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Sample records for community structural shifts

  1. Distributional shifts in size structure of phytoplankton community

    NASA Astrophysics Data System (ADS)

    Waga, H.; Hirawake, T.; Fujiwara, A.; Nishino, S.; Kikuchi, T.; Suzuki, K.; Takao, S.

    2015-12-01

    Increased understanding on how marine species shift their distribution is required for effective conservation of fishery resources under climate change. Previous studies have often predicted distributional shifts of fish using satellite derived sea surface temperature (SST). However, SST may not fully represent the changes in species distribution through food web structure and as such this remains an open issue due to lack of ecological perspective on energy transfer process in the earlier studies. One of the most important factors in ecosystem is composition of phytoplankton community, and its size structure determines energy flow efficiency from base to higher trophic levels. To elucidate spatiotemporal variation in phytoplankton size structure, chlorophyll-a size distribution (CSD) algorithm was developed using spectral variance of phytoplankton absorption coefficient through principal component analysis. Slope of CSD (CSD slope) indicates size structure of phytoplankton community where, strong and weak magnitudes of CSD slope indicate smaller and larger phytoplankton structure, respectively. Shifts in CSD slope and SST were derived as the ratio of temporal trend over the 12-year period (2003-2014) to 2-dimensional spatial gradient and the resulting global median velocity of CSD slope and SST were 0.361 and 0.733 km year-1, respectively. In addition, the velocity of CSD slope monotonically increases with increasing latitude, while relatively complex latitudinal pattern for SST emerged. Moreover, angle of shifts suggest that species are required to shift their distribution toward not limited to simple pole-ward migration, and some regions exhibit opposite direction between the velocity of CSD slope and SST. These findings further imply that combined phytoplankton size structure and SST may contribute for more accurate prediction of species distribution shifts relative to existing studies which only considering variations in thermal niches.

  2. Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

    PubMed

    Adair, Karen L; Wratten, Steve; Lear, Gavin

    2013-06-01

    Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. PMID:23754721

  3. A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary.

    PubMed

    Spietz, Rachel L; Williams, Cheryl M; Rocap, Gabrielle; Horner-Devine, M Claire

    2015-01-01

    Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA-a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L(-1). This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L(-1)), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems. PMID:26270047

  4. A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

    PubMed Central

    Spietz, Rachel L.; Williams, Cheryl M.; Rocap, Gabrielle; Horner-Devine, M. Claire

    2015-01-01

    Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems. PMID:26270047

  5. Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress.

    PubMed

    Bharti, Nidhi; Barnawal, Deepti; Maji, Deepamala; Kalra, Alok

    2015-07-01

    The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities. PMID:25542205

  6. Shifts in Fungal and Bacterial Community Structure During Tallgrass Prairie Restoration

    NASA Astrophysics Data System (ADS)

    Shutthanandan, J.; Bailey, V. L.; Bolton, H.; Brockman, F. J.

    2002-12-01

    The cycling of carbon through the microbial community of soils results in both the storage of freshly added carbon in the soil and the release of greenhouse gases such as carbon dioxide to the atmosphere. It is hypothesized that fungi and bacteria cycle carbon differently, and result in different proportions of carbon stored and evolved. The intensive management of a soil will affect these proportions and thus, may also affect the terrestrial carbon cycle. The soil microbial community was monitored in four soils that form a tallgrass prairie restoration chronosequence. The chronosequence was composed of: 1) native tallgrass prairie, 2) farmland restored to tallgrass prairie in 1979, 3) farmland restored to prairie in 1993, and 4) farmland still in production with row crops. The structure of the microbial community was determined by terminal restriction fragment length analysis (T-RFLP) and we focus here on comparing bacterial and fungal domains from agriculture to native conditions. Shifts in the fungal and bacterial communities were detected that indicate that the bacteria recovered faster from changing the land use from farmland back to prairie, while the fungi are more sensitive to the perturbations of invasive agriculture and appear to be taking longer to revert to their original prairie composition. However, it must also be considered that assays of the activities of these two communities indicate that as the restoration progresses, the fungi dominate the degradation of freshly added carbon (the ratio of fungal-to-bacterial activity was 13.5:1 in the 1979 restoration, but only 0.85:1 in the farmland). Identification of this shift in community structure offers insights into monitoring ecosystem restoration and may also suggest opportunities for enhancing carbon storage by allowing marginal lands to revert to a natural condition.

  7. Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors

    NASA Astrophysics Data System (ADS)

    Fu, Bingbing; Liu, Jiwen; Yang, Hongmei; Hsu, Ting Chang; He, Biyan; Dai, Minhan; Kao, Shuh Ji; Zhao, Meixun; Zhang, Xiao-Hua

    2015-04-01

    Anaerobic ammonium oxidation (anammox) plays an important role in the marine nitrogen cycle. The Pearl Estuary, a typical subtropical estuary characterized by hypoxia upstream and high loads of organic matter and inorganic nutrients caused by anthropogenic activities, has received extensive attention. In this study, anammox bacterial community structures in surface sediments along the Pearl Estuary were investigated using 16S rRNA and hydrazine oxidoreductase (HZO) genes. In addition, abundance of anammox bacteria in both water and surface sediments was investigated by quantitative PCR. Obvious anammox bacterial community structure shift was observed in surface sediments, in which the dominant genus changed from "Candidatus Brocadia" or "Candidatus Anammoxoglobus" to "Candidatus Scalindua" along the salinity gradient from freshwater to the open ocean based on 16S rRNA gene and HZO amino acid phylotypes. This distribution pattern was associated with salinity, temperature, pH of overlying water, and particularly C/N ratio. Phylogenetic analysis unraveled a rich diversity of anammox bacteria including four novel clusters provisionally named "Candidatus Jugangensis," "Candidatus Oceanicum," "Candidatus Anammoxidans," and "Candidatus Aestuarianus." The abundance of anammox bacteria in surface sediments, bottom and surface waters ranged from 4.22 × 105 to 2.55 × 106 copies g-1, 1.24 × 104 to 1.01×105 copies L-1, and 8.07×103 to 8.86×105 copies L-1, respectively. The abundance of anammox bacteria in the water column was positively correlated with NO2- and NO3-, and negatively correlated with dissolved oxygen, although an autochthonous source might contribute to the observed abundance of anammox bacteria.

  8. Influence of corallivory, competition, and habitat structure on coral community shifts.

    PubMed

    Lenihan, Hunter S; Holbrook, Sally J; Schmitt, Russell J; Brooks, Andrew J

    2011-10-01

    The species composition of coral communities has shifted in many areas worldwide through the relative loss of important ecosystem engineers such as highly branched corals, which are integral in maintaining reef biodiversity. We assessed the degree to which the performance of recently recruited branching corals was influenced by corallivory, competition, sedimentation, and the interactions between these factors. We also explored whether the species-specific influence of these biotic and abiotic constraints helps to explain recent shifts in the coral community in lagoons of Moorea, French Polynesia. Population surveys revealed evidence of a community shift away from a historically acroporid-dominated community to a pocilloporid- and poritid-dominated community, but also showed that the distribution and abundance of coral taxa varied predictably with location in the lagoon. At the microhabitat scale, branching corals grew mainly on dead or partially dead massive Porites ("bommies"), promontories with enhanced current velocities and reduced sedimentation. A demographic study revealed that growth and survival of juvenile Pocillopora verrucosa and Acropora retusa, the two most common branching species of each taxon, were affected by predation and competition with vermetid gastropods. By 24 months of age, 20-60% of juvenile corals suffered partial predation by corallivorous fishes, and injured corals experienced reduced growth and survival. A field experiment confirmed that partial predation by corallivorous fishes is an important, but habitat-modulated, constraint for branching corals. Competition with vermetid gastropods reduced growth of both branching species but unexpectedly also provided an associational defense against corallivory. Overall, the impact of abiotic constraints was habitat-specific and similar for Acropora and Pocillopora, but biotic interactions, especially corallivory, had a greater negative effect on Acropora than Pocillopora, which may explain the

  9. 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

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

    PubMed

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

    2015-11-01

    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

  11. Structural and functional shifts in zoobenthos induced by organic enrichment — Implications for community recovery potential

    NASA Astrophysics Data System (ADS)

    Villnäs, A.; Perus, J.; Bonsdorff, E.

    2011-01-01

    Habitat change induced by organic enrichment is a growing concern for the sustainability of benthic communities in coastal aquatic environments. This case study describes the spatial and temporal response patterns and the recovery potential of low-diversity benthic communities to organic enrichment at two fish farm locations, during the rearing periods (15 and 20 years, respectively) and the following recovery periods (2 years). The spatial extent of disturbance differed depending on the hydromorphological characteristics of the rearing sites, but degraded macrobenthic communities close to both fish farms were recorded soon after the activity started. Continued organic enrichment resulted in high species turnover-rates and in an altered benthic community composition at both locations. After fish farm abatement, a partial recovery was detected in species richness, but abundance and biomass values were reduced and changes in structural composition remained. Alterations in benthic biological traits were observed at both fish farm locations, implying that organic enrichment might cause changes in benthic community function within low-diversity benthic communities.

  12. Conservation of Forest Birds: Evidence of a Shifting Baseline in Community Structure

    PubMed Central

    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.

    2010-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions/Significance Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., ∼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

  13. Bacterial community structure and function shift across a northern boreal forest fire chronosequence

    PubMed Central

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

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs < 0.1%). Proteobacteria (39%), Acidobacteria (34%) and Actinobacteria (17%) were the most abundant phyla across all sites. Genes involved in C and N cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  14. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal.

    PubMed

    Mao, Yanping; Wang, Zhiping; Li, Liguan; Jiang, Xiaotao; Zhang, Xuxiang; Ren, Hongqiang; Zhang, Tong

    2016-01-01

    A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively. PMID:27547976

  15. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal

    PubMed Central

    Mao, Yanping; Wang, Zhiping; Li, Liguan; Jiang, Xiaotao; Zhang, Xuxiang; Ren, Hongqiang; Zhang, Tong

    2016-01-01

    A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively. PMID:27547976

  16. 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

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  19. Shifts in methanogen community structure and function across a coastal marsh transect: effects of exotic Spartina alterniflora invasion

    PubMed Central

    Yuan, Junji; Ding, Weixin; Liu, Deyan; Kang, Hojeong; Xiang, Jian; Lin, Yongxin

    2016-01-01

    Invasion of Spartina alterniflora in coastal areas of China increased methane (CH4) emissions. To elucidate the underlying mechanisms, we measured CH4 production potential, methanogen community structure and biogeochemical factors along a coastal wetland transect comprised of five habitat regions: open water, bare tidal flat, invasive S. alterniflora marsh and native Suaeda salsa and Phragmites australis marshes. CH4 production potential in S. alterniflora marsh was 10 times higher than that in other regions, and it was significantly correlated with soil organic carbon, dissolved organic carbon and trimethylamine concentrations, but was not correlated with acetate or formate concentrations. Although the diversity of methanogens was lowest in S. alterniflora marsh, invasion increased methanogen abundance by 3.48-fold, compared with native S. salsa and P. australis marshes due to increase of facultative Methanosarcinaceae rather than acetotrophic and hydrogenotrophic methanogens. Ordination analyses suggested that trimethylamine was the primary factor regulating shift in methanogen community structure. Addition of trimethylamine increased CH4 production rates by 1255-fold but only by 5.61- and 11.4-fold for acetate and H2/CO2, respectively. S. alterniflora invasion elevated concentration of non-competitive trimethylamine, and shifted methanogen community from acetotrophic to facultative methanogens, which together facilitated increased CH4 production potential. PMID:26728134

  20. Shifts in methanogen community structure and function across a coastal marsh transect: effects of exotic Spartina alterniflora invasion

    NASA Astrophysics Data System (ADS)

    Yuan, Junji; Ding, Weixin; Liu, Deyan; Kang, Hojeong; Xiang, Jian; Lin, Yongxin

    2016-01-01

    Invasion of Spartina alterniflora in coastal areas of China increased methane (CH4) emissions. To elucidate the underlying mechanisms, we measured CH4 production potential, methanogen community structure and biogeochemical factors along a coastal wetland transect comprised of five habitat regions: open water, bare tidal flat, invasive S. alterniflora marsh and native Suaeda salsa and Phragmites australis marshes. CH4 production potential in S. alterniflora marsh was 10 times higher than that in other regions, and it was significantly correlated with soil organic carbon, dissolved organic carbon and trimethylamine concentrations, but was not correlated with acetate or formate concentrations. Although the diversity of methanogens was lowest in S. alterniflora marsh, invasion increased methanogen abundance by 3.48-fold, compared with native S. salsa and P. australis marshes due to increase of facultative Methanosarcinaceae rather than acetotrophic and hydrogenotrophic methanogens. Ordination analyses suggested that trimethylamine was the primary factor regulating shift in methanogen community structure. Addition of trimethylamine increased CH4 production rates by 1255-fold but only by 5.61- and 11.4-fold for acetate and H2/CO2, respectively. S. alterniflora invasion elevated concentration of non-competitive trimethylamine, and shifted methanogen community from acetotrophic to facultative methanogens, which together facilitated increased CH4 production potential.

  1. Biodiversity, Community Structural Shifts, and Biogeography of Prokaryotes within Antarctic Continental Shelf Sediment

    PubMed Central

    Bowman, John P.; McCuaig, Robert D.

    2003-01-01

    16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment. PMID:12732511

  2. 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. PMID:27068902

  3. 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

  4. Shifts in Microbial Community Structure with Changes in Cathodic Potential in Marine Sediment Microcosms

    NASA Astrophysics Data System (ADS)

    Lam, B. R.; Rowe, A. R.; Nealson, K. H.

    2014-12-01

    Microorganisms comprise more than 90% of the biomass of the ocean. Their ability to thrive and survive in a wide range of environments from oligotrophic waters to the deep subsurface stems from the great metabolic versatility that exists among them. This metabolic versatility has further expanded with the discovery of extracellular electron transport (EET). EET is the capability of microorganisms to transfer electrons to and from insoluble substrates outside of the cell. Much of what is known about EET comes from studies of model metal reducing microorganisms in the groups Shewanellaceae and Geobacteraceae. However, EET is not limited to these metal reducing microorganisms, and may play a large role in the biogeochemical cycling of several elements. We have developed an electrochemical culturing technique designed to target microorganisms with EET ability and tested these methods in marine sediments. The use of electrodes allows for greater control and quantification of electrons flowing to insoluble substrates as opposed to insoluble substrates such as minerals that are often difficult to measure. We have recently shown that poising electrodes at different redox potentials will enrich for different microbial groups and thus possible metabolisms. In marine sediment microcosms, triplicate electrodes were poised at different cathodic (electron donating) potentials (-300, -400, -500 and -600 mV) and incubated for eight weeks. Community analysis of the 16S rRNA revealed that at lower negative potentials (-500 and -600 mV), more sulfate reducing bacteria in the class Deltaproteobacteria were enriched in comparison to the communities at -300 and -400 mV being dominated by microorganisms within Alphaproteobacteria, Gammaproteobacteria, and Clostridia. This can be explained by sulfate (abundant in seawater) becoming a more energetically favorable electron acceptor with lower applied potentials. In addition, communities at higher potentials showed greater enrichment of the

  5. 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.

  6. 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. PMID:25663374

  7. 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

  8. 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. PMID:24594732

  9. [Decline of Activity and Shifts in the Methanotrophic Community Structure of an Ombrotrophic Peat Bog after Wildfire].

    PubMed

    Danilova, O V; Belova, S E; Kulichevskaya, I S; Dedysh, S N

    2015-01-01

    This study examined potential disturbances of methanotrophic communities playing a key role in reducing methane emissions from the peat bog Tasin Borskoye, Vladimir oblast, Russia as a result of the 2007 wildfire. The potential activity of the methane-oxidizing filter in the burned peatland site and the abundance of indigenous methanotrophic bacteria were significantly reduced in comparison to the undisturbed site. Molecular analysis of methanotrophic community structure by means of PCR amplification and cloning of the pmoAgene encoding particulate methane monooxygenase revealed the replacement of typical peat-inhabiting, acidophilic type II methanotrophic bacteria with type I methanotrophs, which are less active in acidic environments. In summary, both the structure and the activity of the methane-oxidizing filter in burned peatland sites underwent significant changes, which were clearly pronounced even after 7 years of the natural ecosystem recovery. These results point to the long-term character of the disturbances caused by wildfire in peatlands. PMID:27169243

  10. 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.

  11. 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. PMID:24176706

  12. The Expansion of Dreissena and Long-term Shifts in Benthic Macroinvertebrate Community Structure in Lake Ontario, 1998-2008

    EPA Science Inventory

    The introduction of Dreissena to the Great lakes has profoundly impacted benthic ecosystems, resulting in the decline of native species and dramatic community restructuring. In Lake Ontario, long-term monitoring has yielded a wealth of detailed information regarding both the exp...

  13. Shifts in microbial community structure and function in light- and dark-grown biofilms driven by warming.

    PubMed

    Romaní, Anna M; Borrego, Carles M; Díaz-Villanueva, Verónica; Freixa, Anna; Gich, Frederic; Ylla, Irene

    2014-08-01

    Biofilms are dynamic players in biogeochemical cycling in running waters and are subjected to environmental stressors like those provoked by climate change. We investigated whether a 2°C increase in flowing water would affect prokaryotic community composition and heterotrophic metabolic activities of biofilms grown under light or dark conditions. Neither light nor temperature treatments were relevant for selecting a specific bacterial community at initial phases (7-day-old biofilms), but both variables affected the composition and function of mature biofilms (28-day-old). In dark-grown biofilms, changes in the prokaryotic community composition due to warming were mainly related to rotifer grazing, but no significant changes were observed in functional fingerprints. In light-grown biofilms, warming also affected protozoan densities, but its effect on prokaryotic density and composition was less evident. In contrast, heterotrophic metabolic activities in light-grown biofilms under warming showed a decrease in the functional diversity towards a specialized use of several carbohydrates. Results suggest that prokaryotes are functionally redundant in dark biofilms but functionally plastic in light biofilms. The more complex and self-serving light-grown biofilm determines a more buffered response to temperature than dark-grown biofilms. Despite the moderate increase in temperature of only 2°C, warming conditions drive significant changes in freshwater biofilms, which responded by finely tuning a complex network of interactions among microbial populations within the biofilm matrix. PMID:24552130

  14. Shifting grassland plant community structure drives positive interactive effects of warming and diversity on aboveground net primary productivity.

    PubMed

    Cowles, Jane M; Wragg, Peter D; Wright, Alexandra J; Powers, Jennifer S; Tilman, David

    2016-02-01

    Ecosystems worldwide are increasingly impacted by multiple drivers of environmental change, including climate warming and loss of biodiversity. We show, using a long-term factorial experiment, that plant diversity loss alters the effects of warming on productivity. Aboveground primary productivity was increased by both high plant diversity and warming, and, in concert, warming (≈1.5 °C average above and belowground warming over the growing season) and diversity caused a greater than additive increase in aboveground productivity. The aboveground warming effects increased over time, particularly at higher levels of diversity, perhaps because of warming-induced increases in legume and C4 bunch grass abundances, and facilitative feedbacks of these species on productivity. Moreover, higher plant diversity was associated with the amelioration of warming-induced environmental conditions. This led to cooler temperatures, decreased vapor pressure deficit, and increased surface soil moisture in higher diversity communities. Root biomass (0-30 cm) was likewise consistently greater at higher plant diversity and was greater with warming in monocultures and at intermediate diversity, but at high diversity warming had no detectable effect. This may be because warming increased the abundance of legumes, which have lower root : shoot ratios than the other types of plants. In addition, legumes increase soil nitrogen (N) supply, which could make N less limiting to other species and potentially decrease their investment in roots. The negative warming × diversity interaction on root mass led to an overall negative interactive effect of these two global change factors on the sum of above and belowground biomass, and thus likely on total plant carbon stores. In total, plant diversity increased the effect of warming on aboveground net productivity and moderated the effect on root mass. These divergent effects suggest that warming and changes in plant diversity are likely to have both

  15. 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. PMID:26743786

  16. Shift in the Use of Migrant Community Languages in Australia

    ERIC Educational Resources Information Center

    Karidakis, Maria; Arunachalam, Dharma

    2016-01-01

    In this paper, we first explore the trends in the maintenance of migrant community languages among the first generation migrants and then the socio-economic variation in the shift in use of community languages. Our analysis showed that language shift to English among first generation migrants has not been uniform, with some migrant groups adopting…

  17. A novel phase shifting structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Singh, Veena; Dubey, Vishesh; Ahmad, Azeem; Singh, Gyanendra; Mehta, D. S.

    2016-03-01

    This paper describes a new and novel phase shifting technique for qualitative as well as quantitative measurement in microscopy. We have developed a phase shifting device which is robust, inexpensive and involves no mechanical movement. In this method, phase shifting is implemented using LED array, beam splitters and defocused projection of Ronchi grating. The light from the LEDs are made incident on the beam splitters at spatially different locations. Due to variation in the geometrical distances of LEDs from the Ronchi grating and by sequentially illuminating the grating by switching on one LED at a time the phase shifted grating patterns are generated. The phase shifted structured patterns are projected onto the sample using microscopic objective lens. The phase shifted deformed patterns are recorded by a CCD camera. The initial alignment of the setup involves a simple procedure for the calibration for equal fringe width and intensity such that the phase shifted fringes are at equal phase difference. Three frame phase shifting algorithm is employed for the reconstruction of the phase map. The method described here is fully automated so that the phase shifted images are recorded just by switching of LEDs and has been used for the shape measurement of microscopic industrial objects. The analysis of the phase shifted images provides qualitative as well as quantitative information about the sample. Thus, the method is simple, robust and low cost compared to PZT devices commonly employed for phase shifting.

  18. 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. PMID:26695154

  19. 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

  20. Shifts in flowering phenology reshape a subalpine plant community

    PubMed Central

    CaraDonna, Paul J.; Iler, Amy M.; Inouye, David W.

    2014-01-01

    Phenology—the timing of biological events—is highly sensitive to climate change. However, our general understanding of how phenology responds to climate change is based almost solely on incomplete assessments of phenology (such as first date of flowering) rather than on entire phenological distributions. Using a uniquely comprehensive 39-y flowering phenology dataset from the Colorado Rocky Mountains that contains more than 2 million flower counts, we reveal a diversity of species-level phenological shifts that bring into question the accuracy of previous estimates of long-term phenological change. For 60 species, we show that first, peak, and last flowering rarely shift uniformly and instead usually shift independently of one another, resulting in a diversity of phenological changes through time. Shifts in the timing of first flowering on average overestimate the magnitude of shifts in the timing of peak flowering, fail to predict shifts in the timing of last flowering, and underrepresent the number of species changing phenology in this plant community. Ultimately, this diversity of species-level phenological shifts contributes to altered coflowering patterns within the community, a redistribution of floral abundance across the season, and an expansion of the flowering season by more than I mo during the course of our study period. These results demonstrate the substantial reshaping of ecological communities that can be attributed to shifts in phenology. PMID:24639544

  1. Shifts in flowering phenology reshape a subalpine plant community.

    PubMed

    CaraDonna, Paul J; Iler, Amy M; Inouye, David W

    2014-04-01

    Phenology--the timing of biological events--is highly sensitive to climate change. However, our general understanding of how phenology responds to climate change is based almost solely on incomplete assessments of phenology (such as first date of flowering) rather than on entire phenological distributions. Using a uniquely comprehensive 39-y flowering phenology dataset from the Colorado Rocky Mountains that contains more than 2 million flower counts, we reveal a diversity of species-level phenological shifts that bring into question the accuracy of previous estimates of long-term phenological change. For 60 species, we show that first, peak, and last flowering rarely shift uniformly and instead usually shift independently of one another, resulting in a diversity of phenological changes through time. Shifts in the timing of first flowering on average overestimate the magnitude of shifts in the timing of peak flowering, fail to predict shifts in the timing of last flowering, and underrepresent the number of species changing phenology in this plant community. Ultimately, this diversity of species-level phenological shifts contributes to altered coflowering patterns within the community, a redistribution of floral abundance across the season, and an expansion of the flowering season by more than I mo during the course of our study period. These results demonstrate the substantial reshaping of ecological communities that can be attributed to shifts in phenology. PMID:24639544

  2. Subgingival Microbiome Shifts and Community Dynamics in Periodontal Diseases.

    PubMed

    Diaz, Patricia I; Hoare, Anilei; Hong, Bo-Young

    2016-07-01

    High-throughput 16S rRNA gene sequencing has allowed the characterization of subgingival microbiome shifts from health to periodontitis identifying health-associated, periodontitis-associated and core species, which preserve their proportions from health to disease. The development of gingivitis is also characterized by distinct shifts. Microbiome shifts resemble microbial successions and result from interspecies interactions and community adaptation to the changing environment as inflammation ensues. Gingivitis-associated and core species are proposed as likely mediators of microbiome transitions. PMID:27514154

  3. Shifts in Rhizoplane Communities of Aquatic Plants after Cadmium Exposure

    PubMed Central

    Stout, Lisa M.; Nüsslein, Klaus

    2005-01-01

    In this study we present the comparative molecular analysis of bacterial communities of the aquatic plant Lemna minor from a contaminated site (RCP) and from a laboratory culture (EPA), as well as each of these with the addition of cadmium. Plants were identified as L. minor by analysis of the rpl16 chloroplast region. Comparative bacterial community studies were based on the analyses of 16S rRNA clone libraries, each containing about 100 clones from the root surfaces of plants. Bacterial communities were compared at three phylogenetic levels of resolution. At the level of bacterial divisions, differences in diversity index scores between treatments, with and without cadmium within the same plant type (EPA or RCP), were small, indicating that cadmium had little effect. When we compared genera within the most dominant group, the β-proteobacteria, differences between unamended and cadmium-amended libraries were much larger. Bacterial diversity increased upon cadmium addition for both EPA and RCP libraries. Analyses of diversity at the phylotype level showed parallel shifts to more even communities upon cadmium addition; that is, percentage changes in diversity indices due to cadmium addition were the same for either plant type, indicating that contamination history might be independent of disturbance-induced diversity shifts. At finer phylogenetic levels of resolution, the effects of cadmium addition on bacterial communities were very noticeable. This study is a first step in understanding the role of aquatic plant-associated microbial communities in phytoremediation of heavy metals. PMID:15870338

  4. Competitive and demographic leverage points of community shifts under climate warming

    PubMed Central

    Sorte, Cascade J. B.; White, J. Wilson

    2013-01-01

    Accelerating rates of climate change and a paucity of whole-community studies of climate impacts limit our ability to forecast shifts in ecosystem structure and dynamics, particularly because climate change can lead to idiosyncratic responses via both demographic effects and altered species interactions. We used a multispecies model to predict which processes and species' responses are likely to drive shifts in the composition of a space-limited benthic marine community. Our model was parametrized from experimental manipulations of the community. Model simulations indicated shifts in species dominance patterns as temperatures increase, with projected shifts in composition primarily owing to the temperature dependence of growth, mortality and competition for three critical species. By contrast, warming impacts on two other species (rendering them weaker competitors for space) and recruitment rates of all species were of lesser importance in determining projected community changes. Our analysis reveals the importance of temperature-dependent competitive interactions for predicting effects of changing climate on such communities. Furthermore, by identifying processes and species that could disproportionately leverage shifts in community composition, our results contribute to a mechanistic understanding of climate change impacts, thereby allowing more insightful predictions of future biodiversity patterns. PMID:23658199

  5. Competitive and demographic leverage points of community shifts under climate warming.

    PubMed

    Sorte, Cascade J B; White, J Wilson

    2013-07-01

    Accelerating rates of climate change and a paucity of whole-community studies of climate impacts limit our ability to forecast shifts in ecosystem structure and dynamics, particularly because climate change can lead to idiosyncratic responses via both demographic effects and altered species interactions. We used a multispecies model to predict which processes and species' responses are likely to drive shifts in the composition of a space-limited benthic marine community. Our model was parametrized from experimental manipulations of the community. Model simulations indicated shifts in species dominance patterns as temperatures increase, with projected shifts in composition primarily owing to the temperature dependence of growth, mortality and competition for three critical species. By contrast, warming impacts on two other species (rendering them weaker competitors for space) and recruitment rates of all species were of lesser importance in determining projected community changes. Our analysis reveals the importance of temperature-dependent competitive interactions for predicting effects of changing climate on such communities. Furthermore, by identifying processes and species that could disproportionately leverage shifts in community composition, our results contribute to a mechanistic understanding of climate change impacts, thereby allowing more insightful predictions of future biodiversity patterns. PMID:23658199

  6. Invertebrate community response to a shifting mosaic of habitat

    USGS Publications Warehouse

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

    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.

  7. Contrasting energy pathways at the community level as a consequence of regime shifts.

    PubMed

    Xu, Jun; Wen, Zhourui; Ke, Zhixin; Zhang, Meng; Zhang, Min; Guo, Nichun; Hansson, Lars-Anders; Xie, Ping

    2014-05-01

    Ecological regime shifts typically result in abrupt changes in ecosystem structure through several trophic levels, which leads to rapid ecosystem reconfiguration between regimes. An interesting aspect of the impact of regime shift is that alternative regimes may induce distinct shifts in energy pathways; these have been less tested than structural changes. This paper addresses this by using stable isotopes to establish the energy pathways in fish communities. We specifically focus on the impact of regime shift on changes of the energy pathways, and how the magnitude and direction of these changes affect the local community. We found that energy pathways significantly varied among the planktivorous, benthivorous, and piscivorous trophic guilds as a result of the alternative regimes. The regime shift from a clear to a turbid state altered the food web towards planktonic energy pathways and truncated food chain length, which is indicative of less ecological efficiency. This was confirmed by the adaptive foraging strategies of prevalent omnivores in the current communities. These structural and functional characteristics of trophic interactions might not facilitate classic trophic cascading effects in such a turbid regime and suppress the system's response to environmental changes, e.g., nutrient loading, and restoration efforts in turbid to clear water regime shifts. PMID:24414311

  8. Language Shift and the Speech Community: Sociolinguistic Change in a Garifuna Community in Belize

    ERIC Educational Resources Information Center

    Ravindranath, Maya

    2009-01-01

    Language shift is the process by which a speech community in a contact situation (i.e. consisting of bilingual speakers) gradually stops using one of its two languages in favor of the other. The causal factors of language shift are generally considered to be social, and researchers have focused on speakers' attitudes (both explicit and unstated)…

  9. Parasites alter community structure.

    PubMed

    Wood, Chelsea L; Byers, James E; Cottingham, Kathryn L; Altman, Irit; Donahue, Megan J; Blakeslee, April M H

    2007-05-29

    Parasites often play an important role in modifying the physiology and behavior of their hosts and may, consequently, mediate the influence hosts have on other components of an ecological community. Along the northern Atlantic coast of North America, the dominant herbivorous snail Littorina littorea structures rocky intertidal communities through strong grazing pressure and is frequently parasitized by the digenean trematode Cryptocotyle lingua. We hypothesized that the effects of parasitism on host physiology would induce behavioral changes in L. littorea, which in turn would modulate L. littorea's influence on intertidal community composition. Specifically, we hypothesized that C. lingua infection would alter the grazing rate of L. littorea and, consequently, macroalgal communities would develop differently in the presence of infected versus uninfected snails. Our results show that uninfected snails consumed 40% more ephemeral macroalgal biomass than infected snails in the laboratory, probably because the digestive system of infected snails is compromised by C. lingua infection. In the field, this weaker grazing by infected snails resulted in significantly greater expansion of ephemeral macroalgal cover relative to grazing by uninfected snails. By decreasing the per-capita grazing rate of the dominant herbivore, C. lingua indirectly affects the composition of the macroalgal community and may in turn affect other species that depend on macroalgae for resources or habitat structure. In light of the abundance of parasites across systems, we suggest that, through trait-mediated indirect effects, parasites may be a common determinant of structure in ecological communities. PMID:17517667

  10. Microbial community structure and function in response to the shift of sulfide/nitrate loading ratio during the denitrifying sulfide removal process.

    PubMed

    Huang, Cong; Li, Zhi-Ling; Chen, Fan; Liu, Qian; Zhao, You-Kang; Zhou, Ji-Zhong; Wang, Ai-Jie

    2015-12-01

    Influence of acetate-C/NO3(-)-N/S(2-) ratio to the functional microbial community during the denitrifying sulfide removal process is poorly understood. Here, phylogenetic and functional bacterial community for elemental sulfur (S(0)) recovery and nitrate (NO3(-)) removal were investigated with the switched S(2-)/NO3(-) molar ratio ranged from 5/2 to 5/9. Optimized S(2-)/NO3(-) ratio was evaluated as 5/6, with the bacterial genera predominated with Thauera, Enterobacter, Thiobacillus and Stappia, and the sqr gene highly expressed. However, insufficient or high loading of acetate and NO3(-) resulted in the low S(0) recovery, and also significantly modified the bacterial community and genetic activity. With S(2-)/NO3(-) ratio of 5/2, autotrophic S(2-) oxidization genera were dominated and NO3(-) reduction activity was low, confirmed by the low expressed nirK gene. In contrast, S(2-)/NO3(-) ratio switched to 5/8 and 5/9 introduced diverse heterotrophic nitrate reduction and S(0) over oxidization genera in accompanied with the highly expressed nirK and sox genes. PMID:26340031

  11. Holocene shifts in the assembly of plant and animal communities implicate human impacts.

    PubMed

    Lyons, S Kathleen; Amatangelo, Kathryn L; Behrensmeyer, Anna K; Bercovici, Antoine; Blois, Jessica L; Davis, Matt; DiMichele, William A; Du, Andrew; Eronen, Jussi T; Faith, J Tyler; Graves, Gary R; Jud, Nathan; Labandeira, Conrad; Looy, Cindy V; McGill, Brian; Miller, Joshua H; Patterson, David; Pineda-Munoz, Silvia; Potts, Richard; Riddle, Brett; Terry, Rebecca; Tóth, Anikó; Ulrich, Werner; Villaseñor, Amelia; Wing, Scott; Anderson, Heidi; Anderson, John; Waller, Donald; Gotelli, Nicholas J

    2016-01-01

    Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity. PMID:26675730

  12. Shifts in soil testate amoeba communities associated with forest diversification.

    PubMed

    Bobrov, Anatoly A; Zaitsev, Andrei S; Wolters, Volkmar

    2015-05-01

    We studied changes of testate amoeba communities associated with the conversion of spruce monocultures into mixed beech-fir-spruce forests in the Southern Black Forest Mountains (Germany). In this region, forest conversion is characterized by a gradual development of beech undergrowth within thinned spruce tree stands leading to multiple age continuous cover forests with a diversified litter layer. Strong shifts in the abundance of testate amoeba observed in intermediate stages levelled off to monoculture conditions again after the final stage of the conversion process had been reached. The average number of species per conversion stage (i.e., local richness) did not respond strongly to forest conversion, but the total number of species (i.e., regional richness) was considerably higher in the initial stage than in the mixed forests, due to the large number of hygrophilous species inhabiting spruce monocultures. Functional diversity of the testate amoeba community, however, significantly increased during the conversion process. This shift was closely associated with improved C and N availability as well as higher niche diversity in the continuous cover stands. Lower soil acidity in these forests coincided with a higher relative abundance of eurytopic species. Our results suggest that testate amoeba communities are much more affected by physicochemical properties of the soil than directly by litter diversity. PMID:25820471

  13. Regime Shift in an Exploited Fish Community Related to Natural Climate Oscillations

    PubMed Central

    Auber, Arnaud; Travers-Trolet, Morgane; Villanueva, Maria Ching; Ernande, Bruno

    2015-01-01

    Identifying the various drivers of marine ecosystem regime shifts and disentangling their respective influence are critical tasks for understanding biodiversity dynamics and properly managing exploited living resources such as marine fish communities. Unfortunately, the mechanisms and forcing factors underlying regime shifts in marine fish communities are still largely unknown although climate forcing and anthropogenic pressures such as fishing have been suggested as key determinants. Based on a 24-year-long time-series of scientific surveys monitoring 55 fish and cephalopods species, we report here a rapid and persistent structural change in the exploited fish community of the eastern English Channel from strong to moderate dominance of small-bodied forage fish species with low temperature preferendum that occurred in the mid-1990s. This shift was related to a concomitant warming of the North Atlantic Ocean as attested by a switch of the Atlantic Multidecadal Oscillation from a cold to a warm phase. Interestingly, observed changes in the fish community structure were opposite to those classically induced by exploitation as larger fish species of higher trophic level increased in abundance. Despite not playing a direct role in the regime shift, fishing still appeared as a forcing factor affecting community structure. Moreover, although related to climate, the regime shift may have been facilitated by strong historic exploitation that certainly primed the system by favoring the large dominance of small-bodied fish species that are particularly sensitive to climatic variations. These results emphasize that particular attention should be paid to multidecadal natural climate variability and its interactions with both fishing and climate warming when aiming at sustainable exploitation and ecosystem conservation. PMID:26132268

  14. Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation.

    PubMed

    Werner, Jeffrey J; Garcia, Marcelo L; Perkins, Sarah D; Yarasheski, Kevin E; Smith, Samuel R; Muegge, Brian D; Stadermann, Frank J; DeRito, Christopher M; Floss, Christine; Madsen, Eugene L; Gordon, Jeffrey I; Angenent, Largus T

    2014-06-01

    Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity. PMID:24657858

  15. Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression

    PubMed Central

    Henne, Karsten; Fuchs, Felix; Kruth, Sebastian; Horz, Hans-Peter; Conrads, Georg

    2014-01-01

    Background Oral Campylobacter species have been found to be associated with periodontitis progression. While the etiological significance of Campylobacter rectus is quite established, the association of C. gracilis, C. concisus, and C. curvus with health or disease remains contradictory. Objectives This study hypothesizes that the proportion of species within the Campylobacter genus rather than the absolute abundance of a single species is a suitable indicator for periodontitis progression. Design Subgingival plaque from 90 periodontitis patients and gingival sulcus fluid of 32 healthy individuals were subjected to a newly developed nested PCR approach, in which all Campylobacter spp. were amplified simultaneously. The resulting mixture of 16S-rRNA-gene-amplicons were separated by single-stranded conformation polymorphism (SSCP) gel electrophoresis, followed by sequencing and identification of excised bands and relative quantification of band intensities. In all samples, the abundance of selected periodontitis marker species was determined based on DNA hybridization on a microarray. Results The highly prevalent Campylobacter community was composed of varying proportions of C. rectus, C. gracilis, C. concisus, and C. curvus. Cluster analysis based on SSCP-banding pattern resulted in distinct groups which in turn coincided with significant differences in abundance of established periodontitis marker species (Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum) and progression. Conclusions The shift in the Campylobacter community composition seems to display the general microbial community shift during clinical progression in a simplified manner. The focus on members of the Campylobacter in this study suggests that this genus can be an indicator of ecological changes in the subgingival oral microflora. PMID:25412608

  16. EXAFS Energy Shift and Structural Parameters

    NASA Astrophysics Data System (ADS)

    Kelly, Shelly D.; Ravel, Bruce

    2007-02-01

    In EXAFS analysis, the energy shift parameter is used to align the theoretical calculated spectrum to the energy grid of the measured spectrum. Unrealistically large energy shift values, sometimes in excess of 20 eV, are at times published in research articles. We therefore see the need for a concise discussion of the EXAFS energy shift parameter. This paper is intended as a learning tool for the proper alignment of theory to measured EXAFS spectra and proper interpretation of the energy shift parameter.

