, Graham J. C.

2009-11-01

European intertidal salt marshes are important nursery sites for juvenile fish and crustaceans. Due to the increasing threat of habitat loss, the seasonal changes of salt marsh fish communities need to be understood in order to appreciate the ecological and economic importance of the saltmarsh habitat. This study was the first in Great Britain to investigate the seasonal changes of salt marsh fish communities and the variation in community structure between closely located marsh habitats. Between February 2007 and March 2008, five marshes on three estuaries of the Essex coastline were sampled using flume nets to block off intertidal creeks at high tide. Fourteen fish species were caught. The community overall was dominated by three species that made up 91.6% of the total catch: the common goby Pomatoschistus microps (46.2% of the total catch), juvenile herring Clupea harengus (24.3%), and juvenile and larval sea bass Dicentrarchus labrax (21.2%). Cluster analysis demonstrated clear seasonal patterns, with some community structures unique to specific marshes or estuaries. The marsh fish community shifts from a highly diverse community during spring, to a community dominated by D. labrax and P. microps in autumn, and low diversity during winter months. Gravimetric stomach content analysis of fish community identified three main trophic guilds; macroinvertivores, planktivores and omnivores. The macroinvertivore feeding guild contained D. labrax and P. microps, the two most frequently occurring species. This investigation demonstrates the importance of British salt marshes as nursery habitats for commercial fish species.

Community structure detection based on the neighbor node degree information

NASA Astrophysics Data System (ADS)

Tang, Li-Ying; Li, Sheng-Nan; Lin, Jian-Hong; Guo, Qiang; Liu, Jian-Guo

2016-11-01

Community structure detection is of great significance for better understanding the network topology property. By taking into account the neighbor degree information of the topological network as the link weight, we present an improved Nonnegative Matrix Factorization (NMF) method for detecting community structure. The results for empirical networks show that the largest improved ratio of the Normalized Mutual Information value could reach 63.21%. Meanwhile, for synthetic networks, the highest Normalized Mutual Information value could closely reach 1, which suggests that the improved method with the optimal λ can detect the community structure more accurately. This work is helpful for understanding the interplay between the link weight and the community structure detection.

Modelling Vulnerability and Range Shifts in Ant Communities Responding to Future Global Warming in Temperate Forests

PubMed Central

Kim, Sung-Soo; Chun, Jung Hwa; Park, Young-Seuk

2016-01-01

Global warming is likely leading to species’ distributional shifts, resulting in changes in local community compositions and diversity patterns. In this study, we applied species distribution models to evaluate the potential impacts of temperature increase on ant communities in Korean temperate forests, by testing hypotheses that 1) the risk of extinction of forest ant species would increase over time, and 2) the changes in species distribution ranges could drive upward movements of ant communities and further alter patterns of species richness. We sampled ant communities at 335 evenly distributed sites across South Korea and modelled the future distribution range for each species using generalized additive models. To account for spatial autocorrelation, autocovariate regressions were conducted prior to generalized additive models. Among 29 common ant species, 12 species were estimated to shrink their suitable geographic areas, whereas five species would benefit from future global warming. Species richness was highest at low altitudes in the current period, and it was projected to be highest at the mid-altitudes in the 2080s, resulting in an upward movement of 4.9 m yr−1. This altered the altitudinal pattern of species richness from a monotonic-decrease curve (common in temperate regions) to a bell-shaped curve (common in tropical regions). Overall, ant communities in temperate forests are vulnerable to the on-going global warming and their altitudinal movements are similar to other faunal communities. PMID:27504632

Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure.

PubMed

Arpino, James A J; Reddington, Samuel C; Halliwell, Lisa M; Rizkallah, Pierre J; Jones, D Dafydd

2014-06-10

Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFP(G4Δ)) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFP(G4Δ) retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFP(G4Δ) structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Soil shapes community structure through fire.

PubMed

Ojeda, Fernando; Pausas, Juli G; Verdú, Miguel

2010-07-01

Recurrent wildfires constitute a major selecting force in shaping the structure of plant communities. At the regional scale, fire favours phenotypic and phylogenetic clustering in Mediterranean woody plant communities. Nevertheless, the incidence of fire within a fire-prone region may present strong variations at the local, landscape scale. This study tests the prediction that woody communities on acid, nutrient-poor soils should exhibit more pronounced phenotypic and phylogenetic clustering patterns than woody communities on fertile soils, as a consequence of their higher flammability and, hence, presumably higher propensity to recurrent fire. Results confirm the predictions and show that habitat filtering driven by fire may be detected even in local communities from an already fire-filtered regional flora. They also provide a new perspective from which to consider a preponderant role of fire as a key evolutionary force in acid, infertile Mediterranean heathlands.

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

PubMed Central

Liu, Huiying; Mi, Zhaorong; Lin, Li; Wang, Yonghui; Zhang, Zhenhua; Zhang, Fawei; Wang, Hao; Liu, Lingli; Zhu, Biao; Cao, Guangmin; Zhao, Xinquan; Sanders, Nathan J.; Reich, Peter B.

