A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing.

PubMed

Oono, Ryoko

2017-01-01

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions 'how and why are communities different?' This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences.

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing

PubMed Central

2017-01-01

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions ‘how and why are communities different?’ This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences. PMID:29253889

Mapping spatial patterns of denitrifiers at large scales (Invited)

NASA Astrophysics Data System (ADS)

Philippot, L.; Ramette, A.; Saby, N.; Bru, D.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

2010-12-01

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

Mapping the distribution of the denitrifier community at large scales (Invited)

NASA Astrophysics Data System (ADS)

Philippot, L.; Bru, D.; Ramette, A.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

2010-12-01

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 740 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle.

PubMed

Ferrari, Renata; Marzinelli, Ezequiel M; Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F; Byrne, Maria; Malcolm, Hamish A; Williams, Stefan B; Steinberg, Peter D

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate 'no-take' and 'general-use' (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5-10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle

PubMed Central

Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F.; Byrne, Maria; Malcolm, Hamish A.; Williams, Stefan B.; Steinberg, Peter D.

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate ‘no-take’ and ‘general-use’ (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5–10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales. PMID:29547656

Ecological impacts of large-scale disposal of mining waste in the deep sea

PubMed Central

Hughes, David J.; Shimmield, Tracy M.; Black, Kenneth D.; Howe, John A.

2015-01-01

Deep-Sea Tailings Placement (DSTP) from terrestrial mines is one of several large-scale industrial activities now taking place in the deep sea. The scale and persistence of its impacts on seabed biota are unknown. We sampled around the Lihir and Misima island mines in Papua New Guinea to measure the impacts of ongoing DSTP and assess the state of benthic infaunal communities after its conclusion. At Lihir, where DSTP has operated continuously since 1996, abundance of sediment infauna was substantially reduced across the sampled depth range (800–2020 m), accompanied by changes in higher-taxon community structure, in comparison with unimpacted reference stations. At Misima, where DSTP took place for 15 years, ending in 2004, effects on community composition persisted 3.5 years after its conclusion. Active tailings deposition has severe impacts on deep-sea infaunal communities and these impacts are detectable at a coarse level of taxonomic resolution. PMID:25939397

Ecological impacts of large-scale disposal of mining waste in the deep sea.

PubMed

Hughes, David J; Shimmield, Tracy M; Black, Kenneth D; Howe, John A

2015-05-05

Deep-Sea Tailings Placement (DSTP) from terrestrial mines is one of several large-scale industrial activities now taking place in the deep sea. The scale and persistence of its impacts on seabed biota are unknown. We sampled around the Lihir and Misima island mines in Papua New Guinea to measure the impacts of ongoing DSTP and assess the state of benthic infaunal communities after its conclusion. At Lihir, where DSTP has operated continuously since 1996, abundance of sediment infauna was substantially reduced across the sampled depth range (800-2020 m), accompanied by changes in higher-taxon community structure, in comparison with unimpacted reference stations. At Misima, where DSTP took place for 15 years, ending in 2004, effects on community composition persisted 3.5 years after its conclusion. Active tailings deposition has severe impacts on deep-sea infaunal communities and these impacts are detectable at a coarse level of taxonomic resolution.

[Impacts of large hydropower station on benthic algal communities].

PubMed

Jia, Xing-Huan; Jiang, Wan-Xiang; Li, Feng-Qing; Tang, Tao; Duan, Shu-Gui; Cai, Qing-Hua

2009-07-01

To investigate the impacts of large hydropower station in Gufu River on benthic algae, monthly samplings were conducted from September 2004 to June 2007 at the site GF04 which was impacted by the hydropower station, with the site GL03 in Gaolan River as reference. During sampling period, no significant differences were observed in the main physicochemical variables between GF04 and GL03, but the hydrodynamics differed significantly. GL03 was basically at a status of slow flow; while GF04, owing to the discharging from the reservoir, was at a riffle status during more than 60% of the sampling period. Such a difference in hydrodynamics induced significant differences in the community similarity of benthic algae and the relative abundance of unattached diatoms, erect diatoms, and stalked diatoms between GF04 and GL03, which could better reflect the impacts of irregular draw-off by large hydropower station on river eco-system.

Estimating the Size of a Large Network and its Communities from a Random Sample

PubMed Central

Chen, Lin; Karbasi, Amin; Crawford, Forrest W.

2017-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = (V, E) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G(W) be the induced subgraph in G of the vertices in W. In addition to G(W), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K, and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios. PMID:28867924

Estimating the Size of a Large Network and its Communities from a Random Sample.

PubMed

Chen, Lin; Karbasi, Amin; Crawford, Forrest W

2016-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = ( V, E ) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G ( W ) be the induced subgraph in G of the vertices in W . In addition to G ( W ), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K , and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios.

Psychometric Properties of the Penn State Worry Questionnaire for Children in a Large Clinical Sample

ERIC Educational Resources Information Center

Pestle, Sarah L.; Chorpita, Bruce F.; Schiffman, Jason

2008-01-01

The Penn State Worry Questionnaire for Children (PSWQ-C; Chorpita, Tracey, Brown, Collica, & Barlow, 1997) is a 14-item self-report measure of worry in children and adolescents. Although the PSWQ-C has demonstrated favorable psychometric properties in small clinical and large community samples, this study represents the first psychometric…

Identifying Etiological Agents Causing Diarrhea in Low Income Ecuadorian Communities

PubMed Central

Vasco, Gabriela; Trueba, Gabriel; Atherton, Richard; Calvopiña, Manuel; Cevallos, William; Andrade, Thamara; Eguiguren, Martha; Eisenberg, Joseph N. S.

2014-01-01

Continued success in decreasing diarrheal disease burden requires targeted interventions. To develop such interventions, it is crucial to understand which pathogens cause diarrhea. Using a case-control design we tested stool samples, collected in both rural and urban Ecuador, for 15 pathogenic microorganisms. Pathogens were present in 51% of case and 27% of control samples from the urban community, and 62% of case and 18% of control samples collected from the rural community. Rotavirus and Shigellae were associated with diarrhea in the urban community; co-infections were more pathogenic than single infection; Campylobacter and Entamoeba histolytica were found in large numbers in cases and controls; and non-typhi Salmonella and enteropathogenic Escherichia coli were not found in any samples. Consistent with the Global Enteric Multicenter Study, focused in south Asia and sub-Saharan Africa, we found that in Ecuador a small group of pathogens accounted for a significant amount of the diarrheal disease burden. PMID:25048373

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. ningkang@qibebt.ac.cn Supplementary data are available at Bioinformatics online.

A novel storage system for cryoEM samples.

PubMed

Scapin, Giovanna; Prosise, Winifred W; Wismer, Michael K; Strickland, Corey

2017-07-01

We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources. Copyright © 2017. Published by Elsevier Inc.

Online personal ads: community and sex, virtually.

PubMed

Gudelunas, David

2005-01-01

This study samples 200 personal advertisements from the online gay and lesbian global Web portal PlanetOut. This data, along with survey responses completed by advertisers included in the sample, are used to frame a discussion on the use of online gay and lesbian spaces and communities. Despite interacting in a global space, data showed that advertisers remained aware of their local identities. Differences between advertisers were most notable between gender and whether they logged on in a small or large town. Advertisers were interested in interacting locally, eager to move from online to offline communication, often-times not overly concerned with maintaining anonymity, and not interested in toying with multiple identities. Users of PlanetOut personals largely did not consider themselves part of a virtual gay and lesbian community even when they recognized the existence of a local geographically-based gay and lesbian community. However, the dynamic nature of online personal advertisements did allow for a new type of interactive advertisement that does differ from previous print forums.

Bacterial community changes in an industrial algae production system.

PubMed

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

PubMed

Ambrosini, Roberto; Musitelli, Federica; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Mayer, Christoph; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Franzetti, Andrea

2017-05-01

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km 2 of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

Short-term variability and long-term change in the composition of the littoral zone fish community in Spirit Lake, Iowa

USGS Publications Warehouse

Pierce, C.L.; Sexton, M.D.; Pelham, M.E.; Larscheid, J.G.

2001-01-01

We assessed short-term variability and long-term change in the composition of the littoral fish community in Spirit Lake, Iowa. Fish were sampled in several locations at night with large beach seines during spring, summer and fall of 1995-1998. Long-term changes were inferred from comparison with a similar study conducted over 70 y earlier in Spirit Lake. We found 26 species in the littoral zone. The number of species per sample ranged from 4 to 18, averaging 11.8. The average number of species per sample was higher at stations with greater vegetation density. A distinct seasonal pattern was evident in the number of species collected per sample in most years, increasing steadily from spring to fall. Patterns of variability within our 1995-1998 study period suggest that: (1) numerous samples are necessary to adequately characterize a littoral fish community, (2) sampling should be done when vegetation and young-of-year densities are highest and (3) sampling during a single year is inadequate to reveal the full community. The number of native species has declined by approximately 25% over the last 70 y. A coincident decline in littoral vegetation and associated habitat changes during the same period are likely causes of the long-term community change.

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

The Community as Classroom: Multiple Perspectives on Student Learning.

ERIC Educational Resources Information Center

Kerrigan, Seanna; Gelmon, Sherrill; Spring, Amy

2003-01-01

Reports on the multiple perspectives of students, community members, and faculty to document the affect of student participation in service-learning courses. The study examined in this article used a large sample size and multiple qualitative and quantitative methods over several years. The results indicate that service learning affects students…

Size matters: The contribution of mega-infauna to the food webs and ecosystem services of an Oregon estuary - 9-30-12

EPA Science Inventory

Large-bodied invertebrates (bivalves, polychaetes, burrowing shrimps) are common to infaunal communities of NE Pacific estuaries, but their contribution to estuarine community structure, function and ecosystem services is poorly understood because they are difficult to sample and...

House dust fungal communities' characterization: a double take on the six by sixty by six (6 × 60 × 6) project

NASA Astrophysics Data System (ADS)

Amaro, Raquel; Coelho, Sónia D.; Pastorinho, M. Ramiro; Taborda-Barata, Luís; Vaz-Patto, Maria A.; Monteiro, Marisa; Nepomuceno, Miguel C. S.; Lanzinha, Joăo C. G.; Teixeira, Joăo P.; Pereira, Cristiana C.; Sousa, Ana C. A.

2016-11-01

Fungi are a group of microbes that are found with particular incidence in the indoor environment. Their direct toxicity or capability of generating toxic compounds has been associated with a large number of adverse health effects, such as infectious diseases and allergies. Given that in modern society people spend a large part of their time indoors; fungal communities' characterization of this environmental compartment assumes paramount importance in the comprehension of health effects. House dust is an easy to obtain, time-integrative matrix, being its use in epidemiological studies on human exposure to environmental contaminants highly recommended. Furthermore, dust can carry a great variety of fungal content that undergoes a large number of processes that modulate and further complexify human exposure. Our study aims to identify and quantify the fungal community on house dust samples collected using two different methodologies (an approach not often seen in the literature): active (vacuum cleaner bags) and passive sampling (dust settled in petri dishes). Sampling was performed as part of the ongoing 6 × 60 × 6 Project in which six houses from Covilhă (Portugal), with building dates representative of six decades, were studied for a period of sixty days.

Comparative Initial and Sustained Engagement in Web-based Training by Behavioral Healthcare Providers in New York State.

PubMed

Talley, Rachel; Chiang, I-Chin; Covell, Nancy H; Dixon, Lisa

2018-06-01

Improved dissemination is critical to implementation of evidence-based practice in community behavioral healthcare settings. Web-based training modalities are a promising strategy for dissemination of evidence-based practice in community behavioral health settings. Initial and sustained engagement of these modalities in large, multidisciplinary community provider samples is not well understood. This study evaluates comparative engagement and user preferences by provider type in a web-based training platform in a large, multidisciplinary community sample of behavioral health staff in New York State. Workforce make-up among platform registrants was compared to the general NYS behavioral health workforce. Training completion by functional job type was compared to characterize user engagement and preferences. Frequently completed modules were classified by credit and requirement incentives. High initial training engagement across professional role was demonstrated, with significant differences in initial and sustained engagement by professional role. The most frequently completed modules across functional job types contained credit or requirement incentives. The analysis demonstrated that high engagement of a web-based training in a multidisciplinary provider audience can be achieved without tailoring content to specific professional roles. Overlap between frequently completed modules and incentives suggests a role for incentives in promoting engagement of web-based training. These findings further the understanding of strategies to promote large-scale dissemination of evidence-based practice in community behavioral health settings.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

PubMed

Tapio, Ilma; Shingfield, Kevin J; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J; Wallace, R John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

PubMed Central

Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint. PMID:26986467

Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses.

PubMed

Fuka, Mirna Mrkonjić; Wallisch, Stefanie; Engel, Marion; Welzl, Gerhard; Havranek, Jasmina; Schloter, Michael

2013-01-01

Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening.

Dynamics of Bacterial Communities during the Ripening Process of Different Croatian Cheese Types Derived from Raw Ewe's Milk Cheeses

PubMed Central

Fuka, Mirna Mrkonjić; Wallisch, Stefanie; Engel, Marion; Welzl, Gerhard; Havranek, Jasmina; Schloter, Michael

2013-01-01

Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening. PMID:24278315

Psychopathic Traits in a Large Community Sample: Links to Violence, Alcohol Use, and Intelligence

ERIC Educational Resources Information Center

Neumann, Craig S.; Hare, Robert D.

2008-01-01

Numerous studies conducted with offender or forensic psychiatric samples have revealed that individuals with psychopathic traits are at risk for violence and other externalizing psychopathology. These traits appear to be continuously distributed in these samples, leading investigators to speculate on the presence of such traits in the general…

High-resolution phylogenetic microbial community profiling

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

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance ourmore » knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.« less

Lot quality assurance sampling for screening communities hyperendemic for Schistosoma mansoni.

PubMed

Rabarijaona, L P; Boisier, P; Ravaoalimalala, V E; Jeanne, I; Roux, J F; Jutand, M A; Salamon, R

2003-04-01

Lot quality assurance sampling (LQAS) was evaluated for rapid low cost identification of communities where Schistosoma mansoni infection was hyperendemic in southern Madagascar. In the study area, S. mansoni infection shows very focused and heterogeneous distribution requiring multifariousness of local surveys. One sampling plan was tested in the field with schoolchildren and several others were simulated in the laboratory. Randomization and stool specimen collection were performed by voluntary teachers under direct supervision of the study staff and no significant problem occurred. As expected from Receiver Operating Characteristic (ROC) curves, all sampling plans allowed correct identification of hyperendemic communities and of most of the hypoendemic ones. Frequent misclassifications occurred for communities with intermediate prevalence and the cheapest plans had very low specificity. The study confirmed that LQAS would be a valuable tool for large scale screening in a country with scarce financial and staff resources. Involving teachers, appeared to be quite feasible and should not lower the reliability of surveys. We recommend that the national schistosomiasis control programme systematically uses LQAS for identification of communities, provided that sample sizes are adapted to the specific epidemiological patterns of S. mansoni infection in the main regions.

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

PubMed Central

Edel-Hermann, Véronique; Gautheron, Nadine; Durling, Mikael Brandström; Kolseth, Anna-Karin; Steinberg, Christian; Persson, Paula; Friberg, Hanna

2015-01-01

Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology. PMID:26519387

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

USGS Publications Warehouse

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

2005-01-01

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

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales.

PubMed

Bautista-de Los Santos, Quyen Melina; Schroeder, Joanna L; Blakemore, Oliver; Moses, Jonathan; Haffey, Mark; Sloan, William; Pinto, Ameet J

2016-03-01

High-throughput and deep DNA sequencing, particularly amplicon sequencing, is being increasingly utilized to reveal spatial and temporal dynamics of bacterial communities in drinking water systems. Whilst the sampling and methodological biases associated with PCR and sequencing have been studied in other environments, they have not been quantified for drinking water. These biases are likely to have the greatest effect on the ability to characterize subtle spatio-temporal patterns influenced by process/environmental conditions. In such cases, intra-sample variability may swamp any underlying small, systematic variation. To evaluate this, we undertook a study with replication at multiple levels including sampling sites, sample collection, PCR amplification, and high throughput sequencing of 16S rRNA amplicons. The variability inherent to the PCR amplification and sequencing steps is significant enough to mask differences between bacterial communities from replicate samples. This was largely driven by greater variability in detection of rare bacteria (relative abundance <0.01%) across PCR/sequencing replicates as compared to replicate samples. Despite this, we captured significant changes in bacterial community over diurnal time-scales and find that the extent and pattern of diurnal changes is specific to each sampling location. Further, we find diurnal changes in bacterial community arise due to differences in the presence/absence of the low abundance bacteria and changes in the relative abundance of dominant bacteria. Finally, we show that bacterial community composition is significantly different across sampling sites for time-periods during which there are typically rapid changes in water use. This suggests hydraulic changes (driven by changes in water demand) contribute to shaping the bacterial community in bulk drinking water over diurnal time-scales. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacteria as Emerging Indicators of Soil Condition

PubMed Central

Hermans, Syrie M.; Buckley, Hannah L.; Case, Bradley S.; Curran-Cournane, Fiona; Taylor, Matthew

2016-01-01

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future. PMID:27793827

Bacteria as Emerging Indicators of Soil Condition.

PubMed

Hermans, Syrie M; Buckley, Hannah L; Case, Bradley S; Curran-Cournane, Fiona; Taylor, Matthew; Lear, Gavin

2017-01-01

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future. Copyright © 2016 American Society for Microbiology.

College Student Migration.

ERIC Educational Resources Information Center

Fenske, R. H.; And Others

This study examines the background characteristics of two large national samples of first-time enrolled freshmen who (a) attended college within their state of residence but away from their home community, (b) migrated to a college in an adjacent state, (c) migrated to a college in a distant state, and (d) attended college in their home community.…

Dullgren extraction of soil mites (Acarina): Effect of refrigeration time on extraction efficiency

Treesearch

Michelle B. Lakly; D.A. Crossley

2000-01-01

Soil microarthropods constitute one of the most species rich communities in . forest ecosystems (Crossley & Blair, 1991). The effects of soil fauna in these systems on decomposition rates, nutrient regeneration and soil structure have been well documented; however, dependable estimates of population size and community structure largely depend upon adequate sampling...

Learning Communities: Foundations for First-Year Students' Development of Pluralistic Outcomes

ERIC Educational Resources Information Center

Soria, Krista M.; Mitchell, Tania D.

2015-01-01

The purpose of this study was to investigate the associations between first-year undergraduates' (n = 1,701) participation in learning communities and their development of leadership and multicultural competence. The sample included first-year students who were enrolled at six large, public research universities in 2012 and completed the Student…

Anxiety and depressive symptoms related to parenthood in a large Norwegian community sample: the HUNT2 study.

PubMed

Rimehaug, Tormod; Wallander, Jan

2010-07-01

The study compared anxiety and depression prevalence between parents and non-parents in a society with family- and parenthood-friendly social politics, controlling for family status and family history, age, gender, education and social class. All participants aged 30-49 (N = 24,040) in the large, non-sampled Norwegian HUNT2 community health study completed the Hospital Anxiety and Depression Scales. The slightly elevated anxiety and depression among non-parents compared to parents in the complete sample was not confirmed as statistically significant within any subgroups. Married parents and (previously unmarried) cohabiting parents did not differ in portraying low anxiety and depression prevalence. Anxiety was associated with single parenthood, living alone or being divorced, while elevated depression was found only among those living alone. Burdening selection and cultural/political context are suggested as interpretative perspectives on the contextual and personal influences on the complex relationship between parenthood and mental health.

The Relationship between Large Cavum Septum Pellucidum and Antisocial Behavior, Callous-Unemotional Traits and Psychopathy in Adolescents

ERIC Educational Resources Information Center

White, Stuart F.; Brislin, Sarah; Sinclair, Stephen; Fowler, Katherine A.; Pope, Kayla; Blair, R. James R.

2013-01-01

Background: The presence of a large cavum septum pellucidum (CSP) has been previously associated with antisocial behavior/psychopathic traits in an adult community sample. Aims: The current study investigated the relationship between a large CSP and symptom severity in disruptive behavior disorders (DBD; conduct disorder and oppositional defiant…

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

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

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

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

PubMed

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

2017-01-01

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

Spatial Variation in Particulate Matter Components over a Large Urban Area

PubMed Central

Fruin, Scott; Urman, Robert; Lurmann, Fred; McConnell, Rob; Gauderman, James; Rappaport, Ed; Franklin, Meredith; Gilliland, Frank D.; Shafer, Martin; Gorski, Patrick; Avol, Ed

2014-01-01

To characterize exposures to particulate matter (PM) and its components, we performed a large sampling study of small-scale spatial variation in size-resolved particle mass and composition. PM was collected in size ranges of < 0.2, 0.2-to-2.5, and 2.5-to-10 μm on a scale of 100s to 1000s of meters to capture local sources. Within each of eight Southern California communities, up to 29 locations were sampled for rotating, month-long integrated periods at two different times of the year, six months apart, from Nov 2008 through Dec 2009. Additional sampling was conducted at each community’s regional monitoring station to provide temporal coverage over the sampling campaign duration. Residential sampling locations were selected based on a novel design stratified by high- and low-predicted traffic emissions and locations over- and under-predicted from previous dispersion model and sampling comparisons. Primary vehicle emissions constituents, such as elemental carbon (EC), showed much stronger patterns of association with traffic than pollutants with significant secondary formation, such as PM2.5 or water soluble organic carbon. Associations were also stronger during cooler times of the year (Oct through Mar). Primary pollutants also showed greater within-community spatial variation compared to pollutants with secondary formation contributions. For example, the average cool-season community mean and standard deviation (SD) for EC were 1.1 and 0.17 μg/m3, respectively, giving a coefficient of variation (CV) of 18%. For PM2.5, average mean and SD were 14 and 1.3 μg/m3, respectively, with a CV of 9%. We conclude that within-community spatial differences are important for accurate exposure assessment of traffic-related pollutants. PMID:24578605

Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes.