  17. Regime shifts in marine communities: a complex systems perspective on food web dynamics

    PubMed Central

    Yletyinen, Johanna; Bodin, Örjan; Weigel, Benjamin; Nordström, Marie C.; Bonsdorff, Erik; Blenckner, Thorsten

    2016-01-01

    Species composition and habitats are changing at unprecedented rates in the world's oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs. PMID:26888032

  18. Regime shifts in marine communities: a complex systems perspective on food web dynamics.

    PubMed

    Yletyinen, Johanna; Bodin, Örjan; Weigel, Benjamin; Nordström, Marie C; Bonsdorff, Erik; Blenckner, Thorsten

    2016-02-24

    Species composition and habitats are changing at unprecedented rates in the world's oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs. PMID:26888032

  19. Temporal Shifts in Microbial Communities in Nonpregnant African-American Women with and without Bacterial Vaginosis

    PubMed Central

    Wertz, John; Isaacs-Cosgrove, Natasha; Holzman, Claudia; Marsh, Terence L.

    2008-01-01

    Bacterial vaginosis (BV) has been described as an increase in the number of anaerobic and facultatively anaerobic bacteria relative to lactobacilli in the vaginal tract. Several undesirable consequences of this community shift can include irritation, white discharge, an elevated pH, and increased susceptibility to sexually transmitted infections. While the etiology of the condition remains ill defined, BV has been associated with adverse reproductive and pregnancy outcomes. In order to describe the structure of vaginal communities over time we determined the phylogenetic composition of vaginal communities from seven women sampled at multiple points using 16S rRNA gene sequencing. We found that women with no evidence of BV had communities dominated by lactobacilli that appeared stable over our sampling periods while those with BV had greater diversity and decreased stability overtime. In addition, only Lactobacillus iners was found in BV positive communities. PMID:19277101

  20. A shift from exploitation to interference competition with increasing density affects population and community dynamics.

    PubMed

    Holdridge, Erica M; Cuellar-Gempeler, Catalina; terHorst, Casey P

    2016-08-01

    Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of protozoa and bacteria under different combinations of protozoan density and basal resource availability. We then solved a dynamic predator-prey model for parameters of the functional response using population growth rates measured in our experiment. As population density increased, competition shifted from exploitation to interference, and competition was less dependent on resource levels. Surprisingly, the effect of resources was weakest when competition was the most intense. We found that at low population densities, competition was largely exploitative and resource availability had a large effect on population growth rates, but the effect of resources was much weaker at high densities. This shift in competitive mechanism could have implications for interspecific competition, trophic interactions, community diversity, and natural selection. We also tested whether this shift in the mechanism of competition with protozoa density affected the structure of the bacterial prey community. We found that both resources and protozoa density affected the structure of the bacterial prey community, suggesting that competitive mechanism may also affect trophic interactions. PMID:27551386

  1. Can the freshwater bacterial communities shift to the "marine-like" taxa?

    PubMed

    Zhang, Lei; Gao, Guang; Tang, Xiangming; Shao, Keqiang

    2014-11-01

    A mesocosm experiment was used to study the response of a freshwater bacterial community to increasing salinity. Bacterial community composition in the control and saline groups was analyzed using polymerase chain reaction (PCR)-terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes, followed by clonal sequencing of eight selected samples. Cluster analysis and phylogenetic analysis revealed that the bacterial communities in pre- and post-salt addition samples were significantly different. Detailed analysis showed: (i) the existing bacterial taxa markedly declined from freshwater to hypersaline habitats, although some taxa maintain balanced growth over a small salinity range through inter-genus changes in community structures; (ii) the addition of salt induced a clear shift in the community structure toward a striking increase in the relative abundance of the latent "marine-like" genera (e.g., Alcanivorax and Roseovarius). The reasons may be that freshwater bacteria adapt to live in low salt concentrations and low osmotic pressure. They were not adapted to high concentrations of salt, and their acute response to increasing salinity resulted in significantly decreased numbers. However, as the salinity increases, rare members of the ever-present community (rare or dormant bacterial taxa in the "microbial seed bank") rise to the fore, while previous dominant members drop away. This study provides direct evidence for bacterial succession from halosensitive taxa in freshwater to halotolerant ones in response to water salinization. PMID:24687773

  2. Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG).

    PubMed

    He, Xia; So, Mark Jason; de Los Reyes, Francis L

    2016-08-01

    To understand the effect of daily bioaugmentation in full-scale grease interceptors (GIs), we compared the microbial communities occurring in two full-scale GIs during bioaugmented and non-bioaugmented cycles. The changes in microbial communities were determined using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene clone library construction. Differences in the microbial community structure between control and bioaugmented cycles were observed in all cases, although the dominant terminal restriction fragments in the biological product were not detected. The addition of bioaugmentation products and changes in the GI microbial ecology were related to differences in GI performance. Understanding the shifts due to bioaugmentation will result in more informed assessments of the benefits of bioadditives on FOG removal in GIs as well as the effects on downstream sewer lines. PMID:26921180

  3. Recent disturbances augment community shifts in coral assemblages in Moorea, French Polynesia

    NASA Astrophysics Data System (ADS)

    Pratchett, M. S.; Trapon, M.; Berumen, M. L.; Chong-Seng, K.

    2011-03-01

    Coral reefs are often subject to disturbances that can cause enduring changes in community structure and abundance of coral reef organisms. In Moorea, French Polynesia, frequent disturbances between 1979 and 2003 caused marked shifts in taxonomic composition of coral assemblages. This study explores recent changes in live cover and taxonomic structure of coral communities on the north coast of Moorea, French Polynesia, to assess whether coral assemblages are recovering (returning to a previous Acropora-dominated state) or continuing to move towards an alternative community structure. Coral cover declined by 29.7% between July 2003 and March 2009, mostly due to loss of Acropora and Montipora spp. Coral mortality varied among habitats, with highest levels of coral loss on the outer reef slope (7-20 m depth). In contrast, there was limited change in coral cover within the lagoon, and coral cover actually increased on the reef crest. Observed changes in coral cover and composition correspond closely with the known feeding preferences and observed spatial patterns of Acanthaster planci L., though observed coral loss also coincided with at least one episode of coral bleaching, as well as persistent populations of the corallivorous starfish Culcita novaeguineae Muller & Troschel. While climate change poses an important and significant threat to the future structure and dynamics coral reef communities, outbreaks of A. planci remain a significant cause of coral loss in Moorea. More importantly, these recent disturbances have followed long-term shifts in the structure of coral assemblages, and the relative abundance of both Pocillopora and Porites continue to increase due to disproportionate losses of Acropora and Montipora. Moreover, Pocillopora and Porites dominate assemblages of juvenile corals, suggesting that there is limited potential for a return to an Acropora-dominated state, last recorded in 1979.

  4. Climate Change and Eutrophication Induced Shifts in Northern Summer Plankton Communities

    PubMed Central

    Suikkanen, Sanna; Pulina, Silvia; Engström-Öst, Jonna; Lehtiniemi, Maiju; Lehtinen, Sirpa; Brutemark, Andreas

    2013-01-01

    Marine ecosystems are undergoing substantial changes due to human-induced pressures. Analysis of long-term data series is a valuable tool for understanding naturally and anthropogenically induced changes in plankton communities. In the present study, seasonal monitoring data were collected in three sub-basins of the northern Baltic Sea between 1979 and 2011 and statistically analysed for trends and interactions between surface water hydrography, inorganic nutrient concentrations and phyto- and zooplankton community composition. The most conspicuous hydrographic change was a significant increase in late summer surface water temperatures over the study period. In addition, salinity decreased and dissolved inorganic nutrient concentrations increased in some basins. Based on redundancy analysis (RDA), warming was the key environmental factor explaining the observed changes in plankton communities: the general increase in total phytoplankton biomass, Cyanophyceae, Prymnesiophyceae and Chrysophyceae, and decrease in Cryptophyceae throughout the study area, as well as increase in rotifers and decrease in total zooplankton, cladoceran and copepod abundances in some basins. We conclude that the plankton communities in the Baltic Sea have shifted towards a food web structure with smaller sized organisms, leading to decreased energy available for grazing zooplankton and planktivorous fish. The shift is most probably due to complex interactions between warming, eutrophication and increased top-down pressure due to overexploitation of resources, and the resulting trophic cascades. PMID:23776676

  5. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  6. A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico.

    PubMed

    Newell, Silvia E; Eveillard, Damien; McCarthy, Mark J; Gardner, Wayne S; Liu, Zhanfei; Ward, Bess B

    2014-02-01

    The Gulf of Mexico is affected by hurricanes and suffers seasonal hypoxia. The Deepwater Horizon oil spill impacted every trophic level in the coastal region. Despite their importance in bioremediation and biogeochemical cycles, it is difficult to predict the responses of microbial communities to physical and anthropogenic disturbances. Here, we quantify sediment ammonia-oxidizing archaeal (AOA) community diversity, resistance and resilience, and important geochemical factors after major hurricanes and the oil spill. Dominant AOA archetypes correlated with different geochemical factors, suggesting that different AOA are constrained by distinct parameters. Diversity was lowest after the hurricanes, showing weak resistance to physical disturbances. However, diversity was highest during the oil spill and coincided with a community shift, suggesting a new alternative stable state sustained for at least 1 year. The new AOA community was not significantly different from that at the spill site 1 year after the spill. This sustained shift in nitrifier community structure may be a result of oil exposure. PMID:24596268

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

    USGS Publications Warehouse

    Anderson, P.J.; Piatt, J.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 (1953-1997) 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.

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

    USGS Publications Warehouse

    Anderson, P.J.; Piatt, J.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.

  9. 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.

  10. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  11. Voluntary Associations and Community Structure.

    ERIC Educational Resources Information Center

    Dillman, Don A.; And Others

    This study examined overlapping membership of voluntary associations as the basis of a statistical technique for analyzing community structure. An underlying assumption was that organizations select certain membership linkages in preference to others within a community. Thus one would expect to find points of integration and cleavage among…

  12. 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. PMID:23842653

  13. 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

  14. The Japanese Immigrant Community in Brazil: Language Contact and Shift.

    ERIC Educational Resources Information Center

    Kanazawa, Hiroki; Loveday, Leo

    1988-01-01

    Studies language contact and language shift among different generations of Japanese immigrants in Brazil. The social factors involved in the abandonment of the ethnic (Japanese) code is considered. Results indicate that, typically, ethnic identity switch is accompanied by mother tongue replacement with Portuguese by the third generation.…

  15. 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. PMID:24668014

  16. 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

  17. Export flux and stability as regulators of community composition in pelagic marine biological communities: Implications for regime shifts [review article

    NASA Astrophysics Data System (ADS)

    Laws, Edward

    2004-02-01

    Regime shifts occur when a system transitions from one stable configuration to another. Such abrupt changes in biological communities may reflect small changes in environmental conditions such as temperature, oxygen concentration, or irradiance. Although it seems clear that biological communities are not randomly organized with respect to their functional components, there is disagreement concerning the factors that control that organization. In this paper, I examine the implications of assuming that the composition of pelagic marine biological communities evolves to a condition of maximum stability or resilience. At temperatures of 25 °C or less, a model based on this hypothesis predicts abrupt and discontinuous transitions from configurations associated with low export ratios to configurations associated with high export ratios as the rate of primary production increases. Comparison between field data and model predictions shows very good agreement at low and high production rates, but the field data do not support a step-function transition from low to high export ratios at intermediate rates of production. Instead, the field data are consistent with the assumption that food webs effect the transition between high and low ef ratio modes by reconfiguring themselves in a more-or-less continuous manner. The configurations associated with these transitions are at least locally more resilient than any similar food web structure.

  18. Morphological and Compositional Shifts in an Experimental Bacterial Community Influenced by Protists with Contrasting Feeding Modes

    PubMed Central

    Simek, K.; Vrba, J.; Pernthaler, J.; Posch, T.; Hartman, P.; Nedoma, J.; Psenner, R.

    1997-01-01

    In a two-stage continuous-flow system, we studied the impacts of different protozoan feeding modes on the morphology and taxonomic structure of mixed bacterial consortia, which were utilizing organic carbon released by a pure culture of a Rhodomonas sp. grown on inorganic medium in the first stage of the system. Two of three second stages operated in parallel were inoculated by a bacterivorous flagellate, Bodo saltans, and an algivorous ciliate, Urotricha furcata, respectively. The third vessel served as a control. In two experiments, where algal and bacterial populations grew at rates and densities typical for eutrophic waters, we compared community changes of bacteria, algae, and protozoa under quasi-steady-state conditions and during the transient stage after the protozoan inoculation. In situ hybridization with fluorescent oligonucleotide probes and cultivation-based approaches were used to tentatively analyze the bacterial community composition. Initially the cell size distribution and community structure of all cultivation vessels showed similar patterns, with a dominance of 1- to 2.5-(mu)m-long rods from the beta subdivision of the phylum Proteobacteria ((beta)-Proteobacteria). Inoculation with the ciliate increased bacterial growth in this substrate-controlled variant, seemingly via a recycling of nutrients and substrate released by grazing on algae, but without any detectable effect on the composition of bacterial assemblage. In contrast, an inoculation with the bacterivore, B. saltans, resulted in a decreased proportion of the (beta)-Proteobacteria. One part of the assemblage (<4% of total bacterial numbers), moreover, produced large grazing-resistant threadlike cells. As B. saltans ingested only cells of <3 (mu)m, this strategy yielded a refuge for (symbl)70% of total bacterial biomass from being grazed. Another consequence of the heavy predation in this variant was a shift to the numerical dominance of the (alpha)-Proteobacteria. The enhanced

  19. 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

  20. Bee community shifts with landscape context in a tropical countryside.

    PubMed

    Brosi, Berry J; Daily, Gretchen C; Ehrlich, Paul R

    2007-03-01

    The ongoing scientific controversy over a putative "global pollination crisis" underscores the lack of understanding of the response of bees (the most important taxon of pollinators) to ongoing global land-use changes. We studied the effects of distance to forest, tree management, and floral resources on bee communities in pastures (the dominant land-use type) in southern Costa Rica. Over two years, we sampled bees and floral resources in 21 pastures at three distance classes from a large (approximately 230-ha) forest patch and of three common types: open pasture; pasture with remnant trees; and pasture with live fences. We found no consistent differences in bee diversity or abundance with respect to pasture management or floral resources. Bee community composition, however, was strikingly different at forest edges as compared to deforested countryside only a few hundred meters from forest. At forest edges, native social stingless bees (Apidae: Meliponini) comprised approximately 50% of the individuals sampled, while the alien honeybee Apis mellifera made up only approximately 5%. Away from forests, meliponines dropped to approximately 20% of sampled bees, whereas Apis increased to approximately 45%. Meliponine bees were also more speciose at forest edge sites than at a distance from forest, their abundance decreased with continuous distance to the nearest forest patch, and their species richness was correlated with the proportion of forest cover surrounding sample sites at scales from 200 to 1200 m. Meliponines and Apis together comprise the eusocial bee fauna of the study area and are unique in quickly recruiting foragers to high-quality resources. The diverse assemblage of native meliponine bees covers a wide range of body sizes and flower foraging behavior not found in Apis, and populations of many bee species (including Apis), are known to fluctuate considerably from year to year. Thus, the forest-related changes in eusocial bee communities we found may have

  1. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

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

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  2. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  3. Methanogenic community shift in anaerobic batch digesters treating swine wastewater.

    PubMed

    Kim, Woong; Lee, Seungyong; Shin, Seung Gu; Lee, Changsoo; Hwang, Kwanghyun; Hwang, Seokhwan

    2010-09-01

    Qualitative and quantitative molecular analysis techniques were used to determine associations between differences in methanogenic microbial communities and the efficiency of batch anaerobic digesters. Two bioreactors were initially seeded with anaerobic sludge originating from a local municipal wastewater treatment plant and then supplemented with swine wastewater. Differences were observed in the total amount of methane produced in the two bioreactors (7.9L/L, and 4.5L/L, respectively). To explain these differences, efforts were taken to characterize the microbial populations present using a PCR-based DGGE analysis with methanogenic primer and probe sets. The groups Methanomicrobiales (MMB), Methanobacteriales (MBT), and Methanosarcinales (MSL) were detected, but Methanococcales (MCC) was not detected. Following this qualitative assay, real-time PCR was used to investigate quantitative differences in the populations of these methanogenic orders. MMB was found to be the dominant order present and its abundance patterns were different in the two digesters. The population profiles of the other methanogenic groups also differed. Through redundancy analysis, correlations between the concentrations of the different microbes and chemical properties such as volatile fatty acids were calculated. Correlations between MBT and MSL populations and chemical properties were found to be consistent in both digesters, however, differences were observed in the correlations between MMB and propionate. These results suggest that interactions between populations of MMB and other methanogens affected the final methane yield, despite MMB remaining the dominant group overall. The exact details of why changes in the MMB community caused different profiles of methane production could not be ascertained. However, this research provides evidence that microbial behavior is important for regulating the performance of anaerobic processes. PMID:20692007

  4. Bacterioplankton Community Shifts in an Arctic Lake Correlate with Seasonal Changes in Organic Matter Source

    PubMed Central

    Crump, Byron C.; Kling, George W.; Bahr, Michele; Hobbie, John E.

    2003-01-01

    Seasonal shifts in bacterioplankton community composition in Toolik Lake, a tundra lake on the North Slope of Alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (DOM). A shift in community composition, measured by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes, occurred at 4°C in near-surface waters beneath seasonal ice and snow cover in spring. This shift was associated with an annual peak in bacterial productivity ([14C]leucine incorporation) driven by the large influx of labile terrestrial DOM associated with snow meltwater. A second shift occurred after the flux of terrestrial DOM had ended in early summer as ice left the lake and as the phytoplankton community developed. Bacterioplankton communities were composed of persistent populations present throughout the year and transient populations that appeared and disappeared. Most of the transient populations could be divided into those that were advected into the lake with terrestrial DOM in spring and those that grew up from low concentrations during the development of the phytoplankton community in early summer. Sequencing of DNA in DGGE bands demonstrated that most bands represented single ribotypes and that matching bands from different samples represented identical ribotypes. Bacteria were identified as members of globally distributed freshwater phylogenetic clusters within the α- and β-Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides group, and the Actinobacteria. PMID:12676708

  5. 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

  6. Shift in a large river fish assemblage: body-size and trophic structure dynamics.

    PubMed

    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

  7. 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. PMID:26322496

  8. Shifting Regimes and Changing Interactions in the Lake Washington, U.S.A., Plankton Community from 1962–1994

    PubMed Central

    Francis, Tessa B.; Wolkovich, Elizabeth M.; Scheuerell, Mark D.; Katz, Stephen L.; Holmes, Elizabeth E.; Hampton, Stephanie E.

    2014-01-01

    Understanding how changing climate, nutrient regimes, and invasive species shift food web structure is critically important in ecology. Most analytical approaches, however, assume static species interactions and environmental effects across time. Therefore, we applied multivariate autoregressive (MAR) models in a moving window context to test for shifting plankton community interactions and effects of environmental variables on plankton abundance in Lake Washington, U.S.A. from 1962–1994, following reduced nutrient loading in the 1960s and the rise of Daphnia in the 1970s. The moving-window MAR (mwMAR) approach showed shifts in the strengths of interactions between Daphnia, a dominant grazer, and other plankton taxa between a high nutrient, Oscillatoria-dominated regime and a low nutrient, Daphnia-dominated regime. The approach also highlighted the inhibiting influence of the cyanobacterium Oscillatoria on other plankton taxa in the community. Overall community stability was lowest during the period of elevated nutrient loading and Oscillatoria dominance. Despite recent warming of the lake, we found no evidence that anomalous temperatures impacted plankton abundance. Our results suggest mwMAR modeling is a useful approach that can be applied across diverse ecosystems, when questions involve shifting relationships within food webs, and among species and abiotic drivers. PMID:25338087

  9. 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

  10. 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

  11. 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. PMID:26903635

  12. Community-wide changes in intertaxonomic temporal co-occurrence resulting from phenological shifts.

    PubMed

    Hua, Fangyuan; Hu, Junhua; Liu, Yang; Giam, Xingli; Lee, Tien Ming; Luo, Hao; Wu, Jia; Liang, Qiaoyi; Zhao, Jian; Long, Xiaoyan; Pang, Hong; Wang, Biao; Liang, Wei; Zhang, Zhengwang; Gao, Xuejie; Zhu, Jiang

    2016-05-01

    Global climate change is known to affect the assembly of ecological communities by altering species' spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species' temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here, we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon groups from 329 local meteorological observatories across China. We show that widespread shifts in phenology have resulted in community-wide changes in the temporal overlap between taxa that are dominated by extensions, and that these changes are largely due to taxa's altered span of temporal occurrence rather than the degree of synchrony in phenological shifts. Importantly, our findings also suggest that climate change may have led to less phenological mismatch than generally presumed, and that the context under which to discuss the ecological consequences of phenological shifts should be expanded beyond asynchronous shifts. PMID:26680152

  13. 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.

  14. Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators?

    PubMed

    Poirier, Simon; Bize, Ariane; Bureau, Chrystelle; Bouchez, Théodore; Chapleur, Olivier

    2016-09-01

    Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L. Final AD performance was not impaired up to 1.00 g/L. However, progressive shifts in microbial community structure were detected from 0.50 g/L. The methanogenic function was maintained along with increasing initial phenol concentrations up to 2.00 g/L thanks to the emergence of genus Methanoculleus at the expense of Methanosarcina. Within syntrophic populations, family Syntrophomonadaceae proportion was gradually reduced by phenol while Synergistaceae gained in importance in the microbiome. Moreover, at 2.00 g/L, the relative abundance of families belonging to order Clostridiales dropped, leading to the predominance of populations assigned to order Bacteroidales even though it did not prevent final AD performance deterioration. It illustrates the high level of adaptability of archaeal and bacterial communities and suggests the possibility of determining early warning microbial indicators associated with phenol inhibition. PMID:27208731

  15. 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.

  16. Changes in Soil Microbial Community Structure with Flooding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  17. Measurement of isotope shifts and hyperfine structure in Zr II

    NASA Astrophysics Data System (ADS)

    Rosner, S. D.; Holt, R. A.

    2016-06-01

    We have applied fast-ion-beam laser-fluorescence spectroscopy to measure the isotope shifts (IS) of 51 optical transitions in the wavelength range 420.6–461.4 nm and the hyperfine structures (hfs) of 11 even parity and 30 odd parity levels in Zr II. The IS and many of the hfs measurements are the first for these transitions and levels. These atomic data are very important for astrophysical studies of chemical abundances, allowing correction for saturation and the effects of blended lines. They also provide important constraints on stellar diffusion modeling and provide a benchmark for theoretical atomic structure calculations.

  18. Detection of community structure in networks based on community coefficients

    NASA Astrophysics Data System (ADS)

    Lu, Hu; Wei, Hui

    2012-12-01

    Determining community structure in networks is fundamental to the analysis of the structural and functional properties of those networks, including social networks, computer networks, and biological networks. Modularity function Q, which was proposed by Newman and Girvan, was once the most widely used criterion for evaluating the partition of a network into communities. However, modularity Q is subject to a serious resolution limit. In this paper, we propose a new function for evaluating the partition of a network into communities. This is called community coefficient C. Using community coefficient C, we can automatically identify the ideal number of communities in the network, without any prior knowledge. We demonstrate that community coefficient C is superior to the modularity Q and does not have a resolution limit. We also compared the two widely used community structure partitioning methods, the hierarchical partitioning algorithm and the normalized cuts (Ncut) spectral partitioning algorithm. We tested these methods on computer-generated networks and real-world networks whose community structures were already known. The Ncut algorithm and community coefficient C were found to produce better results than hierarchical algorithms. Unlike several other community detection methods, the proposed method effectively partitioned the networks into different community structures and indicated the correct number of communities.

  19. 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

  20. 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. PMID:25714833

  1. 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…

  2. 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. PMID:25009065

  3. 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

  4. 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. PMID:23568711

  5. Discovering Network Structure Beyond Communities

    PubMed Central

    Nishikawa, Takashi; Motter, Adilson E.

    2011-01-01

    To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest. PMID:22355667

  6. Shift of Bacterial Community in Synanthropic Mite Tyrophagus putrescentiae Induced by Fusarium Fungal Diet

    PubMed Central

    Hubert, Jan; Nesvorná, Marta; Ságová-Marečková, Markéta; Kopecký, Jan

    2012-01-01

    Background Tyrophagus putrescentiae (Acari: Astigmata) and Fusarium sp. co-occur in poorly managed grain. In a laboratory experiment, mite grazing resulted in significant reduction of fungal mycelium on cultivation plates. The destruction of mycelium appeared to be a result of an interaction between the mites, fungi and associated bacteria. Methodology and Principal Findings A laboratory experiment was performed to simulate a situation of grain multiinfested by mites and Fusarium fungi. Changes of mite-associated bacterial community in T. putrescentiae were described in 3 habitats: (i) T. putrescentiae mites from a rearing diet prior to their transfer to fungal diet; (ii) fungal mycelium before mite introduction; (iii) mites after 7 day diet of each Fusarium avenaceum, F. culmorum, F. poae and F. verticillioides. Bacterial communities were characterized by 16 S rRNA gene sequencing. In total, 157 nearly full-length 16 S rRNA gene sequences from 9 samples representing selected habitats were analyzed. In the mites, the shift from rearing to fungal diet caused changes in mite associated bacterial community. A diverse bacterial community was associated with mites feeding on F. avenaceum, while feeding on the other three Fusarium spp. led to selection of a community dominated by Bacillaceae. Conclusions/Significance The work demonstrated changes of bacterial community associated with T. putrescentiae after shift to fungal diets suggesting selection for Bacillaceae species known as chitinase producers, which might participate in the fungal mycelium hydrolysis. PMID:23119013

  7. Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance: Implications from microbial community shift.

    PubMed

    Cho, Si-Kyung; Kim, Dong-Hoon; Quince, Christopher; Im, Wan-Taek; Oh, Sae-Eun; Shin, Seung Gu

    2016-09-01

    To elucidate the enhanced methane yield from organic wastes, the effects of low-strength ultrasonication on the microbial community structures in upflow anaerobic sludge blanket reactors were for the first time analyzed using pyrosequencing. Interestingly, a more even microbial community was observed in the ultrasonicated granules than in the control, which could compensate for the decreased richness and resulted in comparable (archaea) or even higher (bacteria) diversity. The ultrasonicated granules contained higher levels of δ-Proteobacteria, of which many are reportedly potential syntrophs, as well as methanogenic genera Methanosaeta, Methanotorris, and Methanococcus. The increased presence of syntrophic bacteria with their methanogenic partners was discussed with respect to hydrogen flux; their selective proliferation seems to be responsible for the enhanced anaerobic performance. This study is the first research shedding light on the novel function of low-strength ultrasound shifting the microbial structure towards better biogas production performance, and will facilitate application of low-strength ultrasound to other bioprocesses. PMID:27150761

  8. Functional shifts in unvegetated, perhumid, recently-deglaciated soils do not correlate with shifts in soil bacterial community composition.

    PubMed

    Sattin, Sarah R; Cleveland, Cory C; Hood, Eran; Reed, Sasha C; King, Andrew J; Schmidt, Steven K; Robeson, Michael S; Ascarrunz, Nataly; Nemergut, Diana R

    2009-12-01

    Past work in recently deglaciated soils demonstrates that microbial communities undergo shifts prior to plant colonization. To date, most studies have focused on relatively 'long' chronosequences with the ability to sample plant-free sites over at least 50 years of development. However, some recently deglaciated soils feature rapid plant colonization and questions remain about the relative rate of change in the microbial community in the unvegetated soils of these chronosequences. Thus, we investigated the forelands of the Mendenhall Glacier near Juneau, AK, USA, where plants rapidly establish. We collected unvegetated samples representing soils that had been ice-free for 0, 1, 4, and 8 years. Total nitrogen (N) ranged from 0.00 approximately 0.14 mg/g soil, soil organic carbon pools ranged from 0.6 approximately 2.3 mg/g soil, and both decreased in concentration between the 0 and 4 yr soils. Biologically available phosphorus (P) and pH underwent similar dynamics. However, both pH and available P increased in the 8 yr soils. Nitrogen fixation was nearly undetectable in the most recently exposed soils, and increased in the 8 yr soils to approximately 5 ng N fixed/cm(2)/h, a trend that was matched by the activity of the soil N-cycling enzymes urease and beta-l,4-N-acetyl-glucosa-minidase. 16S rRNA gene clone libraries revealed no significant differences between the 0 and 8 yr soils; however, 8 yr soils featured the presence of cyanobacteria, a division wholly absent from the 0 yr soils. Taken together, our results suggest that microbes are consuming allochtonous organic matter sources in the most recently exposed soils. Once this carbon source is depleted, a competitive advantage may be ceded to microbes not reliant on in situ nutrient sources. PMID:20127458

  9. Significant Scales in Community Structure

    PubMed Central

    Traag, V. A.; Krings, G.; Van Dooren, P.

    2013-01-01

    Many complex networks show signs of modular structure, uncovered by community detection. Although many methods succeed in revealing various partitions, it remains difficult to detect at what scale some partition is significant. This problem shows foremost in multi-resolution methods. We here introduce an efficient method for scanning for resolutions in one such method. Additionally, we introduce the notion of “significance” of a partition, based on subgraph probabilities. Significance is independent of the exact method used, so could also be applied in other methods, and can be interpreted as the gain in encoding a graph by making use of a partition. Using significance, we can determine “good” resolution parameters, which we demonstrate on benchmark networks. Moreover, optimizing significance itself also shows excellent performance. We demonstrate our method on voting data from the European Parliament. Our analysis suggests the European Parliament has become increasingly ideologically divided and that nationality plays no role. PMID:24121597

  10. Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus

    PubMed Central

    Stratil, Stephanie B; Neulinger, Sven C; Knecht, Henrik; Friedrichs, Anette K; Wahl, Martin

    2013-01-01

    The thallus surface of the brown macroalga Fucus vesiculosus is covered by a specific biofilm community. This biofilm supposedly plays an important role in the interaction between host and environment. So far, we know little about compositional or functional shifts of this epibiotic bacterial community under changing environmental conditions. In this study, the response of the microbiota to different temperatures with respect to cell density and community composition was analyzed by nonculture-based methods (denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene). Redundancy analysis showed that despite high variability among host individuals temperature accounted for 20% of the variation in the bacterial community composition, whereas cell density did not differ between groups. Across all samples, 4341 bacterial operational taxonomic units (OTUs) at a 97% similarity level were identified. Eight percent of OTUs were significantly correlated with low, medium, and high temperatures. Notably, the family Rhodobacteraceae increased in relative abundance from 20% to 50% with increasing temperature. OTU diversity (evenness and richness) was higher at 15°C than at the lower and higher temperatures. Considering their known and presumed ecological functions for the host, change in the epibacterial community may entail shifts in the performance of the host alga. PMID:23568841

  11. 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

  12. 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

  13. Regime shift in sandy beach microbial communities following Deepwater Horizon oil spill remediation efforts.

    PubMed

    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

  14. 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

  15. 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. PMID:19916089

  16. 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. PMID:26397118

  17. Dynamic insight into protein structure utilizing red edge excitation shift.

    PubMed

    Chattopadhyay, Amitabha; Haldar, Sourav

    2014-01-21

    Proteins are considered the workhorses in the cellular machinery. They are often organized in a highly ordered conformation in the crowded cellular environment. These conformations display characteristic dynamics over a range of time scales. An emerging consensus is that protein function is critically dependent on its dynamics. The subtle interplay between structure and dynamics is a hallmark of protein organization and is essential for its function. Depending on the environmental context, proteins can adopt a range of conformations such as native, molten globule, unfolded (denatured), and misfolded states. Although protein crystallography is a well established technique, it is not always possible to characterize various protein conformations by X-ray crystallography due to transient nature of these states. Even in cases where structural characterization is possible, the information obtained lacks dynamic component, which is needed to understand protein function. In this overall scenario, approaches that reveal information on protein dynamics are much appreciated. Dynamics of confined water has interesting implications in protein folding. Interfacial hydration combines the motion of water molecules with the slow moving protein molecules. The red edge excitation shift (REES) approach becomes relevant in this context. REES is defined as the shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of absorption spectrum. REES arises due to slow rates (relative to fluorescence lifetime) of solvent relaxation (reorientation) around an excited state fluorophore in organized assemblies such as proteins. Consequently, REES depends on the environment-induced motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. In the case of a protein, the confined water in the protein creates a dipolar field that acts as the solvent for a fluorophore

  18. 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

  19. 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. PMID:26324852

  20. 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. PMID:27504632

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

    SciTech Connect

    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. 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.

  2. A shift in microbial community composition as a result of a natural temporal change in in a hot spring ecosystem

    NASA Astrophysics Data System (ADS)

    Hamilton, T. L.; Havig, J. R.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.; Peters, J.

    2011-12-01

    Strong physical and geochemical gradients in geothermal springs generate a multiplicity of ecological niches capable of supporting a diverse array of microbial populations and their associated ecological functions. Combining geochemical data with thermodynamic calculations enables predictions of the most likely energy sources supporting these diverse communities. Recent results from spatially- and geochemically-distinct springs in Yellowstone National Park, WY suggest that the structure and composition of microbial communities in geothermal environments can be predicted on the basis of geochemical measurements and associated energetic calculations. Obsidian Pool, a high temperature chemotrophic thermal feature in Yellowstone National Park, WY, has undergone decrease in pH from 6.8 to 4.3 over the past 11 years, a likely result of increased vapor phase input. This documented decrease in pH was accompanied by extensive variation in other geochemical analytes, including numerous redox sensitive compounds. Many of these compounds can be used as a source of energy by microbial populations, although the energetics associated with their utilization vary widely as a function of pH. For example, the energetics associated with redox transformation of iron (e.g., Fe2+ and Fe3+) and sulfur (S2-, So) vary widely with pH, while the energetics associated with redox transformation of nitrogen compounds (e.g., NH4+, NO2-, and NO3-) do so to a much lesser degree. Given that spatial variation in the availability of inorganic sources of energy and the energetics associated with their utilization has been shown to influence the composition of communities in geothermal environments, we hypothesized that a temporal shift, such as that observed in Obsidian Pool, would select for microbial communities that reflect this change. We evaluated this hypothesis using pyrotag sequencing and qPCR of archaeal and bacterial 16S rRNA genes. The data reveal a shift in community structure and

  3. Ontogenetic shifts in trait-mediated mechanisms of plant community assembly.

    PubMed

    Lasky, Jesse R; Bachelot, Bénédicte; Muscarella, Robert; Schwartz, Naomi; Forero-Montaña, Jimena; Nytch, Christopher J; Swenson, Nathan G; Thompson, Jill; Zimmerman, Jess K; Uriarte, Maria

    2015-08-01

    Identifying the processes that maintain highly diverse plant communities remains a central goal in ecology. Species variation in growth and survival rates across ontogeny, represented by tree size classes and life history stage-specific niche partitioning, are potentially important mechanisms for promoting forest diversity. However, the role of ontogeny in mediating competitive dynamics and promoting functional diversity is not well understood, particular in high-diversity systems such as tropical forests. The interaction between interspecific functional trait variation and ontogenetic shifts in competitive dynamics may yield insights into the ecophysiological mechanisms promoting community diversity. We investigated how functional trait (seed size, maximum height, SLA, leaf N, and wood density) associations with growth, survival, and response to competing neighbors differ among seedlings and two size classes of trees in a subtropical rain forest in Puerto Rico. We used a hierarchical Bayes model of diameter growth and survival to infer trait relationships with ontogenetic change in competitive dynamics. Traits were more strongly associated with average growth and survival than with neighborhood interactions, and were highly consistent across ontogeny for most traits. The associations between trait values and tree responses to crowding by neighbors showed significant shifts as trees grew. Large trees exhibited greater growth as the difference in species trait values among neighbors increased, suggesting trait-associated niche partitioning was important for the largest size class. Our results identify potential axes of niche partitioning and performance-equalizing functional trade-offs across ontogeny, promoting species coexistence in this diverse forest community. PMID:26405741

  4. Microbial community compositional shifts in bleached colonies of the Brazilian reef-building coral Siderastrea stellata.

    PubMed

    Lins-de-Barros, Monica M; Cardoso, Alexander M; Silveira, Cynthia B; Lima, Joyce L; Clementino, Maysa M; Martins, Orlando B; Albano, Rodolpho M; Vieira, Ricardo P

    2013-01-01

    The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes. PMID:22864853

  5. Simple probabilistic algorithm for detecting community structure

    NASA Astrophysics Data System (ADS)

    Ren, Wei; Yan, Guiying; Liao, Xiaoping; Xiao, Lan

    2009-03-01

    With the growing number of available social and biological networks, the problem of detecting the network community structure is becoming more and more important which acts as the first step to analyze these data. The community structure is generally regarded as that nodes in the same community tend to have more edges and less if they are in different communities. We propose a simple probabilistic algorithm for detecting community structure which employs expectation-maximization (SPAEM). We also give a criterion based on the minimum description length to identify the optimal number of communities. SPAEM can detect overlapping nodes and handle weighted networks. It turns out to be powerful and effective by testing simulation data and some widely known data sets.

  6. Community Structure in Directed Networks

    NASA Astrophysics Data System (ADS)

    Leicht, E. A.; Newman, M. E. J.

    2008-03-01

    We consider the problem of finding communities or modules in directed networks. In the past, the most common approach to this problem has been to ignore edge direction and apply methods developed for community discovery in undirected networks, but this approach discards potentially useful information contained in the edge directions. Here we show how the widely used community finding technique of modularity maximization can be generalized in a principled fashion to incorporate information contained in edge directions. We describe an explicit algorithm based on spectral optimization of the modularity and show that it gives demonstrably better results than previous methods on a variety of test networks, both real and computer generated.

  7. Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient.