2018-01-01

The structure and function of alpine grassland ecosystems, including their extensive soil carbon stocks, are largely shaped by temperature. The Tibetan Plateau in particular has experienced significant warming over the past 50 y, and this warming trend is projected to intensify in the future. Such climate change will likely alter plant species composition and net primary production (NPP). Here we combined 32 y of observations and monitoring with a manipulative experiment of temperature and precipitation to explore the effects of changing climate on plant community structure and ecosystem function. First, long-term climate warming from 1983 to 2014, which occurred without systematic changes in precipitation, led to higher grass abundance and lower sedge abundance, but did not affect aboveground NPP. Second, an experimental warming experiment conducted over 4 y had no effects on any aspect of NPP, whereas drought manipulation (reducing precipitation by 50%), shifted NPP allocation belowground without affecting total NPP. Third, both experimental warming and drought treatments, supported by a meta-analysis at nine sites across the plateau, increased grass abundance at the expense of biomass of sedges and forbs. This shift in functional group composition led to deeper root systems, which may have enabled plant communities to acquire more water and thus stabilize ecosystem primary production even with a changing climate. Overall, our study demonstrates that shifting plant species composition in response to climate change may have stabilized primary production in this high-elevation ecosystem, but it also caused a shift from aboveground to belowground productivity. PMID:29666319

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

PubMed

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

2018-04-17

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

Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments

DOE PAGES

Christensen, Geoff A.; Somenahally, Anil C.; Moberly, James G.; ...

2017-11-17

Neurotoxic methylmercury (MeHg) is produced by anaerobic Bacteria and Archaea possessing the genes hgcAB, but it is unknown how organic substrate and electron acceptor availability impacts the distribution and abundance of these organisms. We evaluated the impact of organic substrate amendments on mercury (Hg) methylation rates, microbial community structure, and the distribution of hgcAB + microbes with sediments. Sediment slurries were amended with short-chain fatty acids, alcohols, or a polysaccharide. Minimal increases in MeHg were observed following lactate, ethanol, and methanol amendments, while a significant decrease (~70%) was observed with cellobiose incubations. Postincubation, microbial diversity was assessed via 16S rRNAmore » amplicon sequencing. The presence of hgcAB + organisms was assessed with a broad-range degenerate PCR primer set for both genes, while the presence of microbes in each of the three dominant clades of methylators (Deltaproteobacteria, Firmicutes, and methanogenic Archaea) was measured with clade-specific degenerate hgcA quantitative PCR (qPCR) primer sets. The predominant microorganisms in unamended sediments consisted of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Clade-specific qPCR identified hgcA + Deltaproteobacteria and Archaea in all sites but failed to detect hgcA + Firmicutes. Cellobiose shifted the communities in all samples to ~90% non-hgcAB-containing Firmicutes (mainly Bacillus spp. and Clostridium spp.). These results suggest that either expression of hgcAB is downregulated or, more likely given the lack of 16S rRNA gene presence after cellobiose incubation, Hg-methylating organisms are largely outcompeted by cellobiose degraders or degradation products of cellobiose. These results represent a step toward understanding and exploring simple methodologies for controlling MeHg production in the environment. Methylmercury (MeHg) is a neurotoxin produced by microorganisms that bioacummulates in the

Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments

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

Christensen, Geoff A.; Somenahally, Anil C.; Moberly, James G.

Neurotoxic methylmercury (MeHg) is produced by anaerobic Bacteria and Archaea possessing the genes hgcAB, but it is unknown how organic substrate and electron acceptor availability impacts the distribution and abundance of these organisms. We evaluated the impact of organic substrate amendments on mercury (Hg) methylation rates, microbial community structure, and the distribution of hgcAB + microbes with sediments. Sediment slurries were amended with short-chain fatty acids, alcohols, or a polysaccharide. Minimal increases in MeHg were observed following lactate, ethanol, and methanol amendments, while a significant decrease (~70%) was observed with cellobiose incubations. Postincubation, microbial diversity was assessed via 16S rRNAmore » amplicon sequencing. The presence of hgcAB + organisms was assessed with a broad-range degenerate PCR primer set for both genes, while the presence of microbes in each of the three dominant clades of methylators (Deltaproteobacteria, Firmicutes, and methanogenic Archaea) was measured with clade-specific degenerate hgcA quantitative PCR (qPCR) primer sets. The predominant microorganisms in unamended sediments consisted of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Clade-specific qPCR identified hgcA + Deltaproteobacteria and Archaea in all sites but failed to detect hgcA + Firmicutes. Cellobiose shifted the communities in all samples to ~90% non-hgcAB-containing Firmicutes (mainly Bacillus spp. and Clostridium spp.). These results suggest that either expression of hgcAB is downregulated or, more likely given the lack of 16S rRNA gene presence after cellobiose incubation, Hg-methylating organisms are largely outcompeted by cellobiose degraders or degradation products of cellobiose. These results represent a step toward understanding and exploring simple methodologies for controlling MeHg production in the environment. Methylmercury (MeHg) is a neurotoxin produced by microorganisms that bioacummulates in the

Taxonomies of networks from community structure

PubMed Central

Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2014-01-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: they can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi. PMID:23030977

Taxonomies of networks from community structure

NASA Astrophysics Data System (ADS)

Onnela, Jukka-Pekka; Fenn, Daniel J.; Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2012-09-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: They can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary

Femtosecond-pulse inscription of fiber Bragg gratings with single or multiple phase-shifts in the structure

NASA Astrophysics Data System (ADS)

Wolf, Alexey; Dostovalov, Alexandr; Skvortsov, Mikhail; Raspopin, Kirill; Parygin, Alexandr; Babin, Sergey

2018-05-01

In this work, long high-quality fiber Bragg gratings with phase shifts in the structure are inscribed directly in the optical fiber by point-by-point technique using femtosecond laser pulses. Phase shifts are introduced during the inscription process with a piezoelectric actuator, which rapidly shifts the fiber along the direction of its movement in a chosen point of the grating with a chosen shift value. As examples, single and double π phase shifts are introduced in fiber Bragg gratings with a length up to 34 mm in passive fibers, which provide corresponding transmission peaks with bandwidth less than 1 pm. It is shown that 37 mm π -phase-shifted grating inscribed in an active Er-doped fiber forms high-quality DFB laser cavity generating single-frequency radiation at 1550 nm with bandwidth of 20 kHz and signal-to-noise ratio of >70 dB. The inscription technique has a high degree of performance and flexibility and can be easily implemented in fibers of various types.