PubMed

Potgieter, Sarah; Pinto, Ameet; Sigudu, Makhosazana; du Preez, Hein; Ncube, Esper; Venter, Stephanus

2018-08-01

Long-term spatial-temporal investigations of microbial dynamics in full-scale drinking water distribution systems are scarce. These investigations can reveal the process, infrastructure, and environmental factors that influence the microbial community, offering opportunities to re-think microbial management in drinking water systems. Often, these insights are missed or are unreliable in short-term studies, which are impacted by stochastic variabilities inherent to large full-scale systems. In this two-year study, we investigated the spatial and temporal dynamics of the microbial community in a large, full scale South African drinking water distribution system that uses three successive disinfection strategies (i.e. chlorination, chloramination and hypochlorination). Monthly bulk water samples were collected from the outlet of the treatment plant and from 17 points in the distribution system spanning nearly 150 km and the bacterial community composition was characterised by Illumina MiSeq sequencing of the V4 hypervariable region of the 16S rRNA gene. Like previous studies, Alpha- and Betaproteobacteria dominated the drinking water bacterial communities, with an increase in Betaproteobacteria post-chloramination. In contrast with previous reports, the observed richness, diversity, and evenness of the bacterial communities were higher in the winter months as opposed to the summer months in this study. In addition to temperature effects, the seasonal variations were also likely to be influenced by changes in average water age in the distribution system and corresponding changes in disinfectant residual concentrations. Spatial dynamics of the bacterial communities indicated distance decay, with bacterial communities becoming increasingly dissimilar with increasing distance between sampling locations. These spatial effects dampened the temporal changes in the bulk water community and were the dominant factor when considering the entire distribution system. However, temporal variations were consistently stronger as compared to spatial changes at individual sampling locations and demonstrated seasonality. This study emphasises the need for long-term studies to comprehensively understand the temporal patterns that would otherwise be missed in short-term investigations. Furthermore, systematic long-term investigations are particularly critical towards determining the impact of changes in source water quality, environmental conditions, and process operations on the changes in microbial community composition in the drinking water distribution system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment.

PubMed

Dzieciol, Monika; Schornsteiner, Elisa; Muhterem-Uyar, Meryem; Stessl, Beatrix; Wagner, Martin; Schmitz-Esser, Stephan

2016-04-16

Sanitation protocols are applied on a daily basis in food processing facilities to prevent the risk of cross-contamination with spoilage organisms. Floor drain water serves along with product-associated samples (slicer dust, brine or cheese smear) as an important hygiene indicator in monitoring Listeria monocytogenes in food processing facilities. Microbial communities of floor drains are representative for each processing area and are influenced to a large degree by food residues, liquid effluents and washing water. The microbial communities of drain water are steadily changing, whereas drain biofilms provide more stable niches. Bacterial communities of four floor drains were characterized using 16S rRNA gene pyrosequencing to better understand the composition and exchange of drain water and drain biofilm communities. Furthermore, the L. monocytogenes contamination status of each floor drain was determined by applying cultivation-independent real-time PCR quantification and cultivation-dependent detection according to ISO11290-1. Pyrosequencing of 16S rRNA genes of drain water and drain biofilm bacterial communities yielded 50,611 reads, which were clustered into 641 operational taxonomic units (OTUs), affiliated to 16 phyla dominated by Proteobacteria, Firmicutes and Bacteroidetes. The most abundant OTUs represented either product- (Lactococcus lactis) or fermentation- and food spoilage-associated phylotypes (Pseudomonas mucidolens, Pseudomonas fragi, Leuconostoc citreum, and Acetobacter tropicalis). The microbial communities in DW and DB samples were distinct in each sample type and throughout the whole processing plant, indicating the presence of indigenous specific microbial communities in each processing compartment. The microbiota of drain biofilms was largely different from the microbiota of the drain water. A sampling approach based on drain water alone may thus only provide reliable information on planktonic bacterial cells but might not allow conclusions on the bacterial composition of the microbiota in biofilms. Copyright © 2016. Published by Elsevier B.V.

Anthropogenic disturbance and biodiversity of marine benthic communities in Antarctica: a regional comparison.

PubMed

Stark, Jonathan S; Kim, Stacy L; Oliver, John S

2014-01-01

The impacts of two Antarctic stations in different regions, on marine sediment macrofaunal communities were compared: McMurdo, a very large station in the Ross Sea; and Casey, a more typical small station in East Antarctica. Community structure and diversity were compared along a gradient of anthropogenic disturbance from heavily contaminated to uncontaminated locations. We examined some of the inherent problems in comparing data from unrelated studies, such as different sampling methods, spatial and temporal scales of sampling and taxonomic uncertainty. These issues generated specific biases which were taken into account when interpreting patterns. Control sites in the two regions had very different communities but both were dominated by crustaceans. Community responses to anthropogenic disturbance (sediment contamination by metals, oils and sewage) were also different. At McMurdo the proportion of crustaceans decreased in disturbed areas and polychaetes became dominant, whereas at Casey, crustaceans increased in response to disturbance, largely through an increase in amphipods. Despite differing overall community responses there were some common elements. Ostracods, cumaceans and echinoderms were sensitive to disturbance in both regions. Capitellid, dorvelleid and orbiniid polychaetes were indicative of disturbed sites. Amphipods, isopods and tanaids had different responses at each station. Biodiversity and taxonomic distinctness were significantly lower at disturbed locations in both regions. The size of the impact, however, was not related to the level of contamination, with a larger reduction in biodiversity at Casey, the smaller, less polluted station. The impacts of small stations, with low to moderate levels of contamination, can thus be as great as those of large or heavily contaminated stations. Regional broad scale environmental influences may be important in determining the composition of communities and thus their response to disturbance, but there are some generalizations regarding responses which will aid future management of stations.

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef.

PubMed

Säde, Elina; Penttinen, Katri; Björkroth, Johanna; Hultman, Jenni

2017-04-01

Understanding the factors influencing meat bacterial communities is important as these communities are largely responsible for meat spoilage. The composition and structure of a bacterial community on a high-O 2 modified-atmosphere packaged beef product were examined after packaging, on the use-by date and two days after, to determine whether the communities at each stage were similar to those in samples taken from different production lots. Furthermore, we examined whether the taxa associated with product spoilage were distributed across production lots. Results from 16S rRNA amplicon sequencing showed that while the early samples harbored distinct bacterial communities, after 8-12 days storage at 6 °C the communities were similar to those in samples from different lots, comprising mainly of common meat spoilage bacteria Carnobacterium spp., Brochothrix spp., Leuconostoc spp. and Lactococcus spp. Interestingly, abundant operational taxonomic units associated with product spoilage were shared between the production lots, suggesting that the bacteria enable to spoil the product were constant contaminants in the production chain. A characteristic succession pattern and the distribution of common spoilage bacteria between lots suggest that both the packaging type and the initial community structure influenced the development of the spoilage bacterial community. Copyright © 2016 Elsevier Ltd. All rights reserved.

TaqMan Real-Time PCR Assays To Assess Arbuscular Mycorrhizal Responses to Field Manipulation of Grassland Biodiversity: Effects of Soil Characteristics, Plant Species Richness, and Functional Traits▿ †

PubMed Central

König, Stephan; Wubet, Tesfaye; Dormann, Carsten F.; Hempel, Stefan; Renker, Carsten; Buscot, François

2010-01-01

Large-scale (temporal and/or spatial) molecular investigations of the diversity and distribution of arbuscular mycorrhizal fungi (AMF) require considerable sampling efforts and high-throughput analysis. To facilitate such efforts, we have developed a TaqMan real-time PCR assay to detect and identify AMF in environmental samples. First, we screened the diversity in clone libraries, generated by nested PCR, of the nuclear ribosomal DNA internal transcribed spacer (ITS) of AMF in environmental samples. We then generated probes and forward primers based on the detected sequences, enabling AMF sequence type-specific detection in TaqMan multiplex real-time PCR assays. In comparisons to conventional clone library screening and Sanger sequencing, the TaqMan assay approach provided similar accuracy but higher sensitivity with cost and time savings. The TaqMan assays were applied to analyze the AMF community composition within plots of a large-scale plant biodiversity manipulation experiment, the Jena Experiment, primarily designed to investigate the interactive effects of plant biodiversity on element cycling and trophic interactions. The results show that environmental variables hierarchically shape AMF communities and that the sequence type spectrum is strongly affected by previous land use and disturbance, which appears to favor disturbance-tolerant members of the genus Glomus. The AMF species richness of disturbance-associated communities can be largely explained by richness of plant species and plant functional groups, while plant productivity and soil parameters appear to have only weak effects on the AMF community. PMID:20418424

The effects of forest conversion to oil palm on ground-foraging ant communities depend on beta diversity and sampling grain.

PubMed

Wang, Wendy Y; Foster, William A

2015-08-01

Beta diversity - the variation in species composition among spatially discrete communities - and sampling grain - the size of samples being compared - may alter our perspectives of diversity within and between landscapes before and after agricultural conversion. Such assumptions are usually based on point comparisons, which do not accurately capture actual differences in total diversity. Beta diversity is often not rigorously examined. We investigated the beta diversity of ground-foraging ant communities in fragmented oil palm and forest landscapes in Sabah, Malaysia, using diversity metrics transformed from Hill number equivalents to remove dependences on alpha diversity. We compared the beta diversities of oil palm and forest, across three hierarchically nested sampling grains. We found that oil palm and forest communities had a greater percentage of total shared species when larger samples were compared. Across all grains and disregarding relative abundances, there was higher beta diversity of all species among forest communities. However, there were higher beta diversities of common and very abundant (dominant) species in oil palm as compared to forests. Differences in beta diversities between oil palm and forest were greatest at the largest sampling grain. Larger sampling grains in oil palm may generate bigger species pools, increasing the probability of shared species with forest samples. Greater beta diversity of all species in forest may be attributed to rare species. Oil palm communities may be more heterogeneous in common and dominant species because of variable community assembly events. Rare and also common species are better captured at larger grains, boosting differences in beta diversity between larger samples of forest and oil palm communities. Although agricultural landscapes support a lower total diversity than natural forests, diversity especially of abundant species is still important for maintaining ecosystem stability. Diversity in agricultural landscapes may be greater than expected when beta diversity is accounted for at large spatial scales.

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

PubMed

Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

2014-01-17

The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw hydrolysate might be responsible for the large relative abundance of sulfate reducing bacteria.

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

PubMed Central

2014-01-01

Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw hydrolysate might be responsible for the large relative abundance of sulfate reducing bacteria. PMID:24433535

The sexual attitudes and lifestyles of London's Eastern Europeans (SALLEE Project): design and methods.

PubMed

Evans, Alison R; Parutis, Violetta; Hart, Graham; Mercer, Catherine H; Gerry, Christopher; Mole, Richard; French, Rebecca S; Imrie, John; Burns, Fiona

2009-10-30

Since May 2004, ten Central and Eastern European (CEE) countries have joined the European Union, leading to a large influx of CEE migrants to the United Kingdom (UK). The SALLEE project (sexual attitudes and lifestyles of London's Eastern Europeans) set out to establish an understanding of the sexual lifestyles and reproductive health risks of CEE migrants. CEE nationals make up a small minority of the population resident in the UK with no sampling frame from which to select a probability sample. There is also difficulty estimating the socio-demographic and geographical distribution of the population. In addition, measuring self-reported sexual behaviour which is generally found to be problematic, may be compounded among people from a range of different cultural and linguistic backgrounds. This paper will describe the methods adopted by the SALLEE project to address these challenges. The research was undertaken using quantitative and qualitative methods: a cross-sectional survey of CEE migrants based on three convenience samples (recruited from community venues, sexual health clinics and from the Internet) and semi-structured in-depth interviews with a purposively selected sample of CEE migrants. A detailed social mapping exercise of the CEE community was conducted prior to commencement of the survey to identify places where CEE migrants could be recruited. A total of 3,005 respondents took part in the cross-sectional survey, including 2,276 respondents in the community sample, 357 in the clinic sample and 372 in the Internet sample. 40 in-depth qualitative interviews were undertaken with a range of individuals, as determined by the interview quota matrix. The SALLEE project has benefited from using quantitative research to provide generalisable data on a range of variables and qualitative research to add in-depth understanding and interpretation. The social mapping exercise successfully located a large number of CEE migrants for the community sample and is recommended for other migrant populations, especially when little or no official data are available for this purpose. The project has collected timely data that will help us to understand the sexual lifestyles, reproductive health risks and health service needs of CEE communities in the UK.

DEVELOPMENT OF A MULTIMETRIC INDEX FOR ASSESSING THE BIOLOGICAL CONDITION OF THE OHIO RIVER

EPA Science Inventory

The use of fish communities to assess environmental quality is common for streams, but a standard methodology for large rivers is largely undeveloped. We developed an index to assess the condition of fish assemblages along 1580 km of the Ohio River. Representative samples of th...

The Relationship of Learning Communities to Engineering Students' Perceptions of the Freshman Year Experience, Academic Performance, and Persistence

ERIC Educational Resources Information Center

Tolley, Patricia Ann Separ

2009-01-01

The purpose of this correlational study was to examine the effects of a residential learning community and enrollment in an introductory engineering course to engineering students' perceptions of the freshman year experience, academic performance, and persistence. The sample included students enrolled in a large, urban, public, research university…

Fathers' Early Contributions to Children's Language Development in Families from Low-Income Rural Communities

ERIC Educational Resources Information Center

Pancsofar, Nadya; Vernon-Feagans, Lynne

2010-01-01

This study utilized a large sample of two-parent families from low-income rural communities to examine the contributions of father education and vocabulary, during picture book interactions with their infants at 6 months of age, to children's subsequent communication development at 15 months and expressive language development at 36 months. After…

Community Violence, School-Related Protective Factors, and Psychosocial Outcomes in Urban Youth

ERIC Educational Resources Information Center

Ludwig, Kristy A.; Warren, Jared S.

2009-01-01

This study examined the relationship of two putative school-based protective factors--student identification with school and perceived teacher support--to psychosocial outcomes in a sample of urban youth exposed to community violence. Participants were 175 high school students ages 14-19 in grades 9-12 from a large urban school district. Results…

Sleep Habits, Insomnia, and Daytime Sleepiness in a Large and Healthy Community-Based Sample of New Zealanders

PubMed Central

Wilsmore, Bradley R.; Grunstein, Ronald R.; Fransen, Marlene; Woodward, Mark; Norton, Robyn; Ameratunga, Shanthi

2013-01-01

Study Objectives: To determine the relationship between sleep complaints, primary insomnia, excessive daytime sleepiness, and lifestyle factors in a large community-based sample. Design: Cross-sectional study. Setting: Blood donor sites in New Zealand. Patients or Participants: 22,389 individuals aged 16-84 years volunteering to donate blood. Interventions: N/A. Measurements: A comprehensive self-administered questionnaire including personal demographics and validated questions assessing sleep disorders (snoring, apnea), sleep complaints (sleep quantity, sleep dissatisfaction), insomnia symptoms, excessive daytime sleepiness, mood, and lifestyle factors such as work patterns, smoking, alcohol, and illicit substance use. Additionally, direct measurements of height and weight were obtained. Results: One in three participants report < 7-8 h sleep, 5 or more nights per week, and 60% would like more sleep. Almost half the participants (45%) report suffering the symptoms of insomnia at least once per week, with one in 5 meeting more stringent criteria for primary insomnia. Excessive daytime sleepiness (evident in 9% of this large, predominantly healthy sample) was associated with insomnia (odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50 to 2.05), depression (OR 2.01, CI 1.74 to 2.32), and sleep disordered breathing (OR 1.92, CI 1.59 to 2.32). Long work hours, alcohol dependence, and rotating work shifts also increase the risk of daytime sleepiness. Conclusions: Even in this relatively young, healthy, non-clinical sample, sleep complaints and primary insomnia with subsequent excess daytime sleepiness were common. There were clear associations between many personal and lifestyle factors—such as depression, long work hours, alcohol dependence, and rotating shift work—and sleep problems or excessive daytime sleepiness. Citation: Wilsmore BR; Grunstein RR; Fransen M; Woodward M; Norton R; Ameratunga S. Sleep habits, insomnia, and daytime sleepiness in a large and healthy community-based sample of New Zealanders. J Clin Sleep Med 2013;9(6):559-566. PMID:23772189

Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metad...

Predictive Value of Callous-Unemotional Traits in a Large Community Sample

ERIC Educational Resources Information Center

Moran, Paul; Rowe, Richard; Flach, Clare; Briskman, Jacqueline; Ford, Tamsin; Maughan, Barbara; Scott, Stephen; Goodman, Robert

2009-01-01

Objective: Callous-unemotional (CU) traits in children and adolescents are increasingly recognized as a distinctive dimension of prognostic importance in clinical samples. Nevertheless, comparatively little is known about the longitudinal effects of these personality traits on the mental health of young people from the general population. Using a…

Use of PFU protozoan community structural and functional characteristics in assessment of water quality in a large, highly polluted freshwater lake in China.

PubMed

Xu, Muqi; Cao, Hong; Xie, Ping; Deng, Daogui; Feng, Weisong; Xu, Jian

2005-07-01

Structural and functional parameters of protozoan communities colonizing on PFU (polyurethane foam unit) artificial substrate were assessed as indicators of water quality in the Chaohu Lake, a large, shallow and highly polluted freshwater lake in China. Protozoan communities were sampled 1, 3, 6, 9 and 14 days after exposure of PFU artificial substrate in the lake during October 2003. Four study stations with the different water quality gradient changes along the lake were distinguishable in terms of differences in the community's structural (species richness, individual abundance, etc.) and functional parameters (protozoan colonization rates on PFU). The concentrations of TP, TN, COD and BOD as the main chemical indicators of pollution at the four sampling sites were also obtained each year during 2002-2003 for comparison with biological parameters. The results showed that the species richness and PFU colonization rate decreased as pollution intensity increased and that the Margalef diversity index values calculated at four sampling sites also related to water quality. The three functional parameters based on the PFU colonization process, that is, S(eq), G and T90%, were strongly related to the pollution status of the water. The number of protozoan species colonizing on PFU after exposure of 1 to 3 days was found to give a clear comparative indication of the water quality at the four sampling stations. The research provides further evidence that the protozoan community may be utilized effectively in the assessment of water quality and that the PFU method furnishes rapid, cost-effective and reliable information that may be useful for measuring responses to pollution stress in aquatic ecosystems.

Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters.

PubMed

Dussud, C; Meistertzheim, A L; Conan, P; Pujo-Pay, M; George, M; Fabre, P; Coudane, J; Higgs, P; Elineau, A; Pedrotti, M L; Gorsky, G; Ghiglione, J F

2018-05-01

Plastic pollution is widespread in ocean ecosystems worldwide, but it is unknown if plastic offers a unique habitat for bacteria compared to communities in the water column and attached to naturally-occurring organic particles. The large set of samples taken during the Tara-Mediterranean expedition revealed for the first time a clear niche partitioning between free-living (FL), organic particle-attached (PA) and the recently introduced plastic marine debris (PMD). Bacterial counts in PMD presented higher cell enrichment factors than generally observed for PA fraction, when compared to FL bacteria in the surrounding waters. Taxonomic diversity was also higher in the PMD communities, where higher evenness indicated a favorable environment for a very large number of species. Cyanobacteria were particularly overrepresented in PMD, together with essential functions for biofilm formation and maturation. The community distinction between the three habitats was consistent across the large-scale sampling in the Western Mediterranean basin. 'Plastic specific bacteria' recovered only on the PMD represented half of the OTUs, thus forming a distinct habitat that should be further considered for understanding microbial biodiversity in changing marine ecosystems. Copyright © 2017. Published by Elsevier Ltd.

Inventory and analysis of natural vegetation and related resources from space and high altitude photography

NASA Technical Reports Server (NTRS)

Poulton, C. E.

1972-01-01

A multiple sampling technique was developed whereby spacecraft photographs supported by aircraft photographs could be used to quantify plant communities. Large scale (1:600 to 1:2,400) color infrared aerial photographs were required to identify shrub and herbaceous species. These photos were used to successfully estimate a herbaceous standing crop biomass. Microdensitometry was used to discriminate among specific plant communities and individual plant species. Large scale infrared photography was also used to estimate mule deer deaths and population density of northern pocket gophers.