    PubMed

    Morrow, Kathleen M; Fiore, Cara L; Lesser, Michael P

    2016-06-01

    The giant barrel sponge, Xestospongia muta, is a high microbial abundance sponge found on Caribbean coral reefs along shallow to mesophotic depth gradients where multiple abiotic factors change with depth. Sponges were collected along a depth gradient at Little Cayman (LC) and Lee Stocking Island (LSI), and the microbiome of these samples was analysed using 16S rRNA amplicon sequencing. Statistically significant shifts in community structure and dissimilarity (∼ 40%) were detected from 10 to 90 m in LC sponges, but a similar shift was not identified in sponges from 10 to 60 m at LSI (only 17% dissimilar). Additionally, inorganic nutrient levels steadily increased with depth at LSI but not at LC. Based on bulk stable isotopic variability, sponges collected from LC were generally more enriched in (15) N and less enriched in (13) C as depth increased, suggesting a transition from dependency on photoautotrophy to heterotrophy as depth increased. Patterns of stable isotopic enrichment were largely invariant at LSI, which is also reflected in the more stable microbial community along the depth gradient. It appears that environmental factors that change with depth may contribute to differences in X. muta microbial assemblages, demonstrating the importance of contemporaneous environmental sampling in studies of the microbiome of sponges. PMID:26769079

  8. 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

  9. Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill

    PubMed Central

    Kandalepas, Demetra; Blum, Michael J.; Van Bael, Sunshine A.

    2015-01-01

    Symbiotic associations can be disrupted by disturbance or by changing environmental conditions. Endophytes are fungal and bacterial symbionts of plants that can affect performance. As in more widely known symbioses, acute or chronic stressor exposure might trigger disassociation of endophytes from host plants. We tested this hypothesis by examining the effects of oil exposure following the Deepwater Horizon (DWH) oil spill on endophyte diversity and abundance in Spartina alterniflora – the foundational plant in northern Gulf coast salt marshes affected by the spill. We compared bacterial and fungal endophytes isolated from plants in reference areas to isolates from plants collected in areas with residual oil that has persisted for more than three years after the DWH spill. DNA sequence-based estimates showed that oil exposure shifted endophyte diversity and community structure. Plants from oiled areas exhibited near total loss of leaf fungal endophytes. Root fungal endophytes exhibited a more modest decline and little change was observed in endophytic bacterial diversity or abundance, though a shift towards hydrocarbon metabolizers was found in plants from oiled sites. These results show that plant-endophyte symbioses can be disrupted by stressor exposure, and indicate that symbiont community disassembly in marsh plants is an enduring outcome of the DWH spill. PMID:25923203

  10. Prokaryotic community structure and respiration during long-term incubations

    PubMed Central

    Baltar, Federico; Lindh, Markus V; Parparov, Arkadi; Berman, Tom; Pinhassi, Jarone

    2012-01-01

    Despite the importance of incubation assays for studies in microbial ecology that frequently require long confinement times, few reports are available in which changes in the assemblage structure of aquatic prokaryotes were monitored during long-term incubations. We measured rates of dissolved organic carbon degradation and microbial respiration by consumption of dissolved oxygen (DO) in four experiments with Lake Kinneret near-surface water and, concomitantly, we analyzed the variability in prokaryotic community structure during long-term dark bottle incubations. During the first 24 h, there were only minor changes in bacterial community composition. Thereafter there were marked changes in the prokaryotic community structure during the incubations. In contrast, oxygen consumption rates (a proxy for both respiration and dissolved organic carbon degradation rates) remained stable for up to 10–23 days. This study is one of the first to examine closely the phylo-genetic changes that occur in the microbial community of untreated freshwater during long-term (days) incubations in dark, sealed containers. Novel information on the diversity of the main bacterial phylotypes that may be involved in dissolved organic matter degradation in lake Kinneret is also provided. Our results suggest that, under certain ecological settings, constant community metabolic rates can be maintained as a result of shifts in community composition. PMID:22950026

  11. 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.

  12. Protein structure prediction using global optimization by basin-hopping with NMR shift restraints

    NASA Astrophysics Data System (ADS)

    Hoffmann, Falk; Strodel, Birgit

    2013-01-01

    Computational methods that utilize chemical shifts to produce protein structures at atomic resolution have recently been introduced. In the current work, we exploit chemical shifts by combining the basin-hopping approach to global optimization with chemical shift restraints using a penalty function. For three peptides, we demonstrate that this approach allows us to find near-native structures from fully extended structures within 10 000 basin-hopping steps. The effect of adding chemical shift restraints is that the α and β secondary structure elements form within 1000 basin-hopping steps, after which the orientation of the secondary structure elements, which produces the tertiary contacts, is driven by the underlying protein force field. We further show that our chemical shift-restraint BH approach also works for incomplete chemical shift assignments, where the information from only one chemical shift type is considered. For the proper implementation of chemical shift restraints in the basin-hopping approach, we determined the optimal weight of the chemical shift penalty energy with respect to the CHARMM force field in conjunction with the FACTS solvation model employed in this study. In order to speed up the local energy minimization procedure, we developed a function, which continuously decreases the width of the chemical shift penalty function as the minimization progresses. We conclude that the basin-hopping approach with chemical shift restraints is a promising method for protein structure prediction.

  13. Community structure in the phonological network

    PubMed Central

    Siew, Cynthia S. Q.

    2013-01-01

    Community structure, which refers to the presence of densely connected groups within a larger network, is a common feature of several real-world networks from a variety of domains such as the human brain, social networks of hunter-gatherers and business organizations, and the World Wide Web (Porter et al., 2009). Using a community detection technique known as the Louvain optimization method, 17 communities were extracted from the giant component of the phonological network described in Vitevitch (2008). Additional analyses comparing the lexical and phonological characteristics of words in these communities against words in randomly generated communities revealed several novel discoveries. Larger communities tend to consist of short, frequent words of high degree and low age of acquisition ratings, and smaller communities tend to consist of longer, less frequent words of low degree and high age of acquisition ratings. Real communities also contained fewer different phonological segments compared to random communities, although the number of occurrences of phonological segments found in real communities was much higher than that of the same phonological segments in random communities. Interestingly, the observation that relatively few biphones occur very frequently and a large number of biphones occur rarely within communities mirrors the pattern of the overall frequency of words in a language (Zipf, 1935). The present findings have important implications for understanding the dynamics of activation spread among words in the phonological network that are relevant to lexical processing, as well as understanding the mechanisms that underlie language acquisition and the evolution of language. PMID:23986735

  14. Herbivory and dominance shifts among exotic and congeneric native plant species during plant community establishment.

    PubMed

    Engelkes, Tim; Meisner, Annelein; Morriën, Elly; Kostenko, Olga; Van der Putten, Wim H; Macel, Mirka

    2016-02-01

    Invasive exotic plant species often have fewer natural enemies and suffer less damage from herbivores in their new range than genetically or functionally related species that are native to that area. Although we might expect that having fewer enemies would promote the invasiveness of the introduced exotic plant species due to reduced enemy exposure, few studies have actually analyzed the ecological consequences of this situation in the field. Here, we examined how exposure to aboveground herbivores influences shifts in dominance among exotic and phylogenetically related native plant species in a riparian ecosystem during early establishment of invaded communities. We planted ten plant communities each consisting of three individuals of each of six exotic plant species as well as six phylogenetically related natives. Exotic plant species were selected based on a rapid recent increase in regional abundance, the presence of a congeneric native species, and their co-occurrence in the riparian ecosystem. All plant communities were covered by tents with insect mesh. Five tents were open on the leeward side to allow herbivory. The other five tents were completely closed in order to exclude insects and vertebrates. Herbivory reduced aboveground biomass by half and influenced which of the plant species dominated the establishing communities. Exposure to herbivory did not reduce the total biomass of natives more than that of exotics, so aboveground herbivory did not selectively enhance exotics during this early stage of plant community development. Effects of herbivores on plant biomass depended on plant species or genus but not on plant status (i.e., exotic vs native). Thus, aboveground herbivory did not promote the dominance of exotic plant species during early establishment of the phylogenetically balanced plant communities. PMID:26481795

  15. Catastrophic regime shifts in coral communities exposed to physical disturbances: simulation results from object-oriented 3-dimensional coral reef model.

    PubMed

    Tam, Tze-wai; Ang, Put O

    2009-07-21

    A 3-dimensional individual-based model, the ReefModel, was developed to simulate the dynamical structure of coral reef community using object-oriented techniques. Interactions among functional groups of reef organisms were simulated in the model. The behaviours of these organisms were described with simple mechanistic rules that were derived from their general behaviours (e.g. growing habits, competitive mechanisms, response to physical disturbance) observed in natural coral reef communities. The model was implemented to explore the effects of physical disturbance on the dynamical structure of a 3-coral community that was characterized with three functional coral groups: tabular coral, foliaceous coral and massive coral. Simulation results suggest that (i) the integration of physical disturbance and differential responses (disturbance sensitivity and growing habit) of corals plays an important role in structuring coral communities; (ii) diversity of coral communities can be maximal under intermediate level of acute physical disturbance; (iii) multimodality exists in the final states and dynamic regimes of individual coral group as well as coral community structure, which results from the influence of small random spatial events occurring during the interactions among the corals in the community, under acute and repeated physical disturbances. These results suggest that alternative stable states and catastrophic regime shifts may exist in a coral community under unstable physical environment. PMID:19306887

  16. Community shift from phototrophic to chemotrophic sulfide oxidation following anoxic holomixis in a stratified seawater lake.

    PubMed

    Pjevac, Petra; Korlević, Marino; Berg, Jasmine S; Bura-Nakić, Elvira; Ciglenečki, Irena; Amann, Rudolf; Orlić, Sandi

    2015-01-01

    Most stratified sulfidic holomictic lakes become oxygenated after annual turnover. In contrast, Lake Rogoznica, on the eastern Adriatic coast, has been observed to undergo a period of water column anoxia after water layer mixing and establishment of holomictic conditions. Although Lake Rogoznica's chemistry and hydrography have been studied extensively, it is unclear how the microbial communities typically inhabiting the oxic epilimnion and a sulfidic hypolimnion respond to such a drastic shift in redox conditions. We investigated the impact of anoxic holomixis on microbial diversity and microbially mediated sulfur cycling in Lake Rogoznica with an array of culture-independent microbiological methods. Our data suggest a tight coupling between the lake's chemistry and occurring microorganisms. During stratification, anoxygenic phototrophic sulfur bacteria were dominant at the chemocline and in the hypolimnion. After an anoxic mixing event, the anoxygenic phototrophic sulfur bacteria entirely disappeared, and the homogeneous, anoxic water column was dominated by a bloom of gammaproteobacterial sulfur oxidizers related to the GSO/SUP05 clade. This study is the first report of a community shift from phototrophic to chemotrophic sulfide oxidizers as a response to anoxic holomictic conditions in a seasonally stratified seawater lake. PMID:25344237

  17. Community Shift from Phototrophic to Chemotrophic Sulfide Oxidation following Anoxic Holomixis in a Stratified Seawater Lake

    PubMed Central

    Korlević, Marino; Berg, Jasmine S.; Bura-Nakić, Elvira; Ciglenečki, Irena; Amann, Rudolf; Orlić, Sandi

    2014-01-01

    Most stratified sulfidic holomictic lakes become oxygenated after annual turnover. In contrast, Lake Rogoznica, on the eastern Adriatic coast, has been observed to undergo a period of water column anoxia after water layer mixing and establishment of holomictic conditions. Although Lake Rogoznica's chemistry and hydrography have been studied extensively, it is unclear how the microbial communities typically inhabiting the oxic epilimnion and a sulfidic hypolimnion respond to such a drastic shift in redox conditions. We investigated the impact of anoxic holomixis on microbial diversity and microbially mediated sulfur cycling in Lake Rogoznica with an array of culture-independent microbiological methods. Our data suggest a tight coupling between the lake's chemistry and occurring microorganisms. During stratification, anoxygenic phototrophic sulfur bacteria were dominant at the chemocline and in the hypolimnion. After an anoxic mixing event, the anoxygenic phototrophic sulfur bacteria entirely disappeared, and the homogeneous, anoxic water column was dominated by a bloom of gammaproteobacterial sulfur oxidizers related to the GSO/SUP05 clade. This study is the first report of a community shift from phototrophic to chemotrophic sulfide oxidizers as a response to anoxic holomictic conditions in a seasonally stratified seawater lake. PMID:25344237

  18. 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

  19. Coral-algal phase shifts alter fish communities and reduce fisheries production.

    PubMed

    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

  20. 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. PMID:26371310

  1. 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.

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

    PubMed Central

    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. 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. PMID:26371310

  3. 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.

  4. Social significance of community structure: statistical view.

    PubMed

    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. PMID:25679651

  5. RANGELAND COMMUNITIES: STRUCTURE, FUNCTION, AND CLASSIFICATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the vegetational attributes of rangelands is critical to their management. Yet incorporating vegetation structure, function, and classification into a single chapter is an ambitious goal and an attempt to blur the boundaries between classical community ecology that characterize patterns...

  6. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.

    PubMed

    Newton, Ryan J; Huse, Susan M; Morrison, Hilary G; Peake, Colin S; Sogin, Mitchell L; McLellan, Sandra L

    2013-01-01

    Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand

  7. Task shifting-perception of stake holders about adequacy of training and supervision for community mental health workers in Ghana.

    PubMed

    Agyapong, Vincent I O; Osei, Akwasi; Mcloughlin, Declan M; McAuliffe, Eilish

    2016-06-01

    There is growing interest in the effectiveness of task shifting as a strategy for addressing expanding health care challenges in settings with shortages of qualified health personnel. The aim of this study is to examine the perception of stakeholders about the adequacy of training, supervision and support offered to community mental health workers (CMHWs) in Ghana. To address this aim we designed and administered self-completed, semi-structured questionnaires adapted to three specific stakeholder groups in Ghana. The questionnaires were administered to 11 psychiatrists, 29 health policy implementers/coordinators and 164 CMHWs, across Ghana, including 71 (43.3%) Community Psychiatric Nurses (CPNs), 19 (11.6%) Clinical Psychiatric Officers (CPOs) and 74 (45.1%) Community Mental Health Officers (CMHOs). Almost all the stakeholders believed CMHWs in Ghana receive adequate training for the role they are expected to play although many identify some gaps in the training of these mental health workers for the expanded roles they actually play. There were statistically significant differences between the different CMHW groups and the types of in-service training they said they had attended, the frequency with which their work was supervised, and the frequency with which they received feedback from supervisors. CPOs were more likely to attend all the different kinds of in-service training than CMHOs and CPNs, while CMHOs were more likely than CPOs and CPNs to report that their work is never supervised or that they rarely or never receive feedback from supervisors. There was disparity between what CMHWs said were their experiences and the perception of policy makers with respect to the types of in-service training that is available to CMHWs. There is a need to review the task shifting arrangements, perhaps with a view to expanding it to include more responsibilities, and therefore review the curriculum of the training institution for CMHWs and also to offer them regular in

  8. 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

  9. 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. PMID:26714167

  10. 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

  11. Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost

    PubMed Central

    Liebner, Susanne; Ganzert, Lars; Kiss, Andrea; Yang, Sizhong; Wagner, Dirk; Svenning, Mette M.

    2015-01-01

    The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs. PMID:26029170

  12. Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost.

    PubMed

    Liebner, Susanne; Ganzert, Lars; Kiss, Andrea; Yang, Sizhong; Wagner, Dirk; Svenning, Mette M

    2015-01-01

    The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs. PMID:26029170

  13. Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

    PubMed

    Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

    2016-05-01

    The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples. PMID:26841890

  14. Deciphering Network Community Structure by Surprise

    PubMed Central

    Aldecoa, Rodrigo; Marín, Ignacio

    2011-01-01

    The analysis of complex networks permeates all sciences, from biology to sociology. A fundamental, unsolved problem is how to characterize the community structure of a network. Here, using both standard and novel benchmarks, we show that maximization of a simple global parameter, which we call Surprise (S), leads to a very efficient characterization of the community structure of complex synthetic networks. Particularly, S qualitatively outperforms the most commonly used criterion to define communities, Newman and Girvan's modularity (Q). Applying S maximization to real networks often provides natural, well-supported partitions, but also sometimes counterintuitive solutions that expose the limitations of our previous knowledge. These results indicate that it is possible to define an effective global criterion for community structure and open new routes for the understanding of complex networks. PMID:21909420

  15. Simple Nuclear Structure in Cd-129111 from Atomic Isomer Shifts

    NASA Astrophysics Data System (ADS)

    Yordanov, D. T.; Balabanski, D. L.; Bissell, M. L.; Blaum, K.; Budinčević, I.; Cheal, B.; Flanagan, K.; Frömmgen, N.; Georgiev, G.; Geppert, Ch.; Hammen, M.; Kowalska, M.; Kreim, K.; Krieger, A.; Meng, J.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Rajabali, M. M.; Papuga, J.; Schmidt, S.; Zhao, P. W.

    2016-01-01

    Isomer shifts have been determined in 111-129>Cd by high-resolution laser spectroscopy at CERN-ISOLDE. The corresponding mean square charge-radii changes, from the 1 /2+ and the 3 /2+ ground states to the 11 /2- isomers, have been found to follow a distinct parabolic dependence as a function of the atomic mass number. Since the isomers have been previously associated with simplicity due to the linear mass dependence of their quadrupole moments, the regularity of the isomer shifts suggests a higher order of symmetry affecting the ground states in addition. A comprehensive description assuming nuclear deformation is found to accurately reproduce the radii differences in conjunction with the known quadrupole moments. This intuitive interpretation is supported by covariant density functional theory.

  16. Evidence of Community Structure in Biomedical Research Grant Collaborations

    PubMed Central

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

    2014-01-01

    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

  17. Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean.

    PubMed

    Yu, Zheng; Yang, Jun; Liu, Lemian; Zhang, Wenjing; Amalfitano, Stefano

    2015-01-01

    The Southern Ocean is among the least explored marine environments on Earth, and still little is known about regional and vertical variability in the diversity of Antarctic marine prokaryotes. In this study, the bacterioplankton community in both epipelagic and mesopelagic waters was assessed at two adjacent stations by high-throughput sequencing and quantitative PCR. Water temperature was significantly higher in the superficial photic zone, while higher salinity and dissolved oxygen were recorded in the deeper water layers. The highest abundance of the bacterioplankton was found at a depth of 75 m, corresponding to the deep chlorophyll maximum layer. Both Alphaproteobacteria and Gammaproteobacteria were the most abundant taxa throughout the water column, while more sequences affiliated to Cyanobacteria and unclassified bacteria were identified from surface and the deepest waters, respectively. Temperature was the most significant environmental variable affecting the bacterial community structure. The bacterial community composition displayed significant differences at the epipelagic layers between two stations, whereas those in the mesopelagic waters were more similar to each other. Our results indicated that the epipelagic bacterioplankton might be dominated by short-term environmental variable conditions, whereas the mesopelagic communities appeared to be structured by longer water-mass residence time and relative stable environmental factors. PMID:26256889

  18. Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean

    PubMed Central

    Yu, Zheng; Yang, Jun; Liu, Lemian; Zhang, Wenjing; Amalfitano, Stefano

    2015-01-01

    The Southern Ocean is among the least explored marine environments on Earth, and still little is known about regional and vertical variability in the diversity of Antarctic marine prokaryotes. In this study, the bacterioplankton community in both epipelagic and mesopelagic waters was assessed at two adjacent stations by high-throughput sequencing and quantitative PCR. Water temperature was significantly higher in the superficial photic zone, while higher salinity and dissolved oxygen were recorded in the deeper water layers. The highest abundance of the bacterioplankton was found at a depth of 75 m, corresponding to the deep chlorophyll maximum layer. Both Alphaproteobacteria and Gammaproteobacteria were the most abundant taxa throughout the water column, while more sequences affiliated to Cyanobacteria and unclassified bacteria were identified from surface and the deepest waters, respectively. Temperature was the most significant environmental variable affecting the bacterial community structure. The bacterial community composition displayed significant differences at the epipelagic layers between two stations, whereas those in the mesopelagic waters were more similar to each other. Our results indicated that the epipelagic bacterioplankton might be dominated by short-term environmental variable conditions, whereas the mesopelagic communities appeared to be structured by longer water-mass residence time and relative stable environmental factors. PMID:26256889

  19. Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters.

    PubMed

    Carey, Daniel E; Zitomer, Daniel H; Kappell, Anthony D; Choi, Melinda J; Hristova, Krassimira R; McNamara, Patrick J

    2016-08-10

    Triclosan, an antimicrobial chemical found in consumer personal care products, has been shown to stimulate antibiotic resistance in pathogenic bacteria. Although many studies focus on antibiotic resistance pertinent to medical scenarios, resistance developed in natural and engineered environments is less studied and has become an emerging concern for human health. In this study, the impacts of chronic triclosan (TCS) exposure on antibiotic resistance genes (ARGs) and microbial community structure were assessed in lab-scale anaerobic digesters. TCS concentrations from below detection to 2500 mg kg(-1) dry solids were amended into anaerobic digesters over 110 days and acclimated for >3 solid retention time values. Four steady state TCS concentrations were chosen (30-2500 mg kg(-1)). Relative abundance of mexB, a gene coding for a component of a multidrug efflux pump, was significantly higher in all TCS-amended digesters (30 mg kg(-1) or higher) relative to the control. TCS selected for bacteria carrying tet(L) and against those carrying erm(F) at concentrations which inhibited digester function; the pH decrease associated with digester failure was suspected to cause this selection. Little to no impact of TCS was observed on intI1 relative abundance. Microbial communities were also surveyed by high-throughput 16S rRNA gene sequencing. Compared to the control digesters, significant shifts in community structure towards clades containing commensal and pathogenic bacteria were observed in digesters containing TCS. Based on these results, TCS should be included in studies and risk assessments that attempt to elucidate relationships between chemical stressors (e.g. antibiotics), antibiotic resistance genes, and public health. PMID:27291499

  20. Centrality measures for networks with community structure

    NASA Astrophysics Data System (ADS)

    Gupta, Naveen; Singh, Anurag; Cherifi, Hocine

    2016-06-01

    Understanding the network structure, and finding out the influential nodes is a challenging issue in large networks. Identifying the most influential nodes in a network can be useful in many applications like immunization of nodes in case of epidemic spreading, during intentional attacks on complex networks. A lot of research is being done to devise centrality measures which could efficiently identify the most influential nodes in a network. There are two major approaches to this problem: On one hand, deterministic strategies that exploit knowledge about the overall network topology, while on the other end, random strategies are completely agnostic about the network structure. Centrality measures that can deal with a limited knowledge of the network structure are of prime importance. Indeed, in practice, information about the global structure of the overall network is rarely available or hard to acquire. Even if available, the structure of the network might be too large that it is too much computationally expensive to calculate global centrality measures. To that end, a centrality measure is proposed here that requires information only at the community level. Indeed, most of the real-world networks exhibit a community structure that can be exploited efficiently to discover the influential nodes. We performed a comparative evaluation of prominent global deterministic strategies together with stochastic strategies, an available and the proposed deterministic community-based strategy. Effectiveness of the proposed method is evaluated by performing experiments on synthetic and real-world networks with community structure in the case of immunization of nodes for epidemic control.

  1. Integrating macroecological metrics and community taxonomic structure.

    PubMed

    Harte, John; Rominger, Andrew; Zhang, Wenyu

    2015-10-01

    We extend macroecological theory based on the maximum entropy principle from species level to higher taxonomic categories, thereby predicting distributions of species richness across genera or families and the dependence of abundance and metabolic rate distributions on taxonomic tree structure. Predictions agree with qualitative trends reported in studies on hyper-dominance in tropical tree species, mammalian body size distributions and patterns of rarity in worldwide plant communities. Predicted distributions of species richness over genera or families for birds, arthropods, plants and microorganisms are in excellent agreement with data. Data from an intertidal invertebrate community, but not from a dispersal-limited forest, are in excellent agreement with a predicted new relationship between body size and abundance. Successful predictions of the original species level theory are unmodified in the extended theory. By integrating macroecology and taxonomic tree structure, maximum entropy may point the way towards a unified framework for understanding phylogenetic community structure. PMID:26248954

  2. Lagrangian evolution of DMS during the Southern Ocean gas exchange experiment: The effects of vertical mixing and biological community shift

    NASA Astrophysics Data System (ADS)

    Yang, M.; Archer, S. D.; Blomquist, B. W.; Ho, D. T.; Lance, V. P.; Torres, R. J.

    2013-12-01

    Concentrations of dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) are highly variable in time and space. What is driving the variability in DMS(P), and can those variability be explained by physical processes and changes in the biological community? During the Southern Ocean Gas Exchange Experiment (SO GasEx) in the austral fall of 2008, two 3He/SF6 labeled patches were created in the surface water. SF6 and DMS were surveyed continuously in a Lagrangian framework, while direct measurements of air-sea exchange further constrained the gas budgets. Turbulent diffusivity at the base of the mixed layer was estimated from SF6 profiles and used to calculate the vertical fluxes of DMS and nutrients. Increasing mixed layer nutrient concentrations due to mixing were associated with a shift in the phytoplankton community structure, which in turned likely affected the sulfur dynamics on timescales of days. DMS concentration as well as air-sea DMS flux appeared to be decoupled from the DMSP concentration, possibly due to grazing and bacterial DMS production. Contrary to expectations, in an environment with high winds and modest productivity, physical processes (air-sea exchange, photochemistry, vertical mixing) only accounted for a small fraction of DMS loss from the surface water. Among the DMS sinks, inferred biological consumption most likely dominated during SO GasEx.

  3. Closed benchmarks for network community structure characterization

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2012-02-01

    Characterizing the community structure of complex networks is a key challenge in many scientific fields. Very diverse algorithms and methods have been proposed to this end, many working reasonably well in specific situations. However, no consensus has emerged on which of these methods is the best to use in practice. In part, this is due to the fact that testing their performance requires the generation of a comprehensive, standard set of synthetic benchmarks, a goal not yet fully achieved. Here, we present a type of benchmark that we call “closed,” in which an initial network of known community structure is progressively converted into a second network whose communities are also known. This approach differs from all previously published ones, in which networks evolve toward randomness. The use of this type of benchmark allows us to monitor the transformation of the community structure of a network. Moreover, we can predict the optimal behavior of the variation of information, a measure of the quality of the partitions obtained, at any moment of the process. This enables us in many cases to determine the best partition among those suggested by different algorithms. Also, since any network can be used as a starting point, extensive studies and comparisons can be performed using a heterogeneous set of structures, including random ones. These properties make our benchmarks a general standard for comparing community detection algorithms.

  4. Shifting brain asymmetry: the link between meditation and structural lateralization.

    PubMed

    Kurth, Florian; MacKenzie-Graham, Allan; Toga, Arthur W; Luders, Eileen

    2015-01-01

    Previous studies have revealed an increased fractional anisotropy and greater thickness in the anterior parts of the corpus callosum in meditation practitioners compared with control subjects. Altered callosal features may be associated with an altered inter-hemispheric integration and the degree of brain asymmetry may also be shifted in meditation practitioners. Therefore, we investigated differences in gray matter asymmetry as well as correlations between gray matter asymmetry and years of meditation practice in 50 long-term meditators and 50 controls. We detected a decreased rightward asymmetry in the precuneus in meditators compared with controls. In addition, we observed that a stronger leftward asymmetry near the posterior intraparietal sulcus was positively associated with the number of meditation practice years. In a further exploratory analysis, we observed that a stronger rightward asymmetry in the pregenual cingulate cortex was negatively associated with the number of practice years. The group difference within the precuneus, as well as the positive correlations with meditation years in the pregenual cingulate cortex, suggests an adaptation of the default mode network in meditators. The positive correlation between meditation practice years and asymmetry near the posterior intraparietal sulcus may suggest that meditation is accompanied by changes in attention processing. PMID:24643652

  5. Shifting brain asymmetry: the link between meditation and structural lateralization

    PubMed Central

    Kurth, Florian; MacKenzie-Graham, Allan; Toga, Arthur W.

    2015-01-01

    Previous studies have revealed an increased fractional anisotropy and greater thickness in the anterior parts of the corpus callosum in meditation practitioners compared with control subjects. Altered callosal features may be associated with an altered inter-hemispheric integration and the degree of brain asymmetry may also be shifted in meditation practitioners. Therefore, we investigated differences in gray matter asymmetry as well as correlations between gray matter asymmetry and years of meditation practice in 50 long-term meditators and 50 controls. We detected a decreased rightward asymmetry in the precuneus in meditators compared with controls. In addition, we observed that a stronger leftward asymmetry near the posterior intraparietal sulcus was positively associated with the number of meditation practice years. In a further exploratory analysis, we observed that a stronger rightward asymmetry in the pregenual cingulate cortex was negatively associated with the number of practice years. The group difference within the precuneus, as well as the positive correlations with meditation years in the pregenual cingulate cortex, suggests an adaptation of the default mode network in meditators. The positive correlation between meditation practice years and asymmetry near the posterior intraparietal sulcus may suggest that meditation is accompanied by changes in attention processing. PMID:24643652

  6. 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

  7. Jellyfish Modulate Bacterial Dynamic and Community Structure

    PubMed Central

    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

  8. School, Community Leadership, and Election Structure

    ERIC Educational Resources Information Center

    Allen, Ann

    2008-01-01

    This article examines how the political structure of school elections contributes to leadership perspectives related to school-community engagement. Interview data from school superintendents, school board presidents, and city mayors across four cities and two election types were analyzed to determine if differences in school election structure…

  9. 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. PMID:26231415

  10. Invasive toads shift predator-prey densities in animal communities by removing top predators.

    PubMed

    Doody, J Sean; Soanes, Rebekah; Castellano, Christina M; Rhind, David; Green, Brian; McHenry, Colin R; Clulow, Simon

    2015-09-01

    Although invasive species can have substantial impacts on animal communities, cases of invasive species facilitating native species by removing their predators have rarely been demonstrated across vertebrate trophic linkages. The predictable spread of the invasive cane toad (Rhinella marina), however, offered a unique opportunity to quantify cascading effects. In northern Australia, three species of predatory monitor lizards suffered severe population declines due to toad-induced lethal toxic ingestion (yellow-spotted monitor (Varanus panoptes), Mertens' water monitor (V. mertensi), Mitchell's water monitor (V. mitchelli). We, thus, predicted subsequent increases in the abundance and recruitment of prey species due to the reduction of those predators. Toad-induced population-level declines in the water monitor species approached 50% over a five-year period spanning the toad invasion, apparently causing fledging success of the Crimson Finch (Neochmia.phaeton) to increase from 55% to 81%. The consensus of our original and published long-term data is that invasive cane toads are causing predators to lose a foothold on top-down regulation of their prey, triggering shifts in the relative densities of predator and prey in the Australian tropical savannah ecosystem. PMID:26594710

  11. Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms.

    PubMed

    Landa, Marine; Blain, Stéphane; Christaki, Urania; Monchy, Sébastien; Obernosterer, Ingrid

    2016-01-01

    Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements. PMID:26196334

  12. Phylogenetic structure in tropical hummingbird communities

    PubMed Central

    Graham, Catherine H.; Parra, Juan L.; Rahbek, Carsten; McGuire, Jimmy A.

    2009-01-01

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world. PMID:19805042

  13. Phylogenetic structure in tropical hummingbird communities.

    PubMed

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten; McGuire, Jimmy A

    2009-11-17

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world. PMID:19805042

  14. The nested structure of a scavenger community

    PubMed Central

    Selva, Nuria; Fortuna, Miguel A

    2007-01-01

    Scavenging is a widespread phenomenon in vertebrate communities which has rarely been accounted for, in spite of playing an essential role in food webs by enhancing nutrient recycling and community stability. Most studies on scavenger assemblages have often presented an oversimplified view of carrion foraging. Here, we applied for the first time the concept of nestedness to the study of a species-rich scavenger community in a forest ecosystem (Białowieża Primeval Forest, Poland) following a network approach. By analysing one of the most complete datasets existing up to now in a pristine environment, we have shown that the community of facultative scavengers is not randomly assembled but highly nested. A nested pattern means that species-poor carcasses support a subset of the scavenger assemblage occurring at progressively species-rich carcasses. This result contradicts the conventional view of facultative scavenging as random and opportunistic and supports recent findings in scavenging ecology. It also suggests that factors other than competition play a major role in determining community structure. Nested patterns in scavenger communities appear to be promoted by the high diversity in carrion resources and consumers, the differential predictability of the ungulate carcass types and stressful environmental conditions. PMID:17301021

  15. Parasites destabilize host populations by shifting stage-structured interactions.

    PubMed

    Hite, Jessica L; Penczykowski, Rachel M; Shocket, Marta S; Strauss, Alexander T; Orlando, Paul A; Duffy, Meghan A; Cáceres, Carla E; Hall, Spencer R

    2016-02-01

    Should parasites stabilize or destabilize consumer-resource dynamics? Recent theory suggests that parasite-enhanced mortality may confer underappreciated stability to their hosts. We tested this hypothesis using disease in zooplankton. Across both natural and experimental epidemics, bigger epidemics correlated with larger--not smaller--host fluctuations. Thus, we tested two mechanistic hypotheses to explain destabilization or apparent destabilization by parasites. First, enrichment could, in principle, simultaneously enhance both instability and disease prevalence. In natural epidemics, destabilization was correlated with enrichment (indexed by total phosphorous). However, an in situ (lake enclosure) experiment did not support these links. Instead, field and experimental results point to a novel destabilizing mechanism involving host stage structure. Epidemics pushed hosts from relatively more stable host dynamics with less-synchronized juveniles and adults to less stable dynamics with more-synchronized juveniles and adults. Our results demonstrate how links between host stage structure and disease can shape host/consumer-resource stability. PMID:27145618

  16. Community structure and dynamics in social systems

    NASA Astrophysics Data System (ADS)

    Wilkinson, Dennis M.

    This thesis presents applications of statistical physics to the study of the structure and dynamics of social systems, that is, systems whose interactions are based on information exchange. Social systems typically possess a community structure arising from the self organization of groups of interacting components into tightly-knit clusters. An automated method of identifying communities within a network of interactions is first presented. The method includes a statistical component crucial to obtaining accurate results in large, complex systems. It is applied to two real-world social networks, a network of email interactions and a network of related articles in the biomedical literature. The clusters it identifies within these networks are shown to correspond to communities of interrelated components. Next, the dynamics of cooperative problem solving processes on social systems are studied. A simple stochastic model is proposed which captures key aspects of the dynamics which have been empirically observed. Most important among these are the increase in average time to solution and in likelihood of long delays as the system size increases, as well as the log-normal distribution of times to solution. It is shown that a community structure both reduces the average time to solution and decreases the probability of delay. In cases where a system of cooperative efforts does not possess an inherent community structure, the effect of imposing communities is examined. The factor which most affects the dynamics when communities are imposed is shown to be the degree to which individuals neglect information from outside their own communities. The theory of stochastic vector processes is central to the dynamics of social systems and a mathematical study of this subject is presented. Expressions describing the evolution of the moments in the neighborhood of fixed points are obtained for arbitrary systems. Approximation techniques are applied in the small and large noise limits

  17. 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.

  18. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field

    PubMed Central

    Nielsen, Jakob T.; Eghbalnia, Hamid R.; Nielsen, Niels Chr.

    2011-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field. PMID:22293396

  19. Shifting the Starspot Paradigm: Imaging Global Magnetic Structures

    NASA Astrophysics Data System (ADS)

    Roettenbacher, Rachael M.; Monnier, John D.

    2016-01-01

    Stellar magnetism exists in stars across the HR diagram and fuels stellar activity (e.g. flares and starspots). This magnetism affects measurements of fundamental stellar parameters, such as radius and temperature, leading to inaccurate mass and age estimates. In order to better determine stellar parameters, we aim to understand how magnetically-suppressed convection presents as cool regions across the stellar surface. In the standard "spot paradigm" of localized starspots blemishing an otherwise featureless surface, we use precision Kepler data and light curve inversion to study stellar differential rotation and starspot evolution. Contrastingly, by imaging interferometric data collected with the Michigan Infrared Combiner (MIRC) at GSU's Center for High Angular Resolution Astronomy (CHARA) Array, we detect large-scale magnetic structures across the surface of ζ Andromedae. These global regions of suppressed convection cover a large fraction of the surface, likely changing the atmospheric structure of the photosphere and impacting stellar parameter estimates. The large-scale features are at best ambiguous to interpret via established techniques that rely on rotational modulation of spots (e.g. light curve inversion and Doppler imaging). We seek to identify a class of targets where the "spot paradigm" breaks down and gives new insights into a range of phenomena such as long-term changes in flux for active stars, anomalous proper motion of spots derived from precision photometry, and the nature of the stellar dynamo of stars with large convective envelopes.

  20. Identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Chenxi; Duan, Yubing

    2015-07-01

    A wide variety of applications could be formulated to resolve the problem of finding all communities from a given network, ranging from social and biological network analysis to web mining and searching. In this study, we propose the concept of virtual attractive strength between each pair of node in networks, and then give the definition of community structure based on the proposed attractive strength. Furthermore, we present a community detection method by moving vertices to the clusters that produce the largest attractive strengths to them until the division of network reaches unchanged. Experimental results on synthetic and real networks indicate that the proposed approach has favorite effectiveness and fast convergence speed, which provides an efficient method for exploring and analyzing complex systems.

  1. Modularity and community structure in networks.

    PubMed

    Newman, M E J

    2006-06-01

    Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets. PMID:16723398

  2. 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

  3. Multilevel polarization shift keying: Optimum receiver structure and performance evaluation

    SciTech Connect

    Benedetto, S.; Poggiolini, P.T.

    1994-02-01

    Multilevel digital coherent optical modulation schemes based on the state of polarization of a fully polarized lightwave are proposed and analyzed. Based on the complete statistical characterization of the Stokes parameters, extracted though appropriate signal processing in the presence of shot and additive gaussian noise, the optimum maximum likelihood receiver operating symbol by symbol is derived. The exact performance in terms of the average symbol error probability is found. Optimum constellations for the case of equipower 4, 8, 16 and 32 signals are found on the basis of the minimization of the error probability for a given average power. Their performance turns out to be promising as compared to other standard modulation techniques. The spectral analysis of polarization modulated signals is presented. A new receiver structure, which solves the problem of the excess penalties incurred in the presence of channel dichroism, is proposed and analyzed. 22 refs.

  4. A cheating limit for structured communities

    SciTech Connect

    Perelson, Alan S; Gerrish, Philip J

    2008-01-01

    The constructive creativity of natural selection originates from its paradoxical ability to foster cooperation through competition. Cooperating communities ranging from complex societies to somatic tissue are constantly under attack, however, by non-cooperating mutants or transformants, called 'cheaters'. Structure in these communities promotes the formation of cooperating clusters whose competitive superiority can alone be sufficient to thwart outgrowths of cheaters and thereby maintain cooperation. But we find that when cheaters appear too frequently -- exceeding a threshold mutation or transformation rate -- their scattered outgrowths infiltrate and break up cooperating clusters, resulting in a cascading loss of community integrity, a switch to net positive selection for cheaters, and ultimately in the loss of cooperation. We find that this threshold mutation rate is directly proportional to the fitness support received from each cooperating neighbor minus the individual fitness benefit of cheating. When mutation rate also evolves, this threshold is crossed spontaneously after thousands of generations, at which point cheaters rapidly invade. In a structured community, cooperation can persist only if the mutation rate remains below a critical value.

