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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 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. Recruitment of benthic organisms onto a planned artificial reef: shifts in community structure one decade post-deployment.

    PubMed

    Perkol-Finkel, S; Benayahu, Y

    2005-03-01

    Most artificial reef (AR) studies have examined the early colonization stages of benthic communities, while only a few have monitored the development of AR communities beyond the initial successional phases and evaluated the time scale needed for such development. In addition, despite the proliferation of AR studies, comparative studies between artificial and natural reefs (NRs) are scarce. We present here the monitoring results of initial (1-2 year) and progressed (10 year) stages of the developing benthic communities of a purpose-planned AR submerged at Eilat, Israel (Red Sea), and compare them to its adjacent NR. Visual surveys of macro-invertebrates were conducted on the initial stages and coral communities were characterized at the progressed stage, using belt transects. The results demonstrate a distinct shift in species composition of the AR communities along the monitoring periods: from a soft coral dominated community, comprised mainly of Dendronephthya hemprichi, in initial developmental stages of up to two years post-deployment, to a community dominated by the sponge Crella cyatophora at year 10. Distinct differences in coral species count, living cover and diversity were found between the AR and its neighboring NR. We estimate the time frame required to develop a progressed diverse AR community to be well over a decade, even in tropical ecosystems. The factors shaping the species composition of purpose-designed ARs in a coral reef environment, including structural design, spatial orientation, depth and age, are discussed.

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

    PubMed

    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

  12. 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

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

    PubMed

    Ruhl, Henry A; Smith, Kenneth L

    2004-07-23

    A major change in the community structure of the dominant epibenthic megafauna was observed at 4100 meters depth in the northeast Pacific and was synchronous to a major El Niño/La Niña event that occurred between 1997 and 1999. Photographic abundance estimates of epibenthic megafauna from 1989 to 2002 show that two taxa decreased in abundance after 1998 by 2 to 3 orders of magnitude, whereas several other species increased in abundance by 1 to 2 orders of magnitude. These faunal changes are correlated to climate fluctuations dominated by El Niño/La Niña. Megafauna even in remote marine areas appear to be affected by contemporary climatic fluctuations. Such faunal changes highlight the importance of an adequate temporal perspective in describing biodiversity, ecology, and anthropogenic impacts in deep-sea communities. PMID:15273392

  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.

  15. 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

  16. 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

  17. 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

  18. 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

    2015-03-20

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

    PubMed

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

    2016-01-01

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

  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.

  3. Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters.

    PubMed

    Meng, Long; Liu, Han; Bao, Mutai; Sun, Peiyan

    2016-10-15

    This study tracked structure shifts of bacterial compositions before, during and after invading by crude oil to determine the microbial response and explore how temperature, dispersants and nutrients affect the composition of microbial communities or their activities of biodegradation in artificial marine environment. During petroleum hydrocarbons exposed, the composition and functional dynamics of marine microbial communities were altered, favoring bacteria that could utilize this rich carbon source such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes phyla. Low temperature as a dominant factor decreased bacterial richness and catabolic diversity due to abated enzymes activities in correlation with the process of biodegradation. Dispersants exerted no negative consequences on microbial composition, however, bacterial composition by the Chloroflexi, TM6, OP8, Cyanobacteria and Gemmatimonadetes phyla increased. It seemed that more frequent fertilizer application could be equally safe to bacteria and increased significantly the abundance of bacterial strains but Actinobacteria phyla decreased.

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

    PubMed

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

    2016-01-01

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

  5. 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

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

    PubMed

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

    2014-05-01

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

  7. 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

  8. Regime shifts in exploited marine food webs: detecting mechanisms underlying alternative stable states using size-structured community dynamics theory

    PubMed Central

    Gårdmark, Anna; Casini, Michele; Huss, Magnus; van Leeuwen, Anieke; Hjelm, Joakim; Persson, Lennart; de Roos, André M.

    2015-01-01

    Many marine ecosystems have undergone ‘regime shifts’, i.e. abrupt reorganizations across trophic levels. Establishing whether these constitute shifts between alternative stable states is of key importance for the prospects of ecosystem recovery and for management. We show how mechanisms underlying alternative stable states caused by predator–prey interactions can be revealed in field data, using analyses guided by theory on size-structured community dynamics. This is done by combining data on individual performance (such as growth and fecundity) with information on population size and prey availability. We use Atlantic cod (Gadus morhua) and their prey in the Baltic Sea as an example to discuss and distinguish two types of mechanisms, ‘cultivation-depensation’ and ‘overcompensation’, that can cause alternative stable states preventing the recovery of overexploited piscivorous fish populations. Importantly, the type of mechanism can be inferred already from changes in the predators' body growth in different life stages. Our approach can thus be readily applied to monitored stocks of piscivorous fish species, for which this information often can be assembled. Using this tool can help resolve the causes of catastrophic collapses in marine predatory–prey systems and guide fisheries managers on how to successfully restore collapsed piscivorous fish stocks.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Long-term Hg pollution-induced structural shifts of bacterial community in the terrestrial isopod (Porcellio scaber) gut.

    PubMed

    Lapanje, Ales; Zrimec, Alexis; Drobne, Damjana; Rupnik, Maja

    2010-10-01

    In previous studies we detected lower species richness and lower Hg sensitivity of the bacteria present in egested guts of Porcellio scaber (Crustacea, Isopoda) from chronically Hg polluted than from unpolluted environment. Basis for such results were further investigated by sequencing of 16S rRNA genes of mercury-resistant (Hgr) isolates and clone libraries. We observed up to 385 times higher numbers of Hgr bacteria in guts of animals from polluted than from unpolluted environment. The majority of Hgr strains contained merA genes. Sequencing of 16S rRNA clones from egested guts of animals from Hg-polluted environments showed elevated number of bacteria from Pseudomonas, Listeria and Bacteroidetes relatives groups. In animals from pristine environment number of bacteria from Achromobacter relatives, Alcaligenes, Paracoccus, Ochrobactrum relatives, Rhizobium/Agrobacterium, Bacillus and Microbacterium groups were elevated. Such bacterial community shifts in guts of animals from Hg-polluted environment could significantly contribute to P. scaber Hg tolerance.

  14. [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.

  15. [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

  16. 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.

  17. Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields.

    PubMed

    Scavino, Ana Fernandez; Ji, Yang; Pump, Judith; Klose, Melanie; Claus, Peter; Conrad, Ralf

    2013-09-01

    Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture-rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air-dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture-rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture-rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ(13) C in CH4, CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58-75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T-RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture-rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T-RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture-rice rotation, but nevertheless with a

  18. 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.

  19. 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...

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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…

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. Long-term changes in the fish community structure from the Tsushima warm current region of the Japan/East Sea with an emphasis on the impacts of fishing and climate regime shift over the last four decades

    NASA Astrophysics Data System (ADS)

    Tian, Yongjun; Kidokoro, Hideaki; Watanabe, Tatsuro

    2006-02-01

    climatic regime shifts in the North Pacific. These results strongly suggest that the structure of the fish community in the Japan/East Sea was largely affected by climatic and oceanic regime shifts rather than by fishing. There is no evidence showing “fishing down food webs” in the Japan/East Sea. However, in addition to the impacts of abrupt shifts that occurred in the late 1980s, the large predatory and demersal fishes seem to be facing stronger fishing pressure with the collapse of the Japanese sardine.

  12. 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

  13. 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.

  14. 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

  15. Invertebrate community response to a shifting mosaic of habitat

    USGS Publications Warehouse

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

    2008-01-01

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

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

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

    PubMed

    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.

  2. 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

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

    PubMed

    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

  4. Microbial Community Dynamics and Stability during an Ammonia-Induced Shift to Syntrophic Acetate Oxidation

    PubMed Central

    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.

    2014-01-01

    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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. Migration and Father Absence: Shifting Family Structure in Mexico

    PubMed Central

    2013-01-01

    Despite many changing demographic processes in Mexico—declining adult mortality, rising divorce, and rising nonmarital fertility—Mexican children’s family structure has been most affected by rising migration rates. Data from five national surveys spanning three decades demonstrate that since 1976, migration has shifted from the least common to the most common form of father household absence. Presently, more than 1 in 5 children experience a father’s migration by age 15; 1 in 11 experiences his departure to the United States. The proportions are significantly higher among those children born in rural communities and those born to less-educated mothers. The findings emphasize the importance of framing migration as a family process with implications for children’s living arrangements and attendant well-being, particularly in resource-constrained countries. The stability of children’s family life in these regions constitutes a substantial but poorly measured cost of worldwide increases in migration. PMID:23355282

  11. Migration and father absence: shifting family structure in Mexico.

    PubMed

    Nobles, Jenna

    2013-08-01

    Despite many changing demographic processes in Mexico-declining adult mortality, rising divorce, and rising nonmarital fertility-Mexican children's family structure has been most affected by rising migration rates. Data from five national surveys spanning three decades demonstrate that since 1976, migration has shifted from the least common to the most common form of father household absence. Presently, more than 1 in 5 children experience a father's migration by age 15; 1 in 11 experiences his departure to the United States. The proportions are significantly higher among those children born in rural communities and those born to less-educated mothers. The findings emphasize the importance of framing migration as a family process with implications for children's living arrangements and attendant well-being, particularly in resource-constrained countries. The stability of children's family life in these regions constitutes a substantial but poorly measured cost of worldwide increases in migration. PMID:23355282

  12. 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.

  13. Community structure affects behavior.

    PubMed

    Jaenson, C

    1991-06-01

    AID's prevention efforts can benefit from taking into account 5 main aspects (KEPRA) of community structure identified by anthropologists: 1) kinship patterns, 2) economics, 3) politics, 4) religion, and 5) associations. For example, in Uganda among the Basoga and paternal aunt or senga is responsible for female sex education. Such culturally determined patterns need to be targeted in order to enhance education and effectiveness. Economics can reflect differing systems of family support through sexual means. The example given involves a poor family with a teenager in Thailand who exchanges a water buffalo or basic necessity for this daughter's prostitution. Politics must be considered because every society identifies people who have the power to persuade, influence, exchange resources, coerce, or in some way get people to do what is wanted. Utilizing these resources whether its ministers of health, factory owners, or peers is exemplified in the Monterey, Mexico factor floor supervisor and canteen worker introducing to workers the hows and whys of a new AID's education program. His peer status will command more respect than the director with direct authority. Religious beliefs have explanations for causes of sickness or disease, or provide instruction in sex practices. The example given is of a health workers in Uganda discussing AIDS with rural women by saying that we all know that disease and deaths are caused by spells. "But not AIDS - slim. AIDS is different." Associations can help provide educational, economic, and emotional assistance to the AID's effort or families affected.

  14. 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

  15. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    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.

  16. 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.

  17. 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.

  18. 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

  19. Climate change and eutrophication induced shifts in northern summer plankton communities.

    PubMed

    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

  20. Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth.

    PubMed

    Hargreaves, Sarah K; Williams, Ryan J; Hofmockel, Kirsten S

    2015-01-01

    Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.

  1. 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

  2. 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.

  3. 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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed

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

    2015-01-01

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

  7. 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.

  8. Health consequences of shift work and implications for structural design.

    PubMed

    Figueiro, M G; White, R D

    2013-04-01

    The objective of the study was to perform a literature review on the health consequences of working rotating shifts and implications for structural design. A literature search was performed in June 2012 and a selection of the most relevant peer-review articles was included in the present review. Shift workers are more likely to suffer from a circadian sleep disorder characterized by sleepiness and insomnia. Shift work is associated with decreased productivity, impaired safety, diminished quality of life and adverse effects on health. Circadian disruption resulting from rotating shift work has also been associated with increased risk for metabolic syndrome, diabetes, cardiovascular disease and cancer. This article summarizes the known health effects of shift work and discusses how light can be used as a countermeasure to minimize circadian disruption at night while maintaining alertness. In the context of the lighted environment, implications for the design of newborn intensive care units are also discussed. PMID:23536025

  9. 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…

  10. Convergent structure of multitrophic communities over three continents.

    PubMed

    Segar, Simon T; Pereira, Rodrigo A S; Compton, Steve G; Cook, James M

    2013-12-01

    Ecological theory predicts that communities using the same resources should have similar structure, but evolutionary constraints on colonisation and niche shifts may hamper such convergence. Multitrophic communities of wasps exploiting fig fruits, which first evolved about 75MYA, do not show long-term 'inheritance' of taxonomic (lineage) composition or species diversity. However, communities on three continents have converged ecologically in the presence and relative abundance of five insect guilds that we define. Some taxa fill the same niches in each community (phylogenetic niche conservatism). However, we show that overall convergence in ecological community structure depends also on a combination of niche shifts by resident lineages and local colonisations of figs by other insect lineages. Our study explores new ground, and develops new heuristic tools, in combining ecology and phylogeny to address patterns in the complex multitrophic communities of insect on plants, which comprise a large part of terrestrial biodiversity.