The relationship between neuroticism, major depressive disorder and comorbid disorders in Chinese women

PubMed Central

Xia, Jing; He, Qiang; Li, Yihan; Xie, Dong; Zhu, Suoyu; Chen, Jing; Shen, Yuan; Zhang, Ning; Wei, Yan; Chen, Chunfeng; Shen, Jianhua; Zhang, Yan; Gao, Chengge; Li, Youhui; Ding, Jihong; Shen, Wenwu; Wang, Qian; Cao, Meiyue; Liu, Tiebang; Zhang, Jinbei; Duan, Huijun; Bao, Cheng; Ma, Ping; Zhou, Cong; Luo, Yanfang; Zhang, Fengzhi; Liu, Ying; Li, Yi; Jin, Guixing; Zhang, Yutang; Liang, Wei; Chen, Yunchun; Zhao, Changyin; Li, Haiyan; Chen, Yiping; Shi, Shenxun; Kendler, Kenneth S.; Flint, Jonathan; Wang, Xumei

2011-01-01

Objective The personality trait of neuroticism is a risk factor for major depressive disorder (MDD), but this relationship has not been demonstrated in clinical samples from Asia. Methods We examined a large-scale clinical study of Chinese Han women with recurrent major depression and community-acquired controls. Results Elevated levels of neuroticism increased the risk for lifetime MDD (with an odds ratio of 1.37 per SD), contributed to the comorbidity of MDD with anxiety disorders, and predicted the onset and severity of MDD. Our findings largely replicate those obtained in clinical populations in Europe and US but differ in two ways: we did not find a relationship between melancholia and neuroticism; we found lower mean scores for neuroticism (3.6 in our community control sample). Limitations Our findings do not apply to MDD in community-acquired samples and may be limited to Han Chinese women. It is not possible to determine whether the association between neuroticism and MDD reflects a causal relationship. Conclusions Neuroticism acts as a risk factor for MDD in Chinese women, as it does in the West and may particularly predispose to comorbidity with anxiety disorders. Cultural factors may have an important effect on its measurement. PMID:21824661

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Dietary intakes of pesticides based on community duplicate diet samples.

PubMed

Melnyk, Lisa Jo; Xue, Jianping; Brown, G Gordon; McCombs, Michelle; Nishioka, Marcia; Michael, Larry C

2014-01-15

The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from which intake assessments of organophosphate (OP) and pyrethroid pesticides were made. From these nine participants, sixty-seven individual samples were collected and subsequently analyzed by gas chromatography/mass spectrometry. Measured concentrations were used to estimate dietary intakes for individuals and for the community. Individual intakes of total OP and pyrethroid pesticides ranged from 6.7 to 996 ng and 1.2 to 16,000 ng, respectively. The community intake was 256 ng for OPs and 3430 ng for pyrethroid pesticides. The most commonly detected pesticide was permethrin, but the highest overall intake was of bifenthrin followed by esfenvalerate. These data indicate that the community in Apopka, FL, as represented by the nine individuals, was potentially exposed to both OP and pyrethroid pesticides at levels consistent with a dietary model and other field studies in which standard duplicate diet samples were collected. Higher levels of pyrethroid pesticides were measured than OPs, which is consistent with decreased usage of OPs. The diversity of pyrethroid pesticides detected in food samples was greater than expected. Continually changing pesticide usage patterns need to be considered when determining analytes of interest for large scale epidemiology studies. The Community Duplicate Diet Methodology is a tool for researchers to meet emerging exposure measurement needs that will lead to more accurate assessments of intake which may enhance decisions for chemical regulation. Successfully determining the intake of pesticides through the dietary route will allow for accurate assessments of pesticide exposures to a community of individuals, thereby significantly enhancing the research benefit realized from epidemiological exposure studies. © 2013.

Swashed away? Storm impacts on sandy beach macrofaunal communities

NASA Astrophysics Data System (ADS)

Harris, Linda; Nel, Ronel; Smale, Malcolm; Schoeman, David

2011-09-01

Storms can have a large impact on sandy shores, with powerful waves eroding large volumes of sand off the beach. Resulting damage to the physical environment has been well-studied but the ecological implications of these natural phenomena are less known. Since climate change predictions suggest an increase in storminess in the near future, understanding these ecological implications is vital if sandy shores are to be proactively managed for resilience. Here, we report on an opportunistic experiment that tests the a priori expectation that storms impact beach macrofaunal communities by modifying natural patterns of beach morphodynamics. Two sites at Sardinia Bay, South Africa, were sampled for macrofauna and physical descriptors following standard sampling methods. This sampling took place five times at three- to four-month intervals between April 2008 and August 2009. The second and last sampling events were undertaken after unusually large storms, the first of which was sufficiently large to transform one site from a sandy beach into a mixed shore for the first time in living memory. A range of univariate (linear mixed-effects models) and multivariate (e.g. non-metric multidimensional scaling, PERMANOVA) methods were employed to describe trends in the time series, and to explore the likelihood of possible explanatory mechanisms. Macrofaunal communities at the dune-backed beach (Site 2) withstood the effects of the first storm but were altered significantly by the second storm. In contrast, macrofauna communities at Site 1, where the supralittoral had been anthropogenically modified so that exchange of sediments with the beach was limited, were strongly affected by the first storm and showed little recovery over the study period. In line with predictions from ecological theory, beach morphodynamics was found to be a strong driver of temporal patterns in the macrofaunal community structure, with the storm events also identified as a significant factor, likely because of their direct effects on beach morphodynamics. Our results also support those of other studies suggesting that developed shores are more impacted by storms than are undeveloped shores. Whilst recognising we cannot generalise too far beyond our limited study, our results contribute to the growing body of evidence that interactions between sea-level rise, increasing storminess and the expansion of anthropogenic modifications to the shoreline will place functional beach ecosystems under severe pressure over the forthcoming decades and we therefore encourage further, formal testing of these concepts.

Psychometric properties of the Penn State Worry Questionnaire for children in a large clinical sample.

PubMed

Pestle, Sarah L; Chorpita, Bruce F; Schiffman, Jason

2008-04-01

The Penn State Worry Questionnaire for Children (PSWQ-C; Chorpita, Tracey, Brown, Collica, & Barlow, 1997) is a 14-item self-report measure of worry in children and adolescents. Although the PSWQ-C has demonstrated favorable psychometric properties in small clinical and large community samples, this study represents the first psychometric evaluation of the PSWQ-C in a large clinical sample (N = 491). Factor analysis indicated a two-factor structure, in contrast to all previously published findings on the measure. The PSWQ-C demonstrated favorable psychometric properties in this sample, including high internal consistency, high convergent validity with related constructs, and acceptable discriminative validity between diagnostic categories. The performance of the 3 reverse-scored items was closely examined, and results indicated retaining all 14 items.

Molecular comparison of bacterial communities within iron-containing flocculent mats associated with submarine volcanoes along the Kermadec Arc.

PubMed

Hodges, Tyler W; Olson, Julie B

2009-03-01

Iron oxide sheaths and filaments are commonly found in hydrothermal environments and have been shown to have a biogenic origin. These structures were seen in the flocculent material associated with two submarine volcanoes along the Kermadec Arc north of New Zealand. Molecular characterization of the bacterial communities associated with the flocculent samples indicated that no known Fe-oxidizing bacteria dominated the recovered clone libraries. However, clones related to the recently described Fe-oxidizing bacterium Mariprofundus ferrooxydans were obtained from both the iron-containing flocculent (Fe-floc) and sediment samples, and peaks corresponding to Mariprofundus ferrooxydans, as well as the related clones, were observed in several of our terminal restriction fragment length polymorphism profiles. A large group of epsilonproteobacterial sequences, for which there is no cultured representative, dominated clones from the Fe-floc libraries and were less prevalent in the sediment sample. Phylogenetic analyses indicated that several operational taxonomic units appeared to be site specific, and statistical analyses of the clone libraries found that all samples were significantly different from each other. Thus, the bacterial communities in the Fe-floc samples were not more closely related to each other than to the sediment communities.

Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China.

PubMed

Tang, Xiangming; Li, Linlin; Shao, Keqiang; Wang, Boweng; Cai, Xianlei; Zhang, Lei; Chao, Jianying; Gao, Guang

2015-01-01

To elucidate the relationship between particle-attached (PA, ≥ 5.0 μm) and free-living (FL, 0.2-5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37,985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

DOE PAGES

Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; ...

2016-03-21

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using materialmore » from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within general containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. Lastly, a representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.« less

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

PubMed Central

Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; Perry, Kailene; Book, Adam J.; Horn, Heidi A.; Pinto-Tomás, Adrián A.; Currie, Cameron R.

2016-01-01

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation. PMID:26999749

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

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

Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using materialmore » from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within general containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. Lastly, a representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.« less

Mesoscale spatial variability of selected aquatic invertebrate community metrics from a minimally impaired stream segment

USGS Publications Warehouse

Gebler, J.B.

2004-01-01

The related topics of spatial variability of aquatic invertebrate community metrics, implications of spatial patterns of metric values to distributions of aquatic invertebrate communities, and ramifications of natural variability to the detection of human perturbations were investigated. Four metrics commonly used for stream assessment were computed for 9 stream reaches within a fairly homogeneous, minimally impaired stream segment of the San Pedro River, Arizona. Metric variability was assessed for differing sampling scenarios using simple permutation procedures. Spatial patterns of metric values suggest that aquatic invertebrate communities are patchily distributed on subsegment and segment scales, which causes metric variability. Wide ranges of metric values resulted in wide ranges of metric coefficients of variation (CVs) and minimum detectable differences (MDDs), and both CVs and MDDs often increased as sample size (number of reaches) increased, suggesting that any particular set of sampling reaches could yield misleading estimates of population parameters and effects that can be detected. Mean metric variabilities were substantial, with the result that only fairly large differences in metrics would be declared significant at ?? = 0.05 and ?? = 0.20. The number of reaches required to obtain MDDs of 10% and 20% varied with significance level and power, and differed for different metrics, but were generally large, ranging into tens and hundreds of reaches. Study results suggest that metric values from one or a small number of stream reach(es) may not be adequate to represent a stream segment, depending on effect sizes of interest, and that larger sample sizes are necessary to obtain reasonable estimates of metrics and sample statistics. For bioassessment to progress, spatial variability may need to be investigated in many systems and should be considered when designing studies and interpreting data.

Dimensions of Oppositionality in a Brazilian Community Sample: Testing the DSM-5 Proposal and Etiological Links

PubMed Central

Krieger, Fernanda Valle; Polanczyk, Guilherme Vanoni; Goodman, Robert; Rohde, Luis Augusto; Graeff-Martins, Ana Soledade; Salum, Giovanni; Gadelha, Ary; Pan, Pedro; Stahl, Daniel; Stringaris, Argyris

2013-01-01

Objective Investigating dimensions of oppositional symptoms may help to explain heterogeneity of etiology and outcomes for mental disorders across development and provide further empirical justification for the DSM-5–proposed modifications of oppositional defiant disorder (ODD). However, dimensions of oppositionality have not previously been tested in samples outside Europe or the United States. In this study, we used a large Brazilian community sample to compare the fit of different models for dimensions of oppositional symptoms; to examine the association of psychiatric diagnoses and symptoms with dimensions of oppositionality; and to examine the associations between dimensions of oppositionality and parental history of mental disorders. Method A Brazilian community sample of 2,512 children 6 through 12 years old were investigated in this study. Confirmatory factorial analyses were performed to compare the fit of alternative models, followed by linear and logistic regression analyses of associations with psychiatric diagnosis and parental history of psychopathology. Results A three-factor model with irritable, headstrong, and hurtful dimensions fitted best. The irritable dimension showed a strong association with emotional disorders in the child (p<.001) and history of depression (p<.01) and suicidality (p<.05) in the mother. The headstrong dimension was uniquely associated with attention-deficit/hyperactivity disorder (ADHD) in the child (p<.001) and with maternal history of ADHD symptoms (p<.05). The hurtful dimension was specifically associated with conduct disorder (p< .05). Conclusions Our findings from a large community sample of Brazilian children support a distinction between dimensions of oppositionality consistent with current DSM-5 recommendations and provide further evidence for etiological distinctions between these dimensions. PMID:23582870

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology.

PubMed

Datta, Manoshi S; Almada, Amalia A; Baumgartner, Mark F; Mincer, Tracy J; Tarrant, Ann M; Polz, Martin F

2018-06-06

Copepods harbor diverse bacterial communities, which collectively carry out key biogeochemical transformations in the ocean. However, bulk copepod sampling averages over the variability in their associated bacterial communities, thereby limiting our understanding of the nature and specificity of copepod-bacteria associations. Here, we characterize the bacterial communities associated with nearly 200 individual Calanus finmarchicus copepods transitioning from active growth to diapause. We find that all individual copepods sampled share a small set of "core" operational taxonomic units (OTUs), a subset of which have also been found associated with other marine copepod species in different geographic locations. However, most OTUs are patchily distributed across individual copepods, thereby driving community differences across individuals. Among patchily distributed OTUs, we identified groups of OTUs correlated with common ecological drivers. For instance, a group of OTUs positively correlated with recent copepod feeding served to differentiate largely active growing copepods from those entering diapause. Together, our results underscore the power of individual-level sampling for understanding host-microbiome relationships.

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities.

PubMed

Selbmann, Laura; Onofri, Silvano; Coleine, Claudia; Buzzini, Pietro; Canini, Fabiana; Zucconi, Laura

2017-11-01

A wide sampling of rocks, colonized by microbial epi-endolithic communities, was performed along an altitudinal gradient from sea level to 3600 m asl and sea distance from the coast to 100 km inland along the Victoria Land Coast, Antarctica. Seventy-two rock samples of different typology, representative of the entire survey, were selected and studied using denaturing gradient gel electrophoresis to compare variation in fungal diversity according to environmental conditions along this altitudinal and sea distance transect. Lichenized fungi were largely predominant in all the samples studied and the biodiversity was heavily influenced even by minimal local variations. The n-MDS analysis showed that altitude and sea distance affect fungal biodiversity, while sandstone allows the communities to maintain high biodiversity indices. The Pareto-Lorenz curves indicate that all the communities analyzed are highly adapted to extreme conditions but scarcely resilient, so any external perturbation may have irreversible effects on these fragile ecosystems.

Methods for collecting algal samples as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Porter, Stephen D.; Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic algae (periphyton) and phytoplankton communities are characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. This multidisciplinary approach provides multiple lines of evidence for evaluating water-quality status and trends, and for refining an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. Water quality can be characterized by evaluating the results of qualitative and quantitative measurements of the algal community. Qualitative periphyton samples are collected to develop of list of taxa present in the sampling reach. Quantitative periphyton samples are collected to measure algal community structure within selected habitats. These samples of benthic algal communities are collected from natural substrates, using the sampling methods that are most appropriate for the habitat conditions. Phytoplankton samples may be collected in large nonwadeable streams and rivers to meet specific program objectives. Estimates of algal biomass (chlorophyll content and ash-free dry mass) also are optional measures that may be useful for interpreting water-quality conditions. A nationally consistent approach provides guidance on site, reach, and habitat selection, as well as information on methods and equipment for qualitative and quantitative sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data locally, regionally, and nationally.

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

PubMed Central

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. PMID:25909444

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE PAGES

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

2015-07-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

PubMed

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

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

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Composition and structure of macrozooplankton and micronekton communities in the vicinity of free-drifting Antarctic icebergs

NASA Astrophysics Data System (ADS)

Kaufmann, Ronald S.; Robison, Bruce H.; Sherlock, Rob E.; Reisenbichler, Kim R.; Osborn, Karen J.

2011-06-01

Recent warming in the Antarctic has led to increased production of icebergs; however, the ecological effects of icebergs on pelagic communities within the Southern Ocean have not been well-studied. We used a 10 m 2 MOCNESS to collect macrozooplankton and micronekton in the upper 300 m of the water column near free-drifting icebergs in the Atlantic sector of the Southern Ocean during three seasons: December 2005 (late spring), June 2008 (late fall) and March-April 2009 (late summer). Communities were dominated in all three seasons by Antarctic krill ( Euphausia superba) and salps ( Salpa thompsoni), which collectively comprised 60-95% of the community wet biomass in most cases. During our spring and summer cruises, mean biomass was elevated by 3.1-4.3x at a distance of 0.37 km from large icebergs vs. 9.26 km away. These differences were not statistically significant, and no trend in biomass with distance was apparent in samples from fall 2008, when total biomass was an order of magnitude lower. Biomass levels near icebergs during Dec 2005 and Mar-Apr 2009 were comparable to values reported from marginal ice zones, suggesting that waters around icebergs support macrozooplankton and micronekton communities comparable in magnitude to those in some of the most productive areas of the Southern Ocean. Sample variance also was significantly higher within 1.85 km of icebergs during Dec 2005 and Mar-Apr 2009, reflecting increased patchiness on scales sampled by the MOCNESS (20-40×10 3 m 3 filtered per sample). This pattern was not significant during Jun 2008. Large predatory medusae were observed within 1.85 km of icebergs and in Iceberg Alley, an area through which icebergs pass frequently, but were virtually absent in areas remote from icebergs. Small euphausiids showed an inverse distribution, with low densities in areas populated by large medusae. A shift in community composition from a near-iceberg assemblage dominated by herbivores to a carnivore-dominated community in Iceberg Alley may reflect a transition from bottom-up to top-down control with increasing distance and time. Body sizes of dominant species varied seasonally but did not show consistent trends with distance from icebergs. Concentrations of photosynthetic pigments in the guts of E. superba and S. thompsoni corresponded broadly to patterns in surface chlorophyll a concentrations and were comparable to maximum gut pigment concentrations measured in animals collected from highly productive marginal ice zones. Our results suggest that the macrozooplankton and micronekton assemblages near free-drifting icebergs can be quantitatively and qualitatively different from those in surrounding, iceberg-free waters, perhaps due to both bottom-up and top-down processes as well as physical forcing by the passage of a large object through the upper ocean.

Communities of Practice for the Development of Adolescent Civic Engagement: An Empirical Study of Their Correlates in Australia and the United States

ERIC Educational Resources Information Center

Homana, Gary A.

2009-01-01

The relationships between a multidimensional model of school community and civic engagement were examined using survey data collected for the 1999 IEA Civic Education Study from large, nationally representative samples of adolescents in Australia and the United States. This study extends previous research by considering the extent to which…

Community Policing: A Preliminary Assessment of Environmental Impact with Panel Data on Program Implementation in U.S. Cities

ERIC Educational Resources Information Center

He, Ni; Zhao, Jihong; Lovrich, Nicholas P.

2005-01-01

This article examines the environmental impact on the programmatic implementation of community-oriented policing (COP) in large municipal police agencies during the 1990s. Three waves of nationwide surveys (1993, 1996, and 2000) based on a random sample of 281 municipalities and the corresponding police agencies were used for our analysis. Based…

Community Support for the Public Schools in a Large Metropolitan Area. Final Report.

ERIC Educational Resources Information Center

Smith, Ralph V.; And Others

An extensive survey was conducted in 1965 by a team of white and Negro interviewers in an application of ecological theory to a study of the support relationship between the community and its school system. Findings are based upon interview data from a probability sample of 931 respondents selected from the population of persons 21 years of age…

Salivary cortisol in a middle-aged community sample: results from 990 men and women of the KORA-F3 Augsburg study.

PubMed

Lederbogen, Florian; Kühner, Christine; Kirschbaum, Clemens; Meisinger, Christa; Lammich, Josefine; Holle, Rolf; Krumm, Bertram; von Lengerke, Thomas; Wichmann, Heinz-Erich; Deuschle, Michael; Ladwig, Karl-Heinz

2010-09-01

Analysis of salivary cortisol concentrations and derived indices is increasingly used in clinical and scientific medicine. However, comprehensive data on these parameters in the general population are scarce. The aim of this study was to evaluate the concentrations of salivary cortisol in a large middle-aged community sample and to identify major factors associated with altered hormone levels. We conducted a cross-sectional study within the Cooperative Health Research in the Region of Augsburg (KORA)-F3 study. A total of 1484 participants aged 50-69 years (52% women) had agreed to provide four saliva samples during a regular weekday. We measured salivary cortisol concentrations at wake-up (F0), (1/2) h (F(1/2)), 8 h (F8), and 14 h (F14) after waking. We calculated cortisol awakening response (CAR), slope, and area under the curve (AUC(G)) of the circadian cortisol secretion. Sociodemographic and clinical characteristics were evaluated by interview and questionnaires, sampling conditions by protocol. In total, 1208 participants returned saliva samples, exclusion criteria left 990 subjects for final analyses. Salivary cortisol levels were (means+/-s.d.) F0=13.7+/-7.6, F(1/2)=20.5+/-9.8, F8=5.4+/-3.3, and F14=2.0+/-1.8 nmol/l. Earlier sampling times were associated with higher CAR and smaller slope. Cortisol secretion was also influenced by gender and smoking habits. Higher perceived social support was associated with lower AUC(G) and smaller slope. We provide data on salivary cortisol concentrations in a large middle-aged community sample. Gender, sampling time, smoking habits, and perceived social support appeared as determinants of cortisol secretion.

Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages.