  5. Structural shifts in the employment of foreign workers in Austria.

    PubMed

    Biffl, G

    1985-03-01

    The full economic importance of immigration becomes clear only when one examines the concentration of immigrant workers in certain industries and occupations, and this is done in the case of Austria to show the degree of segmentation of the labor market between indigenous and foreign labor. In the course of the 1960s the employment of foreign labor gained importance in Austria. As a consequence, bilateral agreements with the major recruiting countries were made, e.g., with Spain in 1962 and 1969, with Turkey in 1964, and with Yugoslavia in 1966. The reason for the increasing demand for foreign labor was the short supply of indigenous labor due to increasing participation rates and strong economic growth. The demand-pull for foreign labor gained momentum with the onset of the economic boom in 1970, so that by the end of 1973 the number of foreign workers had doubled in comparison to 1970. The 226,800 foreign workers accounted for 8.7% of total employment. The 1974-75 recession and the weak economic development ever since resulted in a decreasing demand for labor. At the same time, the supply of indigenous labor increased as a consequence of a demographic effect and because of increasing participation rates of women. From 1981 to the present, foreign employment decreased again due to the unusually long period of economic stagnation. During 1983, 145,300 foreign workers were engaged, i.e., 5.3% of total employment. The structure for foreign employment now differs greatly from that in the 1960s. The share of women in foreign employment has increased steadily from some 20% in the early 1960s to 31% in 1973 and 40% in 1983 -- a value comparable to the Austrian female share in employment. The reduction of foreign employment since 1973 affected, above all, Yugoslav men. the share of Yugoslavs in foreign employment decreased from 196,300 or 79% in 1973 to 92,200 or 61.7% in 1983. With the duration of foreign employment rising, the disribution of foreign labor over economic

  6. 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

  7. 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. PMID:23869991

  8. From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

    PubMed Central

    Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

    2015-01-01

    Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

  9. From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization.

    PubMed

    Li, Xiaofang; Bond, Philip L; Van Nostrand, Joy D; Zhou, Jizhong; Huang, Longbin

    2015-01-01

    Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

  10. From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

    NASA Astrophysics Data System (ADS)

    Li, Xiaofang; Bond, Philip L.; van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

    2015-08-01

    Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes.

  11. Citrus huanglongbing shapes the structure of bacterial community associated with citrus roots

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To examine the effect of pathogen on the diversity and structure of plant associated bacterial community, we carried out a molecular based analysis using citrus and huanglongbing as host-disease model. 16S rDNA clone library analysis of the citrus roots revealed shifts in the microbial diversity in ...

  12. Microbial community shifts on an anammox reactor after a temperature shock using 454-pyrosequencing analysis.

    PubMed

    Isanta, Eduardo; Bezerra, Tercia; Fernández, Isaac; Suárez-Ojeda, María Eugenia; Pérez, Julio; Carrera, Julián

    2015-04-01

    To explore the changes in the microbial community structure during the recovery process of an anammox reactor after a temperature shock, the 454-pyrosequencing technique was used. The temperature shock reduced the nitrogen removal rate up to 92% compared to that just before the temperature shock, and it took 70 days to recover a similar nitrogen removal rate to that before the temperature shock (ca. 0.30 g N L(-1) d(-1)). Pyrosequencing results indicated that microbial diversity in the reactor decreased as the reactor progressively recovered from the temperature shock. Anammox bacteria were accounted as 6%, 35% and 46% of total sequence reads in samples taken 13, 45 and 166 days after the temperature shock. These results were in agreement with N-removal performance results and anammox activity measured in the reactor during the recovery process. An anammox specific primer was used to precisely determine the anammox species in the biomass samples. PMID:25656864

  13. 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.

  14. 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

  15. The Structure of Executive Functions in Children: A Closer Examination of Inhibition, Shifting, and Updating

    ERIC Educational Resources Information Center

    van der Ven, Sanne H. G.; Kroesbergen, Evelyn H.; Boom, Jan; Leseman, Paul P. M.

    2013-01-01

    An increasing number of studies has investigated the latent factor structure of executive functions. Some studies found a three-factor structure of inhibition, shifting, and updating, but others could not replicate this finding. We assumed that the task choices and scoring methods might be responsible for these contradictory findings. Therefore,…

  16. 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

  17. 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. PMID:25775464

  18. The Shifting Sands of Health Care Delivery: Curriculum Revision and Integration of Community Health Nursing.

    ERIC Educational Resources Information Center

    Conger, Cynthia O'Neill; Baldwin, Joan H.; Abegglen, JoAnn; Callister, Lynn C.

    1999-01-01

    Brigham Young University's nursing curriculum was revised to reflect the community-driven nature of primary health care. Curricular threads of inquiry, practice, stewardship, spirituality, and service are the framework for integrating community health nursing practice. (SK)

  19. Epidemic spreading on complex networks with community structures

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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.

  20. 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

  1. Epidemic spreading on complex networks with community structures.

    PubMed

    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

  2. Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats.

    PubMed

    Wetzels, S U; Mann, E; Metzler-Zebeli, B U; Wagner, M; Klevenhusen, F; Zebeli, Q; Schmitz-Esser, S

    2015-08-01

    Ecological balance in the rumen is highly sensitive to concentrate-rich diets. Yet the effects of these feeding practices on the caprine bacterial epimural microbiome (CBEM), a microbial community with putative important physiological functions in the rumen, are largely unexplored. This study aimed to investigate the effect of dietary concentrate amount on ruminal CBEM. Seventeen growing goats were fed diets with 0 [n=5; 6.2MJ of metabolizable energy (ME)/d], 30 (n=6; 7.3MJ of /d), or 60% (n=6; 10.2MJ of ME/d) concentrate for 6 wk. Two hours after their last feeding, goats were euthanized and tissue samples of the ventral rumen wall were collected, washed in phosphate-buffered saline to detach loosely attached bacteria, and stored at -20°C for further processing. Genomic DNA was isolated from thawed rumen mucosa samples and used for Roche/454 Life Science (Branford, CT) 16S rRNA gene amplicon pyrosequencing yielding 122,458 reads. Pyrosequencing data were clustered into 1,879 operational taxonomic units (OTU; 0.03 distance level). Pyrosequencing revealed Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetes as the most abundant phyla (97.7%). Compared with the 30% group, both the 60 and 0% concentrate groups harbored significantly more Firmicutes and SR1, respectively. On an OTU level, a Bergeriella-related OTU was most abundant in the CBEM, followed by 2 Campylobacter OTU, which responded differently to diets: 1 OTU was significantly increased whereas the other significantly decreased with highest concentrate amount in the diet. At the genus level, the 0% concentrate group harbored increased Kingella-like sequences compared with the other feeding groups. Furthermore, the 0% concentrate group tended to have more Bergeriella than the 30 and 60% concentrate groups. The genus Bergeriella was significantly decreased in the 60% feeding group compared with the other diets. In conclusion, this is the first report of CBEM using deep-sequencing methods on the genus

  3. 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. PMID:25682761

  4. Community-oriented support and research structures

    NASA Astrophysics Data System (ADS)

    Attig, Norbert; Eickermann, Thomas; Gibbon, Paul; Lippert, Thomas

    2009-07-01

    Coordinated by the Partnership for Advanced Computing in Europe (PRACE) Europe is restructuring and strengthening its high-performance computing infrastructure with the aim to create a model HPC ecosystem. At the tip of the pyramid, up to six centres are envisaged that will operate systems of the highest performance class. The HPC Research Infrastructure (HPC-RI) will comprise European, national and regional centres. Science communities are integral partners, strong links will include Grid and Cloud users. The HPC-RI strives at providing scientists all over Europe, on the one hand, with unlimited and independent access to state-of-the-art computer resources in all performance classes and, on the other hand, with a world-class pan-European competence and support network. While the hardware-oriented buildup of the infrastructure is making progress, high-quality user support and software development in the upcoming era of unprecedented parallelism and exascale on the horizon have become the imminent challenges. This has been clearly recognized by the European Commission, who will issue calls for proposals to fund petascale software development in summer 2009. Although traditional support structures are well established in Europe's major supercomputing centres, it is questionable if these structures are able to meet the challenges of the future: in general, support structures are based on cross-disciplinary computer science and mathematics teams; disciplinary computational science support usually is given in an ad-hoc, project-oriented manner. In this paper, we describe our approach to establish a suitable support structure-Simulation Laboratories (SL). SLs are currently being established at the Jülich Supercomputing Centre of the Forschungszentrum Jülich (FZJ) and at the Steinbuch Centre for Computing (SCC) of the Karlsruhe Institute for Technology (KIT) in Germany. While SLs are community-oriented, i.e. each SL focusses on a specific community, they are structured

  5. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    PubMed

    Shen, Yang; Bax, Ad

    2015-01-01

    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 side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 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 (13)C(β) 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

  6. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

    Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

  7. Modeling proteins using a super-secondary structure library and NMR chemical shift information

    PubMed Central

    Menon, Vilas; Vallat, Brinda; Dybas, Joseph M.; Fiser, Andras

    2013-01-01

    Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

  8. [Structural variability of the lithorheophile macrobenthos communities].

    PubMed

    Chertoprud, M V

    2007-01-01

    The relationship between the abundance of taxa and life forms of lithorheophile macrobenthos and its variability were studied based on 200 quantitative samples from six territories of the Palaearctic (Moscow province, northwestern Caucasus, eastern Carpathians, northern Karelia, South Urals, and Altai mountains). The set of taxa predominant in the communities and their ecology are described. It is found that community structure varies strongly, depending on the characteristics of each region, on the size of the watercourse, and on the season. Six types of biocenoses are recognized by means of the Braun-Blanquet method, each characterized by its peculiar set of predominant life forms and families rather similar in different territories. The differences between these types are related to the size and the hydrological conditions of the watercourse. Biocenosis 1 is typical to smal brooks (up to 0.01-0.1 m3/s), characterised by the predominance of detritophagous animals non-specific to the type of food (Gammarus, Nemoura, Limnephilidae). In biocenosis 2a (large brooks with water flow 0.03-0.3 m3/s and velocity 0.1-0.3 m/s), almost immobile shell scrapers (Ancylus, Silo, Agapetes, Glossosoma) are predominant. Biocenosis 2b (large brooks with velocity 0.3-0.5 m/s) have a more or less balanced set of fundamental lithorheophile life forms. Biocenosis 2c (large mountain brooks with velocity 0.5-1 m/s) is characterised by specialized scrapers of the rapids (Epeorus and Diomesa) and filterers (Simuliidae). In biocenosis 3 (small rivers), sedentary filterers (Hydropsychidae, Simulliidae) are predominant; scrapers also play a significant role. Biocenosis 4 (rivers with water flow more than 3 m3/s, thick incrustations, and silted stones on the bottom) has predominant filterers (Hydropsychidae) and vermiform algophagous animals inside the incrustations (Orthocladius, Psychomyia). Significant variability in community structure unrelated to the environmental factors is revealed

  9. Submesoscale dynamics and planktonic community structure

    NASA Astrophysics Data System (ADS)

    Franks, P. J.; Taniguchi, D. A.

    2012-12-01

    The vertical velocities associated with submesoscale dynamics occur on time scales that are resonant with planktonic growth and grazing rates. This resonance may cause submesoscale dynamics to be disproportionately important to planktonic productivity and carbon sequestration. To investigate the role of submesoscale motions on planktonic community structure, we used a continuum size-structured planktonic ecosystem model. The model is based on a traditional NPZ framework, but allows for size dependence of all biological processes. The model was carefully parameterized with data from the literature, and reproduces realistic planktonic size spectra. Perturbing the model with a nutrient pulse similar to that driven by submesoscale upwelling leads to significant perturbations to the ecosystem. Pulses of enhanced biomass propagate from small to large organisms over time scales of days to weeks. We explore the model stability and dynamics, and their dependence on the parameter values, to gain understanding of the potential for submesoscale physical motions to influence planktonic ecosystem dynamics.

  10. 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…

  11. Shifting Models of Welfare: Issues in Relocation from an Institution and the Organization of Community Living

    ERIC Educational Resources Information Center

    Bigby, Christine

    2006-01-01

    The closure of institutions and relocation of people with intellectual disabilities to community living has been the focus of many nations' intellectual disability policies in the past three decades. The author studied the relocation of 58 people from a large institution to 11 small group homes in several Australian communities. Organizational…

  12. Cajun Is Dead--Long Live Cajun: Shifting from a Linguistic to a Cultural Community.

    ERIC Educational Resources Information Center

    Dubois, Sylvie; Melancon, Megan

    1997-01-01

    Surveys the linguistic attitudes and cultural identity of Cajun speakers stratified by age and sex from four communities in Louisiana. Findings reveal that Cajun identity rests fundamentally in the linguistic ability of the speakers and that the criteria established has created considerable tension within the cultural Cajun community. (32…

  13. Language Attitudes, Shift and the Ethnolinguistic Vitality of the Greek Orthodox Community in Istanbul

    ERIC Educational Resources Information Center

    Komondouros, Markos; McEntee-Atalianis, Lisa

    2007-01-01

    The Greek Orthodox community of Istanbul has long existed as a bilingual Greek and Turkish grouping and remains largely unstudied. The sharp decrease in the size of this community to approximately 1000 members raises questions as to the maintenance of Greek in this setting. This study attempts to establish the current status of Greek in the…

  14. 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

  15. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    PubMed

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  16. Monitoring the refinement of crystal structures with (15)N solid-state NMR shift tensor data.

    PubMed

    Kalakewich, Keyton; Iuliucci, Robbie; Mueller, Karl T; Eloranta, Harriet; Harper, James K

    2015-11-21

    The (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 (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 than 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 (15)N tensors at natural abundance is challenging and this limitation is overcome by improved (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 (15)N tensors are at least 5 times more sensitive to crystal structure than (13)C tensors due to nitrogen's greater polarizability and larger range of chemical shifts. PMID:26590548

  17. Common community structure in time-varying networks

    NASA Astrophysics Data System (ADS)

    Zhang, Shihua; Zhao, Junfei; Zhang, Xiang-Sun

    2012-05-01

    In this report we introduce the concept of common community structure in time-varying networks. We propose a novel optimization algorithm to rapidly detect common community structure in such networks. Both theoretical and numerical results show that the proposed method not only can resolve detailed common communities, but also can effectively identify the dynamical phenomena in time-varying networks.

  18. Virioplankton Community Structure in Tunisian Solar Salterns

    PubMed Central

    Boujelben, Ines; Yarza, Pablo; Almansa, Cristina; Villamor, Judith; Maalej, Sami; Santos, Fernando

    2012-01-01

    The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 1010 virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral

  19. Application of the laser ion source for isotope shift and hyperfine structure investigations

    NASA Astrophysics Data System (ADS)

    Barzakh, A. E.; Chubukov, I. Ya.; Fedorov, D. V.; Panteleev, V. N.; Seliverstov, M. D.; Volkov, Yu. M.

    1998-12-01

    A high-efficient method for measuring isotope shifts and hyperfine structures in optical transitions of radioactive atoms is presented. The method is based on application of laser resonance ionization in the mass-separator ion source. The sensitivity of the method is determined by a high efficiency of the laser ion source and low background of the detection system, making use of counting α-particles following the decay of the isotope under investigation. The possibilities of this method are shown in the experiment with 155Yb and 154Tm (I=9). The isotope shifts and electromagnetic moments have been measured.

  20. Community shift of biofilms developed in a full-scale drinking water distribution system switching from different water sources.

    PubMed

    Li, Weiying; Wang, Feng; Zhang, Junpeng; Qiao, Yu; Xu, Chen; Liu, Yao; Qian, Lin; Li, Wenming; Dong, Bingzhi

    2016-02-15

    The bacterial community of biofilms in drinking water distribution systems (DWDS) with various water sources has been rarely reported. In this research, biofilms were sampled at three points (A, B, and C) during the river water source phase (phase I), the interim period (phase II) and the reservoir water source phase (phase III), and the biofilm community was determined using the 454-pyrosequencing method. Results showed that microbial diversity declined in phase II but increased in phase III. The primary phylum was Proteobacteria during three phases, while the dominant class at points A and B was Betaproteobacteria (>49%) during all phases, but that changed to Holophagae in phase II (62.7%) and Actinobacteria in phase III (35.6%) for point C, which was closely related to its water quality. More remarkable community shift was found at the genus level. In addition, analysis results showed that water quality could significantly affect microbial diversity together, while the nutrient composition (e.g. C/N ration) of the water environment might determine the microbial community. Furthermore, Mycobacterium spp. and Pseudomonas spp. were detected in the biofilm, which should give rise to attention. This study revealed that water source switching produced substantial impact on the biofilm community. PMID:26674678

  1. Community Structure and Vietnamese Refugee Adaptation: The Significance of Context.

    ERIC Educational Resources Information Center

    Starr, Paul D.; Roberts, Alden E.

    1982-01-01

    Describes research investigating the effects of community structure on the adjustment of Vietnamese refugees in America. Emphasizes how congruence between individual characteristics and characteristics of the receiving community determine successful refugee adaptation to a new environment. (MJL)

  2. Greenhouse gas emission response to global change may be limited by vegetation community shifts

    EPA Science Inventory

    Coastal marshes experience a confluence of global changes including climate change, sea level rise, exotic species invasion, and eutrophication. These changes are likely to exert new abiotic stressors and affect interspecific interactions that influence vegetation community stru...

  3. Shifts in diversity and function of lake bacterial communities upon glacier retreat.

    PubMed

    Peter, Hannes; Sommaruga, Ruben

    2016-07-01

    Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear. PMID:26771929

  4. Shifts in diversity and function of lake bacterial communities upon glacier retreat

    PubMed Central

    Peter, Hannes; Sommaruga, Ruben

    2016-01-01

    Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear. PMID:26771929

  5. Bipartite Community Structure of eQTLs.

    PubMed

    Platig, John; Castaldi, Peter J; DeMeo, Dawn; Quackenbush, John

    2016-09-01

    Genome Wide Association Studies (GWAS) and expression quantitative trait locus (eQTL) analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects and understanding their combined effect remains a challenge. One hypothesis is that multiple SNPs interact in complex networks to influence functional processes that ultimately lead to complex phenotypes, including disease states. Here we present CONDOR, a method that represents both cis- and trans-acting SNPs and the genes with which they are associated as a bipartite graph and then uses the modular structure of that graph to place SNPs into a functional context. In applying CONDOR to eQTLs in chronic obstructive pulmonary disease (COPD), we found the global network "hub" SNPs were devoid of disease associations through GWAS. However, the network was organized into 52 communities of SNPs and genes, many of which were enriched for genes in specific functional classes. We identified local hubs within each community ("core SNPs") and these were enriched for GWAS SNPs for COPD and many other diseases. These results speak to our intuition: rather than single SNPs influencing single genes, we see groups of SNPs associated with the expression of families of functionally related genes and that disease SNPs are associated with the perturbation of those functions. These methods are not limited in their application to COPD and can be used in the analysis of a wide variety of disease processes and other phenotypic traits. PMID:27618581

  6. Community Structure in Online Collegiate Social Networks

    NASA Astrophysics Data System (ADS)

    Traud, Amanda; Kelsic, Eric; Mucha, Peter; Porter, Mason

    2009-03-01

    Online social networking sites have become increasingly popular with college students. The networks we studied are defined through ``friendships'' indicated by Facebook users from UNC, Oklahoma, Caltech, Georgetown, and Princeton. We apply the tools of network science to study the Facebook networks from these five different universities at a single point in time. We investigate each single-institution network's community structure, which we obtain through partitioning the graph using an eigenvector method. We use both graphical and quantitative tools, including pair-counting methods, which we interpret through statistical analysis and permutation tests to measure the correlations between the network communities and a set of characteristics given by each user (residence, class year, major, and high school). We also analyze the single gender subsets of these networks, and the impact of missing demographical data. Our study allows us to compare the online social networks for the five schools as well as infer differences in offline social interactions. At the schools studied, we were able to define which characteristics of the Facebook users correlate best with friendships.

  7. Long-term regional shifts in plant community composition are largely explained by local deer impact experiments.

    PubMed

    Frerker, Katie; Sabo, Autumn; Waller, Donald

    2014-01-01

    The fact that herbivores and predators exert top-down effects to alter community composition and dynamics at lower trophic levels is no longer controversial, yet we still lack evidence of the full nature, extent, and longer-term effects of these impacts. Here, we use results from a set of replicated experiments on the local impacts of white-tailed deer to evaluate the extent to which such impacts could account for half-century shifts in forest plant communities across the upper Midwest, USA. We measured species' responses to deer at four sites using 10-20 year-old deer exclosures. Among common species, eight were more abundant outside the exclosures, seven were commoner inside, and 16 had similar abundances in- and outside. Deer herbivory greatly increased the abundance of ferns and graminoids and doubled the abundance of exotic plants. In contrast, deer greatly reduced tree regeneration, shrub cover (100-200 fold in two species), plant height, plant reproduction, and the abundance of forbs. None of 36 focal species increased in reproduction or grew taller in the presence of deer, contrary to expectations. We compared these results to data on 50-year regional shifts in species abundances across 62 sites. The effects of herbivory by white-tailed deer accurately account for many of the long-term regional shifts observed in species' abundances (R2 = 0.41). These results support the conjecture that deer impacts have driven many of the regional shifts in forest understory cover and composition observed in recent decades. Our ability to link results from shorter-term, local experiments to regional long-term studies of ecological change strengthens the inferences we can draw from both approaches. PMID:25551827

  8. The network of collaboration among rappers and its community structure

    NASA Astrophysics Data System (ADS)

    Smith, Reginald D.

    2006-02-01

    The social network formed by the collaboration between rappers is studied using standard statistical techniques for analysing complex networks. In addition, the community structure of the rap music community is analysed using a new method that uses weighted edges to determine which connections are most important and revealing among all the communities. The results of this method as well as possible reasons for the structure of the rap music community are discussed.

  9. 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.

  10. Multiplexed Analysis of Peptide Functionality Using Lanthanide-based Structural Shift Reagents

    PubMed Central

    Kerr, Thomas J.; Gant-Branum, Randi L.; McLean, John A.

    2011-01-01

    Functionally selective lanthanide-based ion mobility shift reagents are presented as a method to elucidate protein or peptide structural information as well as relative quantitation of protein expression profiles. Sequence information and site localization of primary amines (n-terminus and lysine), phosphorylation sites, and cysteine residues can be obtained in a data dependent manner using ion mobility-mass spectrometry (IM-MS). The high mass of the incorporated lanthanide ensures a significant shift of where the signal occurs in IM-MS conformation space. Peptide sequence information provided by the use of IM-MS shift reagents allows for both a more confident identification of peptides from complex mixtures and site localization following tandem MS experiments. Stable isotopes of the lanthanide series may also be used as relative quantitation labels since several lanthanides can be utilized in differential sample analyses. PMID:21966243

  11. Experimental verification of isotope shift and hyperfine structure of some even parity levels of neutral Eu

    NASA Astrophysics Data System (ADS)

    Furmann, B.; Stefanska, D.

    2014-09-01

    The results of measurements of the hyperfine structure of 31 classified and four unclassified spectral lines in the europium atom, obtained by using the laser induced fluorescence method, are presented. On the basis of experimental results, the values of the hyperfine structure constants and the isotope shifts for seven hitherto unmeasured levels belonging to even configurations (among them for three entirely new levels with unknown energies) were determined and the respective values known from literature for another 19 levels were verified. Since the motivation for undertaking investigations within this work was an inconsistency in the semi-empirical description of the hyperfine structure and the isotope shifts for some even levels in the europium atom, a detailed discussion of this problem is presented.

  12. Bacterial community shift is induced by dynamic environmental parameters in a changing coastal ecosystem (northern Adriatic, northeastern Mediterranean Sea)--a 2-year time-series study.

    PubMed

    Tinta, T; Vojvoda, J; Mozetič, P; Talaber, I; Vodopivec, M; Malfatti, F; Turk, V

    2015-10-01

    The potential link between the microbial dynamics and the environmental parameters was investigated in a semi-enclosed and highly dynamic coastal system (Gulf of Trieste, northern Adriatic Sea, NE Mediterranean Sea). Our comprehensive 2-year time-series study showed that despite the shallowness of this area, there was a significant difference between the surface and the bottom bacterial community structure. The bottom bacterial community was more diverse than the surface one and influenced by sediment re-suspension. The surface seawater temperature had a profound effect on bacterial productivity, while the bacterial community structure was more affected by freshwater-borne nutrients and phytoplankton blooms. Phytoplankton blooms caused an increase of Gammaproteobacteria (Alteromonadaceae, SAR86 and Vibrionaceae) and shift in dominance from SAR11 to Rhodobacteraceae taxon at the surface. Our results propose the importance of the water mass movements as drivers of freshwater-borne nutrients and of allochthonous microbial taxa. This study emphasizes the prediction power based on association networks analyses that are fed with long-term measurements of microbial and environmental parameters. These interaction maps offer valuable insights into the response of marine ecosystem to climate- and anthropogenic-driven stressors. PMID:24903068

  13. Regime, phase and paradigm shifts: making community ecology the basic science for fisheries

    PubMed Central

    Mangel, Marc; Levin, Phillip S.

    2005-01-01

    Modern fishery science, which began in 1957 with Beverton and Holt, is ca. 50 years old. At its inception, fishery science was limited by a nineteenth century mechanistic worldview and by computational technology; thus, the relatively simple equations of population ecology became the fundamental ecological science underlying fisheries. The time has come for this to change and for community ecology to become the fundamental ecological science underlying fisheries. This point will be illustrated with two examples. First, when viewed from a community perspective, excess production must be considered in the context of biomass left for predators. We argue that this is a better measure of the effects of fisheries than spawning biomass per recruit. Second, we shall analyse a simple, but still multi-species, model for fishery management that considers the alternatives of harvest regulations, inshore marine protected areas and offshore marine protected areas. Population or community perspectives lead to very different predictions about the efficacy of reserves. PMID:15713590

  14. Core level shifts in Cu-Pd alloys as a function of bulk composition and structure

    NASA Astrophysics Data System (ADS)

    Boes, Jacob R.; Kondratyuk, Peter; Yin, Chunrong; Miller, James B.; Gellman, Andrew J.; Kitchin, John R.

    2015-10-01

    CuPd alloys are important materials in hydrogen purification, where they are used as dense Pd-based separation membranes. Cu is added to impart sulfur tolerance and improved mechanical properties. At intermediate compositions and T < 873 K, a BCC alloy (B2) phase occurs, which has superior separation characteristics to those of the FCC phases that form at high Cu and high Pd compositions. Identifying the composition and temperature window where the B2 phase forms is a critical need to enable the design of improved alloys. A composition spread alloy film of Cu and Pd was synthesized. The film was characterized by electron back scatter diffraction and X-ray photoelectron spectroscopy, providing the core level shifts as a function of bulk composition and bulk structure. An anomalous deviation in the Cu core level shift was observed in the composition range 0.33 < xPd < 0.55 over which the B2 phase occurs. Density functional theory calculations were used to simulate core level shifts in the FCC and B2 alloy structures. They suggest that the anomalous deviation in core level shift is due to formation of the ordered B2 phase in this composition range.

  15. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

    PubMed Central

    Staley, Christopher; Gould, Trevor J.; Wang, Ping; Phillips, Jane; Cotner, James B.; Sadowsky, Michael J.

    2014-01-01

    Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of 14 bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046) between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River. PMID:25339945

  16. Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method.

    PubMed

    Tada, Yuya; Grossart, Hans-Peter

    2014-02-01

    In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling. PMID:23985742

  17. Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method

    PubMed Central

    Tada, Yuya; Grossart, Hans-Peter

    2014-01-01

    In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling. PMID:23985742

  18. Going Lean: Impending Money Woes Force Tough Choices, Forecast Fundamental Shift in Community College Funding

    ERIC Educational Resources Information Center

    Joch, Alan

    2011-01-01

    The numbers were already bad, and they keep getting worse, for the Dallas County Community College District (DCCCD). Given the weak economy, administrators planned for a 5 percent reduction in state funding in the 2010-11 academic year. The actual reduction ballooned to more than 7.5 percent, an additional $13 million that DCCCD would be forced to…

  19. Shifting Boundaries: The Challenge of Assessing MTech Community-Based-Visual Arts Research Projects

    ERIC Educational Resources Information Center

    Berman, K.

    2011-01-01

    This article aims to interrogate possible assessment problems arising from a community-based-research mode of research and consider some of the assessment approaches that generate scepticism among some examiners, and endorsement from others. The article explores specific challenges in supervising, accommodating and evaluating diverse candidates…

  20. Runoff and erosional response to a drought-induced shift in a desert grassland community composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigates how drought-induced change in semiarid grassland community composition affected runoff and sediment yield in a small 1.8 ha watershed in southeast Arizona, USA. Three distinct periods in ecosystem composition and associated runoff and sediment yield were identified according ...

  1. Shifting the Role: School-District Superintendents' Experiences as They Build a Learning Community

    ERIC Educational Resources Information Center

    Dickson, John; Mitchell, Coral

    2014-01-01

    This paper presents the findings of a qualitative action-research study that explored how one group of district-level school superintendents conceptualized their role as they built their own learning community. Data analysis yielded four elements that supported the participants' efforts: (a) using a process as an entry point, (b) aligning…

  2. Surprise maximization reveals the community structure of complex networks

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

    How to determine the community structure of complex networks is an open question. It is critical to establish the best strategies for community detection in networks of unknown structure. Here, using standard synthetic benchmarks, we show that none of the algorithms hitherto developed for community structure characterization perform optimally. Significantly, evaluating the results according to their modularity, the most popular measure of the quality of a partition, systematically provides mistaken solutions. However, a novel quality function, called Surprise, can be used to elucidate which is the optimal division into communities. Consequently, we show that the best strategy to find the community structure of all the networks examined involves choosing among the solutions provided by multiple algorithms the one with the highest Surprise value. We conclude that Surprise maximization precisely reveals the community structure of complex networks.

  3. Surprise maximization reveals the community structure of complex networks.

    PubMed

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

    How to determine the community structure of complex networks is an open question. It is critical to establish the best strategies for community detection in networks of unknown structure. Here, using standard synthetic benchmarks, we show that none of the algorithms hitherto developed for community structure characterization perform optimally. Significantly, evaluating the results according to their modularity, the most popular measure of the quality of a partition, systematically provides mistaken solutions. However, a novel quality function, called Surprise, can be used to elucidate which is the optimal division into communities. Consequently, we show that the best strategy to find the community structure of all the networks examined involves choosing among the solutions provided by multiple algorithms the one with the highest Surprise value. We conclude that Surprise maximization precisely reveals the community structure of complex networks. PMID:23320141

  4. Hyperfine structure and isotope shifts of transitions in neutral and singly ionized ytterbium

    NASA Technical Reports Server (NTRS)

    Berends, R. W.; Maleki, L.

    1992-01-01

    The present experimental investigation of the hyperfine structure and isotopic shifts of transitions in neutral and singly-ionized Yb, which constitute a system of some interest to microwave-frequency standards, used counterpropagating pump and probe laser beams directed through a hollow-cathode discharge lamp. The results obtained are in agreement with previous measurements except in the case of the Yb-173(+) 6 2P0 sub 3/2 state, which is more accurately determined.

  5. 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. PMID:25594261

  6. Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

    NASA Astrophysics Data System (ADS)

    Waldrop, M.; Zak, D.; Sinsabaugh, R.

    2002-12-01

    Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

  7. 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

  8. 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. PMID:25126722

  9. Ultrasonic array imaging of multilayer structures using full matrix capture and extended phase shift migration

    NASA Astrophysics Data System (ADS)

    Wu, Haiteng; Chen, Jian; Yang, Keji; Hu, Xuxiao

    2016-04-01

    Multilayer structures have been widely used in industrial fields, and non-destructive evaluation of these structures is of great importance to assure their quality and performance. Recently, ultrasonic array imaging using full matrix capture, e.g. the total focusing method (TFM), has been shown to increase sensitivity to small defects and improve imaging resolution in homogeneous media. However, it cannot be applied to multilayer structures directly, due to the sound velocity variation in different layers and because refraction occurs at layer interfaces, which gives rise to difficulties in determining the propagation path and time. To overcome these problems, an extended phase shift migration (EPSM) is proposed for the full matrix imaging of multilayer structures in this paper. Based on the theory of phase shift migration for monostatic pulse-echo imaging, full matrix imaging using EPSM is derived by extrapolating the wavefields in both transmission and reception, and extended to the multilayer case. The performance of the proposed algorithm is evaluated by full matrix imaging of a two-layer structure with side-drilled holes conducted both in the simulation and the experiment. The results verify that the proposed algorithm is capable of full matrix imaging of a layered structure with a high resolution and signal-to-noise ratio. For comparison, full matrix imaging using the TFM with root-mean-squared velocity is also performed, and the results demonstrate that the proposed algorithm is superior to the TFM in improving both the image quality and resolution.

  10. 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. PMID:25534114

  11. 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.

  12. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  13. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices t...

  14. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed.

    PubMed

    Smalla, K; Wieland, G; Buchner, A; Zock, A; Parzy, J; Kaiser, S; Roskot, N; Heuer, H; Berg, G

    2001-10-01

    The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. PMID:11571180

  15. Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

    PubMed Central

    Smalla, K.; Wieland, G.; Buchner, A.; Zock, A.; Parzy, J.; Kaiser, S.; Roskot, N.; Heuer, H.; Berg, G.

    2001-01-01

    The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. PMID:11571180

  16. Task Shifting Provision of Contraceptive Implants to Community Health Extension Workers: Results of Operations Research in Northern Nigeria

    PubMed Central

    Oguntunde, Olugbenga; Orobaton, Nosa; Otolorin, Emmanuel; Inuwa, Fatima; Alalade, Olubisi; Abegunde, Dele; Danladi, Saba’atu

    2015-01-01

    Background: Contraceptive use remains low in Nigeria, with only 11% of women reporting use of any modern method. Access to long-acting reversible contraceptives (LARCs) is constrained by a severe shortage of human resources. To assess feasibility of task shifting provision of implants, we trained community health extension workers (CHEWs) to insert and remove contraceptive implants in rural communities of Bauchi and Sokoto states in northern Nigeria. Methods: We conducted 2- to 3-week training sessions for 166 selected CHEWs from 82 facilities in Sokoto state (September 2013) and 84 health facilities in Bauchi state (December 2013). To assess feasibility of the task shifting approach, we conducted operations research using a pretest–posttest design using multiple sources of information, including surveys with 151 trained CHEWs (9% were lost to follow-up) and with 150 family planning clients; facility observations using supply checklists (N = 149); direct observation of counseling provided by CHEWs (N = 144) and of their clinical (N = 113) skills; as well as a review of service statistics (N = 151 health facilities). The endline assessment was conducted 6 months after the training in each state. Results: CHEWs inserted a total of 3,588 implants in 151 health facilities over a period of 6 months, generating 10,088 couple-years of protection (CYP). After practicing on anatomic arm models, most CHEWs achieved competency in implant insertions after insertions with 4–5 actual clients. Clinical observations revealed that CHEWs performed implant insertion tasks correctly 90% of the time or more for nearly all checklist items. The amount of information that CHEWs provided clients increased between baseline and endline, and over 95% of surveyed clients reported being satisfied with CHEWs’ services in both surveys. The study found that supervisors not only observed and corrected insertion skills, as needed, during supervisory visits but also encouraged

  17. 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

  18. Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition

    PubMed Central

    Yang, An; Liu, Nana; Tian, Qiuying; Bai, Wenming; Williams, Mark; Wang, Qibing; Li, Linghao; Zhang, Wen-Hao

    2015-01-01

    We evaluated effects of 9-year simulated nitrogen (N) deposition on microbial composition and diversity in the rhizosphere of two dominant temperate grassland species: grass Stipa krylovii and forb Artemisia frigida. Microbiomes in S. krylovii and A. frigida rhizosphere differed, but changed consistently along the N gradient. These changes were correlated to N-induced shifts to plant community. Hence, as plant biomass changed, so did bacterial rhizosphere communities, a result consistent with the role that N fertilizer has been shown to play in altering plant-microbial mutualisms. A total of 23 bacterial phyla were detected in the two rhizospheric soils by pyrosequencing, with Proteobacteria, Acidobacteria, and Bacteroidetes dominating the sequences of all samples. Bacterioidetes and Proteobacteria tended to increase, while Acidobacteria declined with increase in N addition rates. TM7 increased >5-fold in the high N addition rates, especially in S. krylovii rhizosphere. Nitrogen addition also decreased diversity of OTUs (operational taxonomic units), Shannon and Chao1 indices of rhizospheric microbes regardless of plant species. These results suggest that there were both similar but also specific changes in microbial communities of temperate steppes due to N deposition. These findings would contribute to our mechanistic understanding of impacts of N deposition on grassland ecosystem by linking changes in plant traits to their rhizospheric microbes-mediated processes. PMID:26322024

  19. Fragmentation and Management of Ethiopian Moist Evergreen Forest Drive Compositional Shifts of Insect Communities Visiting Wild Arabica Coffee Flowers

    NASA Astrophysics Data System (ADS)

    Berecha, Gezahegn; Aerts, Raf; Muys, Bart; Honnay, Olivier

    2015-02-01

    Coffea arabica is an indigenous understorey shrub of the moist evergreen Afromontane forest of SW Ethiopia. Coffee cultivation here occurs under different forest management intensities, ranging from almost no intervention in the `forest coffee' system to far-reaching interventions that include the removal of competing shrubs and selective thinning of the upper canopy in the `semi-forest coffee' system. We investigated whether increasing forest management intensity and fragmentation result in impacts upon potential coffee pollination services through examining shifts in insect communities that visit coffee flowers. Overall, we netted 2,976 insect individuals on C. arabica flowers, belonging to sixteen taxonomic groups, comprising 10 insect orders. Taxonomic richness of the flower-visiting insects significantly decreased and pollinator community changed with increasing forest management intensity and fragmentation. The relative abundance of honey bees significantly increased with increasing forest management intensity and fragmentation, likely resulting from the introduction of bee hives in the most intensively managed forests. The impoverishment of the insect communities through increased forest management intensity and fragmentation potentially decreases the resilience of the coffee production system as pollination increasingly relies on honey bees alone. This may negatively affect coffee productivity in the long term as global pollination services by managed honey bees are expected to decline under current climate change scenarios. Coffee agroforestry management practices should urgently integrate pollinator conservation measures.

  20. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests.