Changes in predator community structure shifts the efficacy of two warning signals in Arctiid moths.

PubMed

Nokelainen, Ossi; Valkonen, Janne; Lindstedt, Carita; Mappes, Johanna

2014-05-01

Polymorphism in warning coloration is puzzling because positive frequency-dependent selection by predators is expected to promote monomorphic warning signals in defended prey. We studied predation on the warning-coloured wood tiger moth (Parasemia plantaginis) by using artificial prey resembling white and yellow male colour morphs in five separate populations with different naturally occurring morph frequencies. We tested whether predation favours one of the colour morphs over the other and whether that is influenced either by local, natural colour morph frequencies or predator community composition. We found that yellow specimens were attacked less than white ones regardless of the local frequency of the morphs indicating frequency-independent selection, but predation did depend on predator community composition: yellows suffered less attacks when Paridae were abundant, whereas whites suffered less attacks when Prunellidae were abundant. Our results suggest that spatial heterogeneity in predator community composition can generate a geographical mosaic of selection facilitating the evolution of polymorphic warning signals. This is the first time this mechanism gains experimental support. Altogether, this study sheds light on the evolution of adaptive coloration in heterogeneous environments. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Community College Faculty: Making the Paradigm Shift.

ERIC Educational Resources Information Center

Van Ast, John

1999-01-01

Discusses the need for paradigm shifts during the next decade that address the following challenges: (1) the wider range of student ability and mastery; (2) high attrition rates; and (3) differing and often contradicting perceptions of students, faculty, and administration. Contains 180 references. (TGO)

Warming shifts top-down and bottom-up control of pond food web structure and function

PubMed Central

Shurin, Jonathan B.; Clasen, Jessica L.; Greig, Hamish S.; Kratina, Pavel; Thompson, Patrick L.

2012-01-01

The effects of global and local environmental changes are transmitted through networks of interacting organisms to shape the structure of communities and the dynamics of ecosystems. We tested the impact of elevated temperature on the top-down and bottom-up forces structuring experimental freshwater pond food webs in western Canada over 16 months. Experimental warming was crossed with treatments manipulating the presence of planktivorous fish and eutrophication through enhanced nutrient supply. We found that higher temperatures produced top-heavy food webs with lower biomass of benthic and pelagic producers, equivalent biomass of zooplankton, zoobenthos and pelagic bacteria, and more pelagic viruses. Eutrophication increased the biomass of all organisms studied, while fish had cascading positive effects on periphyton, phytoplankton and bacteria, and reduced biomass of invertebrates. Surprisingly, virus biomass was reduced in the presence of fish, suggesting the possibility for complex mechanisms of top-down control of the lytic cycle. Warming reduced the effects of eutrophication on periphyton, and magnified the already strong effects of fish on phytoplankton and bacteria. Warming, fish and nutrients all increased whole-system rates of net production despite their distinct impacts on the distribution of biomass between producers and consumers, plankton and benthos, and microbes and macrobes. Our results indicate that warming exerts a host of indirect effects on aquatic food webs mediated through shifts in the magnitudes of top-down and bottom-up forcing. PMID:23007089

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Functional and phylogenetic structure of island bird communities.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zeng, Di; Baselga, Andrés; Zhao, Yuhao; Li, Jiaqi; Wu, Yiru; Wang, Siyu; Ding, Ping

2017-05-01

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental

Seasonal changes in the assembly mechanisms structuring tropical fish communities.

PubMed

Fitzgerald, Daniel B; Winemiller, Kirk O; Sabaj Pérez, Mark H; Sousa, Leandro M

2017-01-01

Despite growing interest in trait-based approaches to community assembly, little attention has been given to seasonal variation in trait distribution patterns. Mobile animals can rapidly mediate influences of environmental factors and species interactions through dispersal, suggesting that the relative importance of different assembly mechanisms can vary over short time scales. This study analyzes seasonal changes in functional trait distributions of tropical fishes in the Xingu River, a major tributary of the Amazon with large predictable temporal variation in hydrologic conditions and species density. Comparison of observed functional diversity revealed that species within wet-season assemblages were more functionally similar than those in dry-season assemblages. Further, species within wet-season assemblages were more similar than random expectations based on null model predictions. Higher functional richness within dry season communities is consistent with increased niche complementarity during the period when fish densities are highest and biotic interactions should be stronger; however, null model tests suggest that stochastic factors or a combination of assembly mechanisms influence dry-season assemblages. These results demonstrate that the relative influence of community assembly mechanisms can vary seasonally in response to changing abiotic conditions, and suggest that studies attempting to infer a single dominant mechanism from functional patterns may overlook important aspects of the assembly process. During the prolonged flood pulse of the wet season, expanded habitat and lower densities of aquatic organisms likely reduce the influence of competition and predation. This temporal shift in the influence of different assembly mechanisms, rather than any single mechanism, may play a large role in maintaining the structure and diversity of tropical rivers and perhaps other dynamic and biodiverse systems. © 2016 by the Ecological Society of America.