PubMed

Coral, Thomas; Descostes, Michaël; De Boissezon, Hélène; Bernier-Latmani, Rizlan; de Alencastro, Luiz Felippe; Rossi, Pierre

2018-07-01

A large fraction (47%) of the world's uranium is mined by a technique called "In Situ Recovery" (ISR). This mining technique involves the injection of a leaching fluid (acidic or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of dissolved uranium. The present study reports the in-depth alterations brought to autochthonous microbial communities during acidic ISR activities. Water samples were collected from a uranium roll-front deposit that is part of an ISR mine in operation (Tortkuduk, Kazakhstan). Water samples were obtained at a depth of ca 500 m below ground level from several zones of the Uyuk aquifer following the natural redox zonation inherited from the roll front deposit, including the native mineralized orebody and both upstream and downstream adjacent locations. Samples were collected equally from both the entrance and the exit of the uranium concentration plant. Next-generation sequencing data showed that the redox gradient shaped the community structures, within the anaerobic, reduced, and oligotrophic habitats of the native aquifer zones. Acid injection induced drastic changes in the structures of these communities, with a large decrease in both cell numbers and diversity. Communities present in the acidified (pH values < 2) mining areas exhibited similarities to those present in acid mine drainage, with the dominance of Sulfobacillus sp., Leptospirillum sp. and Acidithiobacillus sp., as well as the archaean Ferroplasma sp. Communities located up- and downstream of the mineralized zone under ISR and affected by acidic fluids were blended with additional facultative anaerobic and acidophilic microorganisms. These mixed biomes may be suitable communities for the natural attenuation of ISR mining-affected subsurface through the reduction of metals and sulfate. Assessing the effect of acidification on the microbial community is critical to evaluating the potential for natural attenuation or active bioremediation strategies. Copyright © 2018 Elsevier B.V. All rights reserved.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

A combined parasitological molecular approach for noninvasive characterization of parasitic nematode communities in wild hosts.

PubMed

Budischak, Sarah A; Hoberg, Eric P; Abrams, Art; Jolles, Anna E; Ezenwa, Vanessa O

2015-09-01

Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity of lethal sampling severely restricts the host species that can be studied, the adequacy of sample sizes to assess diversity, the geographic scope of collections and the research questions that can be addressed. Focusing on gastrointestinal nematodes of wild African buffalo, we evaluated whether accurate characterization of nematode communities could be made using a noninvasive technique that combined conventional parasitological approaches with molecular barcoding. To establish the reliability of this new method, we compared estimates of gastrointestinal nematode abundance, prevalence, richness and community composition derived from lethal sampling with estimates derived from our noninvasive approach. Our noninvasive technique accurately estimated total and species-specific worm abundances, as well as worm prevalence and community composition when compared to the lethal sampling method. Importantly, the rate of parasite species discovery was similar for both methods, and only a modest number of barcoded larvae (n = 10) were needed to capture key aspects of parasite community composition. Overall, this new noninvasive strategy offers numerous advantages over lethal sampling methods for studying nematode-host interactions in wildlife and can readily be applied to a range of study systems. © 2015 John Wiley & Sons Ltd.

Community recommendations on biobank governance: Results from a deliberative community engagement in California.

PubMed

Dry, Sarah M; Garrett, Sarah B; Koenig, Barbara A; Brown, Arleen F; Burgess, Michael M; Hult, Jen R; Longstaff, Holly; Wilcox, Elizabeth S; Madrigal Contreras, Sigrid Karina; Martinez, Arturo; Boyd, Elizabeth A; Dohan, Daniel

2017-01-01

United States-based biorepositories are on the cusp of substantial change in regulatory oversight at the same time that they are increasingly including samples and data from large populations, e.g. all patients in healthcare system. It is appropriate to engage stakeholders from these populations in new governance arrangements. We sought to describe community recommendations for biorepository governance and oversight using deliberative community engagement (DCE), a qualitative research method designed to elicit lay perspectives on complex technical issues. We asked for stakeholders to provide input on governance of large biorepositories at the University of California (UC), a public university. We defined state residents as stakeholders and recruited residents from two large metropolitan areas, Los Angeles (LA) and San Francisco (SF). In LA, we recruited English and Spanish speakers; in SF the DCE was conducted in English only. We recruited individuals who had completed the 2009 California Health Interview Survey and were willing to be re-contacted for future studies. Using stratified random sampling (by age, education, race/ethnicity), we contacted 162 potential deliberants of whom 53 agreed to participate and 51 completed the 4-day DCE in June (LA) and September-October (SF), 2013. Each DCE included discussion among deliberants facilitated by a trained staff and simultaneously-translated in LA. Deliberants also received a briefing book describing biorepository operations and regulation. During the final day of the DCE, deliberants voted on governance and oversight recommendations using an audience response system. This paper describes 23 recommendations (of 57 total) that address issues including: educating the public, sharing samples broadly, monitoring researcher behavior, using informative consent procedures, and involving community members in a transparent process of biobank governance. This project demonstrates the feasibility of obtaining meaningful input on biorepository governance from diverse lay stakeholders. Such input should be considered as research institutions respond to changes in biorepository regulation.

The importance of community building for establishing data management and curation practices for physical samples

NASA Astrophysics Data System (ADS)

Ramdeen, S.; Hangsterfer, A.; Stanley, V. L.

2017-12-01

There is growing enthusiasm for curation of physical samples in the Earth Science community (see sessions at AGU, GSA, ESIP). Multiple federally funded efforts aim to develop best practices for curation of physical samples; however, these efforts have not yet been consolidated. Harmonizing these concurrent efforts would enable the community as a whole to build the necessary tools and community standards to move forward together. Preliminary research indicate the various groups focused on this topic are working in isolation, and the development of standards needs to come from the broadest view of `community'. We will investigate the gaps between communities by collecting information about preservation policies and practices from curators, who can provide a diverse cross-section of the grand challenges to the overall community. We will look at existing reports and study results to identify example cases, then develop a survey to gather large scale data to reinforce or clarify the example cases. We will be targeting the various community groups which are working on similar issues, and use the survey to improve the visibility of developed best practices. Given that preservation and digital collection management for physical samples are both important and difficult at present (GMRWG, 2015; NRC, 2002), barriers to both need to be addressed in order to achieve open science goals for the entire community. To address these challenges, EarthCube's iSamples, a research coordination network established to advance discoverability, access, and curation of physical samples using cyberinfrastructure, has formed a working group to collect use cases to examine the breadth of earth scientists' work with physical samples. This research team includes curators of state survey and oceanographic geological collections, and a researcher from information science. In our presentation, we will share our research and the design of the proposed survey. Our goal is to engage the audience in a discussion on next steps towards building this community. References: The Geologic Materials Repository Working Group, 2015, USGS Circular 1410 National Research Council. 2002. Geoscience Data and Collections: National Resources in Peril.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-05-15

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

The coverage of a random sample from a biological community.

PubMed

Engen, S

1975-03-01

A taxonomic group will frequently have a large number of species with small abundances. When a sample is drawn at random from this group, one is therefore faced with the problem that a large proportion of the species will not be discovered. A general definition of quantitative measures of "sample coverage" is proposed, and the problem of statistical inference is considered for two special cases, (1) the actual total relative abundance of those species that are represented in the sample, and (2) their relative contribution to the information index of diversity. The analysis is based on a extended version of the negative binomial species frequency model. The results are tabulated.

Community variations in infant and child mortality in Peru.

PubMed Central

Edmonston, B; Andes, N

1983-01-01

Data from the national Peru Fertility Survey are used to estimate infant and childhood mortality ratios, 1968--77, for 124 Peruvian communities, ranging from small Indian hamlets in the Andes to larger cities on the Pacific coast. Significant mortality variations are found: mortality is inversely related to community population size and is higher in the mountains than in the jungle or coast. Multivariate analysis is then used to assess the influence of community population size, average female education, medical facilities, and altitude on community mortality. Finally, this study concludes that large-scale sample surveys, which include maternal birth history, add useful data for epidemiological studies of childhood mortality. PMID:6886581

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

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

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomicmore » units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.« less

Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

PubMed Central

Wu, Cindy H.; Sercu, Bram; Van De Werfhorst, Laurie C.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Holden, Patricia A.; Andersen, Gary L.

2010-01-01

Background Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. Conclusions/Significance This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health. PMID:20585654

Microbial communities in methane seep sediments along US Atlantic Margin are structured by organic matter and seepage dynamics

NASA Astrophysics Data System (ADS)

Graw, M. F.; Pohlman, J.; Treude, T.; Ruppel, C. D.; Colwell, F. S.

2016-12-01

Methane seeps are dynamic environments on continental margins where subsurface methane reaches the ocean. Microbial communities play a critical role in carbon cycling within seep sediments via organic carbon degradation, methane production, and anaerobic oxidation of methane (AOM), which consumes 20-80% of methane in seep sediments. However, biogeochemical controls on microbial community structure at seeps on a margin-wide scale remain unclear. The passive US Atlantic Margin (USAM) has been identified as a region of active methane seepage. Passive margin seeps have traditionally been understudied relative to seeps on active margins. Passive margins exhibit large cross-margin variability in organic carbon deposition and are anticipated to have divergent seep dynamics from active margins. Thus, the USAM offers a unique opportunity to investigate controls on microbial communities in seep sediments. We undertook analysis of microbial communities inhabiting seep sediments at 6 biogeochemically distinct sites along the USAM. Microbiological samples were co-located with measurements of sediment geochemistry and AOM and sulfate reduction rates. Illumina sequencing of the 16S rRNA gene, using both universal (83 samples) and archaeal-specific (64 samples) primers, and the mcrA gene (18 samples) identified 44 bacterial phyla and 7 archaeal phyla. Seeps in canyons and on open slope, likely representing high and low organic content sediments, hosted distinct communities; the former was dominated by ammonia-oxidizing Marine Group I Thaumarchaeota and the latter by mixotrophic Hadesarchaeota. Seep stability also impacted microbial community structure, and in particular the establishment of an AOM community rather than a Bathyarchaeota-dominated community. These findings contribute to understanding how microbial communities are structured within methane seep sediments and pave the way for investigating broad differences in carbon cycling between seeps on passive and active margins.

Discordance Between Resident and Active Bacterioplankton in Free-Living and Particle-Associated Communities in Estuary Ecosystem.

PubMed

Li, Jia-Ling; Salam, Nimaichand; Wang, Pan-Deng; Chen, Lin-Xing; Jiao, Jian-Yu; Li, Xin; Xian, Wen-Dong; Han, Ming-Xian; Fang, Bao-Zhu; Mou, Xiao-Zhen; Li, Wen-Jun

2018-03-16

Bacterioplankton are the major driving force for biogeochemical cycles in estuarine ecosystems, but the communities that mediate these processes are largely unexplored. We sampled in the Pearl River Estuary (PRE) to examine potential differences in the taxonomic composition of resident (DNA-based) and active (RNA-based) bacterioplankton communities in free-living and particle-associated fractions. MiSeq sequencing data showed that the overall bacterial diversity in particle-associated fractions was higher than in free-living communities. Further in-depth analyses of the sequences revealed a positive correlation between resident and active bacterioplankton communities for the particle-associated fraction but not in the free-living fraction. However, a large overlapping of OTUs between free-living and particle-associated communities in PRE suggested that the two fractions may be actively exchanged. We also observed that the positive correlation between resident and active communities is more prominent among the abundant OTUs (relative abundance > 0.2%). Further, the results from the present study indicated that low-abundance bacterioplankton make an important contribution towards the metabolic activity in PRE.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

PubMed Central

Hug, Laura A; Thomas, Brian C; Brown, Christopher T; Frischkorn, Kyle R; Williams, Kenneth H; Tringe, Susannah G; Banfield, Jillian F

2015-01-01

Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation. PMID:25647349

A metagenomic framework for the study of airborne microbial communities.

PubMed

Yooseph, Shibu; Andrews-Pfannkoch, Cynthia; Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B; Fadrosh, Douglas; Glass, John; Adams, Mark D; Friedman, Robert; Venter, J Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

A Metagenomic Framework for the Study of Airborne Microbial Communities

PubMed Central

Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B.; Fadrosh, Douglas; Glass, John; Adams, Mark D.; Friedman, Robert; Venter, J. Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. PMID:24349140

Effects of landscape gradients on wetland vegetation communities: information for large-scale restoration

USGS Publications Warehouse

Zweig, Christa L.; Kitchens, Wiley M.

2008-01-01

Projects of the scope of the restoration of the Florida Everglades require substantial information regarding ecological mechanisms, and these are often poorly understood. We provide critical base knowledge for Everglades restoration by characterizing the existing vegetation communities of an Everglades remnant, describing how present and historic hydrology affect wetland vegetation community composition, and documenting change from communities described in previous studies. Vegetation biomass samples were collected along transects across Water Conservation Area 3A South (3AS). Ten community types were present between November 2002 and 2005. Separate analyses for key a priori groups (slough, wet prairie, and sawgrass) provided detailed conclusions about effects of historic hydrology on the vegetation of 3AS. Communities were affected by hydrologic variables LIP to four years previous to the sample. We identified wet prairie/slough species such as Eleocharis spp. and Nymphaea odorata as short-term sentinel species of community change. Sawgrass and N. odorata should be monitored for long-term change. Comparisons to preceding studies indicated that many of the communities of previous times, when conditions were drier, no longer exist in our study area and have been replaced by deeper water community types.

The Role of Temperament and Personality in Problem Behaviors of Children with ADHD

ERIC Educational Resources Information Center

De Pauw, Sarah S. W.; Mervielde, Ivan

2011-01-01

This study describes temperament, personality, and problem behaviors in children with Attention-Deficit Hyperactivity Disorder (ADHD) aged 6 to 14 years. It targets differences between an ADHD sample (N=54; 43 boys) and a large community sample (N=465; 393 boys) in means and variances, psychometric properties, and covariation between traits and…

Characterization of the Theta to Beta Ratio in ADHD: Identifying Potential Sources of Heterogeneity

ERIC Educational Resources Information Center

Loo, Sandra K.; Cho, Alexander; Hale, T. Sigi; McGough, James; McCracken, James; Smalley, Susan L.

2013-01-01

Objective: The goal of this study is to characterize the theta to beta ratio (THBR) obtained from electroencephalogram (EEG) measures, in a large sample of community and clinical participants with regard to (a) ADHD diagnosis and subtypes, (b) common psychiatric comorbidities, and (c) cognitive correlates. Method: The sample includes 871…

Satisfaction with Life and Hope: A Look at Age and Marital Status

ERIC Educational Resources Information Center

Bailey, Thomas C.; Snyder, C. R.

2007-01-01

The Adult Trait Hope Scale (Snyder et al., 1991) typically has been administered to samples of college students, and previous researchers have not explored key demographic variables. In a large sample of community persons who were not in college (N = 215), significant differences were detected in Hope Scale scores across differing age groups and…

The College Environment: Contrasts Between CYCC Freshmen and Transfers and a Nationwide Freshman Sample, Fall, 1975.

ERIC Educational Resources Information Center

Kirby, E. B.

In order to analyze the environment of Central YMCA Community College (CYCC), information was requested on the Student Information Form, 1975, which dealt with three large areas: social issues, personal behavior, and future behavior in the noncollege world. This report compares the responses of three student samples--CYCC first-time entering…

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

PubMed

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network.

PubMed

Delafont, Vincent; Bouchon, Didier; Héchard, Yann; Moulin, Laurent

2016-09-01

Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pyrosequencing analysis of the bacterial community in drinking water wells.

PubMed

Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

2013-07-01

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities.

PubMed

Albertsen, Mads; Karst, Søren M; Ziegler, Anja S; Kirkegaard, Rasmus H; Nielsen, Per H

2015-01-01

DNA extraction and primer choice have a large effect on the observed community structure in all microbial amplicon sequencing analyses. Although the biases are well known, no comprehensive analysis has been conducted in activated sludge communities. In this study we systematically explored the impact of a number of parameters on the observed microbial community: bead beating intensity, primer choice, extracellular DNA removal, and various PCR settings. In total, 176 samples were subjected to 16S rRNA amplicon sequencing, and selected samples were investigated through metagenomics and metatranscriptomics. Quantitative fluorescence in situ hybridization was used as a DNA extraction-independent method for qualitative comparison. In general, an effect on the observed community was found on all parameters tested, although bead beating and primer choice had the largest effect. The effect of bead beating intensity correlated with cell-wall strength as seen by a large increase in DNA from Gram-positive bacteria (up to 400%). However, significant differences were present at lower phylogenetic levels within the same phylum, suggesting that additional factors are at play. The best primer set based on in silico analysis was found to underestimate a number of important bacterial groups. For 16S rRNA gene analysis in activated sludge we recommend using the FastDNA SPIN Kit for Soil with four times the normal bead beating and V1-3 primers.

Plant Communities Rather than Soil Properties Structure Arbuscular Mycorrhizal Fungal Communities along Primary Succession on a Mine Spoil

PubMed Central

Krüger, Claudia; Kohout, Petr; Janoušková, Martina; Püschel, David; Frouz, Jan; Rydlová, Jana

2017-01-01

Arbuscular mycorrhizal fungal (AMF) community assembly during primary succession has so far received little attention. It remains therefore unclear, which of the factors, driving AMF community composition, are important during ecosystem development. We addressed this question on a large spoil heap, which provides a mosaic of sites in different successional stages under different managements. We selected 24 sites of c. 12, 20, 30, or 50 years in age, including sites with spontaneously developing vegetation and sites reclaimed by alder plantations. On each site, we sampled twice a year roots of the perennial rhizomatous grass Calamagrostis epigejos (Poaceae) to determine AMF root colonization and diversity (using 454-sequencing), determined the soil chemical properties and composition of plant communities. AMF taxa richness was unaffected by site age, but AMF composition variation increased along the chronosequences. AMF communities were unaffected by soil chemistry, but related to the composition of neighboring plant communities of the sampled C. epigejos plants. In contrast, the plant communities of the sites were more distinctively structured than the AMF communities along the four successional stages. We conclude that AMF and plant community successions respond to different factors. AMF communities seem to be influenced by biotic rather than by abiotic factors and to diverge with successional age. PMID:28473828

Community-based risk assessment of water contamination from high-volume horizontal hydraulic fracturing.

PubMed

Penningroth, Stephen M; Yarrow, Matthew M; Figueroa, Abner X; Bowen, Rebecca J; Delgado, Soraya

2013-01-01

The risk of contaminating surface and groundwater as a result of shale gas extraction using high-volume horizontal hydraulic fracturing (fracking) has not been assessed using conventional risk assessment methodologies. Baseline (pre-fracking) data on relevant water quality indicators, needed for meaningful risk assessment, are largely lacking. To fill this gap, the nonprofit Community Science Institute (CSI) partners with community volunteers who perform regular sampling of more than 50 streams in the Marcellus and Utica Shale regions of upstate New York; samples are analyzed for parameters associated with HVHHF. Similar baseline data on regional groundwater comes from CSI's testing of private drinking water wells. Analytic results for groundwater (with permission) and surface water are made publicly available in an interactive, searchable database. Baseline concentrations of potential contaminants from shale gas operations are found to be low, suggesting that early community-based monitoring is an effective foundation for assessing later contamination due to fracking.

CIHR Candrive Cohort Comparison with Canadian Household Population Holding Valid Driver's Licenses.

PubMed

Gagnon, Sylvain; Marshall, Shawn; Kadulina, Yara; Stinchcombe, Arne; Bédard, Michel; Gélinas, Isabelle; Man-Son-Hing, Malcolm; Mazer, Barbara; Naglie, Gary; Porter, Michelle M; Rapoport, Mark; Tuokko, Holly; Vrkljan, Brenda

2016-06-01

We investigated whether convenience sampling is a suitable method to generate a sample of older drivers representative of the older-Canadian driver population. Using equivalence testing, we compared a large convenience sample of older drivers (Candrive II prospective cohort study) to a similarly aged population of older Canadian drivers. The Candrive sample consists of 928 community-dwelling older drivers from seven metropolitan areas of Canada. The population data was obtained from the Canadian Community Health Survey - Healthy Aging (CCHS-HA), which is a representative sample of older Canadians. The data for drivers aged 70 and older were extracted from the CCHS-HA database, for a total of 3,899 older Canadian drivers. Two samples were demonstrated as equivalent on socio-demographic, health, and driving variables that we compared, but not on driving frequency. We conclude that convenience sampling used in the Candrive study created a fairly representative sample of Canadian older drivers, with a few exceptions.

Seasonal variability in airborne bacterial communities at a high elevation site and their relationship to other air studies and to potential sources

NASA Astrophysics Data System (ADS)

Bowers, R. M.; Mccubbin, I. B.; Hallar, A. G.; Fierer, N.