    PubMed

    Clemmensen, Karina E; Finlay, Roger D; Dahlberg, Anders; Stenlid, Jan; Wardle, David A; Lindahl, Björn D

    2015-03-01

    Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems. We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration. In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition. Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests. PMID:25494880

  1. Climate-driven regime shifts in the biological communities of arctic lakes

    PubMed Central

    Smol, John P.; Wolfe, Alexander P.; Birks, H. John B.; Douglas, Marianne S. V.; Jones, Vivienne J.; Korhola, Atte; Pienitz, Reinhard; Rühland, Kathleen; Sorvari, Sanna; Antoniades, Dermot; Brooks, Stephen J.; Fallu, Marie-Andrée; Hughes, Mike; Keatley, Bronwyn E.; Laing, Tamsin E.; Michelutti, Neal; Nazarova, Larisa; Nyman, Marjut; Paterson, Andrew M.; Perren, Bianca; Quinlan, Roberto; Rautio, Milla; Saulnier-Talbot, Émilie; Siitonen, Susanna; Solovieva, Nadia; Weckström, Jan

    2005-01-01

    Fifty-five paleolimnological records from lakes in the circumpolar Arctic reveal widespread species changes and ecological reorganizations in algae and invertebrate communities since approximately anno Domini 1850. The remoteness of these sites, coupled with the ecological characteristics of taxa involved, indicate that changes are primarily driven by climate warming through lengthening of the summer growing season and related limnological changes. The widespread distribution and similar character of these changes indicate that the opportunity to study arctic ecosystems unaffected by human influences may have disappeared. PMID:15738395

  2. Defined spatial structure stabilizes a synthetic multispecies bacterial community

    PubMed Central

    Kim, Hyun Jung; Boedicker, James Q.; Choi, Jang Wook; Ismagilov, Rustem F.

    2008-01-01

    This paper shows that for microbial communities, “fences make good neighbors.” Communities of soil microorganisms perform critical functions: controlling climate, enhancing crop production, and remediation of environmental contamination. Microbial communities in the oral cavity and the gut are of high biomedical interest. Understanding and harnessing the function of these communities is difficult: artificial microbial communities in the laboratory become unstable because of “winner-takes-all” competition among species. We constructed a community of three different species of wild-type soil bacteria with syntrophic interactions using a microfluidic device to control spatial structure and chemical communication. We found that defined microscale spatial structure is both necessary and sufficient for the stable coexistence of interacting bacterial species in the synthetic community. A mathematical model describes how spatial structure can balance the competition and positive interactions within the community, even when the rates of production and consumption of nutrients by species are mismatched, by exploiting nonlinearities of these processes. These findings provide experimental and modeling evidence for a class of communities that require microscale spatial structure for stability, and these results predict that controlling spatial structure may enable harnessing the function of natural and synthetic multispecies communities in the laboratory. PMID:19011107

  3. Ontogenetic shifts in plant interactions vary with environmental severity and affect population structure.

    PubMed

    le Roux, Peter C; Shaw, Justine D; Chown, Steven L

    2013-10-01

    Environmental conditions and plant size may both alter the outcome of inter-specific plant-plant interactions, with seedlings generally facilitated more strongly than larger individuals in stressful habitats. However, the combined impact of plant size and environmental severity on interactions is poorly understood. Here, we tested explicitly for the first time the hypothesis that ontogenetic shifts in interactions are delayed under increasingly severe conditions by examining the interaction between a grass, Agrostis magellanica, and a cushion plant, Azorella selago, along two severity gradients. The impact of A. selago on A. magellanica abundance, but not reproductive effort, was related to A. magellanica size, with a trend for delayed shifts towards more negative interactions under greater environmental severity. Intermediate-sized individuals were most strongly facilitated, leading to differences in the size-class distribution of A. magellanica on the soil and on A. selago. The A. magellanica size-class distribution was more strongly affected by A. selago than by environmental severity, demonstrating that the plant-plant interaction impacts A. magellanica population structure more strongly than habitat conditions. As ontogenetic shifts in plant-plant interactions cannot be assumed to be constant across severity gradients and may impact species population structure, studies examining the outcome of interactions need to consider the potential for size- or age-related variation in competition and facilitation. PMID:23738758

  4. Isotope shifts and hyperfine structure of the laser-cooling Fe I 358-nm line

    NASA Astrophysics Data System (ADS)

    Huet, N.; Pettens, M.; Bastin, T.

    2015-11-01

    We report on the measurement of the isotope shifts of the 3 d74 s a 5F5-3 d74 p z 5G6o Fe i line at 358 nm between all four stable isotopes ,Fe56Fe54,Fe57 , and Fe58 , as well as the hyperfine structure of that line for Fe57 , the only stable isotope having a nonzero nuclear spin. This line is of primary importance for laser-cooling applications. In addition, an experimental value of the field and specific mass shift coefficients of the transition is reported as well as the hyperfine structure magnetic dipole coupling constant A of the transition excited state in Fe57 , namely A (3 d74 p z 5G6o) =31.241 (48 ) MHz. The measurements were carried out by means of laser-induced fluorescence spectroscopy performed on an isotope-enriched iron atomic beam. All measured frequency shifts are reported with relative uncertainties below one third percent.

  5. 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…

  6. 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…

  7. Runoff and erosional responses to a drought-induced shift in a desert grassland community composition

    NASA Astrophysics Data System (ADS)

    Polyakov, V. O.; Nearing, M. A.; Stone, J. J.; Hamerlynck, E. P.; Nichols, M. H.; Holifield Collins, C. D.; Scott, R. L.

    2010-12-01

    This study investigates how drought-induced change in semiarid grassland community affected runoff and sediment yield in a small watershed in southeast Arizona, USA. Three distinct periods in ecosystem composition and associated runoff and sediment yield were identified according to dominant species: native bunchgrass (1974-2005), forbs (2006), and the invasive grass, Eragrostis lehmanniana (2007-2009). Precipitation, runoff, and sediment yield for each period were analyzed and compared at watershed and plot scales. Average watershed annual sediment yield was 0.16 t ha-1 yr-1. Despite similarities in precipitation characteristics, decline in plant canopy cover during the transition period of 2006 caused watershed sediment yield to increase 23-fold to 1.64 t ha-1 yr-1 comparing with preceding period under native bunchgrasses (0.06 t ha-1 yr-1) or succeeding period under E. lehmanniana (0.06 t ha-1 yr-1). In contrast, measurements on small runoff plots on the hillslopes of the same watershed showed a significant increase in sediment discharge that continued after E. lehmanniana replaced native grasses. Together, these findings suggest alteration in plant community increased sediment yield but that hydrological responses to this event differ at watershed and plot scales, highlighting the geomorphological controls at the watershed scale that determine sediment transport efficiency and storage. Resolving these scalar issues will help identify critical landform features needed to preserve watershed integrity under changing climate conditions.

  8. Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach

    PubMed Central

    Jacquiod, Samuel; Franqueville, Laure; Cécillon, Sébastien; M. Vogel, Timothy; Simonet, Pascal

    2013-01-01

    Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome. PMID:24278158

  9. Structural responses of benthic macroinvertebrate communities from different stream orders to zinc

    SciTech Connect

    Kiffney, P.M.; Clements, W.H. . Dept. of Fishery and Wildlife Biology)

    1994-03-01

    It is well established that benthic invertebrate community structure and function shift in a predictable fashion along longitudinal stream gradients as a result of variation in environmental conditions. The authors research is concerned with experimentally testing whether this shift in community structure influences the response of benthic macroinvertebrates to heavy metals. Using artificial streams, they compared effects of Zn on natural assemblages of benthic macroinvertebrates communities collected from Little Beaver Creek (LBC; a third-order stream) and the Big South Fork of the Cache la Poudre, Colorado, catchment. Organisms collected from LBC and SFP were exposed to 0 or 130 [mu]g/L Zn in indoor experimental streams for 7 d. In general, similar taxa were found at both sites, but densities were generally higher at SFP than at LBC. They observed significant effects at the community and population level as a result of Zn, stream order, and the interaction between Zn and stream order. Specifically, mayflies from both sides were sensitive to Zn, but the magnitude of the response varied between sites. The results indicate that benthic macroinvertebrate communities from different stream order may vary in sensitivity to Zn.

  10. Educational inequality by race in Brazil, 1982-2007: structural changes and shifts in racial classification.

    PubMed

    Marteleto, Leticia J

    2012-02-01

    Despite overwhelming improvements in educational levels and opportunity during the past three decades, educational disadvantages associated with race still persist in Brazil. Using the nationally representative Pesquisa Nacional de Amostra por Domicílio (PNAD) data from 1982 and 1987 to 2007, this study investigates educational inequalities between white, pardo (mixed-race), and black Brazilians over the 25-year period. Although the educational advantage of whites persisted during this period, I find that the significance of race as it relates to education changed. By 2007, those identified as blacks and pardos became more similar in their schooling levels, whereas in the past, blacks had greater disadvantages. I test two possible explanations for this shift: structural changes and shifts in racial classification. I find evidence for both. I discuss the findings in light of the recent race-based affirmative action policies being implemented in Brazilian universities. PMID:22259031

  11. Educational Inequality by Race in Brazil, 1982–2007: Structural Changes and Shifts in Racial Classification

    PubMed Central

    Marteleto, Leticia J.

    2013-01-01

    Despite overwhelming improvements in educational levels and opportunity during the past three decades, educational disadvantages associated with race still persist in Brazil. Using the nationally representative Pesquisa Nacional de Amostra por Domicílio (PNAD) data from 1982 and 1987 to 2007, this study investigates educational inequalities between white, pardo (mixed-race), and black Brazilians over the 25-year period. Although the educational advantage of whites persisted during this period, I find that the significance of race as it relates to education changed. By 2007, those identified as blacks and pardos became more similar in their schooling levels, whereas in the past, blacks had greater disadvantages. I test two possible explanations for this shift: structural changes and shifts in racial classification. I find evidence for both. I discuss the findings in light of the recent race-based affirmative action policies being implemented in Brazilian universities. PMID:22259031

  12. Application of the laser ion source for isotope shift and hyperfine structure investigation

    NASA Astrophysics Data System (ADS)

    Seliverstov, M. D.; Barzakh, A. E.; Chubukov, I. Ya.; Fedorov, D. V.; Panteleev, V. N.; Volkov, Yu. M.

    2000-08-01

    The study of nuclei far from stability requires high sensitivity of the experimental technique. The method of Resonance Ionization Spectroscopy in a Laser Ion Source (RIS/LIS) allows one to carry out measurements of the isotope shifts and hyperfine splittings for isotopes at the production rate about 102 atoms per second. The sensitivity of this method is determined by the high efficiency of the laser ion source and the low background of the detection system afforded by characteristic α particle registration. The isotope shifts and hyperfine structures of 155Yb, 154Tm (I=9 and I=2) and 153Tm (I=11/2) have been measured and the isotopic changes in mean square charge radii and nuclear electromagnetic moments have been determined. The further development of this experimental method - enhanced Target Ion Source system aimed to suppress thermionic background - enables direct detection of the photoions and widens the range of the applicability of the RIS/LIS method.

  13. Stochasticity, complex spatial structure, and the feasibility of the shifting balance theory.

    PubMed

    O'Fallon, Brendan; Adler, Frederick R

    2006-03-01

    Sewall Wright's shifting balance theory of evolution posits a mechanism by which a structured population may escape local fitness optima and find a global optimum. We examine a one-locus, two-allele model of underdominance in populations with differing spatial arrangements of demes, both analytically and with Monte Carlo simulations. We find that inclusion of variance in interpatch connectivities can significantly reduce the number of generations required for fixation of the more favorable allele relative to island and stepping-stone models. Although time to fixation increases with migration rate in all cases, the presence of one or two relatively isolated demes may reduce the number of generations by 80% or more. These results suggest that the shifting balance process may operate under less restrictive conditions than those found with a simple spatial arrangement of demes. PMID:16637490

  14. Combining a weed traits database with a population dynamics model predicts shifts in weed communities

    PubMed Central

    Storkey, J; Holst, N; Bøjer, O Q; Bigongiali, F; Bocci, G; Colbach, N; Dorner, Z; Riemens, M M; Sartorato, I; Sønderskov, M; Verschwele, A

    2015-01-01

    A functional approach to predicting shifts in weed floras in response to management or environmental change requires the combination of data on weed traits with analytical frameworks that capture the filtering effect of selection pressures on traits. A weed traits database (WTDB) was designed, populated and analysed, initially using data for 19 common European weeds, to begin to consolidate trait data in a single repository. The initial choice of traits was driven by the requirements of empirical models of weed population dynamics to identify correlations between traits and model parameters. These relationships were used to build a generic model, operating at the level of functional traits, to simulate the impact of increasing herbicide and fertiliser use on virtual weeds along gradients of seed weight and maximum height. The model generated ‘fitness contours’ (defined as population growth rates) within this trait space in different scenarios, onto which two sets of weed species, defined as common or declining in the UK, were mapped. The effect of increasing inputs on the weed flora was successfully simulated; 77% of common species were predicted to have stable or increasing populations under high fertiliser and herbicide use, in contrast with only 29% of the species that have declined. Future development of the WTDB will aim to increase the number of species covered, incorporate a wider range of traits and analyse intraspecific variability under contrasting management and environments. PMID:26190870

  15. Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil.

    PubMed

    Wan, Chunli; Du, Maoan; Lee, Duu-Jong; Yang, Xue; Ma, Wencheng; Zheng, Lina

    2011-03-01

    Electrokinetic (EK) migration of β-cyclodextrin (β-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m(-1) for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field. PMID:21052991

  16. The structure and evolution of plankton communities

    NASA Astrophysics Data System (ADS)

    Longhurst, Alan R.

    New understanding of the circulation of ancient oceans is not yet matched by progress in our understanding of their pelagic ecology, though it was the planktonic ecosystems that generated our offshore oil and gas reserves. Can we assume that present-day models of ecosystem function are also valid for ancient seas? This question is addressed by a study of over 4000 plankton samples to derive a comprehensive, global description of zooplankton community structure in modern oceans: this shows that copepods form only 50% of the biomass of all plankton, ranging from 70% in polar to 35% in tropical seas. Comparable figures are derived from 14 other taxonomic categories of zooplankton. For trophic groupings, the data indicate globally: geletinous predators - 14%; gelatinous herbivores - 4%; raptorial predators - 33%; macrofiltering herbivores - 20%; macrofiltering omnivores - 25%; and detritivores - 3%. A simple, idealized model for the modern pelagic ecosystem is derived from these percentages which indicates that metazooplankton are not the most important consumers of pico- and nano-plankton production which itself probably constitutes 90% of primary production in warm oceans. This model is then compared with candidate life-forms available in Palaeozoic and Mesozoic oceans to determine to what extent it is also valid for ancient ecosystems: it is concluded that it is probably unnecessary to postulate models fundamentally differing from it in order to accommodate the life-forms, both protozoic and metazoic, known to have populated ancient seas. Remarkably few life-forms have existed which cannot be paralleled in the modern ocean, which contains remarkably few life-forms which cannot be paralleled in the Palaeozoic ocean. As a first assumption, then, it is reasonable to assume that energy pathways were similar in ancient oceans to those we study today.

  17. Community structure and nutrient level control the tolerance of autotrophic biofilm to silver contamination.

    PubMed

    Leflaive, J; Felten, V; Ferriol, J; Lamy, A; Ten-Hage, L; Bec, A; Danger, M

    2015-09-01

    Autotrophic biofilms are complex and fundamental biological compartments of many aquatic ecosystems. Since microbial species differ in their sensitivity to stressors, biofilms have long been proposed for assessing the quality of aquatic ecosystems. Among the many stressors impacting aquatic ecosystems, eutrophication and metal pollution are certainly the most common. Despite that these stressors often occur together, their effects on biofilms have been far much studied separately than interactively. In this study, we evaluated the interactive effects of silver (Ag), a reemerging contaminant, and phosphorus (P), a nutrient often associated with freshwater eutrophication, on the structure and functioning of two types of autotrophic biofilms, one dominated by diatoms and another one dominated by cyanobacteria. We hypothesized that P would alleviate the toxic effects of Ag, either directly, through the contribution of P in metal detoxification processes, or indirectly, through P-mediated shifts in biofilm community compositions and associated divergences in metal tolerance. Results showed that Ag impacted biofilm community structure and functioning but only at unrealistic concentrations (50 μg/L). P availability led to significant shifts in biofilm community composition, these changes being more pronounced in diatom- than those in cyanobacteria-dominated biofilm. In addition, P tended to reduce the impact of Ag but only for the cyanobacteria-dominated biofilm. More generally, our results highlight the preponderant role of the initial community structure and nutrient level on biofilm response to metallic pollutants. PMID:25422116

  18. Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

    PubMed Central

    Jünemann, Sebastian; Prior, Karola; Szczepanowski, Rafael; Harks, Inga; Ehmke, Benjamin; Goesmann, Alexander; Stoye, Jens; Harmsen, Dag

    2012-01-01

    Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in bacterial communities between patients treated by SRP alone versus SRP plus antibiotics. This is the first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight subgingival plaque samples from four patients with chronic periodontitis, taken before and two months after intervention were analyzed. Amplicons from the V6 hypervariable region of the 16S rRNA gene were generated and sequenced each on a 314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs, 3% distance), described by community metrics, and taxonomically classified. Reads ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659 non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in all samples after therapy was observed regardless of the treatment type whereas richness (ACE) showed no correlation. Taxonomic analysis revealed different microbial shifts between both therapy approaches at all taxonomic levels. Most remarkably, the genera Porphyromonas, Tannerella, Treponema, and Filifactor all harboring periodontal pathogenic species were removed almost only in the group treated with SPR and antibiotics. For the species T. forsythia and P. gingivalis results were corroborated by real-time PCR analysis. In the future, hypothesis free metagenomic analysis could be the key in understanding polymicrobial diseases and be used for therapy monitoring. Therefore, as read length continues to increase and cost to decrease, rapid benchtop sequencers like the PGM might finally be used in routine diagnostic. PMID:22870235

  19. Ontogenetic shifts in plant-plant interactions in a rare cycad within angiosperm communities.

    PubMed

    Álvarez-Yépiz, Juan C; Búrquez, Alberto; Dovčiak, Martin

    2014-06-01

    Gymnosperms and angiosperms can co-occur within the same habitats but key plant traits are thought to give angiosperms an evolutionary competitive advantage in many ecological settings. We studied ontogenetic changes in competitive and facilitative interactions between a rare gymnosperm (Dioon sonorense, our target species) and different plant and abiotic neighbours (conspecific-cycads, heterospecific-angiosperms, or abiotic-rocks) from 2007 to 2010 in an arid environment of northwestern Mexico. We monitored survival and growth of seedlings, juveniles, and adults of the cycad Dioon sonorense to evaluate how cycad survival and relative height growth rate (RHGR) responded to intra- and interspecific competition, canopy openness, and nearest neighbour. We tested spatial associations among D. sonorense life stages and angiosperm species and measured ontogenetic shifts in cycad shade tolerance. Canopy openness decreased cycad survival while intraspecific competition decreased survival and RHGR during early ontogeny. Seedling survival was higher in association with rocks and heterospecific neighbours where intraspecific competition was lower. Shade tolerance decreased with cycad ontogeny reflecting the spatial association of advanced stages with more open canopies. Interspecific facilitation during early ontogeny of our target species may promote its persistence in spite of increasing interspecific competition in later stages. We provide empirical support to the long-standing assumption that marginal rocky habitats serve as refugia from angiosperm competition for slow-growing gymnosperms such as cycads. The lack of knowledge of plant-plant interactions in rare or endangered species may hinder developing efficient conservation strategies (e.g. managing for sustained canopy cover), especially under the ongoing land use and climatic changes. PMID:24652529

  20. Community structure of foraminiferal communities within temporal biozones from the western Arctic Ocean

    USGS Publications Warehouse

    Hayek, Lee-Ann C.; Buzas, Martin A.; Osterman, Lisa A.

    2007-01-01

    Community structure is often an overlooked dimension of biodiversity. Knowledge of community structure, the statistical distribution of the relative species abundance vector, makes possible comparisons and contrasts across time, space, and/or environmental conditions. Our results indicate that species of Arctic foraminifera in age-correlated cores from abyssal depths are each best described by log-series distributions. Using this structural information, we were able to determine that structural stability exists for at least 50 ka. The foraminiferal communities in this study show remarkable concordance, distributional similarity and support the neutral theory of biodiversity.

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

    PubMed

    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

  2. Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

    PubMed Central

    Lysøe, Erik; Nordskog, Berit; Brurberg, May Bente

    2014-01-01

    The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development. PMID:25527554

  3. 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. PMID:24358711

  4. Measurement of wavefront structure from large aperture optical components by phase shifting interferometry

    SciTech Connect

    Wolfe, C.R.; Lawson, J.K.; Kellam, M.; Maney, R.T.; Demiris, A.

    1995-05-12

    This paper discusses the results of high spatial resolution measurement of the transmitted or reflected wavefront of optical components using phase shifting interferometry with a wavelength of 6328 {angstrom}. The optical components studied range in size from approximately 50 mm {times} 100 mm to 400 mm {times} 750 mm. Wavefront data, in the form of 3-D phase maps, have been obtained for three regimes of scale length: ``micro roughness``, ``mid-spatial scale``, and ``optical figure/curvature.`` Repetitive wavefront structure has been observed with scale lengths from 10 mm to 100 mm. The amplitude of this structure is typically {lambda}/100 to {lambda}/20. Previously unobserved structure has been detected in optical materials and on the surfaces of components. We are using this data to assist in optimizing laser system design, to qualify optical components and fabrication processes under study in our component development program.

  5. High organic loading treatment for industrial molasses wastewater and microbial community shifts corresponding to system development.

    PubMed

    Kuroda, Kyohei; Chosei, Tomoaki; Nakahara, Nozomi; Hatamoto, Masashi; Wakabayashi, Takashi; Kawai, Toshikazu; Araki, Nobuo; Syutsubo, Kazuaki; Yamaguchi, Takashi

    2015-11-01

    Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. To establish a high organic loading treatment system for industrial molasses wastewater, this study designed a combined system comprising an acidification tank, a thermophilic multi-stage (MS)-upflow anaerobic sludge blanket (UASB) reactor, mesophilic UASB reactor, and down-flow hanging sponge reactor. The average total chemical oxygen demand (COD) and biochemical oxygen demand removal rates were 85%±3% and 95%±2%, respectively, at an organic loading rate of 42kgCODcrm(-3)d(-1) in the MS-UASB reactor. By installation of the acidification tank, the MS-UASB reactor achieved low H2-partial pressure. The abundance of syntrophs such as fatty acid-degrading bacteria increased in the MS-UASB and 2nd-UASB reactors. Thus, the acidification tank contributed to maintaining a favorable environment for syntrophic associations. This study provides new information regarding microbial community composition in a molasses wastewater treatment system. PMID:26241842

  6. Community Shifts in the Surface Microbiomes of the Coral Porites astreoides with Unusual Lesions

    PubMed Central

    Meyer, Julie L.; Paul, Valerie J.; Teplitski, Max

    2014-01-01

    Apical lesions on Porites astreoides were characterized by the appearance of a thin yellow band, which was preceded by bleaching of the coral tissues and followed by a completely denuded coral skeleton, which often harbored secondary macroalgal colonizers. These characteristics have not been previously described in Porites and do not match common Caribbean coral diseases. The lesions were observed only in warmer months and at shallow depths on the fore reef in Belize. Analysis of the microbial community composition based on the V4 hypervariable region of 16S ribosomal RNA genes revealed that the surface microbiomes associated with nonsymptomatic corals were dominated by the members of the genus Endozoicomonas, consistent with other studies. Comparison of the microbiomes of nonsymptomatic and lesioned coral colonies sampled in July and September revealed two distinct groups, inconsistently related to the disease state of the coral, but showing some temporal signal. The loss of Endozoicomonas was characteristic of lesioned corals, which also harbored potential opportunistic pathogens such as Alternaria, Stenotrophomonas, and Achromobacter. The presence of lesions in P. astreoides coincided with a decrease in the relative abundance of Endozoicomonas, rather than the appearance of specific pathogenic taxa. PMID:24937478

  7. Community shifts in the surface microbiomes of the coral Porites astreoides with unusual lesions.

    PubMed

    Meyer, Julie L; Paul, Valerie J; Teplitski, Max

    2014-01-01

    Apical lesions on Porites astreoides were characterized by the appearance of a thin yellow band, which was preceded by bleaching of the coral tissues and followed by a completely denuded coral skeleton, which often harbored secondary macroalgal colonizers. These characteristics have not been previously described in Porites and do not match common Caribbean coral diseases. The lesions were observed only in warmer months and at shallow depths on the fore reef in Belize. Analysis of the microbial community composition based on the V4 hypervariable region of 16S ribosomal RNA genes revealed that the surface microbiomes associated with nonsymptomatic corals were dominated by the members of the genus Endozoicomonas, consistent with other studies. Comparison of the microbiomes of nonsymptomatic and lesioned coral colonies sampled in July and September revealed two distinct groups, inconsistently related to the disease state of the coral, but showing some temporal signal. The loss of Endozoicomonas was characteristic of lesioned corals, which also harbored potential opportunistic pathogens such as Alternaria, Stenotrophomonas, and Achromobacter. The presence of lesions in P. astreoides coincided with a decrease in the relative abundance of Endozoicomonas, rather than the appearance of specific pathogenic taxa. PMID:24937478

  8. Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.

    PubMed

    Theuerl, Susanne; Kohrs, Fabian; Benndorf, Dirk; Maus, Irena; Wibberg, Daniel; Schlüter, Andreas; Kausmann, Robert; Heiermann, Monika; Rapp, Erdmann; Reichl, Udo; Pühler, Alfred; Klocke, Michael

    2015-09-01

    This study provides a comprehensive, long-term microbiological study of a continuously operated, mesophilic, agricultural biogas plant fed with whole-crop silages of maize and rye, cattle manure and cattle slurry. The microbial community structure was accessed by high-throughput 16S rRNA gene amplicon sequencing. For the characterisation of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach as well as a LC-MS/MS approach for protein identification were applied. Our results revealed that the anaerobic digestion is a highly sensitive process: small variations in the process performance induce fluctuations in the microbial community composition and activity. In this context, it could be proven that certain microbial species were better adapted to changing process condition such as temperature (interspecies competition) and that there is a physiological compensation between different microorganisms so that the reactor efficiency was not adversely affected despite of structural and functional changes within the microbial community. PMID:25998656

  9. Fast Lamb wave energy shift approach using fully contactless ultrasonic system to characterize concrete structures

    NASA Astrophysics Data System (ADS)

    Ham, Suyun; Popovics, John S.

    2015-03-01

    Ultrasonic techniques provide an effective non-destructive evaluation (NDE) method to monitor concrete structures, but the need to perform rapid and accurate structural assessment requires evaluation of hundreds, or even thousands, of measurement datasets. Use of a fully contactless ultrasonic system can save time and labor through rapid implementation, and can enable automated and controlled data acquisition, for example through robotic scanning. Here we present results using a fully contactless ultrasonic system. This paper describes our efforts to develop a contactless ultrasonic guided wave NDE approach to detect and characterize delamination defects in concrete structures. The developed contactless sensors, controlled scanning system, and employed Multi-channel Analysis of Surface Waves (MASW) signal processing scheme are reviewed. Then a guided wave interpretation approach for MASW data is described. The presence of delamination is interpreted by guided plate wave (Lamb wave) behavior, where a shift in excited Lamb mode phase velocity, is monitored. Numerically simulated and experimental ultrasonic data collected from a concrete sample with simulated delamination defects are presented, where the occurrence of delamination is shown to be associated with a mode shift in Lamb wave energy.

  10. Biochar decreased microbial metabolic quotient and shifted community composition four years after a single incorporation in a slightly acid rice paddy from southwest China.

    PubMed

    Zheng, Jufeng; Chen, Junhui; Pan, Genxing; Liu, Xiaoyu; Zhang, Xuhui; Li, Lianqing; Bian, Rongjun; Cheng, Kun; Jinwei, Zheng

    2016-11-15

    While numerous studies both in laboratory and field have showed short term impacts of biochar on soil microbial community, there have been comparatively few reports addressing its long term impacts particular in field condition. This study investigated the changes of microbial community activity and composition in a rice paddy four years after a single incorporation of biochar at 20 and 40t/ha. The results indicated that biochar amendment after four years increased soil pH, soil organic C (SOC), total N and C/N ratio and decreased bulk density, particularly for the 40t/ha treatment compared to the control (0t/ha). Though no significant difference was observed in soil basal respiration, biochar amendment increased soil microbial biomass C and resulted in a significantly lower metabolic quotient. Besides, dehydrogenase and β-glucosidase activities were significantly decreased under biochar amendment relative to the control. The results of Illumina Miseq sequencing showed that biochar increased α-diversity of bacteria but decreased that of fungi and changed both bacterial and fungal community structures significantly. Biochar did not change the relative abundances of majority of bacteria at phylum level with the exception of a significant reduction of Actinobacteria, but significantly changed most of bacterial groups at genus level, particularly at 40t/ha. In contrast, biochar significantly decreased the relative abundances of Ascomycota and Basidiomycota by 11% and 66% and increased the relative abundances of Zygomycota by 147% at 40t/ha compared to the non-amended soil. Redundancy analysis (RDA) indicated that biochar induced changes in soil chemical properties, such as pH, SOC and C/N, were important factors driving community composition shifts. This study suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic

  11. Electrically controlled Goos-Hänchen shift of a light beam reflected from the metal-insulator-semiconductor structure.

    PubMed

    Luo, Changyou; Guo, Jun; Wang, Qingkai; Xiang, Yuanjiang; Wen, Shuangchun

    2013-05-01

    We proposed a scheme to manipulate the Goos-Hänchen shift of a light beam reflected from the depletion-type device via external voltage bias. It is shown that the lateral shift of the reflected probe beam can be easily controlled by adjusting the reverse voltage bias and the incidence angle. Using this scheme, the lateral shift can be tuned from negative to positive, without changing the original structure of the depletion-type device. Numerical calculations further indicate that the influence of structure parameters and light wavelength can be reduced via readjustment of the reverse bias. The proposed structure has the potential application for the integrated electronic devices. PMID:23669899

  12. Detecting Community Structure by Using a Constrained Label Propagation Algorithm

    PubMed Central

    Ratnavelu, Kuru

    2016-01-01

    Community structure is considered one of the most interesting features in complex networks. Many real-world complex systems exhibit community structure, where individuals with similar properties form a community. The identification of communities in a network is important for understanding the structure of said network, in a specific perspective. Thus, community detection in complex networks gained immense interest over the last decade. A lot of community detection methods were proposed, and one of them is the label propagation algorithm (LPA). The simplicity and time efficiency of the LPA make it a popular community detection method. However, the LPA suffers from instability detection due to randomness that is induced in the algorithm. The focus of this paper is to improve the stability and accuracy of the LPA, while retaining its simplicity. Our proposed algorithm will first detect the main communities in a network by using the number of mutual neighbouring nodes. Subsequently, nodes are added into communities by using a constrained LPA. Those constraints are then gradually relaxed until all nodes are assigned into groups. In order to refine the quality of the detected communities, nodes in communities can be switched to another community or removed from their current communities at various stages of the algorithm. We evaluated our algorithm on three types of benchmark networks, namely the Lancichinetti-Fortunato-Radicchi (LFR), Relaxed Caveman (RC) and Girvan-Newman (GN) benchmarks. We also apply the present algorithm to some real-world networks of various sizes. The current results show some promising potential, of the proposed algorithm, in terms of detecting communities accurately. Furthermore, our constrained LPA has a robustness and stability that are significantly better than the simple LPA as it is able to yield deterministic results. PMID:27176470

  13. Detecting Community Structure by Using a Constrained Label Propagation Algorithm.

    PubMed

    Chin, Jia Hou; Ratnavelu, Kuru

    2016-01-01

    Community structure is considered one of the most interesting features in complex networks. Many real-world complex systems exhibit community structure, where individuals with similar properties form a community. The identification of communities in a network is important for understanding the structure of said network, in a specific perspective. Thus, community detection in complex networks gained immense interest over the last decade. A lot of community detection methods were proposed, and one of them is the label propagation algorithm (LPA). The simplicity and time efficiency of the LPA make it a popular community detection method. However, the LPA suffers from instability detection due to randomness that is induced in the algorithm. The focus of this paper is to improve the stability and accuracy of the LPA, while retaining its simplicity. Our proposed algorithm will first detect the main communities in a network by using the number of mutual neighbouring nodes. Subsequently, nodes are added into communities by using a constrained LPA. Those constraints are then gradually relaxed until all nodes are assigned into groups. In order to refine the quality of the detected communities, nodes in communities can be switched to another community or removed from their current communities at various stages of the algorithm. We evaluated our algorithm on three types of benchmark networks, namely the Lancichinetti-Fortunato-Radicchi (LFR), Relaxed Caveman (RC) and Girvan-Newman (GN) benchmarks. We also apply the present algorithm to some real-world networks of various sizes. The current results show some promising potential, of the proposed algorithm, in terms of detecting communities accurately. Furthermore, our constrained LPA has a robustness and stability that are significantly better than the simple LPA as it is able to yield deterministic results. PMID:27176470

  14. What Community College Students Value: Delineating a Normative Structure for Community College Students

    ERIC Educational Resources Information Center

    Akin, Renea; Park, Toby J.

    2016-01-01

    This manuscript delineates a normative structure for community college students, outlines how this structure varies by student characteristics, and compares this structure to that of a previously established normative structure identified at a 4-year institution. A total of 512 student survey responses on the College Student Behaviors Inventory…

  15. 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

  16. A stochastic model for detecting overlapping and hierarchical community structure.

    PubMed

    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 l(2,1) 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 l(2,1) 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

  17. Generic criticality of community structure in random graphs

    NASA Astrophysics Data System (ADS)

    Lipowski, Adam; Lipowska, Dorota

    2014-09-01

    We examine a community structure in random graphs of size n and link probability p /n determined with the Newman greedy optimization of modularity. Calculations show that for p <1 communities are nearly identical with clusters. For p =1 the average sizes of a community sav and of the giant community sg show a power-law increase sav˜nα' and sg˜nα. From numerical results we estimate α'≈0.26(1) and α ≈0.50(1) and using the probability distribution of sizes of communities we suggest that α'=α/2 should hold. For p >1 the community structure remains critical: (i) sav and sg have a power-law increase with α'≈α<1 and (ii) the probability distribution of sizes of communities is very broad and nearly flat for all sizes up to sg. For large p the modularity Q decays as Q˜p-0.55, which is intermediate between some previous estimations. To check the validity of the results, we also determine the community structure using another method, namely, a nongreedy optimization of modularity. Tests with some benchmark networks show that the method outperforms the greedy version. For random graphs, however, the characteristics of the community structure determined using both greedy and nongreedy optimizations are, within small statistical fluctuations, the same.

  18. Inhibition of residual n-hexane in anaerobic digestion of lipid-extracted microalgal wastes and microbial community shift.

    PubMed

    Yun, Yeo-Myeong; Shin, Hang-Sik; Lee, Chang-Kyu; Oh, You-Kwan; Kim, Hyun-Woo

    2016-04-01

    Converting lipid-extracted microalgal wastes to methane (CH4) via anaerobic digestion (AD) has the potential to make microalgae-based biodiesel platform more sustainable. However, it is apparent that remaining n-hexane (C6H14) from lipid extraction could inhibit metabolic pathway of methanogens. To test an inhibitory influence of residual n-hexane, this study conducted a series of batch AD by mixing lipid-extracted Chlorella vulgaris with a wide range of n-hexane concentration (∼10 g chemical oxygen demand (COD)/L). Experimental results show that the inhibition of n-hexane on CH4 yield was negligible up to 2 g COD/L and inhibition to methanogenesis became significant when it was higher than 4 g COD/L based on quantitative mass balance. Inhibition threshold was about 4 g COD/L of n-hexane. Analytical result of microbial community profile revealed that dominance of alkane-degrading sulfate-reducing bacteria (SRB) and syntrophic bacteria increased, while that of methanogens sharply dropped as n-hexane concentration increased. These findings offer a useful guideline of threshold n-hexane concentration and microbial community shift for the AD of lipid-extracted microalgal wastes. PMID:25966884

  19. Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora

    PubMed Central

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

    2015-01-01

    Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study. PMID:26082867

  20. 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.

  1. 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.

  2. 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. PMID:23982106

  3. Oak forest exploitation and black-locust invasion caused severe shifts in epiphytic lichen communities in Northern Italy.

    PubMed

    Nascimbene, Juri; Marini, Lorenzo

    2010-10-15

    In the last two centuries, native European oak forests have undergone a dramatic decline related to increasing human pressure for agriculture and urbanization. Oak forests were either completely eradicated and transformed into agricultural landscapes or replaced by second-growth formations. Intensive forest management and the replacement of native forests with production forests or arable lands are recognized amongst the main threats to many lichens in Europe. In this study, we used historical information on the epiphytic lichen biota which was hosted in a native oak-dominated forest of Northern Italy to identify shifts of lichen communities due to the changes in land use which occurred during the last two centuries. We also compared the epiphytic lichen communities inhabiting remnant oak forests with those found in the habitats that have replaced native forests: black-locust forests and agrarian landscapes. Almost all the species sampled during the 19th century are now extinct. The loss of native habitat and the subsequent invasion by black locust were probably the most influential factors which affected the composition of lichen communities, causing the local extinction of most of the species historically recorded. Despite the fact that oak remnants host only a few species which were historically recorded, and that they currently are the lichen poorest habitat in the study region, they host lichen assemblages differing from those of black-locust forests and agrarian stands. In these habitats lichen assemblages are mainly composed of species adapted to well-lit, dry conditions and tolerating air pollution and eutrophication. This pattern is likely to be common also in other lowland and hilly regions throughout Northern Italy where oak forests are targeted among the habitats of conservation concern at the European level. For this reason, a national strategy for biodiversity conservation and monitoring of lowlands forests should provide the framework for local

  4. Ruminal bacterial community shifts in grain-, sugar-, and histidine-challenged dairy heifers.

    PubMed

    Golder, H M; Denman, S E; McSweeney, C; Celi, P; Lean, I J

    2014-01-01

    Ruminal bacterial community composition (BCC) and its associations with ruminal fermentation measures were studied in dairy heifers challenged with combinations of grain, fructose, and histidine in a partial factorial study. Holstein-Friesian heifers (n=30) were randomly allocated to 5 triticale grain-based treatment groups: (1) control (no grain), (2) grain [fed at a dry matter intake (DMI) of 1.2% of body weight (BW)], (3) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI), (4) grain (1.2% of BW DMI) + histidine (6g/head), and (5) grain (0.8% of BW DMI) + fructose (0.4% of BW DMI) + histidine (6g/head). Ruminal fluid was collected using a stomach tube 5, 115, and 215min after consumption of the rations and bacterial 16S ribosomal DNA sequence data was analyzed to characterize bacteria. Large variation among heifers and distinct BCC were evident in a between-group constrained principal components analysis. Bacterial composition in the fructose-fed heifers was positively related to total lactate and butyrate concentrations. Bacterial composition was positively associated with ruminal ammonia, valerate, and histamine concentrations in the grain-fed heifers. The predominant phyla were the Firmicutes (57.6% of total recovered sequences), Bacteroidetes (32.0%), and candidate phylum TM7 (4.0%). Prevotella was the dominant genus. In general, grain or histidine or their interactions with time had minimal effects on the relative abundance of bacterial phyla and families. Fructose increased and decreased the relative abundance of the Firmicutes and Proteobacteria phyla over time, respectively, and decreased the abundance of the Prevotellaceae family over time. The relative abundance of the Streptococcaceae and Veillonellaceae families was increased in the fructose-fed heifers and these heifers over time. A total of 31 operational taxonomic units differed among treatment groups in the 3.6h sampling period, Streptococcus bovis was observed in fructose fed animals. The TM7

  5. 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.