Pressure-Induced Structural Evolution and Band Gap Shifts of Organometal Halide Perovskite-Based Methylammonium Lead Chloride.

PubMed

Wang, Lingrui; Wang, Kai; Xiao, Guanjun; Zeng, Qiaoshi; Zou, Bo

2016-12-15

Organometal halide perovskites are promising materials for optoelectronic devices. Further development of these devices requires a deep understanding of their fundamental structure-property relationships. The effect of pressure on the structural evolution and band gap shifts of methylammonium lead chloride (MAPbCl 3 ) was investigated systematically. Synchrotron X-ray diffraction and Raman experiments provided structural information on the shrinkage, tilting distortion, and amorphization of the primitive cubic unit cell. In situ high pressure optical absorption and photoluminescence spectra manifested that the band gap of MAPbCl 3 could be fine-tuned to the ultraviolet region by pressure. The optical changes are correlated with pressure-induced structural evolution of MAPbCl 3 , as evidenced by band gap shifts. Comparisons between Pb-hybrid perovskites and inorganic octahedra provided insights on the effects of halogens on pressure-induced transition sequences of these compounds. Our results improve the understanding of the structural and optical properties of organometal halide perovskites.

Covariance, correlation matrix, and the multiscale community structure of networks.

PubMed

Shen, Hua-Wei; Cheng, Xue-Qi; Fang, Bin-Xing

2010-07-01

Empirical studies show that real world networks often exhibit multiple scales of topological descriptions. However, it is still an open problem how to identify the intrinsic multiple scales of networks. In this paper, we consider detecting the multiscale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multiscale community structure through the translation and rotation transformations. It is proved that the covariance matrix is the unbiased version of the well-known modularity matrix. We then point out that the translation and rotation transformations fail to deal with the heterogeneous network, which is very common in nature and society. To address this problem, a correlation matrix is proposed through introducing the rescaling transformation into the covariance matrix. Extensive tests on real world and artificial networks demonstrate that the correlation matrix significantly outperforms the covariance matrix, identically the modularity matrix, as regards identifying the multiscale community structure of network. This work provides a novel perspective to the identification of community structure and thus various dimension reduction methods might be used for the identification of community structure. Through introducing the correlation matrix, we further conclude that the rescaling transformation is crucial to identify the multiscale community structure of network, as well as the translation and rotation transformations.

Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

DTIC Science & Technology

2004-09-01

Science 190 and Engineering DOCTORAL DISSERTATION Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj...Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj Massachusetts Institute of Technology Cambridge, Massachusetts 02139 and Woods Hole...Phylogenetic Structure of Two Complex Marine Microbial Communities. Ph.D. Thesis. MIT/WHOI, 2004-11. Approved for publication; distribution unlimited

Investigating Effects of Invasive Species on Plant Community Structure

ERIC Educational Resources Information Center

Franklin, Wilfred

2008-01-01

In this article, the author presents a field study project that explores factors influencing forest community structure and lifts the veil off of "plant blindness." This ecological study consists of three laboratories: (1) preliminary field trip to the study site; (2) plant survey; and (3) analyzing plant community structure with descriptive…

Community Structural Instability, Anomie, Imitation and Adolescent Suicidal Behavior

ERIC Educational Resources Information Center

Thorlindsson, Thorolfur; Bernburg, Jon Gunnar

2009-01-01

The current study examines the contextual effects of community structural characteristics, as well as the mediating role of key social mechanisms, on youth suicidal behavior in Iceland. We argue that the contextual influence of community structural instability on youth suicidal behavior should be mediated by weak attachment to social norms and…

Nutrient addition dramatically accelerates microbial community succession.

PubMed

Knelman, Joseph E; Schmidt, Steven K; Lynch, Ryan C; Darcy, John L; Castle, Sarah C; Cleveland, Cory C; Nemergut, Diana R

2014-01-01

The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients--important drivers of plant succession--affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession.

Nutrient Addition Dramatically Accelerates Microbial Community Succession

PubMed Central

Knelman, Joseph E.; Schmidt, Steven K.; Lynch, Ryan C.; Darcy, John L.; Castle, Sarah C.; Cleveland, Cory C.; Nemergut, Diana R.

2014-01-01

The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession. PMID:25050551

Urbanization drives community shifts towards thermophilic and dispersive species at local and landscape scales.

PubMed

Piano, Elena; De Wolf, Katrien; Bona, Francesca; Bonte, Dries; Bowler, Diana E; Isaia, Marco; Lens, Luc; Merckx, Thomas; Mertens, Daan; van Kerckvoorde, Marc; De Meester, Luc; Hendrickx, Frederik