2012-12-01

Airborne bacteria are a large component of the near-surface atmospheric aerosol; however we know surprisingly little about their spatiotemporal dynamics and even less about their distributions at high-elevation. With this work, we describe seasonal shifts in bacterial abundances, total particle abundances, and bacterial community structure at a high-elevation research station located in Colorado, USA. In addition, we describe the unique composition of these high-elevation airborne bacterial communities as compared to the bacteria commonly observed throughout the lower elevation atmosphere as well as bacteria common to major sources such as leaf surfaces, soils, water bodies and various other surfaces. To address these knowledge gaps, we collected aerosol samples on the rooftop of Storm Peak Laboratory (3200 m ASL) over the course of 2-3 week periods during each of the four calendar seasons. Total bacterial abundances were assessed via flow cytometry, total particle abundances were calculated with an aerodynamic particle sizer, and bacterial communities were characterized using a high-throughput barcoded DNA sequencing approach. The airborne bacterial communities at Storm Peak Lab were then used in a meta-analysis comparing Storm Peak bacteria to other near-surface (lower elevation) bacterial communities and to the communities of likely source environments. Bacterial abundances varied by season, which was similar but not identical to the changes in total particle abundances across the same sampling period. Airborne bacterial community structure varied significantly by season, with the summer communities being the most distinct. Season specific bacterial groups were identified, suggesting that a large proportion of the airborne community may be derived from nearby sources. However following a multi-environment meta-analysis using several air and source derived bacterial community datasets, the high-elevation air communities were the most distinct as compared to the other airborne communities used in the analysis. Furthermore, a very low proportion of the Storm Peak airborne community could be explained by the source environments used in the meta-analysis, suggesting a unique airborne community at high-elevation. High-alpine bacterial communities appear to make up a large fraction of the total atmospheric aerosol, however the different seasonal patterns between bacterial counts and total particle counts suggest that distinct factors control the quantities of different particles making it into the atmosphere. Furthermore, the characteristics of local terrestrial sources that undergo seasonal cycles seem to have a large influence on the airborne communities, but these sources could not explain the occurrence of all airborne bacterial taxa. As airborne bacteria are more commonly being recognized as a ubiquitous component of the atmosphere, a better understanding of their temporal dynamics in the high-alpine environment may give us insight into their many potential roles in atmospheric dynamics, free troposphere atmospheric dispersal patterns, and their role in human and environmental health.

Elemental mapping of large samples by external ion beam analysis with sub-millimeter resolution and its applications

NASA Astrophysics Data System (ADS)

Silva, T. F.; Rodrigues, C. L.; Added, N.; Rizzutto, M. A.; Tabacniks, M. H.; Mangiarotti, A.; Curado, J. F.; Aguirre, F. R.; Aguero, N. F.; Allegro, P. R. P.; Campos, P. H. O. V.; Restrepo, J. M.; Trindade, G. F.; Antonio, M. R.; Assis, R. F.; Leite, A. R.

2018-05-01

The elemental mapping of large areas using ion beam techniques is a desired capability for several scientific communities, involved on topics ranging from geoscience to cultural heritage. Usually, the constraints for large-area mapping are not met in setups employing micro- and nano-probes implemented all over the world. A novel setup for mapping large sized samples in an external beam was recently built at the University of São Paulo employing a broad MeV-proton probe with sub-millimeter dimension, coupled to a high-precision large range XYZ robotic stage (60 cm range in all axis and precision of 5 μ m ensured by optical sensors). An important issue on large area mapping is how to deal with the irregularities of the sample's surface, that may introduce artifacts in the images due to the variation of the measuring conditions. In our setup, we implemented an automatic system based on machine vision to correct the position of the sample to compensate for its surface irregularities. As an additional benefit, a 3D digital reconstruction of the scanned surface can also be obtained. Using this new and unique setup, we have produced large-area elemental maps of ceramics, stones, fossils, and other sort of samples.

Talking About The Smokes: a large-scale, community-based participatory research project.

PubMed

Couzos, Sophia; Nicholson, Anna K; Hunt, Jennifer M; Davey, Maureen E; May, Josephine K; Bennet, Pele T; Westphal, Darren W; Thomas, David P

2015-06-01

To describe the Talking About The Smokes (TATS) project according to the World Health Organization guiding principles for conducting community-based participatory research (PR) involving indigenous peoples, to assist others planning large-scale PR projects. The TATS project was initiated in Australia in 2010 as part of the International Tobacco Control Policy Evaluation Project, and surveyed a representative sample of 2522 Aboriginal and Torres Strait Islander adults to assess the impact of tobacco control policies. The PR process of the TATS project, which aimed to build partnerships to create equitable conditions for knowledge production, was mapped and summarised onto a framework adapted from the WHO principles. Processes describing consultation and approval, partnerships and research agreements, communication, funding, ethics and consent, data and benefits of the research. The TATS project involved baseline and follow-up surveys conducted in 34 Aboriginal community-controlled health services and one Torres Strait community. Consistent with the WHO PR principles, the TATS project built on community priorities and strengths through strategic partnerships from project inception, and demonstrated the value of research agreements and trusting relationships to foster shared decision making, capacity building and a commitment to Indigenous data ownership. Community-based PR methodology, by definition, needs adaptation to local settings and priorities. The TATS project demonstrates that large-scale research can be participatory, with strong Indigenous community engagement and benefits.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2016-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2017-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Factor structure and reliability of the depression, anxiety and stress scales in a large Portuguese community sample.

PubMed

Vasconcelos-Raposo, José; Fernandes, Helder Miguel; Teixeira, Carla M

2013-01-01

The purpose of the present study was to assess the factor structure and reliability of the Depression, Anxiety and Stress Scales (DASS-21) in a large Portuguese community sample. Participants were 1020 adults (585 women and 435 men), with a mean age of 36.74 (SD = 11.90) years. All scales revealed good reliability, with Cronbach's alpha values between .80 (anxiety) and .84 (depression). The internal consistency of the total score was .92. Confirmatory factor analysis revealed that the best-fitting model (*CFI = .940, *RMSEA = .038) consisted of a latent component of general psychological distress (or negative affectivity) plus orthogonal depression, anxiety and stress factors. The Portuguese version of the DASS-21 showed good psychometric properties (factorial validity and reliability) and thus can be used as a reliable and valid instrument for measuring depression, anxiety and stress symptoms.

Community Structure of Decapod Inhabit Dead Coral Pocillopora sp. in Pemuteran, Bali

NASA Astrophysics Data System (ADS)

Pertiwi, N. P. D.; Malik, M. D. A.; Kholilah, N.; Kurniasih, E. M.; Sembiring, A.; Anggoro, A. W.; Ambariyanto; Meyer, C.

2018-02-01

Decapod is one of the cryptic fauna associated with coral reefs, which play an important role and accounts for a major part of the biodiversity in the reef ecosystem. However, this biodiversity is largely overlooked and assessment regarding this biodiversity has not been conducted thoroughly due to lack of resources and the difficulties of sample collection. This research used semi-quantitative sampling methods to assess the community structure of decapod species inhabit dead Pocillopora sp. in Pemuteran, Bali. Two dead coral head of Pocillopora sp. were used as pilot study and sampled at the 8-12 m depth. All decapod found were collected and identify into family level. The result showed 214 decapods found consisting 12 families, with Xanthidae as the most abundant family. Community Index which consisting diversity, uniformity, and dominancy, indicated medium diversity, stable uniformity, and low dominancy of decapod community. This result also indicated no dominancy between families of decapod. Meanwhile, Species Density Index showed the value of 84.58 ± 2.04 individual per m3, with mean diversity of 7.05 ± 2.04 individual per m3 for each family.

Psychometric Characteristics of a Public-Domain Self-Report Measure of Vocational Interests: The Oregon Vocational Interest Scales

PubMed Central

Pozzebon, Julie A.; Visser, Beth A.; Ashton, Michael C.; Lee, Kibeom; Goldberg, Lewis R.

2009-01-01

We investigated the psychometric properties of the Oregon Vocational Interest Scales (ORVIS), a brief public-domain alternative to commercial inventories, in a large community sample and in a college sample. In both samples, we examined the factor structure, scale intercorrelations, and personality correlates of the ORVIS, and in the community sample we also examined the correlations of the ORVIS scales with cognitive abilities and with the scales of a longer, proprietary interest survey. In both samples, all eight scales—Leadership, Organization, Altruism, Creativity, Analysis, Producing, Adventuring, and Erudition—showed wide variation in scores, high internal-consistency reliabilities, and a pattern of high convergent and low discriminant correlations with the scales of the proprietary interest survey. Overall, the results support the construct validity of the scales, which are recommended for use in research on vocational interests and other individual differences. PMID:20155566

Psychometric characteristics of a public-domain self-report measure of vocational interests: the Oregon Vocational Interest Scales.

PubMed

Pozzebon, Julie A; Visser, Beth A; Ashton, Michael C; Lee, Kibeom; Goldberg, Lewis R

2010-03-01

We investigated the psychometric properties of the Oregon Vocational Interest Scales (ORVIS), a brief public-domain alternative to commercial inventories, in a large community sample and in a college sample. In both samples, we examined the factor structure, scale intercorrelations, and personality correlates of the ORVIS, and in the community sample, we also examined the correlations of the ORVIS scales with cognitive abilities and with the scales of a longer, proprietary interest survey. In both samples, all 8 scales-Leadership, Organization, Altruism, Creativity, Analysis, Producing, Adventuring, and Erudition-showed wide variation in scores, high internal-consistency reliabilities, and a pattern of high convergent and low discriminant correlations with the scales of the proprietary interest survey. Overall, the results support the construct validity of the scales, which are recommended for use in research on vocational interests and other individual differences.

The Availability of Web 2.0 Tools from Community College Libraries' Websites Serving Large Student Bodies

ERIC Educational Resources Information Center

Blummer, Barbara; Kenton, Jeffrey M.

2014-01-01

Web 2.0 tools offer academic libraries new avenues for delivering services and resources to students. In this research we report on a content analysis of 100 US community college libraries' Websites for the availability of Web 2.0 applications. We found Web 2.0 tools utilized by 97% of our sample population and many of these sites contained more…

Pre-fire fuel reduction treatments influence plant communities and exotic species 9 years after a large wildfire

Treesearch

Kristen L. Shive; Amanda M. Kuenzi; Carolyn H. Sieg; Peter Z. Fule

2013-01-01

We used a multi-year data set from the 2002 Rodeo-Chediski Fire to detect post-fire trends in plant community response in burned ponderosa pine forests. Within the burn perimeter, we examined the effects of pre-fire fuels treatments on post-fire vegetation by comparing paired treated and untreated sites on the Apache-Sitgreaves National Forest.We sampled these paired...

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

Correlates of firesetting in a community sample of young adolescents.

PubMed

Martin, Graham; Bergen, Helen A; Richardson, Angela S; Roeger, Leigh; Allison, Stephen

2004-03-01

To investigate relationships between firesetting, antisocial behaviour, individual, family and parenting factors in a large community sample of adolescents. A cross-sectional study of students (n = 2596) aged 13 years on average, from 27 schools in South Australia with a questionnaire on firesetting, antisocial behaviour (adapted 21-item Self Report Delinquency Scale), risk-taking, drug use, suicidality, physical and sexual abuse, depressive symptomatology, hopelessness, anxiety, locus of control, self-esteem, family functioning (McMaster Family Assessment Device) and parenting style (Influential Relationships Questionnaire). Data analysis included chi2, anova and logistic regression. Large significant differences are found between firesetters and non-firesetters on all measures. Among adolescents with serious levels of antisocial behaviour (7+ acts included in diagnostic guidelines for DSM-IV conduct disorder), firesetters differ from non-firesetters in reporting more extreme antisocial behaviour (10+ acts), extreme drug use, suicidal behaviour, and perceived failure at school. Gender differences are apparent. A study limitation is the single item assessment of firesetting. Self-report firesetting is strongly associated with extreme antisocial behaviour in young community adolescents, in support of existing evidence from incarcerated delinquent and psychiatric populations. Early detection of community firesetters demands further assessment and intervention. Clinicians should consider its coexistence with serious drug use and high risk-taking (especially in girls), and suicidality, sexual and physical abuse (in boys).

Hiding and feeding in floating seaweed: Floating seaweed clumps as possible refuges or feeding grounds for fishes

NASA Astrophysics Data System (ADS)

Vandendriessche, Sofie; Messiaen, Marlies; O'Flynn, Sarah; Vincx, Magda; Degraer, Steven

2007-02-01

Floating seaweed is considered to be an important habitat for juvenile fishes due to the provision of food, shelter, a visual orientation point and passive transport. The importance of the presence of the highly dynamical seaweed clumps from the North Sea to juvenile neustonic fishes was investigated by analysing both neuston samples (without seaweed) and seaweed samples concerning fish community structure, and length-frequency distributions and feeding habits of five associated fish species. While the neustonic fish community was mainly seasonally structured, the seaweed-associated fish community was more complex: the response of the associated fish species to environmental variables was species specific and probably influenced by species interactions, resulting in a large multivariate distance between the samples dominated by Chelon labrosus and the samples dominated by Cyclopterus lumpus, Trachurus trachurus and Ciliata mustela. The results of the stomach analysis confirmed that C. lumpus is a weedpatch specialist that has a close spatial affinity with the seaweed and feeds intensively on the seaweed-associated invertebrate fauna. Similarly, C. mustela juveniles also fed on the seaweed fauna, but in a more opportunistic way. The shape of the size-frequency distribution suggested enhanced growth when associated with floating seaweed. Chelon labrosus and T. trachurus juveniles were generally large in seaweed samples, but large individuals were also encountered in the neuston. The proportion of associated invertebrate fauna in their diet was of minor importance, compared to the proportions in C. lumpus. Individuals of Syngnathus rostellatus mainly fed on planktonic invertebrates but had a discontinuous size-frequency distribution, suggesting that some of the syngnathids were carried with the seaweed upon detachment and stayed associated. Floating seaweeds can therefore be regarded as ephemeral habitats shared between several fish species (mainly juveniles) that use them for different reasons and with varying intensity.

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica).

PubMed

La Ferla, Rosabruna; Azzaro, Maurizio; Michaud, Luigi; Caruso, Gabriella; Lo Giudice, Angelina; Paranhos, Rodolfo; Cabral, Anderson S; Conte, Antonella; Cosenza, Alessandro; Maimone, Giovanna; Papale, Maria; Rappazzo, Alessandro Ciro; Guglielmin, Mauro

2017-08-01

Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 10 4 -10 5 ) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.

Fisheries Resource Utilization of an Estuarine Borrow Pit in Mobile Bay, Alabama

DTIC Science & Technology

2014-07-01

sampling indicated that both holes supported impoverished benthic assemblages comprised largely of opportunistic, disturbance- adapted infauna. Species...impoverished benthic assemblages comprised largely of opportunistic, disturbance- adapted infauna. The structure of the benthic communities differed...Total % AN Total % BN Gastropod - - - - - - 1 0.3 1 0.07 Total Animals 600 - 20 - 467 - 380 - 1467 - Average. # Animals 120 - 4 - 156 - 126

Community-based water-quality monitoring in the Yukon River Basin and the Kuskokwim Watershed

USGS Publications Warehouse

Herman-Mercer, Nicole M.

2013-01-01

The unique partnership between the USGS and the YRITWC provides mutual benefits by fostering outreach efforts that have been essential for community empowerment and by generating scientific data for prohibitively large and remote regions that would be challenging for USGS scientists to sample as robustly alone. The addition of a new partnership with the KRWC to create a community-based monitoring program will only increase these benefits by growing the spatial extent of data collection and empowering more people to take charge of important science in their own backyard.

A population-based study on health-related quality of life among urban community residents in Shenyang, Northeast of China.

PubMed

Song, Tian; Ding, Yan-wei; Sun, Yan; He, Yi-Ni; Qi, Dian-Jun; Wu, Ying; Wu, Bin; Lang, Lang; Yu, Kai; Zhao, Xin; Zhu, Liang-liang; Wang, Shuang; Yu, Xiao-Song

2015-09-19

Due to the rising standard of living environment and advances in public health and medical care in China, it has been a tendency in recent years that health-related quality of life (HRQoL) has been increasingly acknowledged in community health management. However, large-scale population-based study on evaluating HQRoL in northeast of China was not conducted. This article aims to investigate the HRQoL in community residents in Northeast China and explore the associated factors. Stratified multiple-stage sampling method was used in the cross-sectional survey to investigate HRQoL of community residents in northeast of China. Univariate analysis and multiple linear regressions were used to analyze the factors associated to HRQoL of the community residents. The results were confirmed that HRQoL in general population was well performed for the first time in northeast of China in a large scale population. Community residents had better mental health than physical health. The factors influencing HRQoL included gender, age, educational level, marital status, ethnic group, chronic disease status, having breakfast frequency weekly and sleep quality. However, drinking and smoking habits did not affect residents' HRQoL. In this study, the result of the large-scale survey was satisfactory in northeast of China, providing HRQoL status of community residents. Policies on specific health management in community public health would emphasize on lifestyle behaviors especially eating habits in order to improving HRQoL.

Factor Structure of the Psychopathic Personality Inventory (PPI): Findings from a Large Incarcerated Sample

ERIC Educational Resources Information Center

Neumann, Craig S.; Malterer, Melanie B.; Newman, Joseph P.

2008-01-01

Exploratory factor analysis (EFA) of the Psychopathic Personality Inventory (PPI; S. O. Lilienfeld, 1990; S. O. Lilienfeld & B. P. Andrews, 1996) with a community sample has suggested that the PPI subscales may comprise 2 higher order factors (S. D. Benning, C. J. Patrick, B. M. Hicks, D. M. Blonigen, & R. F. Krueger, 2003). However,…

Corporate psychopathy: Talking the walk.

PubMed

Babiak, Paul; Neumann, Craig S; Hare, Robert D

2010-01-01

There is a very large literature on the important role of psychopathy in the criminal justice system. We know much less about corporate psychopathy and its implications, in large part because of the difficulty in obtaining the active cooperation of business organizations. This has left us with only a few small-sample studies, anecdotes, and speculation. In this study, we had a unique opportunity to examine psychopathy and its correlates in a sample of 203 corporate professionals selected by their companies to participate in management development programs. The correlates included demographic and status variables, as well as in-house 360 degrees assessments and performance ratings. The prevalence of psychopathic traits-as measured by the Psychopathy Checklist-Revised (PCL-R) and a Psychopathy Checklist: Screening Version (PCL: SV) "equivalent"-was higher than that found in community samples. The results of confirmatory factor analysis (CFA) and structural equation modeling (SEM) indicated that the underlying latent structure of psychopathy in our corporate sample was consistent with that model found in community and offender studies. Psychopathy was positively associated with in-house ratings of charisma/presentation style (creativity, good strategic thinking and communication skills) but negatively associated with ratings of responsibility/performance (being a team player, management skills, and overall accomplishments).

Extracting knowledge from the World Wide Web

PubMed Central

Henzinger, Monika; Lawrence, Steve

2004-01-01

The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries. PMID:14745041

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

PubMed

Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Azevedo, Vasco; Ghosh, Preetam; Viana, Marcus; Wattam, Alice R

2017-08-18

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

Unique risk and protective factors for partner aggression in a large scale air force survey.

PubMed

Slep, Amy M Smith; Foran, Heather M; Heyman, Richard E; Snarr, Jeffery D

2010-08-01

The objective of this study is to examine risk factors of physical aggression against a partner in a large representative Active Duty Air Force sample. A stratified sample of 128,950 United States Active Duty members were invited to participate in an Air Force-wide anonymous online survey across 82 bases. The final sample (N = 52,780) was weighted to be representative of the United States Air Force. Backward stepwise regression analyses were conducted to identify unique predictors of partner physical aggression perpetration within and across different ecological levels (individual, family, organization, and community levels). Relationship satisfaction, alcohol problems, financial stress, and number of years in the military were identified as unique predictors of men's and women's perpetration of violence against their partner across ecological levels. Parental status, support from neighbors, personal coping, and support from formal agencies also uniquely predicted men's but not women's perpetration of violence across ecological levels. This study identified specific risk factors of partner violence that may be targeted by prevention and intervention efforts aimed at different levels of impact (e.g., family interventions, community-wide programs).

Initial insights into bacterial succession during human decomposition.

PubMed

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

2015-05-01

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

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints.

PubMed

Mouchet, Maud A; Bouvier, Corinne; Bouvier, Thierry; Troussellier, Marc; Escalas, Arthur; Mouillot, David

2012-03-01

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment. © European Union 2011.

Sampling Migrants from their Social Networks: The Demography and Social Organization of Chinese Migrants in Dar es Salaam, Tanzania.

PubMed

Merli, M Giovanna; Verdery, Ashton; Mouw, Ted; Li, Jing

2016-07-01

The streams of Chinese migration to Africa are growing in tandem with rising Chinese investments and trade flows in and to the African continent. In spite of the high profile of this phenomenon in the media, there are few rich and broad descriptions of Chinese communities in Africa. Reasons for this include the rarity of official statistics on foreign-born populations in African censuses, the absence of predefined sampling frames required to draw representative samples with conventional survey methods and difficulties to reach certain segments of this population. Here, we use a novel network-based approach, Network Sampling with Memory, which overcomes the challenges of sampling 'hidden' populations in the absence of a sampling frame, to recruit a sample of recent Chinese immigrants in Dar es Salaam, Tanzania and collect information on the demographic characteristics, migration histories and social ties of members of this sample. These data reveal a heterogeneous Chinese community composed of "state-led" migrants who come to Africa to work on projects undertaken by large Chinese state-owned enterprises and "independent" migrants who come on their own accord to engage in various types of business ventures. They offer a rich description of the demographic profile and social organization of this community, highlight key differences between the two categories of migrants and map the structure of the social ties linking them. We highlight needs for future research on inter-group differences in individual motivations for migration, economic activities, migration outcomes, expectations about future residence in Africa, social integration and relations with local communities.