  11. Warming and Resource Availability Shift Food Web Structure and Metabolism

    PubMed Central

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

    2009-01-01

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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. Hyperfine structure and isotope shift study in singly ionized lead

    NASA Astrophysics Data System (ADS)

    Wąsowicz, T. J.; Drozdowski, R.; Kwela, J.

    2005-12-01

    Hyperfine structure and isotope shifts in five optical transitions: 424.5 nm (6s^25f ^2textrm{F}_{7/2} 6s^26d^2 textrm{D}_{5/2}), 537.2 nm (6s^25f ^2textrm{F}_{7/2} 6s6p^2 ^4textrm{P}_{5/2}), 554.5 nm (6s^27d ^2textrm{D}_{5/2} 6s^27p ^2textrm{P}_{3/2}), 560.9 nm (6s^27p^2 textrm{P}_{3/2} 6s^27s ^2textrm{S}_{1/2}) and 666.0 nm (6s^27p ^2textrm{P}_{1/2} 6s^27s ^2textrm{S}_{1/2}) of Pb II have been measured. As a light source the discharge tube was used. The hyperfine structure measurements were performed using metallic isotope 207Pb. For isotope shifts measurements natural lead was used. The high resolution spectral apparatus consisted of a silver coated Fabry-Perot etalon and a grating spectrograph combined with a CCD camera used as a detector. In the analysis of the spectra a computer simulation technique was used. The hyperfine structure observations yielded the splitting constants A for seven levels of Pb II. The isotope shift studies enabled to separate the mass and the field shifts and to determine values of changes of the mean square nuclear charge radii.

  19. 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

  20. Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes.

    PubMed

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

    1997-02-01

    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

  1. Community-based rehabilitation programme as a model for task-shifting.

    PubMed

    Dawad, Suraya; Jobson, Geoff

    2011-01-01

    This article explores some of the implications of a non-governmental organisation (NGO) initiated community-based rehabilitation (CBR) programme, for HIV-related task-shifting programmes which have been recommended by the World Health Organisation (WHO) as an important aspect of HIV prevention, treatment and care programmes. The CBR programme is run by multi-skilled community rehabilitation facilitators (CRFs) in a low income, rural context in KwaZulu-Natal, South Africa, and explicitly recognises the multiple facets of disability. As such, the programme focuses on both the physical and social aspects of living with disabilities. A qualitative approach was used to conduct this study, and semi-structured interviews were conducted with beneficiaries of the programme (n = 35), home and community-based care givers (HCBCs) (n = 13), and managers (n = 2). A focus group discussion was conducted with CRFs (n = 5). We found that the CBR programme successfully delivered rehabilitation services at a community level and that multi-skilled CRFs are an effective means of implementing CBR programmes in low-income rural areas. The developmental focus of the programme created a range of benefits for people with disabilities, including: physical rehabilitation, emotional support and counselling, access to grants, social inclusion and accessing assistive devices. Central to the programme's success was the maintenance of relationships and partnerships at different levels in the community, these included relationships between HCBCs and CRFs, between CRFs and therapists, and between the NGO and the various participants in the programme. However, the NGO struggled to maintain a partnership with the relevant government departments and this had important implications for the programmes sustainability. In conclusion, we argue that this programme's use of multi-skilled mid-level workers who have undergone effective training programmes in CBR demonstrates that a wide range of

  2. Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought?

    PubMed

    Evans, Sarah E; Wallenstein, Matthew D; Burke, Ingrid C

    2014-01-01

    Both biogeographical and rainfall manipulation studies show that soil water content can be a strong driver of microbial community composition. However, we do not yet know if these patterns emerge because certain bacterial taxa are better able to survive at dry soil moisture regimes or if they are due to other drought-sensitive ecosystem properties indirectly affecting microbial community composition. In this study, we evaluated (1) whether bacterial community composition changed under an 11-year drought manipulation and (2) whether shifts under drought could be explained by variation in the moisture sensitivity of growth among bacterial taxa (moisture niche partitioning). Using 454 pyrosequencing of 16S rRNA, we observed shifts in bacterial community composition under drought, coincident with changes in other soil properties. We wet-up dry soils from drought plots to five moisture levels, and measured respiration and the composition of actively growing communities using bromodeoxyuridine (BrdU) labeling of DNA. The field drought experiment affected the composition of the active community when incubated at different moisture levels in the laboratory, as well as short-term (36-hour) respiration rates. Independent of history, bacterial communities also displayed strong niche partitioning across the wet-up moisture gradient. Although this indicates that moisture has the potential to drive bacterial community composition under long-term drought, species distributions predicted by response to moisture did not reflect the community composition of plots that were subjected to long-term drought. Bacterial community structure was likely more strongly driven by other environmental factors that changed under long-term drought, or not shaped by response to water level upon wet-up. The approach that we present here for linking niches to community composition could be adapted for other environmental variables to aid in predicting microbial species distributions and community

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

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

    PubMed

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

    2013-05-01

    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.

  5. Warming alters community size structure and ecosystem functioning.

    PubMed

    Dossena, Matteo; Yvon-Durocher, Gabriel; Grey, Jonathan; Montoya, José M; Perkins, Daniel M; Trimmer, Mark; Woodward, Guy

    2012-08-01

    Global warming can affect all levels of biological complexity, though we currently understand least about its potential impact on communities and ecosystems. At the ecosystem level, warming has the capacity to alter the structure of communities and the rates of key ecosystem processes they mediate. Here we assessed the effects of a 4°C rise in temperature on the size structure and taxonomic composition of benthic communities in aquatic mesocosms, and the rates of detrital decomposition they mediated. Warming had no effect on biodiversity, but altered community size structure in two ways. In spring, warmer systems exhibited steeper size spectra driven by declines in total community biomass and the proportion of large organisms. By contrast, in autumn, warmer systems had shallower size spectra driven by elevated total community biomass and a greater proportion of large organisms. Community-level shifts were mirrored by changes in decomposition rates. Temperature-corrected microbial and macrofaunal decomposition rates reflected the shifts in community structure and were strongly correlated with biomass across mesocosms. Our study demonstrates that the 4°C rise in temperature expected by the end of the century has the potential to alter the structure and functioning of aquatic ecosystems profoundly, as well as the intimate linkages between these levels of ecological organization.

  6. Warming alters community size structure and ecosystem functioning.

    PubMed

    Dossena, Matteo; Yvon-Durocher, Gabriel; Grey, Jonathan; Montoya, José M; Perkins, Daniel M; Trimmer, Mark; Woodward, Guy

    2012-08-01

    Global warming can affect all levels of biological complexity, though we currently understand least about its potential impact on communities and ecosystems. At the ecosystem level, warming has the capacity to alter the structure of communities and the rates of key ecosystem processes they mediate. Here we assessed the effects of a 4°C rise in temperature on the size structure and taxonomic composition of benthic communities in aquatic mesocosms, and the rates of detrital decomposition they mediated. Warming had no effect on biodiversity, but altered community size structure in two ways. In spring, warmer systems exhibited steeper size spectra driven by declines in total community biomass and the proportion of large organisms. By contrast, in autumn, warmer systems had shallower size spectra driven by elevated total community biomass and a greater proportion of large organisms. Community-level shifts were mirrored by changes in decomposition rates. Temperature-corrected microbial and macrofaunal decomposition rates reflected the shifts in community structure and were strongly correlated with biomass across mesocosms. Our study demonstrates that the 4°C rise in temperature expected by the end of the century has the potential to alter the structure and functioning of aquatic ecosystems profoundly, as well as the intimate linkages between these levels of ecological organization. PMID:22496185

  7. 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

  8. 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

  9. 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.

  10. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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 ...

  16. 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

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

    PubMed Central

    Barton, Andrew D.; Finkel, Zoe V.; Stock, Charles A.

    2016-01-01

    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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Temperature oscillation coupled with fungal community shifts can modulate warming effects on litter decomposition.

    PubMed

    Dang, Christian K; Schindler, Markus; Chauvet, Eric; Gessner, Mark O

    2009-01-01

    Diel temperature oscillations are a nearly ubiquitous phenomenon, with amplitudes predicted to change along with mean temperatures under global-warming scenarios. Impact assessments of global warming have largely disregarded diel temperature oscillations, even though key processes in ecosystems, such as decomposition, may be affected. We tested the effect of a 5 degrees C temperature increase with and without diel oscillations on litter decomposition by fungal communities in stream microcosms. Five temperature regimes with identical thermal sums (degree days) were applied: constant 3 degrees and 8 degrees C; diel temperature oscillations of 5 degrees C around each mean; and oscillations of 9 degrees C around 8 degrees C. Temperature oscillations around 8 degrees C (warming scenario), but not 3 degrees C (ambient scenario), accelerated decomposition by 18% (5 degrees C oscillations) and 31% (9 degrees C oscillations), respectively, compared to the constant temperature regime at 8 degrees C. Community structure was not affected by oscillating temperatures, although the rise in mean temperature from 3 degrees to 8 degrees C consistently shifted the relative abundance of species. A simple model using temperature-growth responses of the dominant fungal decomposers accurately described the experimentally observed pattern, indicating that the effect of temperature oscillations on decomposition in our warming scenario was caused by strong curvilinear responses of species to warming at low temperature, particularly of the species becoming most abundant at 8 degrees C (Tetracladium marchalianum). These findings underscore the need to consider species-specific temperature characteristics in concert with changes in communities when assessing consequences of global warming on ecosystem processes.

  4. 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…

  5. Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition.

    PubMed

    Simek, Karel; Nedoma, Jirí; Pernthaler, Jakob; Posch, Thomas; Dolan, John R

    2002-08-01

    Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4-6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (delta BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48-72 h and A BCC showed that delta BCC was positively and tightly correlated (r2 = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. bacterial community composition

  6. 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

  7. 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

  8. 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.

  9. Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China.

    PubMed

    Ma, Bin; Lv, Xiaofei; Warren, Alan; Gong, Jun

    2013-11-01

    The effects of salt stress on endophytic prokaryotic communities in plants are largely unknown, and the distribution patterns of bacterial and archaeal endophytes in different tissues of a plant species are rarely compared. We investigated the endophytic bacterial and archaeal communities in roots, stems and leaves of the common reed, Phragmites australis, collected from three tidal zones along a salinity gradient, using terminal restriction fragment (T-RF) length polymorphism analysis of the 16S rRNA genes. The results showed that the bacterial diversity in the roots was significantly higher than that in the leaves, whereas similar archaeal diversity was revealed for either plant tissues or tidal zones. Network analysis revealed that T-RFs were grouped largely by tissue, and the major groups were generally linked by a few common T-RFs. Unique T-RFs in roots were mainly present in plants growing in the supratidal zone, but unique T-RFs in stems and leaves were mainly present in those from the middle and high tidal zones. Non-metric multidimensional scaling ordination and analysis of similarity revealed that bacterial communities were significantly different among tissues (P < 0.05), but similar among tidal zones (P = 0.49). However, the archaeal communities differed among tidal zones (P < 0.05), but were similar among tissues (P = 0.89). This study indicates that: (1) the endophytic archaeal communities are influenced more significantly than the endophytic bacterial communities by soil salinity, and (2) the differential distribution patterns of bacterial and archaeal endophytes in plant tissues along a salinity gradient imply that these two groups play different roles in coastal hydrophytes.

  10. 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.

  11. 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

  12. Plant species loss decreases arthropod diversity and shifts trophic structure.

    PubMed

    Haddad, Nick M; Crutsinger, Gregory M; Gross, Kevin; Haarstad, John; Knops, Johannes M H; Tilman, David

    2009-10-01

    Plant diversity is predicted to be positively linked to the diversity of herbivores and predators in a foodweb. Yet, the relationship between plant and animal diversity is explained by a variety of competing hypotheses, with mixed empirical results for each hypothesis. We sampled arthropods for over a decade in an experiment that manipulated the number of grassland plant species. We found that herbivore and predator species richness were strongly, positively related to plant species richness, and that these relationships were caused by different mechanisms at herbivore and predator trophic levels. Even more dramatic was the threefold increase, from low- to high-plant species richness, in abundances of predatory and parasitoid arthropods relative to their herbivorous prey. Our results demonstrate that, over the long term, the loss of plant species propagates through food webs, greatly decreasing arthropod species richness, shifting a predator-dominated trophic structure to being herbivore dominated, and likely impacting ecosystem functioning and services.