  6. Investigating the Effect of Livestock Grazing and Associated Plant Community Shifts on Carbon and Nutrient Cycling in Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Hewins, D. B.; Chuan, S.; Stolnikova, E.; Bork, E. W.; Carlyle, C. N.; Chang, S. X.

    2015-12-01

    Grassland ecosystems are ubiquitous across the globe covering an estimated 40 % of Earth's terrestrial landmass. These ecosystems are widely valued for providing forage for domestic livestock and a suite of important ecosystem goods and services including carbon (C) storage. Despite storing more than 30 % of soil C globally, the effect of both livestock grazing and the associated change in plant community structure in response to grazing on C and nutrient cycling remains uncertain. To gain a quantitative understanding of the direct and indirect effects of livestock grazing on C and nutrient cycling, we established study sites at 15 existing site localities with paired long-term grazing (ca. 30 y) and non-grazed treatments (totaling 30 unique plant communities). Our sites were distributed widely across Alberta in three distinct grassland bioclimatic zones allowing us to make comparisons across the broad range of climate variability typical of western Canadian grasslands. In each plant community we decomposed 5 common plant species that are known to increase or decrease in response to grazing pressure, a unique plant community sample, and a cellulose paper control. We measured mass loss, initial lignin, C and N concentrations at 0, 1, 3, 6 and 12 months of field incubation. In addition we assayed hydrolytic and oxidative extracellular enzymes associated with for C (n= 5 hydrolytic; phenoloxidase and peroxidase) and nutrients (i.e. N and P; n=1 ea.) cycling from each litter sample at each collection. Our results suggest that by changing the plant community structure, grazing can affect rates of decomposition and associated biogeochemical cycling by changing plant species and associated litter inputs. Moreover, measures of microbial function are controlled by site-specific conditions (e.g. temperature and precipitation), litter chemistry over the course of our incubation.

  7. 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

  8. Ecosystem-Wide Morphological Structure of Leaf-Litter Ant Communities along a Tropical Latitudinal Gradient

    PubMed Central

    Silva, Rogério R.; Brandão, Carlos Roberto F.

    2014-01-01

    General principles that shape community structure can be described based on a functional trait approach grounded on predictive models; increased attention has been paid to factors accounting for the functional diversity of species assemblages and its association with species richness along environmental gradients. We analyze here the interaction between leaf-litter ant species richness, the local communities' morphological structure and fundamental niche within the context of a northeast-southeast latitudinal gradient in one of the world's most species-rich ecosystems, the Atlantic Forest, representing 2,700 km of tropical rainforest along almost 20o of latitude in eastern Brazil. Our results are consistent with an ecosystem-wide pattern in communities' structure, with relatively high species turnover but functionally analogous leaf-litter ant communities' organization. Our results suggest directional shifts in the morphological space along the environmental gradient from overdispersed to aggregated (from North to South), suggesting that primary productivity and environmental heterogeneity (altitude, temperature and precipitation in the case) determine the distribution of traits and regulate the assembly rules, shaping local leaf-litter ant communities. Contrary to the expected and most common pattern along latitudinal gradients, the Atlantic Forest leaf litter ant communities show an inverse pattern in richness, that is, richer communities in higher than in lower latitudes. The morphological specialization of communities showed more morphologically distinct communities at low latitudes and species redundancy at high latitudes. We claim that an inverse latitudinal gradient in primary productivity and environmental heterogeneity across the Atlantic forest may affect morphological diversity and species richness, enhancing species coexistence mechanisms, and producing thus the observed patterns. We suggest that a functional framework based on flexible enough traits

  9. Ecosystem-wide morphological structure of leaf-litter ant communities along a tropical latitudinal gradient.

    PubMed

    Silva, Rogério R; Brandão, Carlos Roberto F

    2014-01-01

    General principles that shape community structure can be described based on a functional trait approach grounded on predictive models; increased attention has been paid to factors accounting for the functional diversity of species assemblages and its association with species richness along environmental gradients. We analyze here the interaction between leaf-litter ant species richness, the local communities' morphological structure and fundamental niche within the context of a northeast-southeast latitudinal gradient in one of the world's most species-rich ecosystems, the Atlantic Forest, representing 2,700 km of tropical rainforest along almost 20° of latitude in eastern Brazil. Our results are consistent with an ecosystem-wide pattern in communities' structure, with relatively high species turnover but functionally analogous leaf-litter ant communities' organization. Our results suggest directional shifts in the morphological space along the environmental gradient from overdispersed to aggregated (from North to South), suggesting that primary productivity and environmental heterogeneity (altitude, temperature and precipitation in the case) determine the distribution of traits and regulate the assembly rules, shaping local leaf-litter ant communities. Contrary to the expected and most common pattern along latitudinal gradients, the Atlantic Forest leaf litter ant communities show an inverse pattern in richness, that is, richer communities in higher than in lower latitudes. The morphological specialization of communities showed more morphologically distinct communities at low latitudes and species redundancy at high latitudes. We claim that an inverse latitudinal gradient in primary productivity and environmental heterogeneity across the Atlantic forest may affect morphological diversity and species richness, enhancing species coexistence mechanisms, and producing thus the observed patterns. We suggest that a functional framework based on flexible enough traits

  10. Fine structures of organic photovoltaic thin films probed by frequency-shift electrostatic force microscopy

    NASA Astrophysics Data System (ADS)

    Araki, Kento; Ie, Yutaka; Aso, Yoshio; Matsumoto, Takuya

    2016-07-01

    The localized charge and electrostatic properties of organic photovoltaic thin films are predominating factors for controlling energy conversion efficiency. The surface potential and electrostatic structures of organic photovoltaic thin films were investigated by frequency shift mode Kelvin force microscopy (KFM) and electrostatic force microscopy (EFM). The KFM images of a poly[2-methoxy-5-(3‧,7‧-dimethyloctyloxy)-1,4-phenylene vinylene]/phenyl-C61-butyric-acid-methyl ester (PCBM) blend thin film reveals that the PCBM domains precipitate as the topmost layer on the thin films. We find fine structures that were not observed in the topography and KFM images. The bias dependence of the EFM images suggests that the EFM contrast reflects the field-induced polarization, indicating the presence of charge trapping sites.

  11. Faculty Scholarship at Community Colleges: Culture, Institutional Structures, and Socialization

    ERIC Educational Resources Information Center

    Morest, Vanessa Smith

    2015-01-01

    This chapter looks at community college faculty engagement in scholarship. Community college faculty spend the majority of their time engaged in teaching, and therefore their scholarship typically focuses on strengthening curriculum and instruction. The paper identifies some of the structural and cultural challenges and supports to scholarship at…

  12. Community Racial Segregation, Electoral Structure, and Minority Representation.

    ERIC Educational Resources Information Center

    Vedlitz, Arnold; Johnson, Charles A.

    1982-01-01

    Community electoral structures and segregation levels affect minority representation. Single-member district electorate systems provide significantly more favorable minority representation levels in segregated communities. In nonsegregated cities type of election system makes little difference in the equality of minority representation. (Author/AM)

  13. Exploratory Visualization of Graphs Based on Community Structure

    ERIC Educational Resources Information Center

    Liu, Yujie

    2013-01-01

    Communities, also called clusters or modules, are groups of nodes which probably share common properties and/or play similar roles within a graph. They widely exist in real networks such as biological, social, and information networks. Allowing users to interactively browse and explore the community structure, which is essential for understanding…

  14. Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

  15. Comparing Metabolic Functionalities, Community Structures, and Dynamics of Herbicide-Degrading Communities Cultivated with Different Substrate Concentrations

    PubMed Central

    Gözdereliler, Erkin; Boon, Nico; Aamand, Jens; De Roy, Karen; Granitsiotis, Michael S.; Albrechtsen, Hans-Jørgen

    2013-01-01

    Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter−1) or high (25 mg liter−1) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and pyrosequencing. The communities also differed in their MCPA-mineralizing activities. The enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low-nucleic acid-content bacteria (LNA bacteria) was correlated with mineralization activity in cultures selected on low herbicide concentrations. This suggests that LNA bacteria may play a role in degradation of low herbicide concentrations in aquifers impacted by agriculture. This study shows that subpopulations of herbicide-degrading bacteria that are adapted to different pesticide concentrations can coexist in the same environment and that using a low herbicide concentration enables enrichment of apparently oligotrophic subpopulations. PMID:23124226

  16. Structural Organization of the Corpus Callosum Predicts Attentional Shifts after Continuous Theta Burst Stimulation

    PubMed Central

    Humphreys, Glyn W.; Sotiropoulos, Stamatios N.; Kennard, Christopher; Cazzoli, Dario

    2015-01-01

    Repetitive transcranial magnetic stimulation (rTMS) applied over the right posterior parietal cortex (PPC) in healthy participants has been shown to trigger a significant rightward shift in the spatial allocation of visual attention, temporarily mimicking spatial deficits observed in neglect. In contrast, rTMS applied over the left PPC triggers a weaker or null attentional shift. However, large interindividual differences in responses to rTMS have been reported. Studies measuring changes in brain activation suggest that the effects of rTMS may depend on both interhemispheric and intrahemispheric interactions between cortical loci controlling visual attention. Here, we investigated whether variability in the structural organization of human white matter pathways subserving visual attention, as assessed by diffusion magnetic resonance imaging and tractography, could explain interindividual differences in the effects of rTMS. Most participants showed a rightward shift in the allocation of spatial attention after rTMS over the right intraparietal sulcus (IPS), but the size of this effect varied largely across participants. Conversely, rTMS over the left IPS resulted in strikingly opposed individual responses, with some participants responding with rightward and some with leftward attentional shifts. We demonstrate that microstructural and macrostructural variability within the corpus callosum, consistent with differential effects on cross-hemispheric interactions, predicts both the extent and the direction of the response to rTMS. Together, our findings suggest that the corpus callosum may have a dual inhibitory and excitatory function in maintaining the interhemispheric dynamics that underlie the allocation of spatial attention. SIGNIFICANCE STATEMENT The posterior parietal cortex (PPC) controls allocation of attention across left versus right visual fields. Damage to this area results in neglect, characterized by a lack of spatial awareness of the side of space

  17. 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

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

    SciTech Connect

    Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

    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 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. 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.

  19. Direct Effect of Carbon Dioxide Concentration on Phytoplankton Community Structure in the Ross Sea, Antarctica

    NASA Astrophysics Data System (ADS)

    Riesselman, C. R.; Tortell, P. D.; Payne, C. D.; Dunbar, R. B.; Ditullio, G. R.

    2006-12-01

    As the largest high-nutrient low-chlorophyll (HNLC) region on the planet, the Southern Ocean plays a critical role in global biogeochemical cycling and climate modulation. Primary productivity and phytoplankton community structure in the waters surrounding Antarctica have demonstrated unique sensitivity to small changes in major and trace element availability and vertical mixing. However, the capacity of changing atmospheric CO2 to restructure Antarctic phytoplankton communities has only recently been proposed. During the austral summer of 2005-2006, the "Controls on Ross Sea Algal Community Structure" (CORSACS) project performed an integrated series of shipboard incubations coupled with polynya water column sampling designed to investigate the interplay of iron, light, and CO2 levels as determinants of primary production and phytoplankton community structure. Results from the CORSACS CO2 manipulation incubation experiment demonstrate substantial shifts in the taxonomic distribution of phytoplankton exposed to an experimental CO2 gradient. Triplicate semi-continuous culture bottles were bubbled with air mixtures containing 100, 370, and 800 ppm CO2, designed to approximate bloom conditions under glacial, modern, and projected future levels of carbon dioxide. At the conclusion of the 18-day incubation, the 100 ppm community was dominated by the small, finely silicified pennate diatom Pseudonitzschia subcurvata, while the abundance of larger, colonial Chaetoceros species increased significantly in the 800 ppm community. These results represent the first evidence that perturbations in atmospheric CO2 have the potential to reorganize phytoplankton community structure in the Southern Ocean, and have implications for both the glacial productivity paradox and the future of polar trophic structure.

  20. 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. PMID:22224595

  1. Artificial neural networks and ecological communities (Book Review: Modelling community structure in freshwater ecosystems)

    USGS Publications Warehouse

    DeAngelis, Donald L.

    2005-01-01

    Review info: Modeling community structure in freshwater ecosystems. Edited by Sovan Lek, Michele Scardi, Piet F.M. Verdonschot, Jean-Pierre Descy, and Young-Seuk Park, 2005. ISBN: 3-540-23940-5, 518 pp.

  2. Edge ratio and community structure in networks

    NASA Astrophysics Data System (ADS)

    Cafieri, Sonia; Hansen, Pierre; Liberti, Leo

    2010-02-01

    A hierarchical divisive algorithm is proposed for identifying communities in complex networks. To that effect, the definition of community in the weak sense of Radicchi [Proc. Natl. Acad. Sci. U.S.A. 101, 2658 (2004)] is extended into a criterion for a bipartition to be optimal: one seeks to maximize the minimum for both classes of the bipartition of the ratio of inner edges to cut edges. A mathematical program is used within a dichotomous search to do this in an optimal way for each bipartition. This includes an exact solution of the problem of detecting indivisible communities. The resulting hierarchical divisive algorithm is compared with exact modularity maximization on both artificial and real world data sets. For two problems of the former kind optimal solutions are found; for five problems of the latter kind the edge ratio algorithm always appears to be competitive. Moreover, it provides additional information in several cases, notably through the use of the dendrogram summarizing the resolution. Finally, both algorithms are compared on reduced versions of the data sets of Girvan and Newman [Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)] and of Lancichinetti [Phys. Rev. E 78, 046110 (2008)]. Results for these instances appear to be comparable.

  3. Growing network model for community with group structure

    NASA Astrophysics Data System (ADS)

    Noh, Jae Dong; Jeong, Hyeong-Chai; Ahn, Yong-Yeol; Jeong, Hawoong

    2005-03-01

    We propose a growing network model for a community with a group structure. The community consists of individual members and groups, gatherings of members. The community grows as a new member is introduced by an existing member at each time step. The new member then creates a new group or joins one of the groups of the introducer. We investigate the emerging community structure analytically and numerically. The group size distribution shows a power-law distribution for a variety of growth rules, while the activity distribution follows an exponential or a power law depending on the details of the growth rule. We also present an analysis of empirical data from online communities the “Groups” in http://www.yahoo.com and the “Cafe” in http://www.daum.net, which show a power-law distribution for a wide range of group sizes.

  4. Community structure of a microbial mat: the phylogenetic dimension.

    PubMed Central

    Risatti, J B; Capman, W C; Stahl, D A

    1994-01-01

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat. Images PMID:7937858

  5. Growing network model for community with group structure.

    PubMed

    Noh, Jae Dong; Jeong, Hyeong-Chai; Ahn, Yong-Yeol; Jeong, Hawoong

    2005-03-01

    We propose a growing network model for a community with a group structure. The community consists of individual members and groups, gatherings of members. The community grows as a new member is introduced by an existing member at each time step. The new member then creates a new group or joins one of the groups of the introducer. We investigate the emerging community structure analytically and numerically. The group size distribution shows a power-law distribution for a variety of growth rules, while the activity distribution follows an exponential or a power law depending on the details of the growth rule. We also present an analysis of empirical data from online communities the "Groups" in http://www.yahoo.com and the "Cafe" in http://www.daum.net, which show a power-law distribution for a wide range of group sizes. PMID:15903517

  6. Community structure of a microbial mat: The phylogenetic dimension

    USGS Publications Warehouse

    Risatti, J.B.; Capman, W.C.; Stahl, D.A.

    1994-01-01

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

  7. Method to find community structures based on information centrality

    NASA Astrophysics Data System (ADS)

    Fortunato, Santo; Latora, Vito; Marchiori, Massimo

    2004-11-01

    Community structures are an important feature of many social, biological, and technological networks. Here we study a variation on the method for detecting such communities proposed by Girvan and Newman and based on the idea of using centrality measures to define the community boundaries [M. Girvan and M. E. J. Newman, Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)]. We develop an algorithm of hierarchical clustering that consists in finding and removing iteratively the edge with the highest information centrality. We test the algorithm on computer generated and real-world networks whose community structure is already known or has been studied by means of other methods. We show that our algorithm, although it runs to completion in a time O(n4) , is very effective especially when the communities are very mixed and hardly detectable by the other methods.

  8. Community structure of a microbial mat: the phylogenetic dimension.

    PubMed

    Risatti, J B; Capman, W C; Stahl, D A

    1994-10-11

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat. PMID:7937858

  9. Exploring community structure in networks by consensus dynamics

    NASA Astrophysics Data System (ADS)

    He, He; Yang, Bo; Hu, Xiaoming

    2016-05-01

    This paper investigates the relationship between community structure and consensus dynamics in complex networks. We analyze the dynamical process towards consensus and show that those sets of densely interconnected nodes corresponding to well-defined communities appear in different time scales. In order to reveal such topological scales, two algorithms built around the idea of visualizing the evolution of different measured quantities are proposed. Then we test our algorithms on a few benchmark graphs whose community structures are already known. Numeric simulations are given to demonstrate the effectiveness and reliability of our methods.

  10. Calibration of spatially phase-shifted DSPI for measurement of large structures.

    PubMed

    Saif, Babak; Eegholm, Bente Hoffmann; Bluth, Marcel; Greenfield, Perry; Hack, Warren; Blake, Peter; Keski-Kuha, Ritva; North-Morris, Michael

    2007-08-10

    We present a method for the calibration of a spatially phase-shifted digital speckle pattern interferometer (SPS-DSPI), which was designed and built for the purpose of testing the James Webb space telescope (JWST) optical structures and related technology development structures. The need to measure dynamic deformations of large, diffuse structures to nanometer accuracy at cryogenic temperature is paramount in the characterization of a large diameter space and terrestrial based telescopes. The techniques described herein apply to any situation, in which high accuracy measurement of diffuse structures are required. The calibration of the instrument is done using a single-crystal silicon gauge. The gauge has four islands of different heights that change in a predictable manner as a function of temperature. The SPS-DSPI is used to measure the relative piston between the islands as the temperature of the gauge is changed. The measurement results are then compared with the theoretical changes in the height of the gauge islands. The maximum deviation of the measured rate of change of the relative piston in nm/K from the expected value is 3.3%. PMID:17694108

  11. Measurement of large cryogenic structures using a spatially phase-shifted digital speckle pattern interferometer.

    PubMed

    Saif, Babak; Bluth, Marcel; Greenfield, Perry; Hack, Warren; Eegholm, Bente Hoffmann; Blake, Peter; Keski-Kuha, Ritva; Feinberg, Lee; Arenberg, Jonathan W

    2008-02-20

    The James Webb Space Telescope (JWST) Backplane Stability Test Article (BSTA) was developed to demonstrate large precision cryogenic structures' technology readiness for use in the JWST. The thermal stability of the BSTA was measured at cryogenic temperatures at the Marshall Space Flight Center (MSFC) X-Ray Calibration Facility (XRCF) and included nearly continuous measurements over a six-week period in the summer of 2006 covering the temperature range from ambient down to 30 Kusing a spatially phase-shifted digital speckle pattern interferometer (SPS-DSPI). The BSTA is a full size, one-sixth section of the JWST primary mirror backplane assembly (PMBA). The BSTA, measuring almost 3 m across, contains most of the prominent structural elements of the backplane and is to our knowledge the largest structure ever measured with SPS-DSPI at cryogenic conditions. The SPS-DSPI measured rigid body motion and deformations of BSTA to nanometer-level accuracy. The SPS-DSPI was developed specifically for the purposes of this test and other tests of large cryogenic structures for JWST. PMID:18288221

  12. Fragmentation alters stream fish community structure in dendritic ecological networks.

    PubMed

    Perkin, Joshuah S; Gido, Keith B

    2012-12-01

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

  13. 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

  14. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere.

    PubMed

    Trivedi, Pankaj; He, Zhili; Van Nostrand, Joy D; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2012-02-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that 'Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in 'Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of 'Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the 'Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the 'Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by 'Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability

  15. Wave stress and coral community structure in Hawaii

    NASA Astrophysics Data System (ADS)

    Dollar, S. J.

    1982-10-01

    The most significant factor determining the structure of Hawaiian reef coral communities is physical disturbance from waves. Sequential analysis of community structure off the west coast of the island of Hawaii shows that variation of wave energy and storm frequency clearly affects organization in time and space. Normal conditions of low wave stress maintain four well-defined reef zones; diversity is highest at intermediate depths and decreases in physically rigorous shallow areas and stable deep reef slopes. Intermediate level storm wave events cause variable effects within the reef zones, but the zonation pattern, as a whole, is maintained. Diversity increases in zones that are dominated by a single species largely through nonlethal fragmentation and transport, but decreases in the zone of most equitable species distribution. Conversely, severe infrequent storm disturbances that cause massive mortality to all coral species wipe out the pattern of community structure and return the entire community to a low diversity early successional stage.

  16. Simultaneous gain and phase-shift enhancements in periodic gain structures

    SciTech Connect

    Yan, R.H.; Chuang, Z.M.; Corzine, S.W.; Coldren, L.A. )

    1990-05-01

    The recently proposed concept of periodic gain, i.e., dividing the active region into segments placed at optical electric-field standing wave maxima, has been shown to greatly reduce the threshold gain requirement of the active media by up to a factor of 2 in high-finesse vertical cavity surface-emitting lasers. The lasing wavelength is determined by the period of the standing wave; however, previous analyses of these structures have failed to show that a similar enhancement effect occurs for the index shift resulting from the active segments as well. In this communication, we show that effects on both gain and index can be rigorously derived from conventional transmission scattering theory.

  17. Evolving friendships and shifting ethical dilemmas: fieldworkers' experiences in a short term community based study in Kenya.

    PubMed

    Kamuya, Dorcas M; Theobald, Sally J; Munywoki, Patrick K; Koech, Dorothy; Geissler, Wenzel P; Molyneux, Sassy C

    2013-04-01

    Fieldworkers (FWs) are community members employed by research teams to support access to participants, address language barriers, and advise on culturally appropriate research conduct. The critical role that FWs play in studies, and the range of practical and ethical dilemmas associated with their involvement, is increasingly recognised. In this paper, we draw on qualitative observation and interview data collected alongside a six month basic science study which involved a team of FWs regularly visiting 47 participating households in their homes. The qualitative study documented how relationships between field workers and research participants were initiated, developed and evolved over the course of the study, the shifting dilemmas FWs faced and how they handled them. Even in this one case study, we see how the complex and evolving relationships between fieldworkers and study participants had important implications for consent processes, access to benefits and mutual understanding and trust. While the precise issues that FWs face are likely to depend on the type of research and the context in which that research is being conducted, we argue that appropriate support for field workers is a key requirement to strengthen ethical research practice and for the long term sustainability of research programmes. PMID:23433316

  18. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

    PubMed Central

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J.

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  19. Correlations of Gut Microbial Community Shift with Hepatic Damage and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure.

    PubMed

    Kan, Haifeng; Zhao, Fuzheng; Zhang, Xu-Xiang; Ren, Hongqiang; Gao, Shixiang

    2015-10-01

    Goldfish (Carassius auratus) were exposed to 0-100 μg/L pentachlorophenol (PCP) for 28 days to investigate the correlations of fish gut microbial community shift with the induced toxicological effects. PCP exposure caused accumulation of PCP in the fish intestinal tract in a time- and dose-dependent manner, while hepatic PCP reached the maximal level after a 21 day exposure. Under the relatively higher PCP stress, the fish body weight and liver weight were reduced and hepatic CAT and SOD activities were inhibited, demonstrating negative correlations with the PCP levels in liver and gut content (R < -0.5 and P < 0.05 each). Pyrosequencing of the 16S rRNA gene indicated that PCP exposure increased the abundance of Bacteroidetes in the fish gut. Within the Bacteroidetes phylum, the Bacteroides genus had the highest abundance, which was significantly correlated with PCP exposure dosage and duration (R > 0.5 and P < 0.05 each). Bioinformatic analysis revealed that Bacteroides showed quantitatively negative correlations with Chryseobacterium, Microbacterium, Arthrobacter, and Legionella in the fish gut, and the Bacteroidetes abundance, Bacteroides abundance, and Firmicutes/Bacteroidetes ratio played crucial roles in the reduction of body weight and liver weight under PCP stress. The results may extend our knowledge regarding the roles of gut microbiota in ecotoxicology. PMID:26378342

  20. Effects of microbially induced transformations and shift in bacterial community on arsenic mobility in arsenic-rich deep aquifer sediments.

    PubMed

    Das, Suvendu; Liu, Chia-Chuan; Jean, Jiin-Shuh; Lee, Chuan-Chun; Yang, Huai-Jen

    2016-06-01

    Elevated concentration of arsenic (As) prevailed in deep aquifers of Chianan Plain, Taiwan. Arsenic release in relation to microbially induced transformations and shift in bacterial communities in deep aquifer sediments of Budai, southwestern Taiwan were investigated using microcosm experiments and substrate amendments over 90 days of anaerobic incubation. The results revealed that As reduction was independent of Fe reduction and a modest rate of sedimentary As release into aqueous phase occurred at the expense of the native organic carbon. Addition of lactate resulted in a parallel increase in As(III) (3.7-fold), Fe(II) (6.2-fold) and Mn (3.5 fold) in aqueous phase compared to un-amended slurries and the enrichment of sequences related to mostly Bacillus, Flavisolibacter, and Geobacter spp, suggesting the important role of these bacteria in As enrichment through reductive dissolution of As-bearing Fe and Mn minerals. The increase in phosphate-extractable As in solid phase with concomitant rise in As in aqueous phase over the course of incubation further attested to the importance of reductive dissolution in promoting As release. Furthermore, the increase in arrA gene abundance with addition of labile carbon suggests that dissimilatory As reduction also may contribute to As enrichment in the water of the deep aquifer of Budai. PMID:26897570

  1. Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood.

    PubMed

    Covino, Stefano; Fabianová, Tereza; Křesinová, Zdena; Čvančarová, Monika; Burianová, Eva; Filipová, Alena; Vořísková, Jana; Baldrian, Petr; Cajthaml, Tomáš

    2016-01-15

    The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix. PMID:26342147

  2. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China.

    PubMed

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  3. 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

  4. Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance.

    PubMed

    Martin, Michael D; Zimmer, Elizabeth A; Olsen, Morten T; Foote, Andrew D; Gilbert, M Thomas P; Brush, Grace S

    2014-04-01

    Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North America, and ragweed populations expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Towards a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed's spatial genetic structure mirrors both the palaeo-record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons, this spatial genetic pattern has changed substantially in the intervening years. Following on previous work relating morphology and genetic expression between plants collected from eastern North America and Western Europe, we speculate that the cluster associated with humans' rapid transformation of the landscape is a likely source of these aggressive invasive populations. PMID:24450363

  5. Nuclear structure corrections to the Lamb shift in μHe3+ and μ3H

    NASA Astrophysics Data System (ADS)

    Nevo Dinur, N.; Ji, C.; Bacca, S.; Barnea, N.

    2016-04-01

    Measuring the 2S-2P Lamb shift in a hydrogen-like muonic atom allows one to extract its nuclear charge radius with a high precision that is limited by the uncertainty in the nuclear structure corrections. The charge radius of the proton thus extracted was found to be 7σ away from the CODATA value, in what has become the yet unsolved "proton radius puzzle". Further experiments currently aim at the isotopes of hydrogen and helium: the precise extraction of their radii may provide a hint at the solution of the puzzle. We present the first ab initio calculation of nuclear structure corrections, including the nuclear polarization correction, to the 2S-2P transition in μHe3+ and μ3H, and assess solid theoretical error bars. Our predictions reduce the uncertainty in the nuclear structure corrections to the level of a few percent and will be instrumental to the on-going μHe3+ experiment. We also support the mirror μ3H system as a candidate for further probing of the nucleon polarizabilities and shedding more light on the puzzle.

  6. Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift

    PubMed Central

    Barstow, Buz; Ando, Nozomi; Kim, Chae Un; Gruner, Sol M.

    2008-01-01

    A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 Å at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold. PMID:18768811

  7. The social structure of microbial community involved in colonization resistance.

    PubMed

    He, Xuesong; McLean, Jeffrey S; Guo, Lihong; Lux, Renate; Shi, Wenyuan

    2014-03-01

    It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as 'Sensor', 'Mediator' and 'Killer', respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of 'Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance. PMID:24088624

  8. The Integration of a Structural Water Gas Shift Catalyst with a Vanadium Alloy Hydrogen Transport Device

    SciTech Connect

    Barton, Thomas; Argyle, Morris; Popa, Tiberiu

    2009-06-30

    This project is in response to a requirement for a system that combines water gas shift technology with separation technology for coal derived synthesis gas. The justification of such a system would be improved efficiency for the overall hydrogen production. By removing hydrogen from the synthesis gas stream, the water gas shift equilibrium would force more carbon monoxide to carbon dioxide and maximize the total hydrogen produced. Additional benefit would derive from the reduction in capital cost of plant by the removal of one step in the process by integrating water gas shift with the membrane separation device. The answer turns out to be that the integration of hydrogen separation and water gas shift catalysis is possible and desirable. There are no significant roadblocks to that combination of technologies. The problem becomes one of design and selection of materials to optimize, or at least maximize performance of the two integrated steps. A goal of the project was to investigate the effects of alloying elements on the performance of vanadium membranes with respect to hydrogen flux and fabricability. Vanadium was chosen as a compromise between performance and cost. It is clear that the vanadium alloys for this application can be produced, but the approach is not simple and the results inconsistent. For any future contracts, large single batches of alloy would be obtained and rolled with larger facilities to produce the most consistent thin foils possible. Brazing was identified as a very likely choice for sealing the membranes to structural components. As alloying was beneficial to hydrogen transport, it became important to identify where those alloying elements might be detrimental to brazing. Cataloging positive and negative alloying effects was a significant portion of the initial project work on vanadium alloying. A water gas shift catalyst with ceramic like structural characteristics was the second large goal of the project. Alumina was added as a

  9. Measuring the significance of community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Hu, Yanqing; Nie, Yuchao; Yang, Hua; Cheng, Jie; Fan, Ying; di, Zengru

    2010-12-01

    Many complex systems can be represented as networks, and separating a network into communities could simplify functional analysis considerably. Many approaches have recently been proposed to detect communities, but a method to determine whether the detected communities are significant is still lacking. In this paper, an index to evaluate the significance of communities in networks is proposed based on perturbation of the network. In contrast to previous approaches, the network is disturbed gradually, and the index is defined by integrating all of the similarities between the community structures before and after perturbation. Moreover, by taking the null model into account, the index eliminates scale effects. Thus, it can evaluate and compare the significance of communities in different networks. The method has been tested in many artificial and real-world networks. The results show that the index is in fact independent of the size of the network and the number of communities. With this approach, clear communities are found to always exist in social networks, but significant communities cannot be found in protein interactions and metabolic networks.

  10. Measuring the robustness of network community structure using assortativity

    PubMed Central

    Shizuka, Daizaburo; Farine, Damien R.

    2016-01-01

    The existence of discrete social clusters, or ‘communities’, is a common feature of social networks in human and nonhuman animals. The level of such community structure in networks is typically measured using an index of modularity, Q. While modularity quantifies the degree to which individuals associate within versus between social communities and provides a useful measure of structure in the social network, it assumes that the network has been well sampled. However, animal social network data is typically subject to sampling errors. In particular, the associations among individuals are often not sampled equally, and animal social network studies are often based on a relatively small set of observations. Here, we extend an existing framework for bootstrapping network metrics to provide a method for assessing the robustness of community assignment in social networks using a metric we call community assortativity (rcom). We use simulations to demonstrate that modularity can reliably detect the transition from random to structured associations in networks that differ in size and number of communities, while community assortativity accurately measures the level of confidence based on the detectability of associations. We then demonstrate the use of these metrics using three publicly available data sets of avian social networks. We suggest that by explicitly addressing the known limitations in sampling animal social network, this approach will facilitate more rigorous analyses of population-level structural patterns across social systems. PMID:26949266

  11. 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. PMID:26259508

  12. Active Women: Perspectives on Their Structural Position in the Community.

    ERIC Educational Resources Information Center

    Moyer, Harriett; And Others

    An exploratory pilot study to determine the personal characteristics of women community leaders and their position in the power structure was conducted in Chippewa and Eau Claire Counties, Wisconsin. The research design involved a comparison of three samples: the traditional power structure identified through reputational techniques; the active…

  13. Benthic community responses to macroalgae invasions in seagrass beds: Diversity, isotopic niche and food web structure at community level

    NASA Astrophysics Data System (ADS)

    Deudero, S.; Box, A.; Vázquez-Luis, M.; Arroyo, N. L.

    2014-04-01

    Trophic paths between species are a useful tool for analysing the impact of species invasions of a biotic community. Species invasions produce changes at trophic level and diversity shifts by replacing native species with species of similar ecological niche. This study focused on the effects of macroalgal invasions on seagrass ecosystems. We conducted two - year bimonthly sampling of a pristine Posidonia oceanica seagrass meadow and dead matte colonized by three Caulerpa species bimonthly. The largest changes in faunal composition were found in meadows colonized by Caulerpa prolifera, where major differences in infaunal taxonomic distinctness were apparent. On the other hand, the infaunal community was quite similar between the two invasive Caulerpa species (Caulerpa taxifolia and Caulerpa racemosa). The isotopic niche based on the main trophic guilds established using stable isotope signatures at community level resulted in a highly compacted and 15N-enriched C. prolifera food web structure, indicating high overlap of food source utilization among faunal components, which is typical of degraded systems. Conversely, the P. oceanica ecosystem presented the most complex food web, while the influence of the 2 invasive species were similar. An attempt to reconstruct the food web at each vegetated habitat revealed high trophic linkages among the different trophic levels with a continuous transition among them by the various trophic guilds suggesting an adaptation response of the different organisms to the new habitat forming species.

  14. Soil bacterial community shifts in response to vegetation and soil temperature change in moist acidic tundra of Northern Alaska

    NASA Astrophysics Data System (ADS)

    Ricketts, M. P.; Gonzalez-Meler, M. A.

    2013-12-01

    The effects of rising temperatures on Earth's ecosystems remain largely unknown and are an active area of research. In temperate systems, plant species often respond directly to climate forcing factors causing complex cascading effects in ecosystem C and nutrient cycling. Similarly, in the Arctic tundra, shifts in aboveground species composition and distribution have been observed in response to warming and other climate change factors, following increases in active layer depth and soil temperature. These abiotic changes provide soil microorganisms access to previously unavailable soil organic matter via thawing soils and increases soil microbial mineralization rates, suggesting that soil microorganisms may be eliciting the plant response. It is hypothesized that this release of nutrients may be providing a competitive advantage to N rich woody species, such as dwarf birch and diamond-leaf willow, over grassy species such as cottongrass tussock. Here we examine how microbial communities respond to increases in soil thermal insulation and vegetative change caused by the accumulation of winter precipitation at a snowfence installed in 1998 at Toolik Field Station, Alaska. In addition to soil temperature, increased snow depth also results in increased surface moisture, soil temperature, and active layer depth. Bacterial phylogenies and relative abundances from soils collected in August of 2012 were determined by sequencing 16S rRNA genes and analyzed using the QIIME software package. We found many significant relative abundance shifts between snow depth treatments (deep, intermediate, low) and soil depths (organic, transition, mineral), most notable of which include in an increase in Deltaproteobacteria in the deep treatment zones, a decrease in Alphaproteobacteria with increased soil depth, and a marked increase in Chloroflexi Anaerolineae (a green non-sulfur bacteria found in a wide range of habitats) in the deep treatment and mineral layers. Other interesting

  15. Comprehensive spectral approach for community structure analysis on complex networks

    NASA Astrophysics Data System (ADS)

    Danila, Bogdan

    2016-02-01

    A simple but efficient spectral approach for analyzing the community structure of complex networks is introduced. It works the same way for all types of networks, by spectrally splitting the adjacency matrix into a "unipartite" and a "multipartite" component. These two matrices reveal the structure of the network from different perspectives and can be analyzed at different levels of detail. Their entries, or the entries of their lower-rank approximations, provide measures of the affinity or antagonism between the nodes that highlight the communities and the "gateway" links that connect them together. An algorithm is then proposed to achieve the automatic assignment of the nodes to communities based on the information provided by either matrix. This algorithm naturally generates overlapping communities but can also be tuned to eliminate the overlaps.

  16. Community structures and role detection in music networks

    NASA Astrophysics Data System (ADS)

    Teitelbaum, T.; Balenzuela, P.; Cano, P.; Buldú, Javier M.

    2008-12-01

    We analyze the existence of community structures in two different social networks using data obtained from similarity and collaborative features between musical artists. Our analysis reveals some characteristic organizational patterns and provides information about the driving forces behind the growth of the networks. In the similarity network, we find a strong correlation between clusters of artists and musical genres. On the other hand, the collaboration network shows two different kinds of communities: rather small structures related to music bands and geographic zones, and much bigger communities built upon collaborative clusters with a high number of participants related through the period the artists were active. Finally, we detect the leading artists inside their corresponding communities and analyze their roles in the network by looking at a few topological properties of the nodes.

  17. Community structures and role detection in music networks.

    PubMed

    Teitelbaum, T; Balenzuela, P; Cano, P; Buldú, Javier M

    2008-12-01

    We analyze the existence of community structures in two different social networks using data obtained from similarity and collaborative features between musical artists. Our analysis reveals some characteristic organizational patterns and provides information about the driving forces behind the growth of the networks. In the similarity network, we find a strong correlation between clusters of artists and musical genres. On the other hand, the collaboration network shows two different kinds of communities: rather small structures related to music bands and geographic zones, and much bigger communities built upon collaborative clusters with a high number of participants related through the period the artists were active. Finally, we detect the leading artists inside their corresponding communities and analyze their roles in the network by looking at a few topological properties of the nodes. PMID:19123615

  18. Isotope Shifts and Hyperfine Structure in Calcium 4snp1P1 and 4snf F Rydberg States

    SciTech Connect

    Muller, P.; Bushaw, Bruce A.; Nortershauser, Wilfried; Wendt, K.