2017-07-01

The increasing conversion of agricultural and natural areas to human-dominated urban landscapes is predicted to lead to a major decline in biodiversity worldwide. Two conditions that typically differ between urban environments and the surrounding landscape are increased temperature, and high patch isolation and habitat turnover rates. However, the extent and spatial scale at which these altered conditions shape biotic communities through selection and/or filtering on species traits are currently poorly understood. We sampled carabid beetles at 81 sites in Belgium using a hierarchically nested sampling design wherein three local-scale (200 × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 × 3 km) urbanization levels. First, we showed that communities sampled in the most urbanized locations and landscapes displayed a distinct species composition at both local and landscape scale. Second, we related community means of species-specific thermal preferences and dispersal capacity (based on European distribution and wing morphology, respectively) to the urbanization gradients. We showed that urban communities consisted on average of species with a preference for higher temperatures and with better dispersal capacities compared to rural communities. These shifts were caused by an increased number of species tolerating higher temperatures, a decreased richness of species with low thermal preference, and an almost complete depletion of species with very low-dispersal capacity in the most urbanized localities. Effects of urbanization were most clearly detected at the local scale, although more subtle effects could also be found at the scale of entire landscapes. Our results demonstrate that urbanization may fundamentally and consistently alter species composition by exerting a strong filtering effect on species dispersal characteristics and favouring replacement by warm-dwelling species. © 2017 John Wiley & Sons Ltd.

A framework for solving ill-structured community problems

NASA Astrophysics Data System (ADS)

Keller, William Cotesworth

A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

PubMed

Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

2017-12-01

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community structure in traffic zones based on travel demand

NASA Astrophysics Data System (ADS)

Sun, Li; Ling, Ximan; He, Kun; Tan, Qian

2016-09-01

Large structure in complex networks can be studied by dividing it into communities or modules. Urban traffic system is one of the most critical infrastructures. It can be abstracted into a complex network composed of tightly connected groups. Here, we analyze community structure in urban traffic zones based on the community detection method in network science. Spectral algorithm using the eigenvectors of matrices is employed. Our empirical results indicate that the traffic communities are variant with the travel demand distribution, since in the morning the majority of the passengers are traveling from home to work and in the evening they are traveling a contrary direction. Meanwhile, the origin-destination pairs with large number of trips play a significant role in urban traffic network's community division. The layout of traffic community in a city also depends on the residents' trajectories.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

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

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more importantmore » than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.« less

Too risky to settle: avian community structure changes in response to perceived predation risk on adults and offspring

USGS Publications Warehouse

Hua, Fangyuan; Fletcher, Robert J.; Sieving, Kathryn E.; Dorazio, Robert M.

2013-01-01

Predation risk is widely hypothesized as an important force structuring communities, but this potential force is rarely tested experimentally, particularly in terrestrial vertebrate communities. How animals respond to predation risk is generally considered predictable from species life-history and natural-history traits, but rigorous tests of these predictions remain scarce. We report on a large-scale playback experiment with a forest bird community that addresses two questions: (i) does perceived predation risk shape the richness and composition of a breeding bird community? And (ii) can species life-history and natural-history traits predict prey community responses to different types of predation risk? On 9 ha plots, we manipulated cues of three avian predators that preferentially prey on either adult birds or offspring, or both, throughout the breeding season. We found that increased perception of predation risk led to generally negative responses in the abundance, occurrence and/or detection probability of most prey species, which in turn reduced the species richness and shifted the composition of the breeding bird community. Species-level responses were largely predicted from the key natural-history trait of body size, but we did not find support for the life-history theory prediction of the relationship between species' slow/fast life-history strategy and their response to predation risk.

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment

PubMed Central

Lipsewers, Yvonne A.; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Meysman, Filip J. R.

2017-01-01

ABSTRACT Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae. The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H2S, S0, and S2O32−) and electron acceptors (O2 and NO3−) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.

PubMed

Lipsewers, Yvonne A; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Sinninghe Damsté, Jaap S; Meysman, Filip J R; Villanueva, Laura; Boschker, Henricus T S

2017-05-15

Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria ( Thiotrichales ) and Epsilonproteobacteria ( Campylobacterales ) were prevalent during spring, whereas Deltaproteobacteria ( Desulfobacterales ) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H 2 S, S 0 , and S 2 O 3 2- ) and electron acceptors (O 2 and NO 3 - ) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A

A Stochastic Model for Detecting Overlapping and Hierarchical Community Structure

PubMed Central

Cao, Xiaochun; Wang, Xiao; Jin, Di; Guo, Xiaojie; Tang, Xianchao

2015-01-01

Community detection is a fundamental problem in the analysis of complex networks. Recently, many researchers have concentrated on the detection of overlapping communities, where a vertex may belong to more than one community. However, most current methods require the number (or the size) of the communities as a priori information, which is usually unavailable in real-world networks. Thus, a practical algorithm should not only find the overlapping community structure, but also automatically determine the number of communities. Furthermore, it is preferable if this method is able to reveal the hierarchical structure of networks as well. In this work, we firstly propose a generative model that employs a nonnegative matrix factorization (NMF) formulization with a l2,1 norm regularization term, balanced by a resolution parameter. The NMF has the nature that provides overlapping community structure by assigning soft membership variables to each vertex; the l2,1 regularization term is a technique of group sparsity which can automatically determine the number of communities by penalizing too many nonempty communities; and hence the resolution parameter enables us to explore the hierarchical structure of networks. Thereafter, we derive the multiplicative update rule to learn the model parameters, and offer the proof of its correctness. Finally, we test our approach on a variety of synthetic and real-world networks, and compare it with some state-of-the-art algorithms. The results validate the superior performance of our new method. PMID:25822148

Change in atmospheric deposition during last half century and its impact on lichen community structure in Eastern Himalaya.