  13. 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

  14. Community detection in networks: Structural communities versus ground truth

    NASA Astrophysics Data System (ADS)

    Hric, Darko; Darst, Richard K.; Fortunato, Santo

    2014-12-01

    Algorithms to find communities in networks rely just on structural information and search for cohesive subsets of nodes. On the other hand, most scholars implicitly or explicitly assume that structural communities represent groups of nodes with similar (nontopological) properties or functions. This hypothesis could not be verified, so far, because of the lack of network datasets with information on the classification of the nodes. We show that traditional community detection methods fail to find the metadata groups in many large networks. Our results show that there is a marked separation between structural communities and metadata groups, in line with recent findings. That means that either our current modeling of community structure has to be substantially modified, or that metadata groups may not be recoverable from topology alone.

  15. 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

  16. 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

  17. Habitat, topographical, and geographical components structuring shrubsteppe bird communities

    USGS Publications Warehouse

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

    2008-01-01

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

  18. 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

  19. 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

  20. Temperature and nutrients are significant drivers of seasonal shift in phytoplankton community from a drinking water reservoir, subtropical China.

    PubMed

    Lv, Hong; Yang, Jun; Liu, Lemian; Yu, Xiaoqing; Yu, Zheng; Chiang, Penchi

    2014-05-01

    Reservoirs are an important source of water supply in many densely populated areas in southeast China. Phytoplankton plays an important role in maintaining the structure and function of these reservoir ecosystems. Understanding of seasonal succession in phytoplankton communities and its driving factors is essential for effective water quality management in drinking-water reservoirs. In this study, water samples were collected monthly at the surface layers of riverine, transitional, and lacustrine zones from May 2010 to April 2011 in Tingxi Reservoir, southeast China. The phytoplankton showed distinct seasonal shifts in community structure at both taxonomic and functional levels. Cyanophyta was the dominant group in summer, especially species of Raphidiopsis in May and Aphanizomenon in June, and cyanobacterial dominance was promoted by both warmer conditions and excessive nutrients loading. Cyanophyta was gradually replaced by Cryptophyta (e.g., Chroomonas caudata) in abundance and by Bacillariophyta (Fragilaria sp. or Synedra sp. and Melosira sp.) in biomass with decreasing temperature. It appeared that seasonal shifts in phytoplankton composition were closely related to climate, nutrient status, and hydrology in this reservoir. Our partial RDA results clearly showed that water temperature and nutrients (TN and TP) were the most critical factors driving phytoplankton community shift in the abundance and biomass data, respectively. Further, with the global warming, cyanobacterial blooms may increase in distribution, duration, and intensity. In our study, the abundance and biomass of cyanobacteria had significant and positive correlations with temperature and phosphorus. Therefore, a stricter limit on nutrient input should be a priority in watershed management to protect drinking water from the effects of cyanobacterial blooms, especially in high-temperature period.

  1. 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

  2. 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

  3. 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.

  4. Transient Shifts in Bacterial Communities Associated with the Temperate Gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea

    PubMed Central

    La Rivière, Marie; Roumagnac, Marie; Garrabou, Joaquim; Bally, Marc

    2013-01-01

    Background Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. Methodology/Principal Findings The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. Conclusion/Significance This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals. However, a transient

  5. Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient.

    PubMed

    Davey, Marie L; Heegaard, Einar; Halvorsen, Rune; Kauserud, Håvard; Ohlson, Mikael

    2013-01-01

    Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low-alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient (P > 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming.

  6. 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.

  7. 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

  8. 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.

  9. Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay.

    PubMed

    Hong, Yiguo; Xu, Xiongrong; Kan, Jinjun; Chen, Feng

    2014-04-01

    Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. Spatial community shift from hard to soft corals in acidified water

    NASA Astrophysics Data System (ADS)

    Inoue, Shihori; Kayanne, Hajime; Yamamoto, Shoji; Kurihara, Haruko

    2013-07-01

    Anthropogenic increases in the partial pressure of CO2 (pCO2) cause ocean acidification, declining calcium carbonate saturation states, reduced coral reef calcification and changes in the compositions of marine communities. Most projected community changes due to ocean acidification describe transitions from hard coral to non-calcifying macroalgal communities; other organisms have received less attention, despite the biotic diversity of coral reef communities. We show that the spatial distributions of both hard and soft coral communities in volcanically acidified, semi-enclosed waters off Iwotorishima Island, Japan, are related to pCO2 levels. Hard corals are restricted to non-acidified low- pCO2 (225μatm) zones, dense populations of the soft coral Sarcophyton elegans dominate medium- pCO2 (831μatm) zones, and both hard and soft corals are absent from the highest- pCO2 (1,465μatm) zone. In CO2-enriched culture experiments, high- pCO2 conditions benefited Sarcophyton elegans by enhancing photosynthesis rates and did not affect light calcification, but dark decalcification (negative net calcification) increased with increasing pCO2. These results suggest that reef communities may shift from reef-building hard corals to non-reef-building soft corals under pCO2 levels (550-970μatm) predicted by the end of this century, and that higher pCO2 levels would challenge the survival of some reef organisms.

  16. 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

  17. 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.

  18. Efficiently inferring community structure in bipartite networks

    NASA Astrophysics Data System (ADS)

    Larremore, Daniel B.; Clauset, Aaron; Jacobs, Abigail Z.

    2014-07-01

    Bipartite networks are a common type of network data in which there are two types of vertices, and only vertices of different types can be connected. While bipartite networks exhibit community structure like their unipartite counterparts, existing approaches to bipartite community detection have drawbacks, including implicit parameter choices, loss of information through one-mode projections, and lack of interpretability. Here we solve the community detection problem for bipartite networks by formulating a bipartite stochastic block model, which explicitly includes vertex type information and may be trivially extended to k-partite networks. This bipartite stochastic block model yields a projection-free and statistically principled method for community detection that makes clear assumptions and parameter choices and yields interpretable results. We demonstrate this model's ability to efficiently and accurately find community structure in synthetic bipartite networks with known structure and in real-world bipartite networks with unknown structure, and we characterize its performance in practical contexts.

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

    PubMed Central

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

    2016-01-01

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

  20. Rapidly shifting baselines in Yangtze fishing communities and local memory of extinct species.

    PubMed

    Turvey, Samuel T; Barrett, Leigh A; Yujiang, Hao; Lei, Zhang; Xinqiao, Zhang; Xianyan, Wang; Yadong, Huang; Kaiya, Zhou; Hart, Tom; Ding, Wang

    2010-06-01

    Local ecological knowledge can provide a unique source of data for conservation, especially in efforts to investigate the status of rare or possibly extinct species, but it is unlikely to remain constant over time. Loss of perspective about past ecological conditions caused by lack of communication between generations may create "shifting baseline syndrome," in which younger generations are less aware of local species diversity or abundance in the recent past. This phenomenon has been widely discussed, but has rarely been examined quantitatively. We present new evidence of shifting baselines in local perception of regional species declines and on the duration of "community memory" of extinct species on the basis of extensive interviews with fishers in communities across the middle-lower Yangtze basin. Many Yangtze species have experienced major declines in recent decades, and the Yangtze River dolphin or baiji (Lipotes vexillifer) and Yangtze paddlefish (Psephurus gladius) may have become extinct during the 21(st) century. Although informants across all age classes were strongly aware of the Yangtze ecosystem's escalating resource depletion and environmental degradation, older informants were more likely to recognize declines in two commercially important fish species, Reeves' shad (Tenualosa reevesii) and Yangtze pufferfish (Takifugu fasciatus), and to have encountered baiji and paddlefish in the past. Age was also a strong predictor of whether informants had even heard of baiji or paddlefish, with younger informants being substantially less likely to recognize either species. A marked decrease in local knowledge about the Yangtze freshwater megafauna matched the time of major population declines of these species from the 1970s onwards, and paddlefish were already unknown to over 70% of all informants below the age of 40 and to those who first started fishing after 1995. This rapid rate of cultural baseline shift suggests that once even megafaunal species cease to

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

    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

  3. 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

  4. 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

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

    PubMed

    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.

  6. Community structure in the phonological network.

    PubMed

    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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. On the use of pseudocontact shifts in the structure determination of metalloproteins.

    PubMed

    Jensen, Malene Ringkjøbing; Hansen, D Flemming; Ayna, Umit; Dagil, Robert; Hass, Mathias A S; Christensen, Hans E M; Led, Jens J

    2006-03-01

    The utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu(2+) metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and (1)H-(15)N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu(+) plastocyanin and Cd(2+)-substituted plastocyanin as the diamagnetic references, it is found that the Cd(2+)-substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu(2+) plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the (15)N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained (1)H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure.

  2. 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.

  3. 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

  4. Climate change effects on soil microarthropod abundance and community structure

    SciTech Connect

    Kardol, Paul; Reynolds, W. Nicholas; Norby, Richard J; Classen, Aimee T

    2011-01-01

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

  5. 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

  6. 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

  7. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill.

    PubMed

    Bik, Holly M; Halanych, Kenneth M; Sharma, Jyotsna; Thomas, W Kelley

    2012-01-01

    Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.

  8. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    PubMed

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  9. Community structure revealed by phase locking.

    PubMed

    Zhou, Ming-Yang; Zhuo, Zhao; Cai, Shi-min; Fu, Zhongqian

    2014-09-01

    Community structure can naturally emerge in paths to synchronization, and scratching it from the paths is a tough issue that accounts for the diverse dynamics of synchronization. In this paper, with assumption that the synchronization on complex networks is made up of local and collective processes, we proposed a scheme to lock the local synchronization (phase locking) at a stable state, meanwhile, suppress the collective synchronization based on Kuramoto model. Through this scheme, the network dynamics only contains the local synchronization, which suggests that the nodes in the same community synchronize together and these synchronization clusters well reveal the community structure of network. Furthermore, by analyzing the paths to synchronization, the relations or overlaps among different communities are also obtained. Thus, the community detection based on the scheme is performed on five real networks and the observed community structures are much more apparent than modularity-based fast algorithm. Our results not only provide a deep insight to understand the synchronization dynamics on complex network but also enlarge the research scope of community detection.

  10. Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2.

    PubMed

    Drigo, Barbara; Pijl, Agata S; Duyts, Henk; Kielak, Anna M; Gamper, Hannes A; Houtekamer, Marco J; Boschker, Henricus T S; Bodelier, Paul L E; Whiteley, Andrew S; van Veen, Johannes A; Kowalchuk, George A

    2010-06-15

    Rising atmospheric CO(2) levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO(2) modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO(2) conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO(2) clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO(2) concentrations and terrestrial ecosystems. PMID:20534474

  11. Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Wang, Jingwei; Zhang, Zhaojing; Zhang, Xuwang; Zhou, Hao; Zhou, Jiti

    2015-01-01

    The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures. PMID:25909735

  12. Finding local community structure in networks

    NASA Astrophysics Data System (ADS)

    Clauset, Aaron

    2005-08-01

    Although the inference of global community structure in networks has recently become a topic of great interest in the physics community, all such algorithms require that the graph be completely known. Here, we define both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time. This algorithm runs in time O(k2d) for general graphs when d is the mean degree and k is the number of vertices to be explored. For graphs where exploring a new vertex is time consuming, the running time is linear, O(k) . We show that on computer-generated graphs the average behavior of this technique approximates that of algorithms that require global knowledge. As an application, we use this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer.

  13. Structure, Relationships, and Community Responsibility.

    ERIC Educational Resources Information Center

    DiTomaso, Nancy; Parks-Yancy, Rochelle; Post, Corinne

    2003-01-01

    Offers several suggestions about how educators' efforts have gone wrong and makes recommendations about what they need to teach students about ethics and management to prepare students more adequately. Concludes that ethics are about structures, processes, and the relationships that endure, get reproduced, and that generate outcomes that affect…

  14. 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.

  15. 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

  16. 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.

  17. Shifting the Starspot Paradigm through Imaging Magnetic Structures and Evolution

    NASA Astrophysics Data System (ADS)

    Roettenbacher, Rachael M.