Sampling Migrants from their Social Networks: The Demography and Social Organization of Chinese Migrants in Dar es Salaam, Tanzania

PubMed Central

Merli, M. Giovanna; Verdery, Ashton; Mouw, Ted; Li, Jing

2016-01-01

The streams of Chinese migration to Africa are growing in tandem with rising Chinese investments and trade flows in and to the African continent. In spite of the high profile of this phenomenon in the media, there are few rich and broad descriptions of Chinese communities in Africa. Reasons for this include the rarity of official statistics on foreign-born populations in African censuses, the absence of predefined sampling frames required to draw representative samples with conventional survey methods and difficulties to reach certain segments of this population. Here, we use a novel network-based approach, Network Sampling with Memory, which overcomes the challenges of sampling ‘hidden’ populations in the absence of a sampling frame, to recruit a sample of recent Chinese immigrants in Dar es Salaam, Tanzania and collect information on the demographic characteristics, migration histories and social ties of members of this sample. These data reveal a heterogeneous Chinese community composed of “state-led” migrants who come to Africa to work on projects undertaken by large Chinese state-owned enterprises and “independent” migrants who come on their own accord to engage in various types of business ventures. They offer a rich description of the demographic profile and social organization of this community, highlight key differences between the two categories of migrants and map the structure of the social ties linking them. We highlight needs for future research on inter-group differences in individual motivations for migration, economic activities, migration outcomes, expectations about future residence in Africa, social integration and relations with local communities. PMID:27746912

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.

PubMed

Vincent, J B; Weiblen, G D; May, G

2016-02-01

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest. © 2015 John Wiley & Sons Ltd.

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

PubMed

Yasir, Muhammad; Azhar, Esam I; Khan, Imran; Bibi, Fehmida; Baabdullah, Rnda; Al-Zahrani, Ibrahim A; Al-Ghamdi, Ahmed K

2015-03-14

Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands. In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples. Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Effects of Hypoxia on the Phylogenetic Composition and Species Distribution of Protists in a Subtropical Harbor.

PubMed

Rocke, Emma; Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin

2016-07-01

Tolo Harbor, a subtropical semi-enclosed coastal water body, is surrounded by an expanding urban community, which contributes to large concentrations of nutrient runoff, leading to algal blooms and localized hypoxic episodes. Present knowledge of protist distributions in subtropical waters during hypoxic conditions is very limited. In this study, therefore, we combined parallel 454 pyrosequencing technology and denaturing gradient gel electrophoresis (DGGE) fingerprint analyses to reveal the protist community shifts before, during, and after a 2-week hypoxic episode during the summer of 2011. Hierarchical clustering for DGGE demonstrated similar grouping of hypoxic samples separately from oxic samples. Dissolved oxygen (DO) concentration and dissolved inorganic nitrogen:phosphate (DIN:PO4) concentrations significantly affected OTU distribution in 454 sequenced samples, and a shift toward a ciliate and marine alveolate clade II (MALV II) species composition occurred as waters shifted from oxic to hypoxic. These results suggest that protist community shifts toward heterotrophic and parasitic tendencies as well as decreased diversity and richness in response to hypoxic outbreaks.

In vitro fermentative capacity of swine large intestine: comparison between native Lantang and commercial Duroc breeds.

PubMed

Cheng, Peng Hui; Liang, Juan Boo; Wu, Yin Bao; Wang, Yan; Tufarelli, Vincenzo; Laudadio, Vito; Liao, Xin Di

2017-08-01

Native Lantang and commercial Duroc pigs were used as animal models to evaluate the differences existing in dietary fiber utilization ability between breeds. Animals were fed the same diet from weaning (4 weeks) to 4 months of age. Neutral detergent fiber (NDF) from wheat bran (as substrate) and fecal samples from the two breeds (as inoculum) were used in an in vitro gas production trial. Results showed that cumulative and maximum gas productions were higher in inocula from Lantang than those from the Duroc breed (P < 0.05). The degradation capacity of NDF for microbiome from Lantang fecal samples were significantly higher compared to Duroc (P < 0.01). The total quantity of short-chain fatty acids and its constituents from the fermentation liquors were different between breeds, suggesting that the dynamic characteristics of fermentation differed between the two breeds. The PCR denaturing gradient gel electrophoresis fingerprint and cluster analysis demonstrated that microbial communities of the two breeds were separated into two clusters and the bacterial community structure of large intestine among the two breed of pigs was different. Our results concluded that Lantang had higher dietary fiber degradation capacity than Duroc pigs, and the higher degradation capacity for the former breed was due to differences in the inherent microbial community in their respective large intestines. © 2016 Japanese Society of Animal Science.

Investigating Temporal Patterns of a Native Bee Community in a Remnant North American Bunchgrass Prairie using Blue Vane Traps

PubMed Central

Kimoto, Chiho; DeBano, Sandra J.; Thorp, Robbin W.; Rao, Sujaya; Stephen, William P.

2012-01-01

Native bees are important ecologically and economically because their role as pollinators fulfills a vital ecosystem service. Pollinators are declining due to various factors, including habitat degradation and destruction. Grasslands, an important habitat for native bees, are particularly vulnerable. One highly imperiled and understudied grassland type in the United States is the Pacific Northwest Bunchgrass Prairie. No studies have examined native bee communities in this prairie type. To fill this gap, the bee fauna of the Zumwalt Prairie, a large, relatively intact remnant of the Pacific Northwest Bunchgrass Prairie, was examined. Native bees were sampled during the summers of 2007 and 2008 in sixteen 40-ha study pastures on a plateau in northeastern Oregon, using a sampling method not previously used in grassland studies—blue vane traps. This grassland habitat contained an abundant and diverse community of native bees that experienced marked seasonal and inter-annual variation, which appears to be related to weather and plant phenology. Temporal variability evident over the entire study area was also reflected at the individual trap level, indicating a consistent response across the spatial scale of the study. These results demonstrate that temporal variability in bee communities can have important implications for long-term monitoring protocols. In addition, the blue vane trap method appears to be well-suited for studies of native bees in large expanses of grasslands or other open habitats, and may be a useful tool for monitoring native bee communities in these systems. PMID:23438086

Investigating temporal patterns of a native bee community in a remnant North American bunchgrass prairie using blue vane traps.

PubMed

Kimoto, Chiho; Debano, Sandra J; Thorp, Robbin W; Rao, Sujaya; Stephen, William P

2012-01-01

Native bees are important ecologically and economically because their role as pollinators fulfills a vital ecosystem service. Pollinators are declining due to various factors, including habitat degradation and destruction. Grasslands, an important habitat for native bees, are particularly vulnerable. One highly imperiled and understudied grassland type in the United States is the Pacific Northwest Bunchgrass Prairie. No studies have examined native bee communities in this prairie type. To fill this gap, the bee fauna of the Zumwalt Prairie, a large, relatively intact remnant of the Pacific Northwest Bunchgrass Prairie, was examined. Native bees were sampled during the summers of 2007 and 2008 in sixteen 40-ha study pastures on a plateau in northeastern Oregon, using a sampling method not previously used in grassland studies-blue vane traps. This grassland habitat contained an abundant and diverse community of native bees that experienced marked seasonal and inter-annual variation, which appears to be related to weather and plant phenology. Temporal variability evident over the entire study area was also reflected at the individual trap level, indicating a consistent response across the spatial scale of the study. These results demonstrate that temporal variability in bee communities can have important implications for long-term monitoring protocols. In addition, the blue vane trap method appears to be well-suited for studies of native bees in large expanses of grasslands or other open habitats, and may be a useful tool for monitoring native bee communities in these systems.

Random forests, a novel approach for discrimination of fish populations using parasites as biological tags.

PubMed

Perdiguero-Alonso, Diana; Montero, Francisco E; Kostadinova, Aneta; Raga, Juan Antonio; Barrett, John

2008-10-01

Due to the complexity of host-parasite relationships, discrimination between fish populations using parasites as biological tags is difficult. This study introduces, to our knowledge for the first time, random forests (RF) as a new modelling technique in the application of parasite community data as biological markers for population assignment of fish. This novel approach is applied to a dataset with a complex structure comprising 763 parasite infracommunities in population samples of Atlantic cod, Gadus morhua, from the spawning/feeding areas in five regions in the North East Atlantic (Baltic, Celtic, Irish and North seas and Icelandic waters). The learning behaviour of RF is evaluated in comparison with two other algorithms applied to class assignment problems, the linear discriminant function analysis (LDA) and artificial neural networks (ANN). The three algorithms are used to develop predictive models applying three cross-validation procedures in a series of experiments (252 models in total). The comparative approach to RF, LDA and ANN algorithms applied to the same datasets demonstrates the competitive potential of RF for developing predictive models since RF exhibited better accuracy of prediction and outperformed LDA and ANN in the assignment of fish to their regions of sampling using parasite community data. The comparative analyses and the validation experiment with a 'blind' sample confirmed that RF models performed more effectively with a large and diverse training set and a large number of variables. The discrimination results obtained for a migratory fish species with largely overlapping parasite communities reflects the high potential of RF for developing predictive models using data that are both complex and noisy, and indicates that it is a promising tool for parasite tag studies. Our results suggest that parasite community data can be used successfully to discriminate individual cod from the five different regions of the North East Atlantic studied using RF.

Ecstasy use and depression: a 4-year longitudinal study among an Australian general community sample.

PubMed

George, Amanda M; Olesen, Sarah; Tait, Robert J

2013-10-01

Longitudinal, population-based studies can better assess the relationship of ecstasy use with depression. We examined whether change in ecstasy use was associated with change in depressive symptoms/probable depression over a 4-year period, among a large Australian sample. The Personality and Total Health project is a longitudinal general community study of Australians from Canberra and Queanbeyan. Data from the youngest cohort when aged 24-30 (N = 2, 128) and 4 years later (N = 1, 977) was included. The Goldberg depression scale and the Brief Patient Health Questionnaire measured depressive symptoms and probable depression, respectively. Multilevel growth models also considered demographics, psychosocial characteristics, and other drug use. Ecstasy use was not associated with long-term depressive symptoms or greater odds of depression in multivariate analyses. Users had more self-reported depressive symptoms when using ecstasy compared to not using. However, differences between people who had and had not ever used ecstasy largely accounted for this. Other factors were more important in the prediction of depression. It would be premature to conclude that ecstasy use is not related to the development of long-term depressive symptoms, given the relatively low level of ecstasy and other drug use in this community sample. Results showed that other factors need to be considered when investigating ecstasy use and depression.

Assessment of Borderline Personality Features in Population Samples: Is the Personality Assessment Inventory-Borderline Features Scale Measurement Invariant across Sex and Age?

ERIC Educational Resources Information Center

De Moor, Marleen H. M.; Distel, Marijn A.; Trull, Timothy J.; Boomsma, Dorret I.

2009-01-01

Borderline personality disorder (BPD) is more often diagnosed in women than in men, and symptoms tend to decline with age. Using a large community sample, the authors investigated whether sex and age differences in four main features of BPD, measured with the "Personality Assessment Inventory-Borderline Features" scale (PAI-BOR; Morey,…

A Taxometric Investigation of the Latent Structure of Worry: Dimensionality and Associations with Depression, Anxiety, and Stress

ERIC Educational Resources Information Center

Olatunji, Bunmi O.; Broman-Fulks, Joshua J.; Bergman, Shawn M.; Green, Bradley A.; Zlomke, Kimberly R.

2010-01-01

Worry has been described as a core feature of several disorders, particularly generalized anxiety disorder (GAD). The present study examined the latent structure of worry by applying 3 taxometric procedures (MAXEIG, MAMBAC, and L-Mode) to data collected from 2 large samples. Worry in the first sample (Study 1) of community participants (n = 1,355)…

CONCEPTS AND APPROACHES FOR THE ...

EPA Pesticide Factsheets

This document is intended to assist users in establishing or refining protocols, including the specific methods related to field sampling, laboratory sample processing, taxonomy, data entry, management and analysis, and final assessment and reporting. It also reviews and provides information on development of monitoring designs to address certain types of environmental questions and approaches for documenting and reporting data quality and performance characteristics for large river biological monitoring. The approaches presented are not intended to replace existing program components but may in some cases be useful for refining them. The goal of this research is to develop methods and indicators that are useful for evaluating the condition of aquatic communities, for assessing the restoration of aquatic communities in response to mitigation and best management practices, and for determining the exposure of aquatic communities to different classes of stressors (i.e., pesticides, sedimentation, habitat alteration).

The effectiveness of large household water storage tanks for protecting the quality of drinking water.

PubMed

Graham, Jay P; VanDerslice, James

2007-06-01

Many communities along the US-Mexico border remain without infrastructure for water and sewage. Residents in these communities often collect and store their water in open 55-gallon drums. This study evaluated changes in drinking water quality resulting from an intervention that provided large closed water storage tanks (2,500-gallons) to individual homes lacking a piped water supply. After the intervention, many of the households did not change the source of their drinking water to the large storage tanks. Therefore, water quality results were first compared based on the source of the household's drinking water: store or vending machine, large tank, or collected from a public supply and transported by the household. Of the households that used the large storage tank as their drinking water supply, drinking water quality was generally of poorer quality. Fifty-four percent of samples collected prior to intervention had detectable levels of total coliforms, while 82% of samples were positive nine months after the intervention (p < 0.05). Exploratory analyses were also carried out to measure water quality at different points between collection by water delivery trucks and delivery to the household's large storage tank. Thirty percent of the samples taken immediately after water was delivered to the home had high total coliforms (> 10 CFU/100 ml). Mean free chlorine levels dropped from 0.43 mg/l, where the trucks filled their tanks, to 0.20 mg/l inside the household's tank immediately after delivery. Results of this study have implications for interventions that focus on safe water treatment and storage in the home, and for guidelines regarding the level of free chlorine required in water delivered by water delivery trucks.

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

PubMed

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

2017-07-01

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

Lead exposure in indigenous communities of the Amazon basin, Peru.

PubMed

Anticona, Cynthia; Bergdahl, Ingvar A; Lundh, Thomas; Alegre, Yuri; Sebastian, Miguel San

2011-12-01

Since 2006, three studies have reported elevated levels of lead (Pb) among the indigenous population of the Corrientes river, in the Amazon basin of Peru. Due to the large evidence of environmental pollution related to oil exploitation in the area, this activity has been suggested as the source of exposure. This study aimed to evaluate Pb levels in the population and environment of two communities exposed and one community non-exposed to the oil exploitation activity. Blood lead levels (BLL) were determined by the instrument Leadcare. A comparison with the graphite furnace atomic absorption technique was performed in order to validate the Leadcare results. Environmental samples were analyzed by inductively coupled plasma atomic emission spectroscopy. Among 361 capillary samples, the mean BLL was 9.4 μg/dl. Mean BLL of the communities exposed (n=171, x¯=9.5 μg/dl) and non-exposed (n=190, x¯=9.2 μg/dl) to the oil activity were not significantly different. Pb levels in environmental samples were below the maximum permissible levels. The sources of exposure could not be identified. Elevated levels of Pb in the oil-non-exposed community pointed out at other sources not yet clarified. Copyright © 2011 Elsevier GmbH. All rights reserved.

Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.

PubMed

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

2018-05-01

The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [<2.5 μm], PM 10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus , Tumebacillus , and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO 2 concentration, relative humidity, PM 10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus , Tumebacillus , and Desulfurispora ) increased significantly on heavy-haze days. In addition, Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze. Copyright © 2018 American Society for Microbiology.

Comparing two fish sampling standards over time: largely congruent results but with caveats

USGS Publications Warehouse

Yule, Daniel L.; Evrard, Lori M.; Cachera, Sébastien; Colon, Michel; Guillard, Jean

2013-01-01

1. We sampled Lake Bourget (surface area = 44 km2) using CEN standard gillnet and provisional standard acoustic survey methods over 3 years (2005, 2010 and 2011) as the fish community responded to re-oligotrophication. A total of 16 species were caught in benthic gillnets and three species in pelagic gillnets. 2. Lake Bourget results were consistent with a recent study (Emmrich et al., Freshwater Biology, 57, 2012, 2436) showing strong correspondence between average biomass-per-unit-effort (BPUE) in standard benthic gillnets and average acoustic volume backscattering when smaller lakes (0.25–5.45 km2) were treated as sample units. 3. The BPUE of whitefish (Coregonus lavaretus), perch (Perca fluviatilis) and roach (Rutilus rutilus) measured by benthic gillnets all declined significantly with increasing bathymetric depth; 93% of nets set at depths >50 m caught zero fish. 4. Pelagic gillnetting indicated that small (20 m) increased significantly after 2005. 5. Both surveys showed whitefish biomass increased significantly during the study, but whitefish ≥25 cm were poorly represented in benthic gillnet catches. Contrary to the acoustic findings, the BPUE of perch and roach in benthic gillnets did not vary significantly over time. This metric is insensitive to changes in size structure in that a high catch of small fish and a low catch of large fish in different years can provide similar average BPUE estimates. 6. We examined correlations between BPUE in benthic gillnets and acoustic methods at fine spatial scales by averaging acoustic backscattering measurements encompassed by buffers of varying size (250–2000 m) around individual gillnets and by averaging samples collected from lake quadrants. Correlations at fines scales were generally poor, and only in 1 year was the quadrant correlation significant. The lack of correlation can be explained, in part, by the two gears sampling different components of the fish community. Conversely, in pelagic habitat, where the fish community was simpler, we found BPUE in pelagic nets to be strongly correlated with acoustic backscattering. 7. With respect to large lakes like Lake Bourget, we hypothesise that the congruence in average biomass measurements provided by these two survey methods occurs because these different community components are responding similarly to a common driver like lake trophic status (or possibly multiple drivers operating in synergy).

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

PubMed Central

Cole, Jessica K; Peacock, Joseph P; Dodsworth, Jeremy A; Williams, Amanda J; Thompson, Daniel B; Dong, Hailiang; Wu, Geng; Hedlund, Brian P

2013-01-01

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (p̂=36.1%), Aeropyrum (p̂=16.6%), the archaeal lineage pSL4 (p̂=15.9%), the archaeal lineage NAG1 (p̂=10.6%) and Thermocrinis (p̂=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (p̂=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles. PMID:23235293

Communities of terrestrial nematodes after different approaches to heathland restoration

NASA Astrophysics Data System (ADS)

Radochova, Petra; Frouz, Jan

2016-04-01

Since the 20th century, the distribution of European heathlands rapidly decreased due to agricultural intensification, heavy use of artificial fertilizers or acidification (Aerts & Heil, 1993). Therefore, various attempts of heathland restoration are under way in these days. Analysis of nematode community composition can be one of the tools suitable for succession evaluation (Ferris et al., 2001). In 2011, 2013 and 2014, soil samples were collected from heathland restoration experiment (launched in 2011) where different restoration methods were applied in a 3 × 3 factorial experiment; existing heathlands were also sampled to identify the target community both in dry and wet heathland. A total of 60 samples of extracted nematodes were analysed for absolute abundance, trophic groups, and genera dominance. Various indices were calculated to describe the nematode community. We were able to prove faster development of wet heathlands towards the target community. However, because of large data variability, there was no significant difference between treatments. Development of wet and dry heathlands differed also in increased proportion of omniphagous nematodes in 2013 and predators in 2014 in dry heathlands. After three years of heathland restoration, nematode community has not yet reached parameters of the target community. References Aerts, R., Heil, G. W., 1993. Heathlands: patterns and processes in a changing environment, 1st ed, Geobotany: 20. Springer Netherlands, Dordrecht, p. 229. Ferris, H., Bongers, T., De Goede, R. G. M., 2001. A framework for soil food web diagnostics: Extension of the nematode faunal analysis oncept. Appl. Soil Ecol. 18, 13-29.

The EuPA Biobank Initiative: Meeting the future challenges of biobanking in proteomics & systems medicine.

PubMed

Wheelock, Åsa M; Paulson, Linda; Litton, Jan-Eric

2015-09-08

In this News & Reviews Discussion, the recently launched EuPA (European Proteomics Association) Biobank Initiative is introduced in the context of current and future challenges in biobanking. The purpose of the initiative is to provide a forumand knowledge platform for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forum and easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, as well as the output and productivity from existing biobanks. The underutilization of biobanks has recently been identified as an emerging issue of biobankingworldwide. Measures to improve our ability to locate and access appropriate sample collections for a wide range of research purposes may enhance both the scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This manuscript is intended as a Discussion piece, and represents a recollection of the presentation under the “EuPA Initiative” session at HUPO/EuPA 2014 in Madrid. The launch of the EuPA (European Proteomics Association) Biobank Initiative in the context of current and future challenges in biobanking is discussed. The purpose of the initiative is to provide a forum and knowledge base for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forumand easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, aswell as the output and productivity fromexisting biobanks. The underutilization of biobanks has recently been identified as a challenge to the well-being and economic sustainability of biobanking worldwide. Measures to improve our ability to localize and access appropriate sample collections for validation studies and other research purposes is thus of benefit bothto scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This article is part of a Special Issue entitled: HUPO 2014.

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean

PubMed Central

Rapp, Josephine Z.; Fernández-Méndez, Mar; Bienhold, Christina; Boetius, Antje

2018-01-01

In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400–500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future. PMID:29875749

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel.