    2000-06-01

    Isotope shifts and hyperfine structure have been measured in 4snp 1P1 and 4snf F Rydberg states for all stable calcium isotopes and the radioisotope 41Ca using high-resolution laser spectroscopy. Triple-resonance excitation via 4s2 1S0 --- 4s4p 1P1 --- 4s4d 1D2 --- Rydberg State was followed by photoionization with a CO2 laser and mass selective ion detection. Isotope shifts for the even-mass isotopes have been analyzed to derive specific mass shift and field shift factors. The apparent isotope shifts for 41Ca and 43Ca exhibit anomalous values that are n-dependent. This is interpreted in terms of hyperfine-induced fine structure mixing, which becomes very pronounced when singlet-triplet fine structure splitting is comparable to the hyperfine interaction energy. Measurements of fine structure splittings for the predominant isotope 40Ca have been used as input parameters for theoretical calculation of the perturbed hyperfine structure. Results obtained by diagonalizing the second-order hyperfine interaction matrices agree very well with experimentally observed spectra.

  19. 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. PMID:19494846

  20. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.

    PubMed

    Moroenyane, I; Chimphango, S B M; Wang, J; Kim, H-K; Adams, Jonathan Miles

    2016-08-01

    The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major

  1. Parasitism, community structure and biodiversity in intertidal ecosystems.

    PubMed

    Mouritsen, K N; Poulin, R

    2002-01-01

    There is mounting evidence that parasites can influence the composition and structure of natural animal communities. In spite of this, it is difficult to assess just how important parasitism is for community structure because very few studies have been designed specifically to address the role of parasites at the community level, no doubt because it is difficult to manipulate the abundance of parasites in field experiments. Here, we bring together a large amount of published information on parasitism in intertidal communities to highlight the potential influence of parasites on the structure and biodiversity of these communities. We first review the impact of metazoan parasites on the survival, reproduction, growth and behaviour of intertidal invertebrates, from both rocky shores and soft-sediment flats. Published evidence suggests that the impact of parasites on individuals is often severe, though their effects at the population level are dependent on prevalence and intensity of infection. We then put this information together in a discussion of the impact of parasitism at the community level. We emphasize two ways in which parasites can modify the structure of intertidal communities. First, the direct impact of parasites on the abundance of key host species can decrease the importance of these hosts in competition or predator-prey interactions with other species. Second, the indirect effects of parasites on the behaviour of their hosts, e.g. burrowing ability or spatial distribution within the intertidal zone, can cause changes to various features of the habitat for other intertidal species, leading to their greater settlement success or to their local disappearance. Our synthesis allows specific predictions to be made regarding the potential impact of parasites in certain intertidal systems, and suggests that parasites must be included in future community studies and food web models of intertidal ecosystems. PMID:12396219

  2. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

    PubMed Central

    Deng, Ye; He, Zhili; Xu, Meiying; Qin, Yujia; Van Nostrand, Joy D.; Wu, Liyou; Roe, Bruce A.; Wiley, Graham; Hobbie, Sarah E.; Reich, Peter B.

    2012-01-01

    Pyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2 (eCO2) on soil microbial communities from 12 replicates each from ambient CO2 (aCO2) and eCO2 settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties. PMID:22307288

  3. Change in Fish Community Structure in the Barents Sea

    PubMed Central

    Aschan, Michaela; Fossheim, Maria; Greenacre, Michael; Primicerio, Raul

    2013-01-01

    Change in oceanographic conditions causes structural alterations in marine fish communities, but this effect may go undetected as most monitoring programs until recently mainly have focused on oceanography and commercial species rather than on whole ecosystems. In this paper, the objective is to describe the spatial and temporal changes in the Barents Sea fish community in the period 1992–2004 while taking into consideration the observed abundance and biodiversity patterns for all 82 observed fish species. We found that the spatial structure of the Barents Sea fish community was determined by abiotic factors such as temperature and depth. The observed species clustered into a deep assemblage, a warm water southern assemblage, both associated with Atlantic water, and a cold water north-eastern assemblage associated with mixed water. The latitude of the cold water NE and warm water S assemblages varied from year to year, but no obvious northward migration was observed over time. In the period 1996–1999 we observed a significant reduction in total fish biomass, abundance, mean fish weight, and a change in community structure including an increase in the pelagic/demersal ratio. This change in community structure is probably due to extremely cold conditions in 1996 impacting on a fish community exposed to historically high fishing rates. After 1999 the fish community variables such as biomass, abundance, mean weight, P/D ratio as well as community composition did not return to levels of the early 90s, although fishing pressure and climatic conditions returned to earlier levels. PMID:23658646

  4. From Structure to Function: the Ecology of Host-Associated Microbial Communities

    PubMed Central

    Robinson, Courtney J.; Bohannan, Brendan J. M.; Young, Vincent B.

    2010-01-01

    Summary: In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota. PMID:20805407

  5. Benchmark model to assess community structure in evolving networks.

    PubMed

    Granell, Clara; Darst, Richard K; Arenas, Alex; Fortunato, Santo; Gómez, Sergio

    2015-07-01

    Detecting the time evolution of the community structure of networks is crucial to identify major changes in the internal organization of many complex systems, which may undergo important endogenous or exogenous events. This analysis can be done in two ways: considering each snapshot as an independent community detection problem or taking into account the whole evolution of the network. In the first case, one can apply static methods on the temporal snapshots, which correspond to configurations of the system in short time windows, and match afterward the communities across layers. Alternatively, one can develop dedicated dynamic procedures so that multiple snapshots are simultaneously taken into account while detecting communities, which allows us to keep memory of the flow. To check how well a method of any kind could capture the evolution of communities, suitable benchmarks are needed. Here we propose a model for generating simple dynamic benchmark graphs, based on stochastic block models. In them, the time evolution consists of a periodic oscillation of the system's structure between configurations with built-in community structure. We also propose the extension of quality comparison indices to the dynamic scenario. PMID:26274223

  6. Gap formation following climatic events in spatially structured plant communities.

    PubMed

    Liao, Jinbao; De Boeck, Hans J; Li, Zhenqing; Nijs, Ivan

    2015-01-01

    Gaps play a crucial role in maintaining species diversity, yet how community structure and composition influence gap formation is still poorly understood. We apply a spatially structured community model to predict how species diversity and intraspecific aggregation shape gap patterns emerging after climatic events, based on species-specific mortality responses. In multispecies communities, average gap size and gap-size diversity increased rapidly with increasing mean mortality once a mortality threshold was exceeded, greatly promoting gap recolonization opportunity. This result was observed at all levels of species richness. Increasing interspecific difference likewise enhanced these metrics, which may promote not only diversity maintenance but also community invasibility, since more diverse niches for both local and exotic species are provided. The richness effects on gap size and gap-size diversity were positive, but only expressed when species were sufficiently different. Surprisingly, while intraspecific clumping strongly promoted gap-size diversity, it hardly influenced average gap size. Species evenness generally reduced gap metrics induced by climatic events, so the typical assumption of maximum evenness in many experiments and models may underestimate community diversity and invasibility. Overall, understanding the factors driving gap formation in spatially structured assemblages can help predict community secondary succession after climatic events. PMID:26114803

  7. 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. PMID:27267720

  8. Benchmark model to assess community structure in evolving networks

    NASA Astrophysics Data System (ADS)

    Granell, Clara; Darst, Richard K.; Arenas, Alex; Fortunato, Santo; Gómez, Sergio

    2015-07-01

    Detecting the time evolution of the community structure of networks is crucial to identify major changes in the internal organization of many complex systems, which may undergo important endogenous or exogenous events. This analysis can be done in two ways: considering each snapshot as an independent community detection problem or taking into account the whole evolution of the network. In the first case, one can apply static methods on the temporal snapshots, which correspond to configurations of the system in short time windows, and match afterward the communities across layers. Alternatively, one can develop dedicated dynamic procedures so that multiple snapshots are simultaneously taken into account while detecting communities, which allows us to keep memory of the flow. To check how well a method of any kind could capture the evolution of communities, suitable benchmarks are needed. Here we propose a model for generating simple dynamic benchmark graphs, based on stochastic block models. In them, the time evolution consists of a periodic oscillation of the system's structure between configurations with built-in community structure. We also propose the extension of quality comparison indices to the dynamic scenario.

  9. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

    PubMed Central

    Stearns, Jennifer C; Davidson, Carla J; McKeon, Suzanne; Whelan, Fiona J; Fontes, Michelle E; Schryvers, Anthony B; Bowdish, Dawn M E; Kellner, James D; Surette, Michael G

    2015-01-01

    The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1–4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease. PMID:25575312

  10. High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats

    PubMed Central

    Liu, Jun-hua; Bian, Gao-rui; Zhu, Wei-yun; Mao, Sheng-yong

    2015-01-01

    High-grain (HG) feeding used in intensive goat production can affect the physiology of the rumen wall, but the changes induced in the epimural bacterial community and host Toll-like receptors (TLRs) are not well understood. In this study, 10 male goats were randomly allocated to two groups and fed either a hay diet (0% grain; n = 5) or an HG diet (65% grain; n = 5). The changes in the ruminal epithelial bacterial community and expression of TLRs during long-term (7 weeks) HG feeding were determined using pyrosequencing and quantitative real-time polymerase chain reaction. Principal coordinate analysis and analysis of molecular variance (AMOVA) results showed that HG feeding caused a strong shift in bacterial composition and structure. At the genus level, our data revealed that it increased the relative abundance of taxa Butyrivibrio, unclassified Clostridiales, Mogibacterium, unclassified Anaerolineaceae, and Succiniclasticum, and decreased the proportion of unclassified Ruminococcaceae, unclassified Rikenellaceae, unclassified Erysipelotrichaceae, Howardella, and unclassified Neisseriaceae. The HG-fed goats also exhibited upregulation of the relative mRNA expression of TLR2, TLR3, and TLR5 in the rumen epithelium (P < 0.05). Correlation analysis revealed that the increase in TLR expression was associated with changes in the relative abundance of ruminal epithelial bacteria. This study provides a first insight into the adaptive response of ruminal epithelial bacterial populations to HG feeding in goats and shows that these changes were associated with alterations in TLR expression. These findings provide new insight into understanding of host–microbial relationships in ruminants. PMID:25784904

  11. High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats.

    PubMed

    Liu, Jun-Hua; Bian, Gao-Rui; Zhu, Wei-Yun; Mao, Sheng-Yong

    2015-01-01

    High-grain (HG) feeding used in intensive goat production can affect the physiology of the rumen wall, but the changes induced in the epimural bacterial community and host Toll-like receptors (TLRs) are not well understood. In this study, 10 male goats were randomly allocated to two groups and fed either a hay diet (0% grain; n = 5) or an HG diet (65% grain; n = 5). The changes in the ruminal epithelial bacterial community and expression of TLRs during long-term (7 weeks) HG feeding were determined using pyrosequencing and quantitative real-time polymerase chain reaction. Principal coordinate analysis and analysis of molecular variance (AMOVA) results showed that HG feeding caused a strong shift in bacterial composition and structure. At the genus level, our data revealed that it increased the relative abundance of taxa Butyrivibrio, unclassified Clostridiales, Mogibacterium, unclassified Anaerolineaceae, and Succiniclasticum, and decreased the proportion of unclassified Ruminococcaceae, unclassified Rikenellaceae, unclassified Erysipelotrichaceae, Howardella, and unclassified Neisseriaceae. The HG-fed goats also exhibited upregulation of the relative mRNA expression of TLR2, TLR3, and TLR5 in the rumen epithelium (P < 0.05). Correlation analysis revealed that the increase in TLR expression was associated with changes in the relative abundance of ruminal epithelial bacteria. This study provides a first insight into the adaptive response of ruminal epithelial bacterial populations to HG feeding in goats and shows that these changes were associated with alterations in TLR expression. These findings provide new insight into understanding of host-microbial relationships in ruminants. PMID:25784904

  12. Retinal chromophore structure and Schiff base interactions in red-shifted channelrhodopsin-1 from Chlamydomonas augustae.

    PubMed

    Ogren, John I; Mamaev, Sergey; Russano, Daniel; Li, Hai; Spudich, John L; Rothschild, Kenneth J

    2014-06-24

    Channelrhodopsins (ChRs), which form a distinct branch of the microbial rhodopsin family, control phototaxis in green algae. Because ChRs can be expressed and function in neuronal membranes as light-gated cation channels, they have rapidly become an important optogenetic tool in neurobiology. While channelrhodopsin-2 from the unicellular alga Chlamydomonas reinhardtii (CrChR2) is the most commonly used and extensively studied optogenetic ChR, little is known about the properties of the diverse group of other ChRs. In this study, near-infrared confocal resonance Raman spectroscopy along with hydrogen-deuterium exchange and site-directed mutagenesis were used to study the structure of red-shifted ChR1 from Chlamydomonas augustae (CaChR1). These measurements reveal that (i) CaChR1 has an all-trans-retinal structure similar to those of the light-driven proton pump bacteriorhodopsin (BR) and sensory rhodopsin II but different from that of the mixed retinal composition of CrChR2, (ii) lowering the pH from 7 to 2 or substituting neutral residues for Glu169 or Asp299 does not significantly shift the ethylenic stretch frequency more than 1-2 cm(-1) in contrast to BR in which a downshift of 7-9 cm(-1) occurs reflecting neutralization of the Asp85 counterion, and (iii) the CaChR1 protonated Schiff base (SB) has stronger hydrogen bonding than BR. A model is proposed to explain these results whereby at pH 7 the predominant counterion to the SB is Asp299 (the homologue to Asp212 in BR) while Glu169 (the homologue to Asp85 in BR) exists in a neutral state. We observe an unusual constancy of the resonance Raman spectra over the broad range from pH 9 to 2 and discuss its implications. These results are in accord with recent visible absorption and current measurements of CaChR1 [Sineshchekov, O. A., et al. (2013) Intramolecular proton transfer in channelrhodopsins. Biophys. J. 104, 807-817; Li, H., et al. (2014) Role of a helix B lysine residue in the photoactive site in

  13. 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

  14. Governance and Management Structures for Community Partnerships: Experiences from the Robert Wood Johnson Foundation's Community Partnerships for Older Adults Program

    ERIC Educational Resources Information Center

    Bolda, Elise J.; Saucier, Paul; Maddux, George L.; Wetle, Terrie; Lowe, Jane Isaacs

    2006-01-01

    Purpose: This article describes early efforts of four community partnerships in Boston, El Paso, Houston, and Milwaukee to address governance and management structures in ways that promote the sustainability of innovative community-based long-term care system improvements. The four communities are grantees of the Community Partnerships for Older…

  15. Ice Cover as a Factor Driving Microbial Community Structure in the Laurentian Great Lakes

    NASA Astrophysics Data System (ADS)

    McKay, R. M.; Beall, B.; Oyserman, B.; Smith, D.; Bullerjahn, G.; Morris, P.; Twiss, M. R.

    2013-12-01

    Lakes serve as rapid responding sentinels of human influence on the natural environment rendering them powerful tools to advance our understanding of a changing climate on microbial community structure and function. Whereas we possess a baseline knowledge of microbial diversity in the Great Lakes, we know little about how these communities respond to the manifestations of climate change. Through collaboration with U.S.- and Canadian Coast Guards, winter surveys have been conducted on Lake Erie since 2007. The surveys have captured extremes in ice extent ranging from expansive ice cover through 2011 to nearly ice-free waters in winter 2012, a condition driven by a warm positive Arctic Oscillation. We showed that dramatic changes in annual ice cover were accompanied by equally dramatic shifts in phytoplankton community structure. Expansive ice cover documented for Lake Erie in winters 2010 and 2011 supported ice-associated phytoplankton blooms dominated by physiologically robust, filamentous centric diatoms. Transcriptomic analysis of the winter bloom offers insights into the success of this psychrophilic community. By comparison, ice free conditions promoted the growth of small-sized cells supported by analysis of size-fractionated chlorophyll a and flow cytometry. The phytoplankton community in winter 2013 was dominated by microplankton-sized filamentous diatoms, coincident with expansive ice cover and thus returning to the size structure of the 2010 and 2011 communities. Reduced size is recognized as a universal ecological response to global warming in aquatic systems although it usually marks a response to climate warming over multiple years, not a single season as reported here. Fig. 1. Winter surveys conducted on Lake Erie over two years demonstrated tight coupling between microplankton Chl a biomass and total Chl a during winter 2010-11 (purple, green), a year of expansive ice cover. A warm positive Arctic Oscillation resulted in negligible ice cover on Lake

  16. Phylogenetic plant community structure along elevation is lineage specific

    PubMed Central

    Ndiribe, Charlotte; Pellissier, Loïc; Antonelli, Silvia; Dubuis, Anne; Pottier, Julien; Vittoz, Pascal; Guisan, Antoine; Salamin, Nicolas

    2013-01-01

    The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages. PMID:24455126

  17. 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

  18. 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...

  19. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

    PubMed Central

    Li, Yan; He, Jinzhi; He, Zhili; Zhou, Yuan; Yuan, Mengting; Xu, Xin; Sun, Feifei; Liu, Chengcheng; Li, Jiyao; Xie, Wenbo; Deng, Ye; Qin, Yujia; VanNostrand, Joy D; Xiao, Liying; Wu, Liyou; Zhou, Jizhong; Shi, Wenyuan; Zhou, Xuedong

    2014-01-01

    Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis. PMID:24671083

  20. 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

  1. Understanding and mitigating tsunami risk for coastal structures and communities

    NASA Astrophysics Data System (ADS)

    Park, Sangki

    Tsunamis have attracted the world's attention over the last decade due to their destructive power and the vast areas they can affect. The 2004 Indian Ocean Tsunami, killed more than 200,000 people, and the 2011 Great Tohoku Japan Earthquake and Tsunami, resulted in 15,000 deaths and an estimated US $300B in damage, are recent examples. An improved understanding of tsunamis and their interactive effects on the built environment will significantly reduce loss of life in tsunamis. In addition, it is important to consider both the effect of the earthquake ground motion and the tsunami it creates for certain coastal regions. A numerical model to predict structural behavior of buildings subjected to successive earthquakes and the tsunamis was developed. Collapse fragilities for structures were obtained by subjecting a structure to a suite of earthquake ground motions. After each motion the numerically damaged structural model was subjected to tsunami wave loading as defined by FEMA P646. This approach was then extended to the community level; a methodology to determine the probability of fatalities for a community as a function of the number of vertical evacuation shelters was computed. Such an approach also considered the location and number of vertical evacuation sites as an optimization problem. Both the single structure cases and the community analyses were presented in terms of fragilities as a function of the earthquake intensity level and evacuation time available. It is envisioned that the approach may be extended to any type of structure as they are typically modeled nonlinearly with strength and stiffness degradation. A logical fragility-based, or performance-based, procedure for vertical evacuation for coastal buildings and for whole communities was developed. A mechanism to obtain a reduction in the collapse risk of structure and more critically maximize the survival rate for a community was a major outcome of this dissertation. The proposed tsunami vertical

  2. Extinction order and altered community structure rapidly disrupt ecosystem functioning.

    PubMed

    Larsen, Trond H; Williams, Neal M; Kremen, Claire

    2005-05-01

    By causing extinctions and altering community structure, anthropogenic disturbances can disrupt processes that maintain ecosystem integrity. However, the relationship between community structure and ecosystem functioning in natural systems is poorly understood. Here we show that habitat loss appeared to disrupt ecosystem functioning by affecting extinction order, species richness and abundance. We studied pollination by bees in a mosaic of agricultural and natural habitats in California and dung burial by dung beetles on recently created islands in Venezuela. We found that large-bodied bee and beetle species tended to be both most extinction-prone and most functionally efficient, contributing to rapid functional loss. Simulations confirmed that extinction order led to greater disruption of function than predicted by random species loss. Total abundance declined with richness and also appeared to contribute to loss of function. We demonstrate conceptually and empirically how the non-random response of communities to disturbance can have unexpectedly large functional consequences. PMID:21352458

  3. Exponential random graph models for networks with community structure

    NASA Astrophysics Data System (ADS)

    Fronczak, Piotr; Fronczak, Agata; Bujok, Maksymilian

    2013-09-01

    Although the community structure organization is an important characteristic of real-world networks, most of the traditional network models fail to reproduce the feature. Therefore, the models are useless as benchmark graphs for testing community detection algorithms. They are also inadequate to predict various properties of real networks. With this paper we intend to fill the gap. We develop an exponential random graph approach to networks with community structure. To this end we mainly built upon the idea of blockmodels. We consider both the classical blockmodel and its degree-corrected counterpart and study many of their properties analytically. We show that in the degree-corrected blockmodel, node degrees display an interesting scaling property, which is reminiscent of what is observed in real-world fractal networks. A short description of Monte Carlo simulations of the models is also given in the hope of being useful to others working in the field.

  4. Seasonal shift in the sensitivity of a natural benthic microalgal community to a herbicide mixture: impact on the protective level of thresholds derived from species sensitivity distributions.

    PubMed

    Larras, Floriane; Montuelle, Bernard; Rimet, Frédéric; Chèvre, Nathalie; Bouchez, Agnès

    2014-08-01

    Seasonal changes in the structure and composition of a benthic microalgal community may lead to different responses to herbicide contamination during different seasons. Consequently, the thresholds derived from risk assessment tools such as species sensitivity distributions (SSDs) must allow for these changes. We built a single-substance SSD for each of four herbicides (atrazine, terbutryn, diuron and isoproturon), which was specific to the sensitivity of the benthic diatoms found in Lake Geneva, in order to derive protective thresholds for a mixture of these four herbicides using the concentration addition model. We then investigated (1) the structural parameters of a Lake Geneva benthic microalgal community during two contrasting seasons (summer 2012 and winter 2013), (2) the response of these communities to a herbicide mixture, and (3) the protective levels of the thresholds derived. The winter community was characterized by having greater biomass, diatom species richness, and diversity metrics, and lower non-diatom species richness than the summer community. The differences in the diatom communities composition in these seasons appeared to be primarily driven by the environmental nitrate concentrations and the temperature. Moreover, the species in the winter community were more resistant to herbicides than those found in the summer community. Consequently, the protective threshold for this herbicide mixture obtained in this study was in fact protective for the winter community, but not for the summer community based on their structural parameters. Thus, the protective level against herbicides of the threshold for the benthic microalgal community should take into account changes in the environmental physico-chemical conditions that strongly influence the structure and composition of the community. The fact that the succession of species over time (i.e., over the seasons) is difficult to predict introduces uncertainties into the estimation of protective

  5. Community Dialogue to Shift Social Norms and Enable Family Planning: An Evaluation of the Family Planning Results Initiative in Kenya

    PubMed Central

    Creanga, Andreea A.; Galavotti, Christine; Wamalwa, Emmanuel

    2016-01-01

    Introduction Use of family planning (FP) is powerfully shaped by social and gender norms, including the perceived acceptability of FP and gender roles that limit women’s autonomy and restrict communication and decision-making between men and women. This study evaluated an intervention that catalyzed ongoing community dialogues about gender and FP in Siaya county, Nyanza Province, Kenya. Specifically, we explored the changes in perceived acceptability of FP, gender norms and use of FP. Methods We used a mixed-method approach. Information on married men and women’s socio-demographic characteristics, pregnancy intentions, gender-related beliefs, FP knowledge, attitudes, and use were collected during county-representative, cross-sectional household surveys at baseline (2009; n11 = 650 women; n12 = 305 men) and endline (2012; n21 = 617 women; n22 = 317 men); exposure to the intervention was measured at endline. We assessed changes in FP use at endline vs. baseline, and fitted multivariate logistic regression models for FP use to examine its association with intervention exposure and explore other predictors of use at endline. In-depth, qualitative interviews with 10 couples at endline further explored enablers and barriers to FP use. Results At baseline, 34.0% of women and 27.9% of men used a modern FP method compared to 51.2% and 52.2%, respectively, at endline (p<0.05). Exposure to FP dialogues was associated with 1.78 (95% CI: 1.20–2.63) times higher odds of using a modern FP method at endline for women, but this association was not significant for men. Women’s use of modern FP was significantly associated with higher spousal communication, control over own cash earnings, and FP self-efficacy. Men who reported high approval of FP were significantly more likely to use modern FP if reporting high approval of FP and more equitable gender beliefs. FP dialogues addressed persistent myths and misconceptions, normalized FP discussions, and increased its

  6. Family Structure, Community Context, and Adolescent Problem Behaviors

    ERIC Educational Resources Information Center

    Hoffman, John P.

    2006-01-01

    A number of models have been proposed to explain the relationship between family structure and adolescent problem behaviors, including several that consider parent-child relations, family income, stress, and residential mobility. However, studies have not explored whether the different types of communities within which families reside affect the…

  7. MICROBIAL COMMUNITY STRUCTURE AND ENZYME ACTIVITIES IN SEMIARID AGRICULTURAL SOILS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of management on the microbial community structure and enzyme activities of three semiarid soils from Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in cotton -peanut (Arachis h...

  8. Changes in Age Structure and Rural Community Growth.

    ERIC Educational Resources Information Center

    McGranahan, David A.

    1985-01-01

    Whatever migration patterns evolve, changes in the age structure mean that rural communities in general can expect fairly stable elementary school population, reduced high school population, slower growth in new business and employment, and continued increase in the elderly population. (JHZ)

  9. The Community Context of Family Structure and Adolescent Drug Use.

    ERIC Educational Resources Information Center

    Hoffmann, John P.

    2002-01-01

    Investigates hypothesis used to explain the relationship between family structure and adolescent drug use, using data from the National Education Longitudinal Study (NELS). Reports that adolescents who resided in single-parent or stepparent families had heightened drug use. Higher adolescent drug use was found in communities with a large…

  10. Relating methanogen community structure and anaerobic digester function.

    PubMed

    Bocher, B T W; Cherukuri, K; Maki, J S; Johnson, M; Zitomer, D H

    2015-03-01

    Much remains unknown about the relationships between microbial community structure and anaerobic digester function. However, knowledge of links between community structure and function, such as specific methanogenic activity (SMA) and COD removal rate, are valuable to improve anaerobic bioprocesses. In this work, quantitative structure-activity relationships (QSARs) were developed using multiple linear regression (MLR) to predict SMA using methanogen community structure descriptors for 49 cultures. Community descriptors were DGGE demeaned standardized band intensities for amplicons of a methanogen functional gene (mcrA). First, predictive accuracy of MLR QSARs was assessed using cross validation with training (n = 30) and test sets (n = 19) for glucose and propionate SMA data. MLR equations correlating band intensities and SMA demonstrated good predictability for glucose (q(2) = 0.54) and propionate (q(2) = 0.53). Subsequently, data from all 49 cultures were used to develop QSARs to predict SMA values. Higher intensities of two bands were correlated with higher SMA values; high abundance of methanogens associated with these two bands should be encouraged to attain high SMA values. QSARs are helpful tools to identify key microorganisms or to study and improve many bioprocesses. Development of new, more robust QSARs is encouraged for anaerobic digestion or other bioprocesses, including nitrification, nitritation, denitrification, anaerobic ammonium oxidation, and enhanced biological phosphorus removal. PMID:25562581

  11. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    ERIC Educational Resources Information Center

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

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

    SciTech Connect

    Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.; Iuliucci, Robbie; Mueller, Karl T.

    2015-11-21

    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 than 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.

  13. Improved chalcopyrite bioleaching by Acidithiobacillus sp. via direct step-wise regulation of microbial community structure.

    PubMed

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

    A direct step-wise regulation strategy of microbial community structure was developed for improving chalcopyrite bioleaching by Acidithiobacillus sp. Specially, the initial microbial proportion between Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans was controlled at 3:1 with additional 2 g/L Fe(2+) for faster initiating iron metabolism. A. thiooxidans biomass was fed via a step-wise strategy (8-12th d) with the microbial proportion 1:1 for balancing community structure and promoting sulfur metabolism in the stationary phase. A. thiooxidans proportion was further improved via another step-wise feeding strategy (14-18th d) with the microbial proportion 1:2 for enhancing sulfur metabolism and weakening jarosite passivation in the later phase. With the community structure-shift control strategy, biochemical reaction was directly regulated for creating a better balance in different phases. Moreover, the final copper ion was increased from 57.1 to 93.2 mg/L, with the productivity 2.33 mg/(Ld). The novel strategy may be valuable in optimization of similar bioleaching process. PMID:26011694

  14. Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Zinke, L.; Carvalho, G.; Lloyd, K. G.; Marshall, I.; Shumaker, A.; Amend, J.

    2014-12-01

    The Baltic Sea Basin (BSB) is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of climatic fluctuations over past tens of thousands of years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates make this an ideal setting to understand the microbial structure of a deep biosphere community in a relatively high carbon, and thus high-energy environment, compared to other deep subsurface sites. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The active microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further refine our understanding of the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

  15. Community structure influences species' abundance along environmental gradients.

    PubMed

    Eloranta, Antti P; Helland, Ingeborg P; Sandlund, Odd T; Hesthagen, Trygve; Ugedal, Ola; Finstad, Anders G

    2016-01-01

    Species' response to abiotic environmental variation can be influenced by local community structure and interspecific interactions, particularly in restricted habitats such as islands and lakes. In temperate lakes, future increase in water temperature and run-off of terrestrial (allochthonous) dissolved organic carbon (DOC) are predicted to alter community composition and the overall ecosystem productivity. However, little is known about how the present community structure and abiotic environmental variation interact to affect the abundance of native fish populations. We used a space-for-time approach to study how local community structure interact with lake morphometric and climatic characteristics (i.e. temperature and catchment productivity) to affect brown trout (Salmo trutta L.) yield in 283 Norwegian lakes located in different biogeographical regions. Brown trout yield (based on data from standardized survey gill net fishing; g 100 m(-2) gill net night(-1)) was generally lower in lakes where other fish species were present than in lakes with brown trout only. The yield showed an overall negative relationship with increasing temperature and a positive relationship with lake shoreline complexity. Brown trout yield was also negatively correlated with DOC load (measured using Normalized Difference Vegetation Index as a proxy) and lake size and depth (measured using terrain slope as a proxy), but only in lakes where other fish species were present. The observed negative response of brown trout yield to increasing DOC load and proportion of the pelagic open-water area is likely due to restricted (littoral) niche availability and competitive dominance of more pelagic fishes such as Arctic charr (Salvelinus alpinus (L.)). Our study highlights that, through competitive interactions, the local community structure can influence the response of a species' abundance to variation in abiotic conditions. Changes in biomass and niche use of top predators (such as the brown

  16. Structure of Benthic Communities along the Taiwan Latitudinal Gradient

    PubMed Central

    De Palmas, Stéphane; Kuo, Chao-Yang; Hsieh, Hernyi Justin; Chen, Chaolun Allen

    2016-01-01

    The distribution and the structure of benthic assemblages vary with latitude. However, few studies have described benthic communities along large latitudinal gradients, and patterns of variation are not fully understood. Taiwan, lying between 21.90°N and 25.30°N, is located at the center of the Philippine-Japan arc and lies at the northern margin of coral reef development. A wide range of habitats is distributed along this latitudinal gradient, from extensive fringing coral reefs at the southern coast to non-reefal communities at the north. In this study, we examined the structure of benthic communities around Taiwan, by comparing its assemblages in four regions, analyzing the effects of the latitudinal gradient, and highlighting regional characteristics. A total of 25 sites, 125 transects, and 2,625 photographs were used to analyze the benthic communities. Scleractinian corals present an obvious gradient of increasing diversity from north to south, whereas macro-algae diversity is higher on the north-eastern coast. At the country scale, Taiwanese coral communities were dominated by turf algae (49%). At the regional scale, we observed an important heterogeneity that may be caused by local disturbances and habitat degradation that smooths out regional differences. In this context, our observations highlight the importance of managing local stressors responsible for reef degradation. Overall, this study provides an important baseline upon which future changes in benthic assemblages around Taiwan can be assessed. PMID:27513665

  17. Mutualistic Interactions and Community Structure in Biological Metacommunities

    NASA Astrophysics Data System (ADS)

    Rikvold, Per Arne; Filotas, Elise; Grant, Martin; Parrott, Lael

    2011-03-01

    The role of space in determining species coexistence and community structure is well established. However, previous studies mainly focus on simple competition and predation systems, and the role of mutualistic interspecies interactions is not well understood. Here we use a spatially explicit metacommunity model, in which new species enter by a mutation process, to study the effect of fitness-dependent dispersal on the structure of communities with interactions comprising mutualism, competition, and exploitation. We find that the diversity and interaction network undergo a nonequilibrium phase transition with increasing dispersal rate. Low dispersion rate favors spontaneous emergence of many dissimilar, strongly mutualistic and species-poor local communities. Due to the local dissimilarities, the global diversity is high. High dispersion rate promotes local biodiversity and supports similar, species-rich local communities with a wide range of interactions. The strong similarity between neighboring local communities leads to reduced global diversity. Supported by NSERC (Canada), FQRNT (Québec), NSF (U.S.A.)

  18. The microbial community structure of the cotton rat nose.

    PubMed

    Chaves-Moreno, Diego; Plumeier, Iris; Kahl, Silke; Krismer, Bernhard; Peschel, Andreas; Oxley, Andrew P A; Jauregui, Ruy; Pieper, Dietmar H

    2015-12-01

    The cotton rat nose is commonly used as a model for Staphylococcus aureus colonization, as it is both physiologically and anatomically comparable to the human nares and can be easily colonized by this organism. However, while the colonization of the human anterior nares has been extensively studied, the microbial community structure of cotton rat noses has not been reported so far. We describe here the microbial community structure of the cotton rat (Sigmodon hispidus) nose through next-generation sequencing of 16S rRNA gene amplicons covering the V1-V2 region and the analysis of nearly full length 16S rRNA genes of the major phylotypes. Roughly half of the microbial community was composed of two undescribed species of the genus Campylobacter, with phylotypes belonging to the genera Catonella, Acholeplasma, Streptobacillus and Capnocytophaga constituting the predominant community members. Thus, the nasal community of the cotton rat is uniquely composed of several novel bacterial species and may not reflect the complex interactions that occur in human anterior nares. Mammalian airway microbiota may, however, be a rich source of hitherto unknown microbes. PMID:26306992

  19. Structure of Benthic Communities along the Taiwan Latitudinal Gradient.

    PubMed

    Ribas-Deulofeu, Lauriane; Denis, Vianney; De Palmas, Stéphane; Kuo, Chao-Yang; Hsieh, Hernyi Justin; Chen, Chaolun Allen

    2016-01-01

    The distribution and the structure of benthic assemblages vary with latitude. However, few studies have described benthic communities along large latitudinal gradients, and patterns of variation are not fully understood. Taiwan, lying between 21.90°N and 25.30°N, is located at the center of the Philippine-Japan arc and lies at the northern margin of coral reef development. A wide range of habitats is distributed along this latitudinal gradient, from extensive fringing coral reefs at the southern coast to non-reefal communities at the north. In this study, we examined the structure of benthic communities around Taiwan, by comparing its assemblages in four regions, analyzing the effects of the latitudinal gradient, and highlighting regional characteristics. A total of 25 sites, 125 transects, and 2,625 photographs were used to analyze the benthic communities. Scleractinian corals present an obvious gradient of increasing diversity from north to south, whereas macro-algae diversity is higher on the north-eastern coast. At the country scale, Taiwanese coral communities were dominated by turf algae (49%). At the regional scale, we observed an important heterogeneity that may be caused by local disturbances and habitat degradation that smooths out regional differences. In this context, our observations highlight the importance of managing local stressors responsible for reef degradation. Overall, this study provides an important baseline upon which future changes in benthic assemblages around Taiwan can be assessed. PMID:27513665

  20. 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.

  1. Quantifying the response of structural complexity and community composition to environmental change in marine communities.

    PubMed

    Ferrari, Renata; Bryson, Mitch; Bridge, Tom; Hustache, Julie; Williams, Stefan B; Byrne, Maria; Figueira, Will

    2016-05-01

    Habitat structural complexity is a key factor shaping marine communities. However, accurate methods for quantifying structural complexity underwater are currently lacking. Loss of structural complexity is linked to ecosystem declines in biodiversity and resilience. We developed new methods using underwater stereo-imagery spanning 4 years (2010-2013) to reconstruct 3D models of coral reef areas and quantified both structural complexity at two spatial resolutions (2.5 and 25 cm) and benthic community composition to characterize changes after an unprecedented thermal anomaly on the west coast of Australia in 2011. Structural complexity increased at both resolutions in quadrats (4 m(2)) that bleached, but not those that did not bleach. Changes in complexity were driven by species-specific responses to warming, highlighting the importance of identifying small-scale dynamics to disentangle ecological responses to disturbance. We demonstrate an effective, repeatable method for quantifying the relationship among community composition, structural complexity and ocean warming, improving predictions of the response of marine ecosystems to environmental change. PMID:26679689

  2. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  3. Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

    PubMed

    Rodrigues, Richard R; Pineda, Rosana P; Barney, Jacob N; Nilsen, Erik T; Barrett, John E; Williams, Mark A

    2015-01-01

    The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen

  4. Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

    PubMed Central

    Rodrigues, Richard R.; Pineda, Rosana P.; Barney, Jacob N.; Nilsen, Erik T.; Barrett, John E.; Williams, Mark A.

    2015-01-01

    The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen

  5. Dynamics of the diversity and structure of the overall and nitrifying microbial community in activated sludge along gradient copper exposures.

    PubMed

    Ouyang, Fan; Ji, Min; Zhai, Hongyan; Dong, Zhao; Ye, Lin

    2016-08-01

    Diversity and composition of the microbial community, especially the nitrifiers, are essential to the treatment efficiency of wastewater in activated sludge systems. Heavy metals commonly present in the wastewater influent such as Cu can alter the community structure of nitrifiers and lower their activity. However, the dynamics of microbial community along a gradient of metal exposure have largely been unexplored, partially due to the limitations in traditional molecular methods. This study explored the dynamics regarding the diversity and community structures of overall and nitrifying microbial communities in activated sludge under intermittent Cu gradient loadings using Illumina sequencing. We created a new local nitrifying bacterial database for sequence BLAST searches. High Cu loadings (>10.9 mg/L) impoverished microbial diversity and altered the microbial community. Overall, Proteobacteria was the predominant phylum in the activated sludge system, in which Zoogloea, Thauera, and Dechloromonas (genera within the Rhodocyclaceae family of the Beta-proteobacteria class) were the dominant genera in the presence of Cu. The abundance of unclassified bacteria at the phylum level increased substantially with increasing Cu loadings. Nitrosomonas and Nitrospira were the predominant nitrifiers. The nitrifying bacterial community changed through increasing abundance and shifting to Cu-tolerant species to reduce the toxic effects of Cu. Our local nitrifying bacterial database helped to improve the resolution of bacterial identification. Our results provide insights into the dynamics of microbial community in response to various metal concentrations in activated sludge systems and improve our understanding regarding the effect of metals on wastewater treatment efficiency. PMID:27098258

  6. Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions.