    Magnetism is present in stars across all masses and evolutionary states. For cool stars with a convective outer envelope, stellar magnetic fields are generated through complex interactions between the convective layer and radiative core due to rotation. Magnetism in cool stars fuels stellar activity, in particular as starspots. Using starspots as a proxy, this work concentrates on imaging stellar magnetism. With state-of-the-art observations and imaging techniques, I investigate shifting the spot paradigm of localized starspots blemishing an otherwise bright surface (analogous to the solar photosphere) to a surface hosting a widespread network of magnetically-suppressed convection. This network is capable of affecting measurements of fundamental stellar parameters, such as radius and temperature, leading to inaccurate mass and age estimates. To accomplish this shift, I use precision Kepler data and a light-curve inversion algorithm for studies of stellar differential rotation and starspot evolution. Additionally, with long-baseline interferometric data collected with the Michigan Infrared Combiner (MIRC) at Georgia State University's Center for High Angular Resolution Astronomy (CHARA) Array, I target the bright, spotted, giant primary stars of close binary (RS CVn) systems. For these stars, I combine interferometric detections with radial velocity data to measure orbital and stellar parameters, which are used in concert with long-term photometric light curves to observe ellipsoidal variations, measure gravity darkening, and isolate the starspot signatures. In direct imaging using the interferometric data, I observe a spotted RS CVn star through an entire rotation period to detect canonical starspots, a polar starspot, and globally-suppressed convection. The regions of magnetically-suppressed convection cover a large fraction of the surface, potentially impacting estimates of stellar parameters. The combination of these efforts provides a start to a new era of

  18. Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function.

    PubMed

    Nadarajah, Nalina; Allen, D Grant; Fulthorpe, Roberta R

    2007-06-01

    The effect of temperature fluctuations on bacterial community structure and function in lab-scale sequencing batch reactors treating bleached kraft mill effluent was investigated. An increase in temperature from 30 to 45 degrees C caused shifts in both bacterial community structure and function. Triplicate reactors were highly similar for 40 days following startup. After the temperature shift, their community structure and function started to diverge from each other and from the control. A multi-response permutation procedure confirmed that the variability in community structure between transient and control reactors were greater than that among the triplicate transient reactors. The fact that these disturbances manifest themselves in different ways in apparently identical reactors suggests a high degree of variability between replicate systems.

  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.

  20. 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

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

    PubMed Central

    Yu, Lifang; Peng, Dangcong; Pan, Ruiling

    2012-01-01

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

  2. 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.

  3. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    PubMed

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  4. 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

  5. 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.

  6. 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…

  7. 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

  8. 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

  9. 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

  10. 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.

  11. Rural community development in China and the industrial shift of the rural population: summary of an international symposium.

    PubMed

    Shao, X

    1991-01-01

    As a summary of an international symposium on rural community development in China, commentary on China's rural reform, the industrial development of the rural population, and urbanization of the rural population and rural population control is provided. The successful reform that has occurred since the Party's 3rd Plenary session of the 11th Central Committee has been the implementation of the household joint production contract responsibility system. Farmers are enthusiastic about their right to land management. Recent focus on the declines and fluctuations in agricultural output has raised many questions. Suggestions have been made to raise agricultural prices and increase investment. Public ownership should remain with household management. The security of longterm ownership of land by individuals is not available, hence individuals are unwilling to make longterm investment. Another opinion was that the stagnation in production was temporary and a course of development; the cause was population pressure. Suggested future development after reforms should involve development of the village social structure. Communities already have a stable social system of blood ties and an administrative system organized by the party, government, and the economy. Communities with these characteristics could invest in the large-scale farming equipment which smaller households cannot afford, and take responsibility for land allocation and management and financial transactions. The role of the community would be a difficult one in balancing income distribution and expanding community benefits. The 2nd major influence on rural development has been growth in rural nonindustrial production in the small town enterprise. The urban policies of household registration and employment limit growth to rural enterprises which may use backward production technology and produce second-rate products. Eventually, rural industry will become both complementary and supplementary to the national

  12. 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.

  13. Climate Shifts and Plant-Community Transformations Affect Nitrogen Cycling in Semi-Arid Rangelands

    NASA Astrophysics Data System (ADS)

    Huber, D. P.; Hardenbrook, S.; Lohse, K. A.; Germino, M. J.; Reinhardt, K.

    2011-12-01

    Semi-arid rangelands are being impacted by climate shifts and plant-community transformations. However, little is known about how these ecosystems will respond to long-term changes in amount and seasonality of precipitation, or how shifts in vegetation modulate the response of plant-soil processes. Semi-arid rangelands are typically characterized by resource islands (perennial shrubs) and contrasting "interplant" (IP) spaces or patch types which may increase the complexity of ecosystem response to climate change. We used an established long-term ecohydrologic experiment (Est. 1993) located in southeastern Idaho to evaluate ecosystem response to changing precipitation seasonality and magnitude. The experiment consists of 3 replicated blocks of 2 vegetation types (a diverse sagebrush steppe assemblage or monoculture of exotic crested wheatgrass, CWG) and 3 irrigation treatments. We hypothesized that increased precipitation will enhance storage of soil organic matter (SOM) due to greater detrital inputs. Rates of nitrogen (N) mineralization and decomposition were also expected to increase relative to ambient treatments. Additionally, we expected that change from native sagebrush to CWG would reduce N availability due to differences in detrital C:N ratios and biomass partitioning. Preliminary results show increased precipitation enhanced carbon pools in native vegetation plots, with SOM in ambient, fall/spring, and summer precipitation treatments of 2.27, 2.73, and 2.71% respectively, and average plot cover of 29, 48, and 40% respectively. Under shrubs, available N increased with increased precipitation (3.5, 4.6, and 5.6 μg-N g-1 soil) although N-cycling rates remained constant. Conversely, IP patches experienced a steady increase in both net N mineralization and nitrification between ambient, fall/spring, and summer precipitation treatments. The IP patches experienced lower absolute values but similar trends in SOM and available N. Crested wheatgrass plots showed

  14. 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

  15. 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.

  16. 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.

  17. Modularity and community structure in networks

    PubMed Central

    Newman, M. E. J.

    2006-01-01

    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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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,…

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  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. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.

    PubMed

    Fritzsching, K J; Yang, Y; Schmidt-Rohr, K; Hong, Mei

    2013-06-01

    We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D (13)C-(13)C, (15)N-(13)C, or 3D (15)N-(13)C-(13)C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D (13)C-(13)C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-Cα-Cβ or N-Cα-Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  15. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    PubMed

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  16. 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

  17. 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.

  18. Parents' Reasons for Community Language Schools: Insight from a High-Shift, Non-Visible, Middle-Class Community

    ERIC Educational Resources Information Center

    Nordstrom, Janica

    2016-01-01

    In the past decade, there has been increased scholarly interest in the purpose and functions of community language schools, also known as heritage, supplementary or complementary schools. In particular, previous studies have focused on schools operating in minority communities deriving from Asian and Eastern-European countries, showing that…

  19. Zooplankton-mediated changes of bacterial community structure.

    PubMed

    Jürgens, K; Arndt, H; Rothhaupt, K O

    1994-01-01

    Enclosure experiments in the mesotrophic Schöhsee in northern Germany were designed to study the impact of metazooplankton on components of the microbial food web (bacteria, flagellates, ciliates). Zooplankton was manipulated in 500-liter epilimnetic mesocosms so that either Daphnia or copepods were dominating, or metazooplankton was virtually absent. The bacterial community responded immediately to changes in zooplankton composition. Biomass, productivity, and especially the morphology of the bacteria changed drastically in the different treatments. Cascading predation effects on the bacterioplankton were transmitted mainly by phagotrophic protozoans which had changed in species composition and biomass. When Daphnia dominated, protozoans were largely suppressed and the original morphological structure of the bacteria (mainly small rods and cocci) remained throughout the experiment. Dominance of copepods or the absence of metazoan predators resulted in a mass appearance of bacterivorous protists (flagellates and ciliates). They promoted a fast decline of bacterial abundance and a shift to the predominance of morphologically inedible forms, mainly long filaments. After 3 days they formed 80-90% of the bacterial biomass. The results indicate that metazooplankton predation on phagotrophic protozoans is a key mechanism for the regulation of bacterioplankton density and community structure.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. [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

  6. [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

  7. 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…

  8. 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…

  9. Utilizing the charge field effect on amide (15)N chemical shifts for protein structure validation.

    PubMed

    Bader, Reto

    2009-01-01

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide (15)N shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such (15)N chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFT-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that (15)N chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

  10. Opinion Dynamics in Populations with Implicit Community Structure

    NASA Astrophysics Data System (ADS)

    Si, Xiameng; Liu, Yun; Zhang, Zhenjiang

    Web encounter facilitate contacts between people from different communities outside space and time. Implicit Community Structure is exhibited because of highly connected links within community and sparse encounters between communities. Considering the imperceptible influence of encounter on opinions, Sznajd updating rules are used to mimic people's behaviors after encountering a stranger in another community. We introduce a model for opinion evolution, in which the interconnectivity between different communities is represented as encounter frequency, and leadership is introduced to control the strength of community's opinion guide. In this scenario, the effects of Implicit Community Structure of contact network on opinion evolution, for asymmetric and random initial distribution but with heterogeneous opinion guide, are investigated respectively. It is shown that large encounter frequency favors consensus of the whole populations and successful opinion spreading, which is qualitatively agree with the results observed in Majority model defined on substrates with predefined community structure.

  11. 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)

  12. Bipartite Community Structure of eQTLs

    PubMed Central

    Platig, John; DeMeo, Dawn; Quackenbush, John

    2016-01-01

    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

  13. 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.

  14. 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

  15. Dynamics and control of diseases in networks with community structure.

    PubMed

    Salathé, Marcel; Jones, James H

    2010-04-08

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

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

    PubMed

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

    2014-10-01

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

  17. Interference competition and temporal niche shifts: elephants and herbivore communities at waterholes.

    PubMed

    Valeix, Marion; Chamaillé-Jammes, Simon; Fritz, Hervé

    2007-09-01

    Scarcity of resources may result in high levels of animal aggregation; interference competition can occur in such a scenario and play a role in resource acquisition. Here, we test the hypothesis that animals could minimize interference competition by shifting their temporal niches in relation to competitors. In Hwange National Park, Zimbabwe, we monitored waterholes in order to study agonistic interactions between elephants and other herbivore species. We also used a long-term data set from a yearly survey of waterhole attendance by herbivores to evaluate the influence of the presence of elephants on the use of waterholes by other herbivore species. Our results show that in drier years, waterholes are crowded with elephants early in the afternoon. In general, the species most affected by interference competition with elephants shift their temporal niches at the waterholes, thus maintaining a constant temporal overlaps with elephants. The species less affected by interference competition with elephants show no temporal niche shifts and increase their temporal overlap with elephants at waterholes, as predicted from a noncompetition hypothesis. This study provides evidence that interference competition with a behaviorally dominant large species influences the temporal niches of smaller species, and suggests that the potential costs associated with interference between elephants and other herbivores at waterholes are linked to shifts in diurnal activities rather than interactions and water acquisition itself.

  18. A Hierarchical Model for Language Maintenance and Language Shift: Focus on the Malaysian Chinese Community

    ERIC Educational Resources Information Center

    Wang, Xiaomei; Chong, Siew Ling

    2011-01-01

    Social factors involved in language maintenance and language shift (LMLS) have been the focus of LMLS studies. Previous studies provide fundamental support for the theoretical development of this research branch. However, there is no discussion regarding the hierarchical order of these social factors, i.e. the degree of importance of various…

  19. 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.

  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. 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...

  2. 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

  3. 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.

  4. Long-Term Regional Shifts in Plant Community Composition Are Largely Explained by Local Deer Impact Experiments

    PubMed Central

    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

  5. Arbuscular mycorrhizal fungal communities and Rhizophagus irregularis populations shift in response to short-term ploughing and fertilisation in a buffer strip.