PubMed

He, Jing; Yi, Li; Hai, Le; Ming, Liang; Gao, Wanting; Ji, Rimutu

2018-01-12

The bacterial community plays important roles in the gastrointestinal tracts (GITs) of animals. However, our understanding of the microbial communities in the GIT of Bactrian camels remains limited. Here, we describe the bacterial communities from eight different GIT segments (rumen, reticulum, abomasum, duodenum, ileum, jejunum, caecum, colon) and faeces determined from 11 Bactrian camels using 16S rRNA gene amplicon sequencing. Twenty-seven bacterial phyla were found in the GIT, with Firmicutes, Verrucomicrobia and Bacteroidetes predominating. However, there were significant differences in microbial community composition between segments of the GIT. In particular, a greater proportion of Akkermansia and Unclassified Ruminococcaceae were found in the large intestine and faecal samples, while more Unclassified Clostridiales and Unclassified Bacteroidales were present in the in forestomach and small intestine. Comparative analysis of the microbiota from different GIT segments revealed that the microbial profile in the large intestine was like that in faeces. We also predicted the metagenomic profiles for the different GIT regions. In forestomach, there was enrichment associated with replication and repair and amino acid metabolism, while carbohydrate metabolism was enriched in the large intestine and faeces. These results provide profound insights into the GIT microbiota of Bactrian camels.

The community structure of over-wintering larval and small juvenile fish in a large estuary

NASA Astrophysics Data System (ADS)

Munk, Peter; Cardinale, Massimiliano; Casini, Michele; Rudolphi, Ann-Christin

2014-02-01

The Skagerrak and Kattegat are estuarine straits of high hydrographical and ecological diversity, situated between the saline waters of the North Sea and the brackish waters of the Baltic Sea. These sustain important nursery grounds of many fish species, of which several overwinter during the larval and early juvenile stages. In order to give more insight into the communities of the overwintering ichthyoplankton in estuarine areas, we examine an annual series of observations from a standard survey carried out 1992-2010. Species differences and annual variability in distributions and abundances are described, and linkages between ichthyoplankton abundances and corresponding hydrographical information are analysed by GAM methods. Communities were dominated by herring, gobies, butterfish, sprat, pipefishes, lemon sole and European eel (i.e. glass eel), and all the sampled species showed large annual fluctuations in abundances. The species showed quite specific patterns of distribution although species assemblages with common distributional characteristics were identified. Within these assemblages, the ichthyoplankton abundances showed linkage to environmental characteristics described by bottom-depth and surface temperature and salinity. Hence the study points to a significant structuring of overwintering ichthyoplankton communities in large estuaries, based on the species habitat choice and its response to physical gradients.

Vegetative community control of freshwater availability: Phoenix Islands case study

NASA Astrophysics Data System (ADS)

Engels, M.; Heinse, R.

2014-12-01

On small low islands with limited freshwater resources, terrestrial plant communities play a large role in moderating freshwater availability. Freshwater demands of vegetative communities are variable depending on the composition of the community. Hence, changes to community structure from production crop introductions, non-native species invasions, and climate change, may have significant implications for freshwater availability. Understanding how vegetative community changes impact freshwater availability will allow for better management and forecasting of limited freshwater supplies. To better understand these dynamics, we investigated three small tropical atolls in the Phoenix Island Protected Area, Kiribati. Despite their close proximity, these islands receive varying amounts of rainfall, are host to different plant communities and two of the islands have abandoned coconut plantations. Using electromagnetic induction, ground penetrating radar, soil samples, climate and satellite data, we present preliminary estimates of vegetative water demand for different tropical plant communities.

Pattern of Antibiotic Resistance Among Community Derived Isolates of Enterobacteriaceae Using Urine Sample: A Study From Northern India

PubMed Central

Lohiya, Ayush; Kapil, Arti; Gupta, Sanjeev Kumar; Misra, Puneet; Rai, Sanjay K.

2015-01-01

Background Despite world-wide evidence of increased antibiotic resistance, there is scarce data on antibiotic resistance in community settings. One of the reason being difficulty in collection of biological specimen (traditionally stool) in community from apparently healthy individuals. Hence, finding an alternative specimen that is easier to obtain in a community setting or in large scale surveys for the purpose, is crucial. We conducted this study to explore the feasibility of using urine samples for deriving community based estimates of antibiotic resistance and to estimate the magnitude of resistance among urinary isolates of Escherichia coli and Klebsiella pneumonia against multiple antibiotics in apparently healthy individuals residing in a rural community of Haryana, North India. Materials and Methods Eligible individuals were apparently healthy, aged 18 years or older. Using the health management information system (HMIS) of Ballabgarh Health Demographic Surveillance System (HDSS), sampling frame was prepared. Potential individuals were identified using simple random sampling. Random urine sample was collected in a sterile container and transported to laboratory under ambient condition. Species identification and antibiotic susceptibility testing for Enterobacteriaceae was done using Clinical Laboratory and Standards Institute (CLSI) 2012 guidelines. Multi-drug resistant (MDR) Enterobacteriaceae, Extended Spectrum Beta Lactamase (ESBL) producing Enterobacteriaceae, and Carbapenem producing Enterobacteriaceae (CRE) were identified from the urine samples. Results A total of 433 individuals participated in the study (non-response rate – 13.4%), out of which 58 (13.4%) were positive for Enterobacteriaceae, 8.1% for E. coli and 5.3% for K. pneumoniae. Resistance against penicillin (amoxicillin/ampicillin) for E. coli and K. pneumoniae was 62.8% and 100.0% respectively. Isolates resistant to co-trimoxazole were 5.7% and 0.0% respectively. None of the isolates were resistant to imipenem, and meropenem. Conclusion and recommendations It is feasible to use urine sample to study magnitude of antibiotic resistance in population based surveys. At community level, resistance to amoxicillin was considerable, negligible for co-trimoxazole, and to higher antibiotics including carbapenems. PMID:26393150

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

Marketing activities of vape shops across racial/ethnic communities.

PubMed

Garcίa, Robert; Sidhu, Anupreet; Allem, Jon-Patrick; Baezconde-Garbanati, Lourdes; Unger, Jennifer B; Sussman, Steve

2016-01-01

There has been a surge in the number of vape shops in the USA. Research on the marketing practices of e-cigarette manufacturers is scarce and even less known are the practices of vape shop retailers. Past research on tobacco marketing has shown differences in the amount and content of marketing material, based on a community's demographic profile. This study examined marketing strategies in vape shops and explored differences among vape shops located in communities that differ by ethnic composition. Data was gathered in 2014 from a pilot-study on vape shops (n=77) in Los Angeles, which documented the characteristics of shops through employee interviews and in-store observations. Data were collected from shops located in communities that were predominantly, African-American (n=20), Hispanic (n=17), Korean (n=18), or non-Hispanic White (n=22). Sixty-one percent of vape shops had advertisements (print ads and posters) for e-cigarettes and 84% offered discounts. Vape shops in Hispanic communities were more likely to have ethnic specific marketing material compared to shops in other communities. All the shops provided customers with free samples, however those in Korean and non-Hispanic White communities had a significantly higher prevalence of customer accessible free samples. Vape shop marketing practices differed by ethnic community. A large majority of shops provided free samples to their customers, a practice which is now banned by the FDA. It will be important to monitor how vape shops will adjust their marketing strategy because of this ban. Future research should expand on the findings presented here to provide regulators with further crucial information.

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

PubMed

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

2017-04-01

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

Complementarity of Rotating Video and Underwater Visual Census for Assessing Species Richness, Frequency and Density of Reef Fish on Coral Reef Slopes

PubMed Central

Mallet, Delphine; Wantiez, Laurent; Lemouellic, Soazig; Vigliola, Laurent; Pelletier, Dominique

2014-01-01

Estimating diversity and abundance of fish species is fundamental for understanding community structure and dynamics of coral reefs. When designing a sampling protocol, one crucial step is the choice of the most suitable sampling technique which is a compromise between the questions addressed, the available means and the precision required. The objective of this study is to compare the ability to sample reef fish communities at the same locations using two techniques based on the same stationary point count method: one using Underwater Visual Census (UVC) and the other rotating video (STAVIRO). UVC and STAVIRO observations were carried out on the exact same 26 points on the reef slope of an intermediate reef and the associated inner barrier reefs. STAVIRO systems were always deployed 30 min to 1 hour after UVC and set exactly at the same place. Our study shows that; (i) fish community observations by UVC and STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of small species were higher for UVC; (iv) density of fished species was higher for STAVIRO and (v) only UVC detected significant differences in fish assemblage structure across reef type at the spatial scale studied. We recommend that the two techniques should be used in a complementary way to survey a large area within a short period of time. UVC may census reef fish within complex habitats or in very shallow areas such as reef flat whereas STAVIRO would enable carrying out a large number of stations focused on large and diver-averse species, particularly in the areas not covered by UVC due to time and depth constraints. This methodology would considerably increase the spatial coverage and replication level of fish monitoring surveys. PMID:24392126

Scale-Dependence of Processes Structuring Dung Beetle Metacommunities Using Functional Diversity and Community Deconstruction Approaches

PubMed Central

da Silva, Pedro Giovâni; Hernández, Malva Isabel Medina

2015-01-01

Community structure is driven by mechanisms linked to environmental, spatial and temporal processes, which have been successfully addressed using metacommunity framework. The relative importance of processes shaping community structure can be identified using several different approaches. Two approaches that are increasingly being used are functional diversity and community deconstruction. Functional diversity is measured using various indices that incorporate distinct community attributes. Community deconstruction is a way to disentangle species responses to ecological processes by grouping species with similar traits. We used these two approaches to determine whether they are improvements over traditional measures (e.g., species composition, abundance, biomass) for identification of the main processes driving dung beetle (Scarabaeinae) community structure in a fragmented mainland-island landscape in southern Brazilian Atlantic Forest. We sampled five sites in each of four large forest areas, two on the mainland and two on the island. Sampling was performed in 2012 and 2013. We collected abundance and biomass data from 100 sampling points distributed over 20 sampling sites. We studied environmental, spatial and temporal effects on dung beetle community across three spatial scales, i.e., between sites, between areas and mainland-island. The γ-diversity based on species abundance was mainly attributed to β-diversity as a consequence of the increase in mean α- and β-diversity between areas. Variation partitioning on abundance, biomass and functional diversity showed scale-dependence of processes structuring dung beetle metacommunities. We identified two major groups of responses among 17 functional groups. In general, environmental filters were important at both local and regional scales. Spatial factors were important at the intermediate scale. Our study supports the notion of scale-dependence of environmental, spatial and temporal processes in the distribution and functional organization of Scarabaeinae beetles. We conclude that functional diversity may be used as a complementary approach to traditional measures, and that community deconstruction allows sufficient disentangling of responses of different trait-based groups. PMID:25822150

Analyzing hidden populations online: topic, emotion, and social network of HIV-related users in the largest Chinese online community.

PubMed

Liu, Chuchu; Lu, Xin

2018-01-05

Traditional survey methods are limited in the study of hidden populations due to the hard to access properties, including lack of a sampling frame, sensitivity issue, reporting error, small sample size, etc. The rapid increase of online communities, of which members interact with others via the Internet, have generated large amounts of data, offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. In this study, we try to understand the multidimensional characteristics of a hidden population by analyzing the massive data generated in the online community. By elaborately designing crawlers, we retrieved a complete dataset from the "HIV bar," the largest bar related to HIV on the Baidu Tieba platform, for all records from January 2005 to August 2016. Through natural language processing and social network analysis, we explored the psychology, behavior and demand of online HIV population and examined the network community structure. In HIV communities, the average topic similarity among members is positively correlated to network efficiency (r = 0.70, p < 0.001), indicating that the closer the social distance between members of the community, the more similar their topics. The proportion of negative users in each community is around 60%, weakly correlated with community size (r = 0.25, p = 0.002). It is found that users suspecting initial HIV infection or first in contact with high-risk behaviors tend to seek help and advice on the social networking platform, rather than immediately going to a hospital for blood tests. Online communities have generated copious amounts of data offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. It is recommended that support through online services for HIV/AIDS consultation and diagnosis be improved to avoid privacy concerns and social discrimination in China.

Spatial and temporal distribution of the vibrionaceae in coastal waters of Hawaii, Australia, and France.

PubMed

Jones, B W; Maruyama, A; Ouverney, C C; Nishiguchi, M K

2007-08-01

Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.

Recent Suicidal Ideation and Suicide Attempts in a Large-Scale Survey of the U.S. Air Force: Prevalences and Demographic Risk Factors

ERIC Educational Resources Information Center

Snarr, Jeffery D.; Heyman, Richard E.; Slep, Amy M. Smith

2010-01-01

One-year prevalences of self-reported noteworthy suicidal ideation and nonfatal suicide attempts were assessed in a large sample of U.S. Air Force active duty members (N = 52,780). Participants completed the 2006 Community Assessment, which was conducted online. Over 3% of male and 5.5% of female participants reported having experienced noteworthy…

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates

USGS Publications Warehouse

Hobbs, Michael T.; Brehme, Cheryl S.

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates.

PubMed

Hobbs, Michael T; Brehme, Cheryl S

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.

Using Realist Synthesis to Develop an Evidence Base from an Identified Data Set on Enablers and Barriers for Alcohol and Drug Program Implementation

ERIC Educational Resources Information Center

Hunter, Barbara; MacLean, Sarah; Berends, Lynda

2012-01-01

The purpose of this paper is to show how "realist synthesis" methodology (Pawson, 2002) was adapted to review a large sample of community based projects addressing alcohol and drug use problems. Our study drew on a highly varied sample of 127 projects receiving funding from a national non-government organisation in Australia between 2002…

Cross-Informant Symptoms from CBCL, TRF, and YSR : Trait and Method Variance in a Normative Sample of Russian Youths

ERIC Educational Resources Information Center

Grigorenko, Elena L.; Geiser, Christian; Slobodskaya, Helena R.; Francis, David J.

2010-01-01

A large community-based sample of Russian youths (n = 841, age M = 13.17 years, SD = 2.51) was assessed with the Child Behavior Checklist (mothers and fathers separately), Teacher's Report Form, and Youth Self-Report. The multiple indicator-version of the correlated trait-correlated method minus one, or CT-C(M-1), model was applied to analyze (a)…

Associations between degraded benthic communities and contaminated sediments: Sabine Lake, Lake Pontchartrain, and Choctawhatchee Bay

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

Engle, V.D.; Summers, J.K.; Macauley, J.M.

1994-12-31

The Environmental Monitoring and Assessment Program for Estuaries (EMAP-E) in the Gulf of Mexico supplements its base sampling effort each year with localized, intensive spatial sampling in selected large estuarine systems. By selecting random locations within 70 km{sup 2} hexagonal areas, individual estuaries were sampled using EMAP methods but at four times the density as base sampling. In 1992, 19 sites were sampled in Lake Pontchartrain, Louisiana. In 1 993, 18 sites were sampled in Sabine Lake, Texas and 12 sites were sampled in Choctawhatchee Bay, Florida. At all sites, sediment grabs were taken and analyzed for benthic species compositionmore » and abundance, for toxicity to Ampelisca, and for organic and inorganic sediment contaminants. An indicator of biotic integrity, the benthic index, was calculated to represent the status of benthic communities. A series of statistical techniques, such as stepwise regression analysis, were employed to determine whether the variation in the benthic index could be associated with variation in sediment contaminants, sediment toxicity, or levels of dissolved oxygen. Spatial distributions of these parameters were examined to determine the geographical co-occurrence of degraded benthic communities and environmental stressors. In Lake Pontchartrain, for example, 85% of the variation in the benthic index was associated with decreased levels of dissolved oxygen, and increased concentrations of PCBs, alkanes, copper, tin, and zinc in the sediments.« less

Effectiveness of Winkler Litter Extraction and Pitfall Traps in Sampling Ant Communities and Functional Groups in a Temperate Forest.

PubMed

Mahon, Michael B; Campbell, Kaitlin U; Crist, Thomas O

2017-06-01

Selection of proper sampling methods for measuring a community of interest is essential whether the study goals are to conduct a species inventory, environmental monitoring, or a manipulative experiment. Insect diversity studies often employ multiple collection methods at the expense of researcher time and funding. Ants (Formicidae) are widely used in environmental monitoring owing to their sensitivity to ecosystem changes. When sampling ant communities, two passive techniques are recommended in combination: pitfall traps and Winkler litter extraction. These recommendations are often based on studies from highly diverse tropical regions or when a species inventory is the goal. Studies in temperate regions often focus on measuring consistent community response along gradients of disturbance or among management regimes; therefore, multiple sampling methods may be unnecessary. We compared the effectiveness of pitfalls and Winkler litter extraction in an eastern temperate forest for measuring ant species richness, composition, and occurrence of ant functional groups in response to experimental manipulations of two key forest ecosystem drivers, white-tailed deer and an invasive shrub (Amur honeysuckle). We found no significant effect of sampling method on the outcome of the ecological experiment; however, we found differences between the two sampling methods in the resulting ant species richness and functional group occurrence. Litter samples approximated the overall combined species richness and composition, but pitfalls were better at sampling large-bodied (Camponotus) species. We conclude that employing both methods is essential only for species inventories or monitoring ants in the Cold-climate Specialists functional group. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

Hunter, C.; Simpson, J.; Kovats, Z.

Sediments from Soda Creek were evaluated using the Sediment Quality Triad as part of investigations being conducted at the Monsanto Company plant in Soda Springs, Idaho. Information collected by an ecological assessment included metal concentrations (arsenic, cadmium, copper, molybdenum, nickel, selenium, silver, and vanadium), benthic fauna community structure, and sediment toxicity. The collected sediments were composed of sandy-silt sized particles, with 2.4% to 9.1% organic carbon. Metal concentrations at sample stations were elevated relative to sediments collected from reference stations. For example, average cadmium concentrations ranged from 13 to 48 mg/kg at sample stations and 0.72 to 3.2 mg/kg atmore » reference stations; selenium concentrations ranged from 4.7 to 91 mg/kg at sample stations and 0.82 to 2.7 mg/kg at reference stations. Soda Creek has a relatively low flow gradient and the benthic fauna at both reference and sample stations was dominated by oligochaete worms and chironomid midge larvae. Taxonomic richness at individual sites ranged from 4.3 to 6.7 and 6 to 10.3 at reference and sample sites, respectively. There was no significant evidence of toxicity at any location sampled. Cluster analysis showed that the benthic community structure of many of the sample stations could not be distinguished from the reference stations. Canonical correlation analysis showed there was a significant relationship between benthic fauna and metal concentration, but there was not a consistent difference between sample and reference stations. For Soda Creek, local phenomena were more significant to benthic community structure than large-scale patterns of metal accumulation. Using the Triad approach, the authors concluded there has been no adverse effect of metal concentrations on the benthic community of Soda Creek.« less

COMPARISON OF LARGE RIVER SAMPLING METHOD USING DIATOM METRICS

EPA Science Inventory

We compared the results of four methods used to assess the algal communities at 60 sites distributed among four rivers. Based on Principle Component Analysis of physical habitat data collected concomitantly with the algal data, sites were separated into those with a mean thalweg...

COMPARISON OF LARGE RIVER SAMPLING METHODS ON ALGAL METRICS

EPA Science Inventory

We compared the results of four methods used to assess the algal communities at 60 sites distributed among four rivers. Based on Principle Component Analysis of physical habitat data collected concomitantly with the algal data, sites were separated into those with a mean thalweg...

Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.

PubMed

Stewart, Frank J; Dalsgaard, Tage; Young, Curtis R; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E; Delong, Edward F

2012-01-01

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

PubMed Central

Stewart, Frank J.; Dalsgaard, Tage; Young, Curtis R.; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E.; DeLong, Edward F.

2012-01-01

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations. PMID:22615914

Comparison of self-reported and biomedical data on hypertension and diabetes: findings from the China Health and Retirement Longitudinal Study (CHARLS)

PubMed Central

Ning, Meng; Zhang, Qiang; Yang, Min

2016-01-01

Objectives We examined the level of agreement between biomedical and self-reported measurements of hypertension and diabetes in a Chinese national community sample, and explored associations of the agreement and possible contextual effects among provinces and geographic regions in China. Design Secondary analysis of a cohort sample. Setting and participants Community samples were drawn from the national baseline survey of the China Health and Retirement Longitudinal Study (CHARLS, 2011–2012) through multistage probability sampling, which included households with members 45 years of age or above with a total sample size of 17 708 individuals. Outcome measures Sensitivity, specificity and κ were used as measurements of agreements or validity; variance of validity measures among provinces and communities was estimated using random-effects models. Results Self-reports for hypertension and diabetes showed high specificity (96.3% and 98.3%, respectively) but low sensitivity (56.3% and 61.5%, respectively). Agreement between self-reported data and biomedical measurements was moderate for both hypertension (κ 0.57) and diabetes (κ 0.65), with respondents who were older, of higher socioeconomic status, better educated and who had hospital admissions in the past 12 months showing stronger agreements than their counterparts. Large and significant variations in the sensitivity among provinces for hypertension, and among communities for both hypertension and diabetes, could neither be attributed to the effects of respondents’ characteristics nor to the contextual effects of city–village differences. Conclusions As a considerable number of people in the overall sample were unaware of their conditions, self-reports will lead to an underestimation of the prevalence of hypertension and diabetes. However, in more developed communities or provinces, self-reported data can be a reliable estimate of the prevalence of the two conditions. Further investigations of contextual effects at provincial and community levels could highlight public health strategies to improve awareness of the two conditions. PMID:26729390

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

PubMed

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

2017-04-01

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

Taenia solium infection in Peru: a collaboration between Peace Corps Volunteers and researchers in a community based study.