    PubMed

    Mueller, Rebecca C; Bohannan, Brendan J M

    2015-09-01

    Global N inputs and atmospheric CO2 concentrations have increased as a result of human activities, and are predicted to increase along with population growth, with potentially negative effects on biodiversity. Using taxonomic and phylogenetic measures, we examined the response of arbuscular mycorrhizal fungi (AMF) to experimental manipulations of N and CO2 at the Jasper Ridge Global Change Experiment. No significant interactions between N and CO2 were observed, but individual effects of N and CO2 were found. Elevated CO2 resulted in changes in phylogenetic similarity, and a shift to phylogenetic clustering of AMF communities. N addition resulted in higher phylogenetic diversity and evenness, with no shifts in community composition and no significant signal for phylogenetic clustering. N addition resulted in an increase in both available N and the N:P ratio in N-amended plots, which suggests that changing patterns of nutrient limitation could have lead to altered species interactions. These findings suggest that elevated levels of N and CO2 altered patterns of AMF community assembly, with potential effects on ecosystem function. PMID:25990297

  7. Effects of coastal upwelling on the structure of macrofaunal communities in SE Brazil

    NASA Astrophysics Data System (ADS)

    Quintana, Cintia O.; Bernardino, Angelo F.; de Moraes, Paula C.; Valdemarsen, Thomas; Sumida, Paulo Y. G.

    2015-03-01

    The effects of coastal upwelling on the structure of macrofaunal communities were investigated in two shallow bays in SE Brazil. Water, sediment and fauna samples were collected at four time-points corresponding to austral summer, fall, winter and spring, respectively. Water column temperature and salinity profiles indicated that upwelling occurred in summer-spring (December and November), but not in fall-winter (April and August). The structure of macrofaunal communities differed consistently between these periods. The sediment content of labile organic matter did not vary as a function of upwelling and could not explain the changes in macrofaunal communities. Rather it appeared that macrofaunal community structure was determined by organic matter quality (i.e. phytoplankton composition), physical disturbance regimes and bottom-water temperature. Physical disturbance caused by S-SE winds, warm water temperatures (up to 26 °C) and resuspension-driven phytoflagellate blooms during non-upwelling were associated to higher density (2511-2525 ind m- 2) and dominance of small opportunistic species such as spionid, paraonid and capitellid polychaetes. In contrast, stable hydrodynamic conditions, diatom blooms and lower water temperatures (down to 18 °C) during upwelling resulted in lower density of macrofauna (796-1387 ind m- 2) and a shift in species composition to relatively large-sized magelonids and carnivorous polychaetes. Therefore, organic matter quality, physical disturbance regimes, and bottom-water temperature were the major factors regulating the life-cycles, composition and density of macrofaunal communities in these less productive subtropical upwelling systems.

  8. 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

  9. Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

    PubMed Central

    Kamilar, Jason M.; Beaudrot, Lydia; Reed, Kaye E.

    2015-01-01

    We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change. PMID:25875361

  10. Drivers of macroinvertebrate community structure in unmodified streams

    PubMed Central

    2014-01-01

    Often simple metrics are used to summarise complex patterns in stream benthic ecology, thus it is important to understand how well these metrics can explain the finer-scale underlying environmental variation often hidden by coarser-scale influences. I sampled 47 relatively pristine streams in the central North Island of New Zealand in 2007 and (1) evaluated the local-scale drivers of macroinvertebrate community structure as well as both diversity and biomonitoring metrics in this unmodified landscape, and (2) assessed whether these drivers were similar for commonly used univariate metrics and multivariate structure. The drivers of community metrics and multivariate structure were largely similar, with % canopy cover and resource supply metrics the most commonly identified environmental drivers in these pristine streams. For an area with little to no anthropogenic influence, substantial variation was explained in the macroinvertebrate community (up to 70% on the first two components of a partial least squares regression), with both uni- and multivariate approaches. This research highlights two important points: (1) the importance of considering natural underlying environmental variation when assessing the response to coarse environmental gradients, and (2) the importance of considering canopy cover presence when assessing the impact of stressors on stream macroinvertebrate communities. PMID:25024926

  11. THE STRUCTURE AND PROCESS OF SCHOOL-COMMUNITY RELATIONS. VOLUME III, THE STRUCTURE OF SCHOOL-COMMUNITY RELATIONS.

    ERIC Educational Resources Information Center

    CARTER, RICHARD F.; AND OTHERS

    TO EVALUATE STRUCTURAL COMPONENTS OF SCHOOL-COMMUNITY RELATIONS, 860 VARIABLES WERE DEFINED FROM THE LITERATURE AND GROUPED INTO 26 DIVISIONS FOR ASSESSMENT AGAINST FOUR SUMMARY CRITERION VARIABLES--(1) ACQUIESCENCE, THE DEGREE TO WHICH VOTERS IN A SCHOOL DISTRICT VIEW FINANCIAL ISSUES FAVORABLY, (2) PARTICIPATION, THE DEGREE TO WHICH VOTERS…

  12. 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

  13. Carbon Accumulation and Microbial Community Structure in Reclaimed Mine Soils

    NASA Astrophysics Data System (ADS)

    Pfiffner, S. M.; Palumbo, A. V.; Tarver, J. D.; Fisher, S.; Cantu, J.; Brandt, C. C.

    2002-12-01

    The objective of this study was to investigate the potential for soil amendments to increase accumulation of carbon in reclaimed soils and the relationship between carbon and microbial community structure. Changes in community structure were determined by signature lipid biomarkers (SLBs) or phospholipid fatty acid methyl esters. PLFA provide estimates of the viable biomass, diversity of prokaryotic and eukaryotic diversity, and indications of physiological stress to the microbial community. Artificial neural network (ANN) analysis has been used to examine the relationship between microbial community structure and soil geochemistry. It was hypothesized that (1) soil amendments would cause changes in the structure of the microbial community and carbon content (2) changes in the structure of the microbial community would be vary between the types of amendments, and (3) analysis of the SLB with an artificial neural network (ANN) would distinguish treatment and provide a insight in to the relationship between changes in soil geochemistry and microbial community. Twenty soils samples from different field plots and at different soil horizon depths were analyzed. Biomass as estimated by PLFA analysis, ranged from 1.9 to 265 nmol/g, which corresponded to cell densities of 4.8 x107 to 6.6 x109 cells/g. In the Wall's Farm and Jenkin's Farm samples the microbial biomass decreased with depth. A horizon soils had biomass values of greater or equal to 120 nmol/g, followed by the A2 horizon,(70 to 100 nmol/g) and the weak B horizon at and (40 to 80 nmo/g). The A2 and B horizon samples showed higher relative abundance of mid-chain branched saturates that are indicative of gram positive prokaryotes and actinomycetes. At Well's Farm, the polyunsaturates indicative of eukaryotes were observed at higher abundances. These changes were related to both the prokaryotic and eukaryotic influences in the microbial community in response to the soil amendments. The correlation between

  14. Bacterial community structure in freshwater springs infested with the invasive plant species Hydrilla verticillata

    PubMed Central

    Gordon-Bradley, N.; Li, N.

    2015-01-01

    The phylogenetic composition and physiological profiles of bacterial communities in freshwater springs were evaluated during the blooming and non-blooming stages of the invasive plant species, Hydrilla verticillata. Community-level physiological profiles (CLPPs) and pyrosequencing of 16S rRNA gene amplicons were used to study potential Hydrilla mediated shifts in the physiological potential and phylogenetic composition of the bacterial community in infested systems. The results of CLPP revealed that the microbes in the Hydrilla invaded sites utilized less substrates during blooming periods than during nonblooming periods of the plant. Spearman’s rank correlation analysis showed some relationships between the relative abundances of bacterial taxa and the Biolog substrate utilization pattern. The relative abundance of the identified taxa showed some striking differences based on the blooming status of Hydrilla and to a lesser extent on site variation. The relative abundance of Actinobacteria, Bacteriodetes, and Verrucomicrobia was generally higher during Hydrilla blooms, while Deltaproteobacteria was generally higher during non-blooming stages of Hydrilla. The detected genera also varied based on the blooming stages of the plant. Based on the findings, it appears that Hydrilla alters the phylogenetic composition and structure of the bacterial community during the blooming stage. PMID:26207069

  15. From one to one million: How does community structure track disturbance across time and space?

    NASA Astrophysics Data System (ADS)

    Webb, A. E.

    2012-12-01

    The rate and severity of disturbances to the biosphere have been increasing over the last millennium due in part to anthropogenic effects, and the results of these disturbances are of increasing interest to the scientific and public communities. This project examines the impact of acidification and global warming on communities across a spectrum of temporal and spatial scales in both modern and fossil systems. Twenty datasets were selected from published zoo- and phyto-plankton literature to represent a temporal and spatial gradient, from small lakes to the open ocean, and from one year to one million years. Each dataset is associated with a proxy for an environmental disturbance (isotopes, pH, sedimentology, etc.) and consists of 15-300 samples across the interval of disturbance. To test the biotic changes induced by disturbance, community structure is measured by quantifying species-abundance distributions using rank-abundance curves and ordinations. A community consists of the individuals present in a given location at a given time, and the relative abundance of different species serves as a proxy for resource-partitioning. Disturbances cause a change in resource-partitioning, either by changing resource availability or by removing/adding species which compete for those resources. Therefore, shifts in resource-partitioning resulting from disturbance can be tracked by changes in community composition. Prior to an environmental disturbance, communities typically consist of many species that evenly partition resources and thereby abundance. After a disturbance, communities are dominated by a few species that can tolerate or thrive in the new conditions. Non-metric multi-dimensional scaling and Bray-Curtis polar ordinations reveal a progression from pre-disturbance communities, through the disturbance, and into the eventual recovery, which may or may not resemble the pre-disturbance communities. Larger disturbances (in terms of spatial extent or temporal duration

  16. Impacts of Size Structure on Intraguild Predation in Pond Communities

    NASA Astrophysics Data System (ADS)

    Crumrine, P. W.

    2005-05-01

    Size structure, the degree to which individuals in a population vary in size, can greatly influence the dynamics of intraguild predation (IGP) within ecological communities. I manipulated the degree of size structure within assemblages of IG predators and IG prey to examine impacts on the direction and intensity of IGP in communities of larval dragonflies and larval water beetles. In pond enclosure studies, Pachydiplax longipennis (IG prey) mortality was lower when exposed to size structured assemblages of Anax junius (IG predator) than when exposed to only large A. junius at the same density. Effects of size-structured assemblages of A. junius on shared prey, Ischnura verticalis, were similar to the effects each size class alone at the same density. Separate experiments with Dytiscid water beetle larvae as IG predators and size-structured assemblages of A. junius as IG prey suggest that IG prey size structure plays only a limited role in mediating shared prey survival. These experiments highlight the importance of size structure as a characteristic that may promote the coexistence of predators in IGP systems.

  17. Triclocarban Influences Antibiotic Resistance and Alters Anaerobic Digester Microbial Community Structure.

    PubMed

    Carey, Daniel E; Zitomer, Daniel H; Hristova, Krassimira R; Kappell, Anthony D; McNamara, Patrick J

    2016-01-01

    Triclocarban (TCC) is one of the most abundant organic micropollutants detected in biosolids. Lab-scale anaerobic digesters were amended with TCC at concentrations ranging from the background concentration of seed biosolids (30 mg/kg) to toxic concentrations of 850 mg/kg to determine the effect on methane production, relative abundance of antibiotic resistance genes, and microbial community structure. Additionally, the TCC addition rate was varied to determine the impacts of acclimation time. At environmentally relevant TCC concentrations (max detect = 440 mg/kg), digesters maintained function. Digesters receiving 450 mg/kg of TCC maintained function under gradual TCC addition, but volatile fatty acid concentrations increased, pH decreased, and methane production ceased when immediately fed this concentration. The concentrations of the mexB gene (encoding for a multidrug efflux pump) were higher with all concentrations of TCC compared to a control, but higher TCC concentrations did not correlate with increased mexB abundance. The relative abundance of the gene tet(L) was greater in the digesters that no longer produced methane, and no effect on the relative abundance of the class 1 integron integrase encoding gene (intI1) was observed. Illumina sequencing revealed substantial community shifts in digesters that functionally failed from increased levels of TCC. More subtle, yet significant, community shifts were observed in digesters amended with TCC levels that did not inhibit function. This research demonstrates that TCC can select for a multidrug resistance encoding gene in mixed community anaerobic environments, and this selection occurs at concentrations (30 mg/kg) that can be found in full-scale anaerobic digesters (U.S. median concentration = 22 mg/kg, mean = 39 mg/kg). PMID:26588246

  18. The seasonal cycle of the Lazarev Sea macrozooplankton community and a potential shift to top-down trophic control in winter

    NASA Astrophysics Data System (ADS)

    Hunt, B. P. V.; Pakhomov, E. A.; Siegel, V.; Strass, V.; Cisewski, B.; Bathmann, U.

    2011-07-01

    Between 2004 and 2008, during the German Southern Ocean GLOBEC programme, four large scale bio-oceanographic surveys were conducted in the Lazarev Sea for the Lazarev Sea Krill Survey (LAKRIS). These surveys were completed in Autumn (April-May) 2004, Summer (December-January) 2005/06, Winter (July-August) 2006, and Summer (December-January) 2007/08. On each occasion macrozooplankton communities were sampled by RMT-8 in the upper 200 m of the water column. Chlorophyll a biomass averaged ˜1.5 mg m -3 (max=8.2 mg m -3) in Summer 05/06, 0.88 mg m -3 (max=2.77 mg m -3) in Summer 07/08, 0.24 mg m -3 (max=0.73 mg m -3) in Autumn 04, and 0.042 mg m -3 (max=0.1 mg m -3) in Winter 06. Macrozooplankton densities did not differ significantly between seasons and were 53, 68, 59, and 48 ind. 1000 m -3 in Summer 05/06, Summer 07/08, Autumn, and Winter, respectively. Total macrozooplankton biomass, however, increased significantly from summer (0.88 and 0.97 g dry weight 1000 m -3 in Summer 05/06 and Summer 07/08, respectively) to Autumn 04 (2.66 g dry weight 1000 m -3) and Winter 06 levels (1.75 g dry weight 1000 m -3). This biomass increase was due to both an increased occurrence of Euphausia superba and fish and a shift to a larger size structure in the latter group. Siphonophores (predominantly Diphyes antarctica), chaetognaths (predominantly Eukrohnia hamata and Sagitta gazellae) and euphausiids (predominantly Thysanoessa macrura and E. superba) contributed >80% to total densities in all four surveys. However, a strong and distinctive change in assemblage structure was observed between seasons. Key amongst these was a shift within the euphausiids from a dominance of T. macrura in summer to that of E. superba in autumn and winter; a winter decrease in E. hamata; an autumn and winter decrease in Tomopteris sp.; and a winter increase in the abundance of the grazers Clio pyramidata sulcata and Ihlea racovitzai, hyperiids, and the myctophid fish Electrona antarctica. Carnivorous

  19. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds

    PubMed Central

    Shen, Yang; Bryan, Philip N; He, Yanan; Orban, John; Baker, David; Bax, Ad

    2010-01-01

    Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA95) and an α/β-fold protein (GB95), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA95 exhibiting the correct fold, this protein proved particularly challenging despite its small size. Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS-Rosetta structure prediction program and yields adequate convergence, even when input chemical shifts are limited to just amide 1HN and 15N or 1HN and 1Hα values. PMID:19998407

  20. 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. PMID:27090691

  1. Protozoan community structure in a fractal soil environment.

    PubMed

    Finlay, B J; Fenchel, T

    2001-09-01

    Protozoan abundance was quantified, and 365 protozoan species were recorded, in 150 soil samples from an upland grassland in Scotland. Across the entire size range (2-200 pm) protozoan species richness varied by a factor of two, whereas abundance increased by a factor of 20 with decreasing body size. As the soil had fractal structure, the relatively flat species curve can be explained if spatial heterogeneity determines species number--for in a fractal environment, heterogeneity will be the same at all spatial scales. Community structure appeared to approach a temporary steady-state about six days after re-hydration of dried soil. A simple model based on combining the fractal character of increasing habitat area at smaller spatial scales, with the weight-specific energy requirements of protozoa, provided theoretical curves of abundance and biovolume on body size which provide a reasonable fit to real data. We suggest two possibilities--that the apparent competence of the theoretical model is fortuitous and the product of poorly understood dynamic elements of the trophic structure in the community; or that key elements of protozoan community structure in a fractal soil environment may be largely explained in terms of habitat space and energy requirements. PMID:11693659

  2. Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil

    PubMed Central

    Pett-Ridge, J.; Firestone, M. K.

    2005-01-01

    Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), “Bacilli,” “Clostridia,” and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods. PMID

  3. A new method in palaeoecology: fish community structure indicates environmental changes

    NASA Astrophysics Data System (ADS)

    Schmölcke, Ulrich; Ritchie, Kenneth

    2010-12-01

    A new method to reconstruct aquatic palaeoenvironments is presented. It is based on a non-metrical ‘fish environment reconstruction index’ (FERI), calculated for the total fish community recorded at an archaeological site. As an example, a FERI is generated for the Baltic Sea using the ecological requirements of northern European fish species. The present study evaluates the proposed method by using fish bone assemblages from a region (the middle Holocene Baltic Sea coast) with well-studied hydrographic history. The bones originate from consecutive human riparian and coastal settlements of hunter-gatherers. The results obtained for the parameters salinity and sediment structure correlate well with geological knowledge. The new method shows a successive change from freshwater to brackish and finally to nearly marine conditions before, during, and towards the end of the marine transgression that created the present Baltic Sea. Additionally, a shift in the sediment structure from muddy to sandy/rocky conditions is recognisable.

  4. Sewing Empowerment: Examining Multiple Identity Shifts as a Mexican Immigrant Woman Develops Expertise in a Sewing Cooperative Community of Practice

    ERIC Educational Resources Information Center

    Vickers, Caroline H.; Deckert, Sharon K.

    2013-01-01

    This article demonstrates how one woman's identity changed as she was empowered through her participation in a sewing cooperative community of practice. A community of practice framework allows examination of participation in ongoing negotiated interactions in which people construct expert and novice identities as they work together. Identity, as…

  5. Root Metaphors, Paradigm Shifts, and Democratically Shared Values: Community Service-Learning as a Bridge-Building Endeavor

    ERIC Educational Resources Information Center

    Sheffield, Eric C.

    2007-01-01

    This paper claims that community service-learning (CSL) projects in schools and universities, if done well, might very well take us--all of us--to important new places. Under the conception of community service and democratic education more generally, CSL projects in schools and universities can take us to "the" most important place: a…

  6. Phylogenetic structure and host abundance drive disease pressure in communities.

    PubMed

    Parker, Ingrid M; Saunders, Megan; Bontrager, Megan; Weitz, Andrew P; Hendricks, Rebecca; Magarey, Roger; Suiter, Karl; Gilbert, Gregory S

    2015-04-23

    Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a 'rare-species advantage'. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry. PMID:25903634

  7. Faunal shift in southern California's coastal fishes: A new assemblage and trophic structure takes hold

    NASA Astrophysics Data System (ADS)

    Miller, Eric F.; McGowan, John A.

    2013-07-01

    Trends in coastal fish abundance indices were examined using a novel 39-year (1972-2010) time series recorded at southern California coastal power plants. Since 1972, the annual mean abundance index significantly declined (r2 = 0.45, p < 0.001). The mean annual biomass index likewise declined but with a large interruption in 2005-2006 when an influx of large bodied, southern species increased the annual means. Ensemble mean abundance indices for fished and unfished species declined at similar rates. Two faunal shifts were identified, 1983-1984 and 1989-1990. The ensemble mean, annual entrapment rate abundance index during the current period (1990-2010) represents only 22% of that recorded during the first and most abundant period, 1972-1983. The mean biogeographic distribution of the assemblage was non-linear over time including a shift south during the 1980s through the 1990s before shifting north in recent years. The northern shift in recent years accompanied higher variability than previously recorded and was likely related to the overall low abundance. Since the early 1980s, the mean trophic level derived from abundance declined. The observed patterns were not correlated with commonly employed composite indices such as the Pacific Decadal Oscillation, but did show some sensitivity to changes in coastal seawater temperature and density over time. Timing of the observed faunal shifts in the fish assemblage was consistent with reported oceanographic shifts. These data suggested factors beyond fishing, such as oceanographic change, have substantially impacted the coastal fishes of southern California.

  8. Community structure of non-coding RNA interaction network.

    PubMed

    Nacher, Jose C

    2013-01-01

    Rapid technological advances have shown that the ratio of non-protein coding genes rises to 98.5% in humans, suggesting that current knowledge on genetic information processing might be largely incomplete. It implies that protein-coding sequences only represent a small fraction of cellular transcriptional information. Here, we examine the community structure of the network defined by functional interactions between non-coding RNAs (ncRNAs) and proteins related bio-macromolecules (PRMs) using a two-fold approach: modularity in bipartite network and k-clique community detection. First, the high modularity scores as well as the distribution of community sizes showing a scaling-law revealed manifestly non-random features. Second, the k-clique sub-graphs and overlaps show that the identified communities of the ncRNA molecules of H. sapiens can potentially be associated with certain functions. These findings highlight the complex modular structure of ncRNA interactions and its possible regulatory roles in the cell. PMID:23545211

  9. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure.

    PubMed

    Hanemaaijer, Mark; Röling, Wilfred F M; Olivier, Brett G; Khandelwal, Ruchir A; Teusink, Bas; Bruggeman, Frank J

    2015-01-01

    Microbial communities play important roles in health, industrial applications and earth's ecosystems. With current molecular techniques we can characterize these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the genetic properties and the dynamic couplings between individual microorganisms give rise to their dynamic activities. Neither do they give insight into what we call "the community state", that is the fluxes and concentrations of nutrients within the community. This knowledge is a prerequisite for rational control and intervention in microbial communities. Therefore, the inference of the community structure from experimental data is a major current challenge. We will argue that this inference problem requires mathematical models that can integrate heterogeneous experimental data with existing knowledge. We propose that two types of models are needed. Firstly, mathematical models that integrate existing genomic, physiological, and physicochemical information with metagenomics data so as to maximize information content and predictive power. This can be achieved with the use of constraint-based genome-scale stoichiometric modeling of community metabolism which is ideally suited for this purpose. Next, we propose a simpler coarse-grained model, which is tailored to solve the inference problem from the experimental data. This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators. The simpler inference models are, in our opinion, key to understanding microbial ecosystems, yet until now, have received remarkably little attention. This has led to the situation where the modeling of microbial communities, using only genome-scale models is currently more a computational, theoretical exercise than a method useful to the experimentalist. PMID:25852671

  10. Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales

    PubMed Central

    Salani, Faezeh Shah; Arndt, Hartmut; Hausmann, Klaus; Nitsche, Frank; Scheckenbach, Frank

    2012-01-01

    Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000–3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales. PMID:22071346

  11. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects.

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest

  12. 77Se Chemical Shift Tensor of L-selenocystine: Experimental NMR Measurements and Quantum Chemical Investigations of Structural Effects

    PubMed Central

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-01-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine’s specialized biological roles, it is of interest to examine their 77Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state 77Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information of selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on 77Se L-selenocystine’s chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10–20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of −180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. −90°, the energy costs to alter the dihedral angle in the range from −120° to −60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. 77Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272±30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3–9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results

  13. Statistical learning of temporal community structure in the hippocampus

    PubMed Central

    Schapiro, Anna C.; Turk-Browne, Nicholas B.; Norman, Kenneth A.; Botvinick, Matthew M.

    2015-01-01

    The hippocampus is involved in the learning and representation of temporal statistics, but little is understood about the kinds of statistics it can uncover. Prior studies have tested various forms of structure that can be learned by tracking the strength of transition probabilities between adjacent items in a sequence. We test whether the hippocampus can learn higher-order structure using sequences that have no variance in transition probability and instead exhibit temporal community structure. We find that the hippocampus is indeed sensitive to this form of structure, as revealed by its representations, activity dynamics, and connectivity with other regions. These findings suggest that the hippocampus is a sophisticated learner of environmental regularities, able to uncover higher-order structure that requires sensitivity to overlapping associations. PMID:26332666

  14. Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure

    PubMed Central

    Rizvi, Fariha Z.; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J.; Krumholz, Lee R.

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  15. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    PubMed

    Sheik, Cody S; Mitchell, Tyler W; Rizvi, Fariha Z; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J; Krumholz, Lee R

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  16. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Laurie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Gunga, H.; Johnston, S.; Westby, C.; Ribeiro, L.; Ploutz-Snyder, R.; Smith, S.

    2015-01-01

    INTRODUCTION: Mechanisms responsible for the ocular structural and functional changes that characterize the visual impairment and intracranial pressure (ICP) syndrome (VIIP) are unclear, but hypothesized to be secondary to the cephalad fluid shift experienced in spaceflight. This study will relate the fluid distribution and compartmentalization associated with long-duration spaceflight with VIIP symptoms. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, can be predicted preflight with acute hemodynamic manipulations, and also if lower body negative pressure (LBNP) can reverse the VIIP effects. METHODS: Physiologic variables will be examined pre-, in- and post-flight in 10 International Space Station crewmembers including: fluid compartmentalization (D2O and NaBr dilution); interstitial tissue thickness (ultrasound); vascular dimensions and dynamics (ultrasound and MRI (including cerebrospinal fluid pulsatility)); ocular measures (optical coherence tomography, intraocular pressure, ultrasound); and ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight measures will be assessed while upright, supine and during 15 deg head-down tilt (HDT). In-flight measures will occur early and late during 6 or 12 month missions. LBNP will be evaluated as a countermeasure during HDT and during spaceflight. RESULTS: The first two crewmembers are in the preflight testing phase. Preliminary results characterize the acute fluid shifts experienced from upright, to supine and HDT postures (increased stroke volume, jugular dimensions and measures of ICP) which are reversed with 25 millimeters Hg LBNP. DISCUSSION: Initial results indicate that acute cephalad fluid shifts may be related to VIIP symptoms, but also may be reversible by LBNP. The effect of a chronic fluid shift has yet to be evaluated. Learning Objectives: Current spaceflight VIIP research is described

  17. Community structure from spectral properties in complex networks

    NASA Astrophysics Data System (ADS)

    Servedio, V. D. P.; Colaiori, F.; Capocci, A.; Caldarelli, G.

    2005-06-01

    We analyze the spectral properties of complex networks focusing on their relation to the community structure, and develop an algorithm based on correlations among components of different eigenvectors. The algorithm applies to general weighted networks, and, in a suitably modified version, to the case of directed networks. Our method allows to correctly detect communities in sharply partitioned graphs, however it is useful to the analysis of more complex networks, without a well defined cluster structure, as social and information networks. As an example, we test the algorithm on a large scale data-set from a psychological experiment of free word association, where it proves to be successful both in clustering words, and in uncovering mental association patterns.

  18. Diversifying Instruction and Shifting Authority: A Cultural Historical Activity Theory (CHAT) Analysis of Classroom Participant Structures

    ERIC Educational Resources Information Center

    Patchen, Terri; Smithenry, Dennis W.

    2014-01-01

    Recent calls asking science teachers to increase student authority by diversifying instruction appear stalled by a lack of empirical evidence supporting the actual implementation of any such shifts. To better support the practical integration of more student-directed inquiry into the science classroom, we consider one teacher's day-to-day…

  19. A global perspective on marine photosynthetic picoeukaryote community structure

    PubMed Central

    Kirkham, Amy R; Lepère, Cécile; Jardillier, Ludwig E; Not, Fabrice; Bouman, Heather; Mead, Andrew; Scanlan, David J

    2013-01-01

    A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change. PMID:23364354

  20. 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-.

  1. Crude Oil Treatment Leads to Shift of Bacterial Communities in Soils from the Deep Active Layer and Upper Permafrost along the China-Russia Crude Oil Pipeline Route

    PubMed Central

    Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

    2014-01-01

    The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099

  2. Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route.

    PubMed

    Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

    2014-01-01

    The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099

  3. 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'. PMID:25535940

  4. Solution structure of Ln(III) complexes with macrocyclic ligands through theoretical evaluation of 1H NMR contact shifts.

    PubMed

    Rodríguez-Rodríguez, Aurora; Esteban-Gómez, David; de Blas, Andrés; Rodríguez-Blas, Teresa; Botta, Mauro; Tripier, Raphaël; Platas-Iglesias, Carlos

    2012-12-17

    Herein, we present a new approach that combines DFT calculations and the analysis of Tb(III)-induced (1)H NMR shifts to quantitatively and accurately account for the contact contribution to the paramagnetic shift in Ln(III) complexes. Geometry optimizations of different Gd(III) complexes with macrocyclic ligands were carried out using the hybrid meta-GGA TPSSh functional and a 46 + 4f(7) effective core potential (ECP) for Gd. The complexes investigated include [Ln(Me-DODPA)](+) (H(2)Me-DODPA = 6,6'-((4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(methylene))dipicolinic acid, [Ln(DOTA)(H(2)O)](-) (H(4)DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate), [Ln(DOTAM)(H(2)O)](3+) (DOTAM = 1,4,7,10- tetrakis[(carbamoyl)methyl]-1,4,7,10-tetraazacyclododecane), and related systems containing pyridyl units (Ln = Gd, Tb). Subsequent all-electron relativistic calculations based on the DKH2 approximation, or small-core ECP calculations, were used to compute the (1)H hyperfine coupling constants (HFCCs) at the ligand nuclei (A(iso) values). The calculated A(iso) values provided direct access to contact contributions to the (1)H NMR shifts of the corresponding Tb(III) complexes under the assumption that Gd and Tb complexes with a given ligand present similar HFCCs. These contact shifts were used to obtain the pseudocontact shifts, which encode structural information as they depend on the position of the nucleus with respect to the lanthanide ion. An excellent agreement was observed between the experimental and calculated pseudocontact shifts using the DFT-optimized geometries as structural models of the complexes in solution, which demonstrates that the computational approach used provides (i) good structural models for the complexes, (ii) accurate HFCCs at the ligand nuclei. The methodology presented in this work can be classified in the context of model-dependent methods, as it relies on the use of a specific molecular structure obtained from DFT

  5. Impacts of global changes and extreme hydroclimatic events on macroinvertebrate community structures in the French Rhône River.

    PubMed

    Daufresne, Martin; Bady, Pierre; Fruget, Jean-François

    2007-03-01

    We assessed the temporal changes in and the relationships between the structures of the macroinvertebrate communities and the environmental conditions of the French Rhône River (the river from Lake Geneva to the Mediterranean Sea) over the last 20 years (1985-2004). Multisite environmental and biological datasets were analysed using multiple CO-inertia analysis (MCOA) and Procrustean analysis. Changes in environmental conditions were mainly marked by an improvement in water quality between 1985 and 1991 and by an increase in water temperature from 1985 onwards due to climate change. Improvement in water quality seemed to delay changes in community structures under global warming. We then observed trends in community structures coupled with high temperatures and a decrease in oxygen content. Interestingly, we observed both gradual changes and rapid switches in community states. These shifts seemed coupled to extreme hydroclimatic events (i.e. pulse disturbances). Floods and the 2003 heatwave enhanced the development of eurytolerant and invasive taxa which were probably able to take advantage of gradual warming environmental conditions. Despite various site-specific "press" constraints (e.g. hydropower schemes, nuclear power plants), similar changes in community structures were observed along the French Rhône River. Such consistency in temporal processes at large geographical scales underlined the strength of hydroclimatic constraints on community dynamics compared to specific local disturbances. Finally, community structures did not show any sign of recovery, and their relative sensitivities to extreme hydroclimatic events seemed to increase with time. Thus, our results suggest that global changes may reduce the resilience of current community states. PMID:17242905

  6. Diatom community structure on in-service cruise ship hulls.

    PubMed

    Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

    2014-10-01

    Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm. PMID

  7. Oceanographic structure drives the assembly processes of microbial eukaryotic communities

    PubMed Central

    Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

    2015-01-01

    Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance–decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community. PMID:25325383

  8. Oceanographic structure drives the assembly processes of microbial eukaryotic communities.

    PubMed

    Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

    2015-04-01

    Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance-decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community. PMID:25325383

  9. Bacterial community structure in aquifers corresponds to stratigraphy

    NASA Astrophysics Data System (ADS)

    Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

    2014-05-01

    So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

  10. Spatial structure of the meroplankton community along a Patagonian fjord - The role of changing freshwater inputs

    NASA Astrophysics Data System (ADS)

    Meerhoff, Erika; Tapia, Fabián J.; Castro, Leonardo R.

    2014-12-01

    Freshwater inputs are major drivers of circulation, hydrographic structure, and productivity patterns along estuarine systems. We assessed the degree to which meroplankton community structure in the Baker/Martinez fjord complex (Chilean Patagonia, 47.5°S) responds to spatial and temporal changes in hydrographic conditions driven by seasonal changes in Baker river outflow. Zooplankton and hydrographic measurements were conducted along the fjord in early spring (October) and late summer (February), when river outflow was minimal and maximal, respectively. Major meroplankton groups found on these surveys were larval barnacles, crabs, bivalves and gastropods. There was a clear change in community structure between October and February, explained by a switch in the numerically dominant group from barnacle to bivalve larvae. This change in community structure was related to changes in hydrographic structure along the fjord, which are mainly associated with seasonal changes in the Baker river outflow. A variance partition analysis showed no significant spatial trend that could account for the variation in meroplankton along the Martinez channel, whereas temporal variability and environmental variables accounted for 36.6% and 27.6% of the variance, respectively. When comparing meroplankton among the Baker and Martinez channels in October, changes in environmental variables explained 44.9% of total variance, whereas spatial variability accounted for 23.5%. Early and late-stage barnacle larvae (i.e. nauplii and cyprids) were more abundant in water with lower temperature, and higher dissolved oxygen and chlorophyll-a concentration, whereas bivalve larvae were more strongly associated to warmer waters. The seasonal shift in numerical dominance, from barnacle larvae in early spring to bivalve larvae in late summer, suggests that reproduction of these groups is triggered by substantially different sets of conditions, both in terms of hydrography and food availability. The

  11. Different Assembly Processes Drive Shifts in Species and Functional Composition in Experimental Grasslands Varying in Sown Diversity and Community History

    PubMed Central

    Roscher, Christiane; Schumacher, Jens; Gerighausen, Uta; Schmid, Bernhard

    2014-01-01

    Background The prevalence of different biotic processes (limiting similarity, weaker competitor exclusion) and historical contingency due to priority effects are in the focus of ongoing discussions about community assembly and non-random functional trait distributions. Methodology/Principal Findings We experimentally manipulated assembly history in a grassland biodiversity experiment (Jena Experiment) by applying two factorially crossed split-plot treatments to all communities: (i) duration of weeding (never weeded since sowing or cessation of weeding after 3 or 6 years); (ii) seed addition (control vs. seed addition 4 years after sowing). Spontaneous colonization of new species in the control treatment without seed addition increased realized species richness and functional richness (FRic), indicating continuously denser packing of niches. Seed addition resulted in forced colonization and increased realized species richness, FRic, functional evenness (FEve) and functional divergence (FDiv), i.e. higher abundances of species with extreme trait values. Furthermore, the colonization of new species led to a decline in FEve through time, suggesting that weaker competitors were reduced in abundance or excluded. Communities with higher initial species richness or with longer time since cessation of weeding were more restricted in the entry of new species and showed smaller increases in FRic after seed addition than other communities. The two assembly-history treatments caused a divergence of species compositions within communities originally established with the same species. Communities originally established with different species converged in species richness and functional trait composition over time, but remained more distinct in species composition. Conclusions/Significance Contrasting biotic processes (limiting similarity, weaker competitor exclusion) increase functional convergence between communities initially established with different species. Historical

  12. Making the links between community structure and individual well-being: community quality of life in Riverdale, Toronto, Canada.

    PubMed

    Raphael, D; Renwick, R; Brown, I; Steinmetz, B; Sehdev, H; Phillips, S

    2001-09-01

    An inquiry into community quality of life was carried out within a framework that recognizes the complex relationship between community structures and individual well-being. Through use of focus groups and key informant interviews, community members, service providers, and elected representatives in a Toronto community considered aspects of their community that affected quality of life. Community members identified strengths of access to amenities, caring and concerned people, community agencies, low-cost housing, and public transportation. Service providers and elected representatives recognized diversity, community agencies and resources, and presence of culturally relevant food stores and services as strengths. At one level, findings were consistent with emerging concepts of social capital. At another level, threats to the community were considered in relation to the hypothesized role neo-liberalism plays in weakening the welfare state. PMID:11439254

  13. Shifts in root-associated microbial communities of Typha latifolia growing in naphthenic acids and relationship to plant health.

    PubMed

    Phillips, Lori A; Armstrong, Sarah A; Headley, John V; Greer, Charles W; Germida, James J

    2010-01-01

    Naphthenic acids (NAs) are a complex mixture of organic acid compounds released during the extraction of crude oil from oil sands operations. The accumulation of toxic NAs in tailings pond water (TPW) is of significant environmental concern, and phytoremediation using constructed wetlands is one remediation option being assessed. Since root-associated microorganisms are an important factor during phytoremediation of organic compounds, this study investigated the impact of NAs on the microbial communities associated with the macrophyte Typha latifolia (cattail). Denaturing gradient gel electrophoresis revealed that the impact of NAs on microbial communities was niche dependent, with endophytic communities being the most stable and bulk water communities being the least stable. The type of NA used was significant to microbial response, with commercial NAs causing greater adverse changes than TPW NAs. In general, plant beneficial bacteria such as diazotrophs were favoured in cattails grown in TPW NAs, while potentially deleterious bacteria such as denitrifying Dechlorospirillum species increased in commercial NA treatments. These findings suggest that NAs may affect plant health by impacting root-associated microbial communities. A better understanding of these impacts may allow researchers to optimize those microbial communities that support plant health, and thus further optimize wetland treatment systems. PMID:21166345

  14. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  15. 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. PMID:27162185

  16. Spatial analysis of early successional, temperate forest community structure

    NASA Astrophysics Data System (ADS)

    Walker, R. H.; Williams, C. A.; MacLean, R. G.; Epstein, H. E.; Vanderhoof, M. K.

    2013-12-01

    The global importance of sequestration of carbon by temperate forests makes characterizing the regrowth of these forests post-disturbance both ecologically and economically important. High intensity disturbances, such as logging, result in substantial alteration of community composition post-disturbance, creating the potential for alterations to the cycling of carbon, water, and nutrients in the ecosystem. Because logging pressure in New England continues to increase, understanding how forest ecosystems in this region respond to disturbance is crucial. This study aims to characterize interspecies interactions within New England forests by identifying synchronous and asynchronous colocation of species following a disturbanc