    PubMed

    Peyret-Guzzon, M; Stockinger, H; Bouffaud, M-L; Farcy, P; Wipf, D; Redecker, D

    2016-01-01

    Short-term effects of soil physical disturbance by ploughing and nitrogen and phosphate fertilisation on arbuscular mycorrhizal fungal (AMF) communities and on intraspecific populations of Rhizophagus irregularis in a buffer strip surrounded by arable fields were studied. Pre-grown Plantago lanceolata plantlets were transplanted into fertilised and/or ploughed experimental plots. After 3 months, the glomeromycotan communities in the roots of these trap plants were analysed using 454 pyrosequencing of a fragment of the RNA polymerase II gene (RPB1). Intraspecific populations of R. irregularis were studied by restriction fragment length polymorphism (RFLP) analysis of the mitochondrial large ribosomal subunit (mtLSU) gene. Soil disturbance significantly increased the diversity of species-level molecular taxa (MTs) and altered community structure, whilst fertilisation alone had no significant effect, unless coupled with ploughing. At the population level, the expected shift from genotypes of R. irregularis typically found in grasslands to those usually found in arable sites was only partially observed. In conclusion, in the short-term, physical soil disturbance, as well as nitrogen fertilisation when coupled with physical soil disturbance, affected AMF community and to a smaller extent population composition. PMID:26023005

  6. Arbuscular mycorrhizal fungal communities and Rhizophagus irregularis populations shift in response to short-term ploughing and fertilisation in a buffer strip.

    PubMed

    Peyret-Guzzon, M; Stockinger, H; Bouffaud, M-L; Farcy, P; Wipf, D; Redecker, D

    2016-01-01

    Short-term effects of soil physical disturbance by ploughing and nitrogen and phosphate fertilisation on arbuscular mycorrhizal fungal (AMF) communities and on intraspecific populations of Rhizophagus irregularis in a buffer strip surrounded by arable fields were studied. Pre-grown Plantago lanceolata plantlets were transplanted into fertilised and/or ploughed experimental plots. After 3 months, the glomeromycotan communities in the roots of these trap plants were analysed using 454 pyrosequencing of a fragment of the RNA polymerase II gene (RPB1). Intraspecific populations of R. irregularis were studied by restriction fragment length polymorphism (RFLP) analysis of the mitochondrial large ribosomal subunit (mtLSU) gene. Soil disturbance significantly increased the diversity of species-level molecular taxa (MTs) and altered community structure, whilst fertilisation alone had no significant effect, unless coupled with ploughing. At the population level, the expected shift from genotypes of R. irregularis typically found in grasslands to those usually found in arable sites was only partially observed. In conclusion, in the short-term, physical soil disturbance, as well as nitrogen fertilisation when coupled with physical soil disturbance, affected AMF community and to a smaller extent population composition.

  7. 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.

  8. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska.

    PubMed

    Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A G; Tiedje, James M; Zhou, Jizhong

    2015-01-01

    Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.

  9. Hyperfine structure and isotope shifts in 733.2 nm mixed forbidden line of Pb I

    NASA Astrophysics Data System (ADS)

    Wąsowicz, T. J.; Drozdowski, R.; Kwela, J.

    2007-05-01

    Studies of the hyperfine structure and isotope shifts in 733.2 nm mixed (M1+E2) multipole line of Pb I are presented. As a light source the electrodeless discharge tube was used. The high resolution spectral apparatus consisted of a silver coated Fabry-Perot etalon and a grating spectrograph combined with a CCD camera used as a detector. In the analysis of the spectra a computer simulation technique was used. The experiments with the isotope 207Pb yielded the hyperfine structure splitting constant A for the 3P1 and 1D2 levels of the 6s26p2 ground configuration. In the experiment with natural lead the isotope shifts between four stable isotopes (204, 206, 207, 208) were measured.

  10. 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.

  11. 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.

  12. 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

  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. 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.

  15. Electronic structure and nuclear magnetic resonance chemical shift of solids and surfaces

    NASA Astrophysics Data System (ADS)

    Pfrommer, Bernd Georg

    Several different topics related to the electronic structure of solids and surfaces are discussed in this thesis. With the quasi-Newton algorithm for relaxing crystal structures and a new ab initio method to compute nuclear magnetic resonance (NMR) chemical shifts, numerical methods are developed and implemented to efficiently compute properties related to the electronic structure. These techniques are then applied to a range of different materials. The quasi-Newton method is used to study the recently discovered high-pressure R8 phase of silicon, and the fcc-hcp high-pressure structural phase transition of xenon. Using the pressure-induced magnetic phase transition of a model atomic hydrogen crystal as a test system, the accuracy of density functional theory in both the generalized gradient approximation (GGA) and the local spin density approximation (LSDA) is compared to variational quantum Monte Carlo (VQMC) calculations (1). Finally, for the first time, the NMR chemical shift of extended systems such as amorphous carbon and the hydrogenated diamond (111) surface are calculated from first principles. 1. In the first chapter, a model body-centered cubic (bcc) atomic hydrogen solid is studied using density functional theory in LSDA and GGA. 2. How a quasi-Newton method can be used to simultaneously relax the internal coordinates and lattice parameters of crystals under pressure is the subject of the second chapter. 3. Chapter three presents a detailed ab initio study of the electronic and structural properties of the recently discovered R8 phase of silicon. 4. In chapter four, the fcc-hcp high pressure structural phase transition of xenon is calculated. 5. Chapter five describes a theory for the ab initio computation of the NMR chemical shift in extended systems, using periodic boundary conditions. 6. In chapter six, the NMR chemical shift spectra of diamond, CVD diamond, and diamond-like amorphous carbon are computed from first principles. 7. Unexpected features

  16. Community structure detection based on the neighbor node degree information

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  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. Shifts in the microbial community, nitrifiers and denitrifiers in the biofilm in a full-scale rotating biological contactor.

    PubMed

    Peng, Xingxing; Guo, Feng; Ju, Feng; Zhang, Tong

    2014-07-15

    The objective of this study was to investigate the microbial community shifts, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath. The microbial consortia were profiled using multiple approaches, including 454 high-throughput sequencing of the V3-V4 region of 16S rRNA gene, clone libraries, and quantitative polymerase chain reaction (qPCR). The results demonstrated that (1) the overall microbial community at different locations had distinct patterns, that is, there were similar microbial communities at the beginnings of the two RBC trains and completely different populations at the ends of the two RBC trains; (2) nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira), increased in relative abundance in the biofilm along the flowpath, whereas denitrifiers (Rhodanobacter, Paracoccus, Thauera, and Azoarcus) markedly decreased; (3) the AOA were subdominant to the AOB in all sampled sections; and (4) strong ecological associations were shown among different bacteria. Overall, the results of this study provided more comprehensive information regarding the biofilm community composition and assemblies in full-scale RBCs.

  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. 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…

  1. 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…

  2. Growing networks of overlapping communities with internal structure.

    PubMed

    Young, Jean-Gabriel; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J

    2016-08-01

    We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships, and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks. PMID:27627327

  3. Growing networks of overlapping communities with internal structure

    NASA Astrophysics Data System (ADS)

    Young, Jean-Gabriel; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J.

    2016-08-01

    We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships, and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks.

  4. Pinning controllability of complex networks with community structure.

    PubMed

    Miao, Qingying; Tang, Yang; Kurths, Jürgen; Fang, Jian-an; Wong, W K

    2013-09-01

    In this paper, we study the controllability of networks with different numbers of communities and various strengths of community structure. By means of simulations, we show that the degree descending pinning scheme performs best among several considered pinning schemes under a small number of pinned nodes, while the degree ascending pinning scheme is becoming more powerful by increasing the number of pinned nodes. It is found that increasing the number of communities or reducing the strength of community structure is beneficial for the enhancement of the controllability. Moreover, it is revealed that the pinning scheme with evenly distributed pinned nodes among communities outperforms other kinds of considered pinning schemes. PMID:24089950

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. A new dynamic null model for phylogenetic community structure

    PubMed Central

    Pigot, Alex L; Etienne, Rampal S

    2015-01-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion – often attributed to negative biotic interactions – are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure. PMID:25560516

  10. A new dynamic null model for phylogenetic community structure.

    PubMed

    Pigot, Alex L; Etienne, Rampal S

    2015-02-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.

  11. A comprehensive study on algal-bacterial communities shift during thiocyanate degradation in a microalga-mediated process.

    PubMed

    Ryu, Byung-Gon; Kim, Woong; Nam, Kibok; Kim, Sungwhan; Lee, Bongsoo; Park, Min S; Yang, Ji-Won

    2015-09-01

    Changes in algal and bacterial communities during thiocyanate (SCN(-)) decomposition in a microalga-mediated process were studied. Pyrosequencing indicated that Thiobacillus bacteria and Micractinium algae predominated during SCN(-) hydrolysis, even after its complete degradation. Principal components analysis and evenness profiles (based on the Pareto-Lorenz curve) suggested that the changes in the bacterial communities were driven by nitrogen and sulfur oxidation, pH changes, and photoautotrophic conditions. The populations of predominant microalgae remained relatively stable during SCN(-) hydrolysis, but the proportion of bacteria - especially nitrifying bacteria - fluctuated. Thus, the initial microalgal population may be crucial in determining which microorganisms dominate when the preferred nitrogen source becomes limited. The results also demonstrated that microalgae and SCN(-)-hydrolyzing bacteria can coexist, that microalgae can be effectively used with these bacteria to completely treat SCN(-), and that the structure of the algal-bacterial community is more stable than the community of nitrifying bacteria alone during SCN(-) degradation.

  12. A comprehensive study on algal-bacterial communities shift during thiocyanate degradation in a microalga-mediated process.

    PubMed

    Ryu, Byung-Gon; Kim, Woong; Nam, Kibok; Kim, Sungwhan; Lee, Bongsoo; Park, Min S; Yang, Ji-Won

    2015-09-01

    Changes in algal and bacterial communities during thiocyanate (SCN(-)) decomposition in a microalga-mediated process were studied. Pyrosequencing indicated that Thiobacillus bacteria and Micractinium algae predominated during SCN(-) hydrolysis, even after its complete degradation. Principal components analysis and evenness profiles (based on the Pareto-Lorenz curve) suggested that the changes in the bacterial communities were driven by nitrogen and sulfur oxidation, pH changes, and photoautotrophic conditions. The populations of predominant microalgae remained relatively stable during SCN(-) hydrolysis, but the proportion of bacteria - especially nitrifying bacteria - fluctuated. Thus, the initial microalgal population may be crucial in determining which microorganisms dominate when the preferred nitrogen source becomes limited. The results also demonstrated that microalgae and SCN(-)-hydrolyzing bacteria can coexist, that microalgae can be effectively used with these bacteria to completely treat SCN(-), and that the structure of the algal-bacterial community is more stable than the community of nitrifying bacteria alone during SCN(-) degradation. PMID:25911193

  13. 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.

  14. RASP: rapid and robust backbone chemical shift assignments from protein structure.

    PubMed

    MacRaild, Christopher A; Norton, Raymond S

    2014-03-01

    Chemical shift prediction has an unappreciated power to guide backbone resonance assignment in cases where protein structure is known. Here we describe Resonance Assignment by chemical Shift Prediction (RASP), a method that exploits this power to derive protein backbone resonance assignments from chemical shift predictions. Robust assignments can be obtained from a minimal set of only the most sensitive triple-resonance experiments, even for spectroscopically challenging proteins. Over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. Applied to experimental data from a challenging 34 kDa protein, RASP assigns 90 % of manually assigned residues using only 40 % of the experimental data required for the manual assignment. RASP has the potential to significantly accelerate the backbone assignment process for a wide range of proteins for which structural information is available, including those for which conventional assignment strategies are not feasible. PMID:24445369

  15. 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.

  16. 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.

  17. Metagenomics Reveals Planktonic Bacterial Community Shifts across a Natural CO2 Gradient in the Mediterranean Sea

    PubMed Central

    Pathak, Ashish; Rodolfo-Metalpa, Riccardo; Milazzo, Marco; Green, Stefan J.; Hall-Spencer, Jason M.

    2015-01-01

    Bacterial communities at a CO2 vent (pH 6.7) were compared with those at control (pH 8.0) and transition sites (pH 7.6) using 16S rRNA metagenomics. Firmicutes and unclassified bacteria dominated across all sites, Proteobacteria, especially Gammaproteobacteria, declined, and Epsilonproteobacteria increased in the vent with an increase in Bacteroidetes at both the vent and transition sites. PMID:25676760

  18. 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

  19. 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

  20. Effects of a synthetic oil on zooplankton community structure

    SciTech Connect

    Hook, L.A.

    1988-01-01

    This study assessed the effects of a coal-derived oil on the structure of zooplankton communities of laboratory pond microcosms and outdoor experimental ponds. Several measures of community structure and multivariate statistical techniques were used to reveal changes in the patterns of zooplankton community structure caused by the perturbation. From these results the basic ecological mechanisms responsible for maintenance of zooplankton community structure were inferred. The comparison of the field, laboratory microcosm, and laboratory bioassay results for the effects of oil provided an empirical basis for predicting pollutant effects on aquatic ecosystems. The responses of the microcosm and pond zooplankton communities to oil treatment were quite similar. Changes in cladoceran densities were the most sensitive indicators of stress in the zooplankton communities. Copepods were slightly less sensitive, and rotifers were least sensitive to oil treatment.