PubMed

Bajpai, Rajesh; Mishra, Seema; Dwivedi, Sanjay; Upreti, Dalip Kumar

2016-08-09

Climatic fluctuations largely affects species turnover and cause major shifts of terrestrial ecosystem. In the present study the five decade old herbarium specimens of lichens were compared with recent collection from Darjeeling district with respect to elements, PAHs accumulation and carbon isotope composition (δ(13)C) to explore the changes in climatic conditions and its impact on lichen flora. The δ(13)C has increased in recent specimens which is in contrast to the assumption that anthropogenic emission leads to δ(13)C depletion in air and increased carbon discrimination in flora. Study clearly demonstrated an increase in anthropogenic pollution and drastic decrease in precipitation while temperature showed abrupt changes during the past five decades resulting in significant change in lichen community structure. The Usneoid and Pertusorioid communities increased, while Physcioid and Cyanophycean decreased, drastically. Lobarian abolished from the study area, however, Calcicoid has been introduced in the recent past. Probably, post-industrial revolution, the abrupt changes in the environment has influenced CO2 diffusion and/C fixation of (lower) plants either as an adaptation strategy or due to toxicity of pollutants. Thus, the short term studies (≤5 decades) might reflect recent micro-environmental condition and lichen community structure can be used as model to study the global climate change.

Change in atmospheric deposition during last half century and its impact on lichen community structure in Eastern Himalaya

PubMed Central

Bajpai, Rajesh; Mishra, Seema; Dwivedi, Sanjay; Upreti, Dalip Kumar

2016-01-01

Climatic fluctuations largely affects species turnover and cause major shifts of terrestrial ecosystem. In the present study the five decade old herbarium specimens of lichens were compared with recent collection from Darjeeling district with respect to elements, PAHs accumulation and carbon isotope composition (δ13C) to explore the changes in climatic conditions and its impact on lichen flora. The δ13C has increased in recent specimens which is in contrast to the assumption that anthropogenic emission leads to δ13C depletion in air and increased carbon discrimination in flora. Study clearly demonstrated an increase in anthropogenic pollution and drastic decrease in precipitation while temperature showed abrupt changes during the past five decades resulting in significant change in lichen community structure. The Usneoid and Pertusorioid communities increased, while Physcioid and Cyanophycean decreased, drastically. Lobarian abolished from the study area, however, Calcicoid has been introduced in the recent past. Probably, post-industrial revolution, the abrupt changes in the environment has influenced CO2 diffusion and/C fixation of (lower) plants either as an adaptation strategy or due to toxicity of pollutants. Thus, the short term studies (≤5 decades) might reflect recent micro-environmental condition and lichen community structure can be used as model to study the global climate change. PMID:27502030

Projected shifts in copepod surface communities in the Mediterranean Sea under several climate change scenarios

NASA Astrophysics Data System (ADS)

Benedetti, F.; Guilhaumon, F.; Adloff, F.; Irisson, J. O.; Ayata, S. D.

2016-02-01

Although future increases in water temperature and future changes in regional circulation are expected to have great impacts on the pelagic food-web, estimates focusing on community-level shifts are still lacking for the planktonic compartment. By combining statistical niche models (or species distribution models) with projections from a regional circulation model, the impact of climate change on copepod epipelagic communities is assessed for the Mediterranean Sea. Habitat suitability maps are generated for 106 of the most abundant copepod species to analyze emerging patterns of diversity at the community level. Using variance analysis, we also quantified the uncertainties associated to our modeling strategy (niche model choice, CO2 emission scenario, boundary forcings of the circulation model). Comparing present and future projections, changes in species richness (alpha diversity) and in community composition (beta diversity, decomposed into turnover and nestedness component) are calculated. Average projections show that copepod communities will mainly experience turn-over processes, with little changes in species richness. Species gains are mainly located in the Gulf of Lions, the Northern Adriatic and the Northern Aegean seas. However, projections are highly variable, especially in the Eastern Mediterranean basin. We show that such variability is mainly driven by the choice of the niche model, through interactions with the CO2 emission scenario or the boundary forcing of the circulation model can be locally important. Finally, the possible impact of the estimated community changes on zooplanktonic functional and phylogenetic diversity is also assessed. We encourage the enlargement of this type of study to other components of the pelagic food-web, and argue that niche models' outputs should always be given along with a measure of uncertainty, and explained in light of a strong theoretical background.

Structural and emulsifying properties of soy protein isolate subjected to acid and alkaline pH-shifting processes.

PubMed

Jiang, Jiang; Chen, Jie; Xiong, Youling L

2009-08-26

Structural unfolding of soy protein isolate (SPI) as induced by holding (0, 0.5, 1, 2, and 4 h) in acidic (pH 1.5-3.5) and alkaline (pH 10.0-12.0) pH solutions, followed by refolding (1 h) at pH 7.0, was analyzed. Changes in emulsifying properties of treated SPI were then examined. The pH-shifting treatments resulted in a substantial increase in protein surface hydrophobicity, intrinsic tryptophan fluorescence intensity, and disulfide-mediated aggregation, along with the exposure of tyrosine. After the pH-shifting processes, soy protein adopted a molten globule-like conformation that largely maintained the original secondary structure and overall compactness but lost some tertiary structure. These structural modifications, consequently, led to markedly improved emulsifying activity of SPI as well as the emulsion stability.

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

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

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

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure.

PubMed

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-09-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

PubMed Central

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-01-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. PMID:24963997

The way to uncover community structure with core and diversity

NASA Astrophysics Data System (ADS)

Chang, Y. F.; Han, S. K.; Wang, X. D.