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

    USGS Publications Warehouse

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

    2003-01-01

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

  2. Shallow water marine sediment bacterial community shifts along a natural CO2 gradient in the Mediterranean Sea off Vulcano, Italy.

    PubMed

    Kerfahi, Dorsaf; Hall-Spencer, Jason M; Tripathi, Binu M; Milazzo, Marco; Lee, Junghoon; Adams, Jonathan M

    2014-05-01

    The effects of increasing atmospheric CO(2) on ocean ecosystems are a major environmental concern, as rapid shoaling of the carbonate saturation horizon is exposing vast areas of marine sediments to corrosive waters worldwide. Natural CO(2) gradients off Vulcano, Italy, have revealed profound ecosystem changes along rocky shore habitats as carbonate saturation levels decrease, but no investigations have yet been made of the sedimentary habitat. Here, we sampled the upper 2 cm of volcanic sand in three zones, ambient (median pCO(2) 419 μatm, minimum Ω(arag) 3.77), moderately CO(2)-enriched (median pCO(2) 592 μatm, minimum Ω(arag) 2.96), and highly CO(2)-enriched (median pCO(2) 1611 μatm, minimum Ω(arag) 0.35). We tested the hypothesis that increasing levels of seawater pCO(2) would cause significant shifts in sediment bacterial community composition, as shown recently in epilithic biofilms at the study site. In this study, 454 pyrosequencing of the V1 to V3 region of the 16S rRNA gene revealed a shift in community composition with increasing pCO(2). The relative abundances of most of the dominant genera were unaffected by the pCO(2) gradient, although there were significant differences for some 5 % of the genera present (viz. Georgenia, Lutibacter, Photobacterium, Acinetobacter, and Paenibacillus), and Shannon Diversity was greatest in sediments subject to long-term acidification (>100 years). Overall, this supports the view that globally increased ocean pCO(2) will be associated with changes in sediment bacterial community composition but that most of these organisms are resilient. However, further work is required to assess whether these results apply to other types of coastal sediments and whether the changes in relative abundance of bacterial taxa that we observed can significantly alter the biogeochemical functions of marine sediments. PMID:24493461

  3. 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

  4. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373

  5. 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…

  6. 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…

  7. 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

  8. 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.

  9. Fragmentation and management of Ethiopian moist evergreen forest drive compositional shifts of insect communities visiting wild Arabica coffee flowers.

    PubMed

    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. PMID:25355631

  10. 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.

  11. 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

  12. 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

  13. Fragmentation and management of Ethiopian moist evergreen forest drive compositional shifts of insect communities visiting wild Arabica coffee flowers.

    PubMed

    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.

  14. 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.

  15. 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

  16. 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

  17. Shifting physical health care responsibilities at a community mental health center.

    PubMed

    Miller, Cindy; Martinez, Ruby

    2003-06-01

    This study assesses the effects of transferring physical health care of consumers from non-nurse case managers to a nurse case manager at a community mental health center. Using a comparative descriptive design, pre- and postintervention surveys were distributed to clinical staff before and after the transfer of responsibilities to determine differences in responses relating to workload and quality of consumer care. Findings suggested that staff had more time to spend on treatment consistent with their education and training, and experienced improved job satisfaction. They reported that consumers' health care improved in terms of quality, efficiency, access, continuity, and follow-up. A chart review revealed that the number of current annual health histories decreased slightly (6%), but annual physical exams increased by 24%. Types of medical appointments were analyzed to note the complexity of health needs of the consumers, with 38% being for routine care and the remaining 62% for chronic, specialty, and acute care. Nurse case managers responsible for overseeing consumers' physical health care would be a valuable addition to community mental health centers. This study suggests improved consumer care and job satisfaction ramifications.

  18. Monitoring bacterial community shifts in bioleaching of Ni-Cu sulfide.

    PubMed

    He, Zhiguo; Zhao, Jiancun; Gao, Fengling; Hu, Yuehua; Qiu, Guanzhou

    2010-11-01

    The microbial ecology of the bioleaching of Ni-Cu sulfide is poorly understood and little effort has been made to handle the microbiological components of these processes. In this study, denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes fragments from bacteria was used to evaluate the changes of the bacterial community in the process of Ni-Cu sulfide bioleaching in a shaken flask system. The results revealed that the bacterial community was disturbed after the addition of Ni-Cu sulfide. Phylogenetic analyses of 16S rRNA fragments revealed that the retrieved sequences clustered together with the genera Acidithiobacillus and Leptospirillum. Multidimensional scaling (MDS) and cluster analysis of DGGE-banding patterns revealed that the process of Ni-Cu sulfide bioleaching in 46days was divided into three stages. During the bioleaching process of Ni-Cu sulfide, Leptospirillum was always dominant. The genera Acidithiobacillus was only detected at early and later stages of the bioleaching process. These results extend our knowledge on microbial dynamics in Ni-Cu sulfide bioleaching, a key issue required to improve commercial applications. PMID:20624605

  19. 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.

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

    PubMed

    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.

  1. 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

  2. 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

  3. 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.

  4. Coastal urbanization leads to remarkable seaweed species loss and community shifts along the SW Atlantic.

    PubMed

    Scherner, Fernando; Horta, Paulo Antunes; de Oliveira, Eurico Cabral; Simonassi, José Carlos; Hall-Spencer, Jason M; Chow, Fungyi; Nunes, José Marcos C; Pereira, Sonia Maria Barreto

    2013-11-15

    Coastal urbanization is rapidly expanding worldwide while its impacts on seaweed communities remain poorly understood. We assessed the impact of urbanization along an extensive latitudinal gradient encompassing three phycogeographical regions in the SW Atlantic. Human population density, number of dwellings, and terrestrial vegetation cover were determined for each survey area and correlated with diversity indices calculated from seaweed percent cover data. Urban areas had significantly lower calcareous algal cover (-38%), and there was significantly less carbonate in the sediment off urban areas than off reference areas. Seaweed richness averaged 26% less in urban areas than in areas with higher vegetation cover. We observed a remarkable decline in Phaeophyceae and a substantial increase of Chlorophyta in urban areas across a wide latitudinal gradient. Our data show that coastal urbanization is causing substantial loss of seaweed biodiversity in the SW Atlantic, and is considerably changing seaweed assemblages.

  5. 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

  6. Magic angle spinning NMR structure determination of proteins from pseudocontact shifts.

    PubMed

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

    2013-06-01

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure.

  7. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests.

    PubMed

    Kembel, Steven W

    2009-09-01

    Patterns of phylogenetic relatedness within communities have been widely used to infer the importance of different ecological and evolutionary processes during community assembly, but little is known about the relative ability of community phylogenetics methods and null models to detect the signature of processes such as dispersal, competition and filtering under different models of trait evolution. Using a metacommunity simulation incorporating quantitative models of trait evolution and community assembly, I assessed the performance of different tests that have been used to measure community phylogenetic structure. All tests were sensitive to the relative phylogenetic signal in species metacommunity abundances and traits; methods that were most sensitive to the effects of niche-based processes on community structure were also more likely to find non-random patterns of community phylogenetic structure under dispersal assembly. When used with a null model that maintained species occurrence frequency in random communities, several metrics could detect niche-based assembly when there was strong phylogenetic signal in species traits, when multiple traits were involved in community assembly, and in the presence of environmental heterogeneity. Interpretations of the causes of community phylogenetic structure should be modified to account for the influence of dispersal.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

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

    PubMed

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

    2014-05-01

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

  15. 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…

  16. 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

  17. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows.

    PubMed

    Cousseau, L; Husemann, M; Foppen, R; Vangestel, C; Lens, L

    2016-10-01

    Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns.

  18. Involvement of medial temporal structures in reflexive attentional shift by gaze

    PubMed Central

    Sato, Wataru; Kubota, Yasutaka; Usui, Keiko; Inoue, Yushi; Murai, Toshiya; Hayashi, Takuji; Toichi, Motomi

    2008-01-01

    Recent studies have revealed that eye gaze triggers reflexive shift of the observer's visuospatial attention to its direction even if it does not predict any events in the environment. To determine whether medial temporal structures are involved in this reflexive gaze processing, an experiment of the gaze-cuing paradigm was carried out in seven epileptic patients who had undergone unilateral temporal lobectomy and nine age- and IQ-matched epileptic controls who had not undergone any surgical treatments. Gaze cues were presented for 200 ms to the unilateral visual field, after which subjects were required to localize targets as quickly as possible. They were also instructed that gaze directions were not predictive of the location of the targets. When the gaze cues stimulated the intact hemisphere in lobectomized patients or either hemisphere in controls, reaction times for correct responses were significantly shorter when gaze directions were toward the targets than away from the targets. This cuing effect was not manifested following stimulation of the lesioned hemisphere in lobectomized patients. These findings suggest that the medial temporal structures, including the amygdala, play a crucial role in the reflexive shift of attention triggered by another person's gaze direction in humans. PMID:19015098

  19. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows.

    PubMed

    Cousseau, L; Husemann, M; Foppen, R; Vangestel, C; Lens, L

    2016-10-01

    Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns. PMID:27273323

  20. 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

  1. 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

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

    PubMed

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

    2012-11-01

    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.

  3. 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.

  4. Virality Prediction and Community Structure in Social Networks

    PubMed Central

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

    2013-01-01

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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts.

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-01

    The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C,Cα,Cβ,N,Hα of Hα chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (AAC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super

  10. Characterization of the structural and functional diversity of indigenous soil microbial communities in smelter-impacted and nonimpacted soils.

    PubMed

    Anderson, Jennifer A H; Hooper, Michael J; Zak, John C; Cox, Stephen B

    2009-03-01

    A century of mining and smelting activity at the Anaconda Smelter site in Anaconda, Montana, USA, has contaminated the surrounding soils and groundwater with metals. Soil microbial communities from six smelter-impacted sites and a nonimpacted site were compared to determine the long-term effects of a gradient of metal concentrations on microbial activity, biomass, functional diversity (Biolog microtiter plates), and structural diversity (denaturant gradient gel electrophoresis of 16S ribosomal DNA). Microbial activity and biomass were decreased in the smelter-impacted soils. Likewise, the functional and structural diversity of the microbial communities native to the smelter-impacted soils were shifted, relative to the microbial community, from the nonimpacted site. These shifts were significantly correlated with soil metal concentration and several soil physicochemical properties (pH, organic matter, NO(3), NH(4), etc.), which provides evidence of the importance of many environmental variables on microbial community dynamics in soils. Preliminary evidence of functional redundancy was observed within microbial communities native to the smelter-impacted sites, based on overlapping carbon substrate utilization patterns. However, due to culture-based selection bias, redundancy pertains only to a subset of the community and may not be ecologically relevant. Nevertheless, the effects of metal contamination on microbial communities in the present study are pronounced and results provide preliminary insight into the complex relationship between soil microbial community structure and function in anthropogenically disturbed soils.

  11. 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.

  12. Disturbance and recovery of microbial community structure and function following Hurricane Frances.

    PubMed

    Yannarell, Anthony C; Steppe, Timothy F; Paerl, Hans W

    2007-03-01

    Disturbance and recovery influence microbial community structure and ecosystem functions in most natural environments. This study from a hypersaline Bahamian lagoon details the response of a benthic cyanobacterial mat to disturbance by Hurricane Frances, a category-4 storm. Clone libraries of cyanobacterial small subunit r-RNA genes and nitrogenase genes revealed significant shifts in cyanobacterial and diazotroph community composition following the hurricane. Post-hurricane clone libraries were dominated by sequences that had been rare in pre-hurricane communities. In spite of this dominance shift, re-colonizing mat communities performed nitrogen fixation and photosynthesis at rates within the normal range of variation measured in the mat at similar salinities. There was a tendency for nitrogen fixation rates from mats re-colonizing sites with hurricane-related sand deposition to be higher than those from mats re-colonizing sites without significant sand deposition. This suggests that the altered communities responded to a carbon : nitrogen imbalance that was particularly pronounced in areas subjected to disturbance by sand burial. The post-hurricane dominance of organisms that had been previously rare suggests that pre-hurricane diversity and functional redundancy contributed to the rapid recovery of ecosystem function in the post-disturbance environment.

  13. 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

  14. Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type

    NASA Astrophysics Data System (ADS)

    Emslie, M. J.; Pratchett, M. S.; Cheal, A. J.; Osborne, K.

    2010-09-01

    The extent to which fish communities are structured by spatial variability in coral reef habitats versus stochastic processes (such as larval supply) is very important in predicting responses to sustained and ongoing habitat degradation. In this study, butterflyfish and benthic communities were surveyed annually over 15 years on 47 reefs (spanning 12° of latitude) of the Great Barrier Reef (GBR). Spatial autocorrelation in the structure of butterflyfish communities versus key differences in reef habitats was investigated to assess the extent to which the structure of these fish communities is influenced by habitat conditions. Benthic communities on each of the 47 reefs were broadly categorised as either: 1. Poritidae/Alcyoniidae, 2. mixed taxa, 3. soft coral or 4. Acropora-dominated habitats. These habitat types most reflected increases in water clarity and wave exposure, moving across the GBR shelf from coastal to outer-shelf environments. In turn, each habitat type also supported very distinct butterflyfish communities. Hard coral feeders were always the dominant butterflyfish species in each community type. However, the numerically dominant species changed according to habitat type, representing spatial replacement of species across the shelf. This study reveals clear and consistent differences in the structure of fish communities among reefs associated with marked differences in habitat structure.

  15. Community structural instability, anomie, imitation and adolescent suicidal behavior.

    PubMed

    Thorlindsson, Thorolfur; Bernburg, Jón Gunnar

    2009-04-01

    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 values (anomie), and contact with suicidal others (suggestion-imitation). The data comes from a national survey of 14-16 years old adolescents. Valid questionnaires were obtained from 7018 students (response rate about 87%). The findings show that the community level of residential mobility has a positive, contextual effect on adolescent suicidal behavior. The findings also indicate that the contextual effect of residential mobility is mediated by both anomie and suggestion-imitation. The findings offer the possibility to identify communities that carry a substantial risk for adolescent suicide as well as the mechanisms that mediate the influence of community structural characteristics on adolescent risk behavior.

  16. Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins.

    PubMed

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

    2016-01-29

    Pseudocontact shifts (PCSs) induced by paramagnetic lanthanides produce pronounced effects in nuclear magnetic resonance spectra, which are easily measured and which deliver valuable long-range structure restraints. Even sparse PCS data greatly enhance the success rate of 3D (3-dimensional) structure predictions of proteins by the modeling program Rosetta. The present work extends this approach to 3D structures of larger proteins, comprising more than 200 residues, which are difficult to model by Rosetta without additional experimental restraints. The new algorithm improves the fragment assembly method of Rosetta by utilizing PCSs generated from paramagnetic lanthanide ions attached at four different sites as the only experimental restraints. The sparse PCS data are utilized at multiple stages, to identify native-like local structures, to rank the best structural models and to rebuild the fragment libraries. The fragment libraries are refined iteratively until convergence. The PCS-driven iterative resampling algorithm is strictly data dependent and shown to generate accurate models for a benchmark set of eight different proteins, ranging from 100 to 220 residues, using solely PCSs of backbone amide protons.

  17. 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

  18. 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

  19. Abrupt shifts in the fish community of the hydrologically variable upper estuary of the Swan River

    NASA Astrophysics Data System (ADS)

    Kanandjembo, A. N.; Potter, I. C.; Platell, M. E.

    2001-09-01

    Fish were sampled in nearshore, shallow waters (<1·5 m deep) and offshore, deeper waters (2·5-5 m) of the saline lower reaches of the Swan and Canning Rivers, which collectively represent the upper Swan-Canning Estuary, by using seine and gill nets, respectively, in each season between winter 1995 and autumn 1997. Seventeen of the 34 fish species caught during the study spawn in the upper estuaries. These species, which include the semi-anadromous Nematalosa vlaminghi, comprised 50·0% of the number of species and 88·8% of the number of fish in shallow waters and 43·8 and 89·9%, respectively, of those in deeper waters. The two most abundant species in shallow waters, Engraulis australis and N. vlaminghi, contributed 36·0 and 19·6%, respectively, to the total numbers of fish in those waters, and the latter species comprised nearly 50% of the catch in deeper waters. During winter, when freshwater discharge increased sharply and salinities declined precipitously, the number of species and abundance of fish in shallow and deeper waters were generally at their lowest and the species composition was the most discrete. This reflected the downstream movement out of the upper estuary of substantial numbers of individuals of species such as N. vlaminghi, Acanthopagrus butcheri, Amniataba caudavittata, Atherinomorus ogilbyi, Atherinosoma elongata and Craterocephalus mugiloides and the upstream movement into the upper estuary of juvenile Mugil cephalus. The overall fish fauna then changed quite abruptly in spring, when large N. vlaminghi, A. butcheri and A. caudavittata became abundant as they migrated into the upper estuary where they then spawned. During summer and autumn, the fauna in the shallows then changed more gradually through, inter alia, the recruitment of juvenile community in winter contrasts with the

  20. 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

  1. 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.

  2. Cascading failures in complex networks with community structure

    NASA Astrophysics Data System (ADS)

    Lin, Guoqiang; di, Zengru; Fan, Ying

    2014-12-01

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

  3. Change in fish community structure in the Barents Sea.

    PubMed

    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.

  4. 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…

  5. 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…

  6. Nanomaterials in Biosolids Inhibit Nodulation, Shift Microbial Community Composition, and Result in Increased Metal Uptake Relative to Bulk/Dissolved Metals.

    PubMed

    Judy, Jonathan D; McNear, David H; Chen, Chun; Lewis, Ricky W; Tsyusko, Olga V; Bertsch, Paul M; Rao, William; Stegemeier, John; Lowry, Gregory V; McGrath, Steve P; Durenkamp, Mark; Unrine, Jason M

    2015-07-21

    We examined the effects of amending soil with biosolids produced from a pilot-scale wastewater treatment plant containing a mixture of metal-based engineered nanomaterials (ENMs) on the growth of Medicago truncatula, its symbiosis with Sinorhizobium meliloti, and on soil microbial community structure. Treatments consisted of soils amended with biosolids generated with (1) Ag, ZnO, and TiO2 ENMs introduced into the influent wastewater (ENM biosolids), (2) AgNO3, Zn(SO4)2, and micron-sized TiO2 (dissolved/bulk metal biosolids) introduced into the influent wastewater stream, or (3) no metal added to influent wastewater (control). Soils were amended with biosolids to simulate 20 years of metal loading, which resulted in nominal metal concentrations of 1450, 100, and 2400 mg kg(-1) of Zn, Ag, and Ti, respectively, in the dissolved/bulk and ENM treatments. Tissue Zn concentrations were significantly higher in the plants grown in the ENM treatment (182 mg kg(-1)) compared to those from the bulk treatment (103 mg kg(-1)). Large reductions in nodulation frequency, plant growth, and significant shifts in soil microbial community composition were found for the ENM treatment compared to the bulk/dissolved metal treatment. These results suggest differences in metal bioavailability and toxicity between ENMs and bulk/dissolved metals at concentrations relevant to regulatory limits.

  7. Phosphate addition and plant species alters microbial community structure in acidic upland grassland soil.

    PubMed

    Rooney, Deirdre C; Clipson, Nicholas J W

    2009-01-01

    Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g(-1) soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g(-1) soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g(-1) soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest

  8. 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

  9. 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.

  10. 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

  11. 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%.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

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

    PubMed

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

    2014-09-14

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

  19. 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.

  20. 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

  1. 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

  2. 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

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

    PubMed Central

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

    2012-01-01

    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

  4. Shifting to structures in physics and biology: a prophylactic for promiscuous realism.

    PubMed

    French, Steven

    2011-06-01

    Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology.

  5. 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

  6. 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

  7. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    PubMed

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  8. Spatial structuring of bacterial communities within individual Ginkgo biloba trees.

    PubMed

    Leff, Jonathan W; Del Tredici, Peter; Friedman, William E; Fierer, Noah

    2015-07-01

    Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. Linking community size structure and ecosystem functioning using metabolic theory

    PubMed Central

    Yvon-Durocher, Gabriel; Allen, Andrew P.

    2012-01-01

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change. PMID:23007088

  16. 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.

  17. 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

  18. Past, Present, and Future Variations in Community College Organizational Structure.

    ERIC Educational Resources Information Center

    Underwood, James C.; Hammons, James O.

    1999-01-01

    Presents the results of a 1991 survey of 118 community college presidents, which elicited details about how their colleges were organized five years prior to and in 1991, as well as their preferred organization structures for the future. Reports variations in structure by three college size categories (enrollment levels) and indicates significant…

  19. Changing Community Structure and Income Distribution: A Structural Equation Model.

    ERIC Educational Resources Information Center

    Wheelock, Gerald C.

    A preliminary model of community economic development processes, consisting of a system of simultaneous equations, is used to describe how these processes influence changes in median family income and income inequality. The analysis was performed on 61 racially mixed counties in Alabama, using 1960-70 census data. Social and demographic variables…

  20. 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.

  1. 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

  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. 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

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

    PubMed

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

    2014-11-15

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

  6. 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

  7. 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

  8. 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

  9. Temporary and permanent wetland macroinvertebrate communities: Phylogenetic structure through time

    NASA Astrophysics Data System (ADS)

    Silver, Carly A.; Vamosi, Steven M.; Bayley, Suzanne E.

    2012-02-01

    Water permanence has been previously identified as an important factor affecting macroinvertebrate diversity and abundance in wetlands. Here, we repeatedly sampled the macroinvertebrate communities in 16 permanent and 14 temporary wetlands in Alberta, Canada. Temporary wetlands were predicted to have more closely related taxa and reduced species richness due to the specialized adaptations required to survive in a temporary habitat. We analyzed the species richness (SR) and phylogenetic structure of communities, focusing on three measures of relatedness: Phylogenetic Distance (PD), Net Related Index (NRI) and Nearest Taxon Index (NTI). We also examined the influence of taxonomic scale on resulting phylogenetic structure. Overall, taxa were more diverse and abundant in permanent wetlands. As expected, PD and SR were greatest in permanent wetlands. NTI and NRI metrics suggest permanent wetland communities are primarily structured by biotic interactions, such as competition and predation. Conversely, temporary wetland communities appear to be affected more by environmental filtering, with fewer groups being able to survive and reproduce in the relatively limited time that these environments contain water. Insect and dipteran assemblages differed from the patterns found when examining all taxa together for communities for both permanent and temporary wetlands, tending to become more phylogenetically clustered as the season progressed. Conversely, lophotrochozoan and gastropod assemblages closely matched the patterns observed for full communities in permanent wetlands, suggesting a role for biotic interactions. Given the contrasting patterns observed for permanent and temporary wetlands, macroinvertebrate diversity at the landscape level may be best conserved by maintaining both habitat types.

  10. 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

  11. 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.

  12. Random field Ising model and community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Son, S.-W.; Jeong, H.; Noh, J. D.

    2006-04-01

    We propose a method to determine the community structure of a complex network. In this method the ground state problem of a ferromagnetic random field Ising model is considered on the network with the magnetic field Bs = +∞, Bt = -∞, and Bi≠s,t=0 for a node pair s and t. The ground state problem is equivalent to the so-called maximum flow problem, which can be solved exactly numerically with the help of a combinatorial optimization algorithm. The community structure is then identified from the ground state Ising spin domains for all pairs of s and t. Our method provides a criterion for the existence of the community structure, and is applicable equally well to unweighted and weighted networks. We demonstrate the performance of the method by applying it to the Barabási-Albert network, Zachary karate club network, the scientific collaboration network, and the stock price correlation network. (Ising, Potts, etc.)

  13. Characterization of bacterial community structure on a weathered pegmatitic granite.

    PubMed

    Gleeson, Deirdre B; Kennedy, Nabla M; Clipson, Nicholas; Melville, Karrie; Gadd, Geoffrey M; McDermott, Frank P

    2006-05-01

    This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.