2018-07-01

Communities are ubiquitous in nature and society. Individuals that share common properties often self-organize to form communities. Avoiding the shortages of computation complexity, pre-given information and unstable results in different run, in this paper, we propose a simple and efficient method to deepen our understanding of the emergence and diversity of communities in complex systems. By introducing the rational random selection, our method reveals the hidden deterministic and normal diverse community states of community structure. To demonstrate this method, we test it with real-world systems. The results show that our method could not only detect community structure with high sensitivity and reliability, but also provide instructional information about the hidden deterministic community world and the real normal diverse community world by giving out the core-community, the real-community, the tide and the diversity. Thizs is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in complex systems.

The community structure of the global corporate network.

PubMed

Vitali, Stefania; Battiston, Stefano

2014-01-01

We investigate the community structure of the global ownership network of transnational corporations. We find a pronounced organization in communities that cannot be explained by randomness. Despite the global character of this network, communities reflect first of all the geographical location of firms, while the industrial sector plays only a marginal role. We also analyze the meta-network in which the nodes are the communities and the links are obtained by aggregating the links among firms belonging to pairs of communities. We analyze the network centrality of the top 50 communities and we provide a quantitative assessment of the financial sector role in connecting the global economy.

The Community Structure of the Global Corporate Network

PubMed Central

Vitali, Stefania; Battiston, Stefano

2014-01-01

We investigate the community structure of the global ownership network of transnational corporations. We find a pronounced organization in communities that cannot be explained by randomness. Despite the global character of this network, communities reflect first of all the geographical location of firms, while the industrial sector plays only a marginal role. We also analyze the meta-network in which the nodes are the communities and the links are obtained by aggregating the links among firms belonging to pairs of communities. We analyze the network centrality of the top 50 communities and we provide a quantitative assessment of the financial sector role in connecting the global economy. PMID:25126722

Light Structures Phototroph, Bacterial and Fungal Communities at the Soil Surface

PubMed Central

Davies, Lawrence O.; Schäfer, Hendrik; Marshall, Samantha; Bramke, Irene; Oliver, Robin G.; Bending, Gary D.

2013-01-01

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere. PMID:23894406

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure

PubMed Central

Hatton, Jasmine J.; Stevenson, Timothy J.; Buck, C. Loren; Duddleston, Khrystyne N.

2017-01-01

Summary We examined the effect of diet on pre-hibernation fattening and the gut microbiota of captive arctic ground squirrels (Urocitellus parryii). We measured body composition across time and gut microbiota density, diversity, and function prior to and after five-weeks on control, high-fat, low-fat (18%, 40%, and 10% energy from fat, respectively), or restricted calorie (50% of control) diets. Squirrels fattened at the same rate and to the same degree on all diets. Additionally, we found no differences in gut microbiota diversity or short chain fatty acid production across time or with diet. Analysis of the gut microbial transcriptome indicated differences in community function among diet groups, but not across time, and revealed shifts in the relative contribution of function at a taxonomic level. Our results demonstrate that pre-hibernation fattening of arctic ground squirrels is robust to changes in diet and is accomplished by more than increased food intake. Although our analyses did not uncover a definitive link between host fattening and the gut microbiota, and suggest the squirrels may possess a gut microbial community structure that is unresponsive to dietary changes, studies manipulating diet earlier in the active season may yet uncover a relationship between host diet, fattening and gut microbiota. PMID:28251799

A spectral method to detect community structure based on distance modularity matrix

NASA Astrophysics Data System (ADS)

Yang, Jin-Xuan; Zhang, Xiao-Dong

2017-08-01

There are many community organizations in social and biological networks. How to identify these community structure in complex networks has become a hot issue. In this paper, an algorithm to detect community structure of networks is proposed by using spectra of distance modularity matrix. The proposed algorithm focuses on the distance of vertices within communities, rather than the most weakly connected vertex pairs or number of edges between communities. The experimental results show that our method achieves better effectiveness to identify community structure for a variety of real-world networks and computer generated networks with a little more time-consumption.

How mammalian predation contributes to tropical tree community structure.

PubMed

Paine, C E Timothy; Beck, Harald; Terborgh, John

2016-12-01

The recruitment of seedlings from seeds is the key demographic transition for rain forest trees. Though tropical forest mammals are known to consume many seeds, their effects on tree community structure remain little known. To evaluate their effects, we monitored 8,000 seeds of 24 tree species using exclosure cages that were selectively permeable to three size classes of mammals for up to 4.4 years. Small and medium-bodied mammals removed many more seeds than did large mammals, and they alone generated beta diversity and negative density dependence, whereas all mammals reduced diversity and shaped local species composition. Thus, small and medium-bodied mammals more strongly contributed to community structure and promoted species coexistence than did large mammals. Given that seedling recruitment is seed limited for most species, alterations to the composition of the community of mammalian seed predators is expected to have long-term consequences for tree community structure in tropical forests. © 2016 by the Ecological Society of America.

Short- versus long-term responses to changing CO2 in a coastal dinoflagellate bloom: implications for interspecific competitive interactions and community structure.