  14. Characterization of fungal community structure on a weathered pegmatitic granite.

    PubMed

    Gleeson, Deirdre B; Clipson, Nicholas; Melville, Karrie; Gadd, Geoffrey M; McDermott, Frank P

    2005-10-01

    This study exploited the contrasting major element chemistry of adjacent, physically separable crystals of framework and sheet silicates in a pegmatitic granite to investigate the mineralogical influences of fungal community structure on mineral surfaces. Large intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were individually extracted, together with whole-rock granite. Environmental scanning electron microscopy (ESEM) revealed a diversity of fungal structures, with microcolonial fungi and fungal hyphae clearly visible on surfaces of all mineral types. Fungal automated ribosomal intergenic spacer analysis (FARISA) was used to generate a ribotype profile for each mineral sample and a randomization test revealed that ribotype profiles, or community fingerprints, differed between different mineral types. Canonical correspondence analysis (CCA) revealed that mineral chemistry affected individual fungal ribotypes, and strong relationships were found between certain ribotypes and particular chemical elements. This finding was further supported by analysis of variance (ANOVA) of the 16 most abundant ribotypes within the community. Significantly, individual ribotypes were largely restricted to single mineral types and ribotypes clustered strongly on the basis of mineral type. CCA also revealed that Al, Si, and Ca had a significant impact on fungal community structure within this system. These results show that fungal community structure was driven by the chemical composition of mineral substrates, indicating selective pressure by individual chemical elements on fungal populations in situ.

  15. Functional structure of biological communities predicts ecosystem multifunctionality.

    PubMed

    Mouillot, David; Villéger, Sébastien; Scherer-Lorenzen, Michael; Mason, Norman W H

    2011-01-01

    The accelerating rate of change in biodiversity patterns, mediated by ever increasing human pressures and global warming, demands a better understanding of the relationship between the structure of biological communities and ecosystem functioning (BEF). Recent investigations suggest that the functional structure of communities, i.e. the composition and diversity of functional traits, is the main driver of ecological processes. However, the predictive power of BEF research is still low, the integration of all components of functional community structure as predictors is still lacking, and the multifunctionality of ecosystems (i.e. rates of multiple processes) must be considered. Here, using a multiple-processes framework from grassland biodiversity experiments, we show that functional identity of species and functional divergence among species, rather than species diversity per se, together promote the level of ecosystem multifunctionality with a predictive power of 80%. Our results suggest that primary productivity and decomposition rates, two key ecosystem processes upon which the global carbon cycle depends, are primarily sustained by specialist species, i.e. those that hold specialized combinations of traits and perform particular functions. Contrary to studies focusing on single ecosystem functions and considering species richness as the sole measure of biodiversity, we found a linear and non-saturating effect of the functional structure of communities on ecosystem multifunctionality. Thus, sustaining multiple ecological processes would require focusing on trait dominance and on the degree of community specialization, even in species-rich assemblages.

  16. Effects of Pressure-shift Freezing on the Structural and Physical Properties of Gelatin Hydrogel Matrices

    PubMed Central

    Kim, Byeongsoo; Gil, Hyung Bae; Min, Sang-Gi; Lee, Si-Kyung; Choi, Mi-Jung

    2014-01-01

    This study investigates the effects of the gelatin concentration (10-40%, w/v), freezing temperatures (from -20℃ to -50℃) and freezing methods on the structural and physical properties of gelatin matrices. To freeze gelatin, the pressure-shift freezing (PSF) is being applied at 0.1 (under atmospheric control), 50 and 100 MPa, respectively. The freezing point of gelatin solutions decrease with increasing gelatin concentrations, from -0.2℃ (10% gelatin) to -6.7℃ (40% gelatin), while the extent of supercooling did not show any specific trends. The rheological properties of the gelatin indicate that both the storage (G') and loss (G") moduli were steady in the strain amplitude range of 0.1-10%. To characterize gelatin matrices formed by the various freezing methods, the ice crystal sizes which were being determined by the scanning electron microscopy (SEM) are affected by the gelatin concentrations. The ice crystal sizes are affected by gelatin concentrations and freezing temperature, while the size distributions of ice crystals depend on the freezing methods. Smaller ice crystals are being formed with PSF rather than under the atmospheric control where the freezing temperature is above -40℃. Thus, the results of this study indicate that the PSF processing at a very low freezing temperature (-50℃) offers a potential advantage over commercial atmospheric freezing points for the formation of small ice crystals. PMID:26760743

  17. 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

  18. Phytoplankton community structure and dynamics in the river influenced margin of the Northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Chakraborty, S.; Lohrenz, S. E.

    2010-12-01

    Coastal ocean margins especially those which are dominated by large river systems such as the Mississippi River are characterized by high variability in fluxes of both organic and inorganic matter. The current lack of reliable estimates of carbon fluxes in large river systems contributes to uncertainties in global carbon fluxes. Autotrophic (photosynthesis) and heterotrophic (respiration) processes strongly influence carbon fluxes in river-dominated coastal margins and are dependent on the phytoplankton community structure, community composition. Knowledge of the functional specialization of the planktonic community structure is critical in understanding biogeochemical cycling in these ecosystems. As a part of the GulfCarbon program and associated projects funded through NSF, NASA and NOAA, we examined the the composition and biomass of the phytoplankton community in northern Gulf of Mexico coastal waters influenced by the Mississippi River. Taxonomic composition, size indices and biomass of phytoplankton community were determined along several cross-shelf transects. A cross-shelf gradient of in chlorophyll-a was consistently observed in association with low salinity water masses related to freshwater inputs from the Mississippi River and other rivers. Shifts in phytoplankton community spatially were found to be associated with the salinity gradient along the shelf waters. Seasonal differences were also observed and were closely related to the river discharge and nutrient dynamics. Extensive, quality controlled data sets such as these will help to better understand the effects of plankton community on the seawater pCO2 variations and to refine regional carbon fluxes and contributions of coastal waters to the global carbon budget.

  19. 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

  20. 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

  1. 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…

  2. Phylogenetic plant community structure along elevation is lineage specific.

    PubMed

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

    2013-12-01

    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.

  3. 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

  4. 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

  5. Community structural characteristics and the adoption of fluoridation.

    PubMed Central

    Smith, R A

    1981-01-01

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

  6. Methane production and microbial community structure for alkaline pretreated waste activated sludge.

    PubMed

    Sun, Rui; Xing, Defeng; Jia, Jianna; Zhou, Aijuan; Zhang, Lu; Ren, Nanqi

    2014-10-01

    Alkaline pretreatment was studied to analyze the influence on waste activated sludge (WAS) reduction, methane production and microbial community structure during anaerobic digestion. Methane production from alkaline pretreated sludge (A-WAS) (pH = 12) increased from 251.2 mL/Ld to 362.2 mL/Ld with the methane content of 68.7% compared to raw sludge (R-WAS). Sludge reduction had been improved, and volatile suspended solids (VSS) removal rate and protein reduction had increased by ∼ 10% and ∼ 35%, respectively. The bacterial and methanogenic communities were analyzed using 454 pyrosequencing and clone libraries of 16S rRNA gene. Remarkable shifts were observed in microbial community structures after alkaline pretreatment, especially for Archaea. The dominant methanogenic population changed from Methanosaeta for R-WAS to Methanosarcina for A-WAS. In addition to the enhancement of solubilization and hydrolysis of anaerobic digestion of WAS, alkaline pretreatment showed significant impacts on the enrichment and syntrophic interactions between microbial communities.

  7. 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

  8. 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.

  9. 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.

  10. 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…

  11. Geometrical Structure and Interface Dependence of Bias Stress Induced Threshold Voltage Shift in C60-Based OFETs

    PubMed Central

    2014-01-01

    The influence of the nature of interface between organic semiconductor and gate dielectric on bias stress electrical stability of n-type C60-based organic field effect transistors (OFETs) was studied. The bias stress induced threshold voltage (Vth) shift was found to depend critically on the OFET device structure: the direction of Vth shift in top-gate OFETs was opposite to that in bottom-gate OFETs, while the use of the dual-gate OFET structure resulted in just very small variations in Vth. The opposite direction of Vth shift is attributed to the different nature of interfaces between C60 semiconductor and Parylene dielectric in these devices. The Vth shift to more positive voltages upon bias stress in bottom-gate C60-OFET was similar to that observed for other n-type semiconductors and rationalized by electron trapping in the dielectric or at the gate dielectric/C60 interface. The opposite direction of Vth shift in top-gate C60-OFETs is attributed to free radical species created in the course of Parylene deposition on the surface of C60 during device fabrication, which produce plenty of hole traps. It was also realized that the dual-gate OFETs gives stable characteristics, which are immune to bias stress effects. PMID:25142130

  12. Mission and Structure: The Community College in a Global Context.

    ERIC Educational Resources Information Center

    Levin, John S.

    This is an investigation of globalization and its effects upon seven community colleges in Canada and the U.S. As a study of organizational change, the investigation addresses the alteration of processes and structures over the 1990s, brought about in part by globalization and institutional responses to globalization. This report has 11 chapters,…

  13. 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

  14. Perception of Community Dissatisfaction and School Organizational Structures.

    ERIC Educational Resources Information Center

    Leiter, Jeffrey

    1983-01-01

    The effects of school personnel's perceptions of community dissatisfaction are examined on school structures of normative consensus, upward communication, and exchanges of help. The analysis uses questionnaire data from school personnel of 34 schools to compare the explanatory utility of four theoretical perspectives. (Author/PN)

  15. 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...

  16. Reactivity-Structure-Based Rate Estimation Rules for Alkyl Radical H Atom Shift and Alkenyl Radical Cycloaddition Reactions.

    PubMed

    Wang, Kun; Villano, Stephanie M; Dean, Anthony M

    2015-07-16

    Intramolecular H atom shift reactions of alkyl radicals and cycloaddition reactions of alkenyl radicals are two important reaction classes in hydrocarbon combustion and pyrolysis. In this work, we derive high-pressure rate estimation rules that are based on the results of electronic structure calculations at the CBS-QB3 level of theory combined with transition state theory calculations. The rules for the H atom shift reactions of alkyl radicals cover the 1,2- up to the 1,7-H shifts. The rules for the cycloaddition reactions of alkenyl radicals are for both the endo- and exo-cycloaddition and include the formation of three- to seven-member ring products. The results are in good agreement with available experiment measurements and other theoretical studies. Both types of reactions proceed via cyclic transition state structures. The impact of ring size and substituent groups on pre-exponential factors and activation energies are discussed in the context of a Benson-type structure-reactivity relationship. Similar relationships between the pre-exponential factors and the number of internal rotors lost in formation of the transition state are derived for both H-shift and cycloaddition reactions. The activation energies are found to be more complicated. The ring strain contribution to the barrier is much lower for the exo-cycloaddition reactions than it is for the other two investigated reaction systems. The ring strains for the H-shift and endo-cycloaddition are similar to one another and are comparable to that of cycloalkanes for three- to six-member rings, but are significantly lower for the larger rings. The results suggest that the 1,6-H shift and 1,7-endo-cycloaddition reactions might be faster than previous estimates. PMID:25563061

  17. Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters.

    PubMed

    Cabrol, Léa; Urra, Johana; Rosenkranz, Francisca; Kroff, Pablo Araya; Plugge, Caroline M; Lesty, Yves; Chamy, Rolando

    2015-01-01

    The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD.

  18. 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

  19. 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.

  20. 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

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

    PubMed

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

    2011-10-01

    Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. PMID:23761342

  2. Effects of Phenol Feeding Pattern on Microbial Community Structure and Cometabolism of Trichloroethylene

    PubMed Central

    Shih, C.; Davey, M. E.; Zhou, J.; Tiedje, J. M.; Criddle, C. S.

    1996-01-01

    Cometabolism of trichloroethylene (TCE) by phenol-fed enrichments was evaluated in four reactors with distinct phenol feeding patterns. The reactors were inoculated from the same source, operated at the same average dilution rate, and received the same mass of phenol over time. Only the timing of phenol addition differed. Reactor C received phenol continuously; reactor SC5 received phenol semicontinuously--alternating between 5 h of feed and 3 h without feed; reactor SC2 alternated between 2 h of feed and 6 h without feed; and reactor P received a single pulse every 24 h. The structure of the enrichments and their capacity for TCE transformation were analyzed. In long-term operation, reactors C and SC5 were dominated by fungi, had higher levels of predators, were more susceptible to biomass fluctuations, and exhibited reduced capacity for TCE transformation. Reactors P and SC2 were characterized by lower levels of fungi, higher bacterial biomass, higher concentrations of TCE-degrading organisms, and higher rates of TCE transformation. After 200 days of operation, rates of TCE transformation increased 10-fold in reactor P, resulting in TCE transformation rates that were 20 to 100 times higher than the rates of the other reactor communities. The cause of this shift is unknown. Isolates capable of the highest rates of TCE transformation were obtained from reactor P. We conclude that cometabolic activity depends upon microbial community structure and that the community structure can be manipulated by altering the growth substrate feeding pattern. PMID:16535382

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.)