PubMed

Tatters, Avery O; Schnetzer, Astrid; Fu, Feixue; Lie, Alle Y A; Caron, David A; Hutchins, David A

2013-07-01

Increasing pCO2 (partial pressure of CO2 ) in an "acidified" ocean will affect phytoplankton community structure, but manipulation experiments with assemblages briefly acclimated to simulated future conditions may not accurately predict the long-term evolutionary shifts that could affect inter-specific competitive success. We assessed community structure changes in a natural mixed dinoflagellate bloom incubated at three pCO2 levels (230, 433, and 765 ppm) in a short-term experiment (2 weeks). The four dominant species were then isolated from each treatment into clonal cultures, and maintained at all three pCO2 levels for approximately 1 year. Periodically (4, 8, and 12 months), these pCO2 -conditioned clones were recombined into artificial communities, and allowed to compete at their conditioning pCO2 level or at higher and lower levels. The dominant species in these artificial communities of CO2 -conditioned clones differed from those in the original short-term experiment, but individual species relative abundance trends across pCO2 treatments were often similar. Specific growth rates showed no strong evidence for fitness increases attributable to conditioning pCO2 level. Although pCO2 significantly structured our experimental communities, conditioning time and biotic interactions like mixotrophy also had major roles in determining competitive outcomes. New methods of carrying out extended mixed species experiments are needed to accurately predict future long-term phytoplankton community responses to changing pCO2 . © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

SEMICONDUCTOR INTEGRATED CIRCUITS: A quasi-3-dimensional simulation method for a high-voltage level-shifting circuit structure

NASA Astrophysics Data System (ADS)

Jizhi, Liu; Xingbi, Chen

2009-12-01

A new quasi-three-dimensional (quasi-3D) numeric simulation method for a high-voltage level-shifting circuit structure is proposed. The performances of the 3D structure are analyzed by combining some 2D device structures; the 2D devices are in two planes perpendicular to each other and to the surface of the semiconductor. In comparison with Davinci, the full 3D device simulation tool, the quasi-3D simulation method can give results for the potential and current distribution of the 3D high-voltage level-shifting circuit structure with appropriate accuracy and the total CPU time for simulation is significantly reduced. The quasi-3D simulation technique can be used in many cases with advantages such as saving computing time, making no demands on the high-end computer terminals, and being easy to operate.

Shifting Practices Toward Recovery-Oriented Care Through an E-Recovery Portal in Community Mental Health Care: A Mixed-Methods Exploratory Study

PubMed Central

Strand, Monica; Eng, Lillian Sofie; Børøsund, Elin; Varsi, Cecilie; Ruland, Cornelia

2017-01-01

Background Mental health care is shifting from a primary focus on symptom reduction toward personal recovery-oriented care, especially for persons with long-term mental health care needs. Web-based portals may facilitate this shift, but little is known about how such tools are used or the role they may play in personal recovery. Objective The aim was to illustrate uses and experiences with the secure e-recovery portal “ReConnect” as an adjunct to ongoing community mental health care and explore its potential role in shifting practices toward recovery. Methods ReConnect was introduced into two Norwegian mental health care communities and used for 6 months. The aim was to support personal recovery and collaboration between service users and health care providers. Among inclusion criteria for participation were long-term care needs and at least one provider willing to interact with service users through ReConnect. The portal was designed to support ongoing collaboration as each service user-provider dyad/team found appropriate and consisted of (1) a toolbox of resources for articulating and working with recovery processes, such as status/goals/activities relative to life domains (eg, employment, social network, health), medications, network map, and exercises (eg, sleep hygiene, mindfulness); (2) messaging with providers who had partial access to toolbox content; and (3) a peer support forum. Quantitative data (ie, system log, questionnaires) were analyzed using descriptive statistics. Qualitative data (eg, focus groups, forum postings) are presented relative to four recovery-oriented practice domains: personally defined recovery, promoting citizenship, working relationships, and organizational commitment. Results Fifty-six participants (29 service users and 27 providers) made up 29 service user-provider dyads. Service users reported having 11 different mental health diagnoses, with a median 2 (range 1-7) diagnoses each. The 27 providers represented nine different

A high-latitude coral community with an uncertain future: Stetson Bank, northwestern Gulf of Mexico

NASA Astrophysics Data System (ADS)

DeBose, J. L.; Nuttall, M. F.; Hickerson, E. L.; Schmahl, G. P.

2013-03-01

Limited data exist that detail trends in benthic community composition of high-latitude coral communities. As anthropogenic stressors are projected to increase in number and intensity, long-term monitoring datasets are essential to understanding community stability and ecosystem resilience. In 1993, a long-term monitoring program was initiated at Stetson Bank, in the Gulf of Mexico. Over the course of this monitoring, a major shift in community structure occurred, in which the coral-sponge community was replaced by an algal-dominated community. During the initial years of this study, the coral community at Stetson Bank was relatively stable. Beginning in the late 1990s, sponge cover began a steady decline from over 30 % to less than 25 %. Then, in 2005, the benthic community underwent a further significant change when living coral cover declined from 30 % to less than 8 % and sponges declined to less than 20 % benthic cover. This abrupt shift corresponded with a Caribbean-wide bleaching event in 2005 that caused major mortality of Stetson Bank corals. Previous bleaching events at Stetson Bank did not result in wide-scale coral mortality. Several environmental parameters may have contributed to the rapid decline in this benthic community. We suggest that the combined effects of coastal runoff and elevated temperatures contributed to the observed shift. We present an analysis of 15 years of monitoring data spanning from 1993 to 2008; this dataset provides both a biological baseline and a multiyear trend analysis of the community structure for a high-latitude coral-sponge community in the face of changing climatic conditions.