PubMed

Watts, Nathaniel S; Pajuelo, Monica; Clark, Taryn; Loader, Maria-Cristina I; Verastegui, Manuela R; Sterling, Charles; Friedland, Jon S; Garcia, Hector H; Gilman, Robert H

2014-01-01

Neurocysticercosis is a leading cause of seizures and epilepsy in most of the world, and it occurs when Taenia solium larval cysts infect the central nervous system. T. solium tapeworm infection is endemic in much of Peru, but there are scarce data on the prevalence in many rural highland communities where it is likely to be hyper-endemic. Peace Corps Volunteers live and work in these communities; however, to our knowledge, they have not been used to facilitate public health research. We utilized Peace Corps Volunteers to estimate the prevalence of T. solium tapeworm infection in seven rural communities in northern Peru. A convenience non-random sampling frame was used. Peace Corps Volunteers facilitated the collection of stool samples (N = 2,328), which were analyzed by sedimentation and microscopy. Niclosamide treatment and purgation preceded species identification, which was done by PCR-REA. Taenia sp. egg-positive stool samples were found in three of the seven communities we surveyed. The overall prevalence of Taenia sp. egg positivity was 2.1% (49/2,328) (95% CI = 1.6-2.8%) with prevalence up to 4.3% (42/977) (95% CI = 3.1-5.8%) by community. All 34 of the specimens tested by PCR-REA were T. solium. The overall prevalence of T. solium tapeworm infection was 1.5% (34/2,328) (95% CI = 1.0-2.0%). Prevalence up to 2.9% (28/977) (95% CI = 1.9-4.1%) by community was observed. This study recorded high T. solium tapeworm prevalence, and identified hyper-endemic rural communities. It demonstrates that synergy between researchers and Peace Corps Volunteers can be an effective means to conducting large-scale, community-based studies in remote areas of Peru.

Mining Consumer Health Vocabulary from Community-Generated Text

PubMed Central

Vydiswaran, V.G. Vinod; Mei, Qiaozhu; Hanauer, David A.; Zheng, Kai

2014-01-01

Community-generated text corpora can be a valuable resource to extract consumer health vocabulary (CHV) and link them to professional terminologies and alternative variants. In this research, we propose a pattern-based text-mining approach to identify pairs of CHV and professional terms from Wikipedia, a large text corpus created and maintained by the community. A novel measure, leveraging the ratio of frequency of occurrence, was used to differentiate consumer terms from professional terms. We empirically evaluated the applicability of this approach using a large data sample consisting of MedLine abstracts and all posts from an online health forum, MedHelp. The results show that the proposed approach is able to identify synonymous pairs and label the terms as either consumer or professional term with high accuracy. We conclude that the proposed approach provides great potential to produce a high quality CHV to improve the performance of computational applications in processing consumer-generated health text. PMID:25954426

A Survey of Residents' Perceptions of the Effect of Large-Scale Economic Developments on Perceived Safety, Violence, and Economic Benefits.

PubMed

Fabio, Anthony; Geller, Ruth; Bazaco, Michael; Bear, Todd M; Foulds, Abigail L; Duell, Jessica; Sharma, Ravi

2015-01-01

Emerging research highlights the promise of community- and policy-level strategies in preventing youth violence. Large-scale economic developments, such as sports and entertainment arenas and casinos, may improve the living conditions, economics, public health, and overall wellbeing of area residents and may influence rates of violence within communities. To assess the effect of community economic development efforts on neighborhood residents' perceptions on violence, safety, and economic benefits. Telephone survey in 2011 using a listed sample of randomly selected numbers in six Pittsburgh neighborhoods. Descriptive analyses examined measures of perceived violence and safety and economic benefit. Responses were compared across neighborhoods using chi-square tests for multiple comparisons. Survey results were compared to census and police data. Residents in neighborhoods with the large-scale economic developments reported more casino-specific and arena-specific economic benefits. However, 42% of participants in the neighborhood with the entertainment arena felt there was an increase in crime, and 29% of respondents from the neighborhood with the casino felt there was an increase. In contrast, crime decreased in both neighborhoods. Large-scale economic developments have a direct influence on the perception of violence, despite actual violence rates.

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

PubMed Central

Kable, Mary E.; Srisengfa, Yanin; Laird, Miles; Zaragoza, Jose; McLeod, Jeremy; Heidenreich, Jessie

2016-01-01

ABSTRACT Currently, the bacterial composition of raw milk in tanker trucks and the outcomes of transfer and storage of that milk at commercial processing facilities are not well understood. We set out to identify the bacteria in raw milk collected for large-scale dairy product manufacturing. Raw bovine milk samples from 899 tanker trucks arriving at two dairy processors in San Joaquin Valley of California during three seasons (spring, summer, and fall) were analyzed by community 16S rRNA gene sequencing. This analysis revealed highly diverse bacterial populations, which exhibited seasonal differences. Raw milk collected in the spring contained the most diverse bacterial communities, with the highest total cell numbers and highest proportions being those of Actinobacteria. Even with this complexity, a core microbiota was present, consisting of 29 taxonomic groups and high proportions of Streptococcus and Staphylococcus and unidentified members of Clostridiales. Milk samples were also collected from five large-volume silos and from 13 to 25 tankers whose contents were unloaded into each of them during 2 days in the summer. Transfer of the milk to storage silos resulted in two community types. One group of silos contained a high proportion of Streptococcus spp. and was similar in that respect to the tankers that filled them. The community found in the other group of silos was distinct and dominated by Acinetobacter. Overall, despite highly diverse tanker milk community structures, distinct milk bacterial communities were selected within the processing facility environment. This knowledge can inform the development of new sanitation procedures and process controls to ensure the consistent production of safe and high-quality dairy products on a global scale. PMID:27555305

Cognitive complaints correlate with depression rather than concurrent objective cognitive impairment in the SAGE baseline sample

PubMed Central

Zlatar, Zvinka Z.; Moore, Raeanne C.; Palmer, Barton W.; Thompson, Wesley K.; Jeste, Dilip V.

2014-01-01

Objective Whether subjective cognitive complaints are suggestive of depression or concurrent cognitive impairment in older adults without dementia remains unclear. The current study examined this question in a large (N=1,000), randomly-selected community-based sample of adults ages 51-99 without a formal diagnosis of dementia (Successful AGing Evaluation study-SAGE). Methods The modified Telephone Interview for Cognitive Status (TICS-m) measured objective cognitive function, the Cognitive Failures Questionnaire (CFQ) measured subjective cognitive complaints, and the Patient Health Questionnaire (PHQ-9) measured depression. Spearman rho correlations and linear regression models were conducted to examine the relationship among variables in the baseline SAGE sample. Results There was a weak association between TICS-m and CFQ scores (rho= -.12); however a moderate to large association was observed for CFQ and PHQ-9 (rho= .44). Scores on the CFQ were not associated with TICS-m scores (β=-.03, p=.42) after controlling for PHQ-9 and variables of interest, such as age, gender, ethnicity, and physical functioning, while PHQ-9 was significantly associated with CFQ scores (β=.46, p<.001) after controlling for variables of interest. Conclusions Subjective cognitive complaints are more likely related to symptoms of depression rather than concurrent cognitive impairment in a large cross-section of community-dwelling adults without a formal diagnosis of dementia. PMID:24614203

The size of an ethno-cultural community as a social determinant of health for Chinese seniors.

PubMed

Chau, Shirley; Lai, Daniel W L

2011-12-01

The present study investigated the link between the sizes of the Chinese community to the health of Chinese seniors in Canada. A secondary data analysis of survey data from a representative sample of 2,272 Chinese older adults aged 55 and over was conducted. Hierarchical regression analyses were performed to assess the effects of the size of Chinese communities in Chinese seniors' health. Chinese seniors residing in the community with a small Chinese population reported better physical and mental health than the Chinese seniors residing in communities with a larger Chinese population. The findings were contrary to expectations that health of Chinese seniors should be higher in cities with large Chinese communities. These findings raise new questions for future investigations into the dynamics and impact of ethnic community size, and the importance of studying intragroup differences within ethno-cultural groups to better understand health disparities in ethnic groups.

Temporal Stability of the Human Skin Microbiome.

PubMed

Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

2016-05-05

Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states. Copyright © 2016 Elsevier Inc. All rights reserved.

Prevalence of Sexual Dysfunctions

PubMed Central

Simons, Jeffrey; Carey, Michael P.

2008-01-01

Ten years of research that has provided data regarding the prevalence of sexual dysfunctions is reviewed. A thorough review of the literature identified 52 studies that have been published in the 10 years since an earlier review by Spector and Carey (1990). Community samples indicate a current prevalence of 0 - 3% for male orgasmic disorder, 0 - 5% for erectile disorder, and 0 - 3% for male hypoactive sexual desire disorder. Pooling current and 1-year figures provides community prevalence estimates of 7 - 10% for female orgasmic disorder and 4 - 5% for premature ejaculation. Stable community estimates of the current prevalence for the other sexual dysfunctions remain unavailable. Prevalence estimates obtained from primary care and sexuality clinic samples are characteristically higher. Although a relatively large number of studies have been conducted since Spector and Carey’s (1990) review, the lack of methodological rigor of many studies limits the confidence that can be placed in these findings. PMID:11329727

Recruitment and baseline characteristics of the Community of Voices choir study to promote the health and well-being of diverse older adults.

PubMed

Johnson, Julene K; Gregorich, Steven E; Acree, Michael; Nápoles, Anna M; Flatt, Jason D; Pounds, Dana; Pabst, Alexandria; Stewart, Anita L

2017-12-01

To describe the recruitment and baseline results of the Community of Voices study that aims to examine the effect of a community choir intervention on the health and well-being of older adults from diverse racial/ethnic and socioeconomic backgrounds. Using community-based participatory research methods, we recruited adults age 60 and over from 12 Administration on Aging-supported senior centers in San Francisco into a 2-arm cluster-randomized controlled trial of the community choir intervention. Multiple outreach methods were used. We tracked outreach, screening, and recruitment metrics and collected demographics and baseline outcomes via community-based, interviewer-administered surveys and performance measures of cognition, physical function, and psychosocial variables. The study contacted 819 individuals, screened 636, and enrolled 390 diverse older adults over a 42-month, phased recruitment period. The mean age was 71.2 (SD = 7.3), and the majority were women. Two-thirds of the sample are non-white, and 20% of participants reported having financial hardship. Outreach and recruitment methods used in the Community of Voices trial facilitated enrollment of a large proportion of minority and lower-SES older adults in the final sample. Similar recruitment approaches could serve as a model for recruiting diverse racial/ethnic and socioeconomic older adults into research.

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows.

PubMed

Tapio, Ilma; Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R John; Bayat, Ali R; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Shingfield, Kevin J; Vilkki, Johanna

2017-01-01

The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions.

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

PubMed Central

Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R. John; Bayat, Ali R.; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Vilkki, Johanna

2017-01-01

The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions. PMID:28704445

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area

PubMed Central

Leight, Andrew K.; Crump, Byron C.; Hood, Raleigh R.

2018-01-01

Routine monitoring of shellfish growing waters for bacteria indicative of human sewage pollution reveals little about the bacterial communities that co-occur with these indicators. This study investigated the bacterial community, potential pathogens, and fecal indicator bacteria in 40 water samples from a shellfish growing area in the Chesapeake Bay, USA. Bacterial community composition was quantified with deep sequencing of 16S rRNA gene amplicons, and absolute gene abundances were estimated with an internal standard (Thermus thermophilus genomes). Fecal coliforms were quantified by culture, and Vibrio vulnificus and V. parahaemolyticus with quantitative PCR. Fecal coliforms and V. vulnificus were detected in most samples, and a diverse assemblage of potential human pathogens were detected in all samples. These taxa followed two general patterns of abundance. Fecal coliforms and 16S rRNA genes for Enterobacteriaceae, Aeromonas, Arcobacter, Staphylococcus, and Bacteroides increased in abundance after a 1.3-inch rain event in May, and, for some taxa, after smaller rain events later in the season, suggesting that these are allochthonous organisms washed in from land. Clostridiaceae and Mycobacterium 16S rRNA gene abundances increased with day of the year and were not positively related to rainfall, suggesting that these are autochthonous organisms. Other groups followed both patterns, such as Legionella. Fecal coliform abundance did not correlate with most other taxa, but were extremely high following the large rainstorm in May when they co-occurred with a broad range of potential pathogen groups. V. vulnificus were absent during the large rainstorm, and did not correlate with 16S rRNA abundances of Vibrio spp. or most other taxa. These results highlight the complex nature of bacterial communities and the limited utility of using specific bacterial groups as indicators of pathogen presence. PMID:29593669

Self-Efficacy and Nutrition Education: A Study of the Effect of an Intervention with Faith Community Nurses.

PubMed

Gotwals, Beth

2018-02-01

The faith community provides an important access point for practice focused on population health at a time when health issues such as obesity and overweight are affecting large number of Americans. The purpose of this study was to examine faith community nurses' self-efficacy perceptions following a nutrition educational intervention. A convenience sample of 92 faith community nurses were randomly assigned to experimental and control groups. The t-distribution analysis revealed significant differences between the nutrition knowledge self-efficacy (p = .016) and nutrition counseling self-efficacy (p = .010) post-test scores for the experimental and control groups. This type of educational intervention provides a model to be used with faith community nurses as they integrate faith and health in this setting.

Consistency of Bottom Fish Communities in the Beaufort Sea Within and Between Years

NASA Astrophysics Data System (ADS)

Norcross, B.; Holladay, B.

2016-02-01

Fish communities in the Arctic may be indicators of change due to climate and oil and gas exploration. An initial benchmark is generally established by sampling a set of sites in multiple years sequentially to estimate interannual variability. Standard practice is to conduct one trawl haul per station. Establishing the annual frequency of sampling and minimum number of hauls per station necessary to detect changes in demersal fish communities is essential to designing a monitoring program. Using small bottom trawls, we assessed interannual variability of bottom fish communities between 2013 and 2014 in the eastern US Beaufort Sea at eight depths 20-1000 m on each of four transects. In 2014, to determine if one haul per station was representative of a site, replicate hauls were made at stations along one transect at the US-Canada border. The similarity among replicate hauls within a single year was excellent, indicating that one haul per station was representative of fish communities. There were distinctly different bottom fish communities on the Beaufort Sea shelf (20-100 m) and slope (200-1000 m). Shelf communities had higher abundances of smaller fishes; whereas slope communities had fewer, but larger, individuals. There was no change in fish abundance between years, but there was interannual variability in the biomass of fish communities on the slope. However, as few fishes were captured at deep stations, the difference between catching and not catching a single large heavy fish affected relative biomass significantly, which may distort the conclusion of interannual variability. Furthermore, these replicate hauls occurred in the eastern Beaufort Sea, which appears to have fewer fish species and in lower abundance than the western Beaufort Sea. The similarity within replicates may not be as striking in a more diverse environment, however this study shows that in this region of the Arctic, it is likely sufficient to forego replicate sampling at a station in one year and season, and sequential years of sampling in that season, when characterizing bottom fish communities within a long-term study of community stability.

Rapid screening for perceived cognitive impairment in major depressive disorder.

PubMed

Iverson, Grant L; Lam, Raymond W

2013-05-01

Subjectively experienced cognitive impairment is common in patients with mood disorders. The British Columbia Cognitive Complaints Inventory (BC-CCI) is a 6-item scale that measures perceived cognitive problems. The purpose of this study is to examine the reliability of the scale in healthy volunteers and depressed patients and to evaluate the sensitivity of the measure to perceived cognitive problems in depression. Participants were 62 physician-diagnosed inpatients or outpatients with depression, who had independently confirmed diagnoses on the Structured Clinical Interview for DSM-IV, and a large sample of healthy community volunteers (n=112). The internal consistency reliability of the BC-CCI was α=.86 for patients with depression and α=.82 for healthy controls. Principal components analyses revealed a one-factor solution accounting for 54% of the total variability in the control sample and a 2-factor solution (cognitive impairment and difficulty with expressive language) accounting for 76% of the variance in the depression sample. The total score difference between the groups was very large (Cohen's d=2.2). The BC-CCI has high internal consistency in both depressed patients and community controls, despite its small number of items. The test is sensitive to cognitive complaints in patients with depression.

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

PubMed

Gilbert, Jack A; Field, Dawn; Huang, Ying; Edwards, Rob; Li, Weizhong; Gilna, Paul; Joint, Ian

2008-08-22

Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

Classification of medication incidents associated with information technology.

PubMed

Cheung, Ka-Chun; van der Veen, Willem; Bouvy, Marcel L; Wensing, Michel; van den Bemt, Patricia M L A; de Smet, Peter A G M

2014-02-01

Information technology (IT) plays a pivotal role in improving patient safety, but can also cause new problems for patient safety. This study analyzed the nature and consequences of a large sample of IT-related medication incidents, as reported by healthcare professionals in community pharmacies and hospitals. The medication incidents submitted to the Dutch central medication incidents registration (CMR) reporting system were analyzed from the perspective of the healthcare professional with the Magrabi classification. During classification new terms were added, if necessary. The principal source of the IT-related problem, nature of error. Additional measures: consequences of incidents, IT systems, phases of the medication process. From March 2010 to February 2011 the CMR received 4161 incidents: 1643 (39.5%) from community pharmacies and 2518 (60.5%) from hospitals. Eventually one of six incidents (16.1%, n=668) were related to IT; in community pharmacies more incidents (21.5%, n=351) were related to IT than in hospitals (12.6%, n=317). In community pharmacies 41.0% (n=150) of the incidents were about choosing the wrong medicine. Most of the erroneous exchanges were associated with confusion of medicine names and poor design of screens. In hospitals 55.3% (n=187) of incidents concerned human-machine interaction-related input during the use of computerized prescriber order entry. These use problems were also a major problem in pharmacy information systems outside the hospital. A large sample of incidents shows that many of the incidents are related to IT, both in community pharmacies and hospitals. The interaction between human and machine plays a pivotal role in IT incidents in both settings.

Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique.

PubMed

Nam, Young-Do; Park, So-lim; Lim, Seong-Il

2012-04-01

Kochujang is a traditional Korean fermented food that is made with red pepper, glutinous rice, salt, and soybean. Kochujang is fermented by naturally occurring microorganisms through which it obtains various health-promoting properties. In this study, the bacterial diversities of 9 local and 2 commercial brands of kochujang were analyzed with a barcoded pyrosequencing technique targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. Through the analysis of 13524 bacterial pyrosequences, 223 bacterial species were identified, most of which converged on the phylum Firmicutes (average 93.1%). All of the kochujang samples were largely populated (>90.9% of abundance) by 12 bacterial families, and Bacillaceae showed the highest abundance in all but one sample. Bacillus subtilis and B. licheniformis were the most dominant bacterial species and were broadly distributed among the kochujang samples. Each sample contained a high abundance of region-specific bacterial species, such as B. sonorensis, B. pumilus, Weissella salipiscis, and diverse unidentified Bacillus species. Phylotype- and phylogeny-based community comparison analysis showed that the microbial communities of the two commercial brands were different from those of the local brands. Moreover, each local brand kochujang sample had region-specific microbial community reflecting the manufacturing environment. © 2012 Institute of Food Technologists®

Microbial Community Composition of Tap Water and Biofilms Treated with or without Copper-Silver Ionization.

PubMed

Stüken, Anke; Haverkamp, Thomas H A; Dirven, Hubert A A M; Gilfillan, Gregor D; Leithaug, Magnus; Lund, Vidar

2018-03-20

Copper-silver ionization (CSI) is an in-house water disinfection method primarily installed to eradicate Legionella bacteria from drinking water distribution systems (DWDS). Its effect on the abundance of culturable Legionella and Legionella infections has been documented in several studies. However, the effect of CSI on other bacteria in DWDS is largely unknown. To investigate these effects, we characterized drinking water and biofilm communities in a hospital using CSI, in a neighboring building without CSI, and in treated drinking water at the local water treatment plant. We used 16S rDNA amplicon sequencing and Legionella culturing. The sequencing results revealed three distinct water groups: (1) cold-water samples (no CSI), (2) warm-water samples at the research institute (no CSI), and (3) warm-water samples at the hospital (after CSI; ANOSIM, p < 0.001). Differences between the biofilm communities exposed and not exposed to CSI were less clear (ANOSIM, p = 0.022). No Legionella were cultured, but limited numbers of Legionella sequences were recovered from all 25 water samples (0.2-1.4% relative abundance). The clustering pattern indicated local selection of Legionella types (Kruskal-Wallis, p < 0.001). Furthermore, one unclassified Betaproteobacteria OTU was highly enriched in CSI-treated warm water samples at the hospital (Kruskal-Wallis, p < 0.001).

Prevalence of antibiotic resistance genes in bacterial communities associated with Cladophora glomerata mats along the nearshore of Lake Ontario.

PubMed

Ibsen, Michael; Fernando, Dinesh M; Kumar, Ayush; Kirkwood, Andrea E

2017-05-01

The alga Cladophora glomerata can erupt in nuisance blooms throughout the lower Great Lakes. Since bacterial abundance increases with the emergence and decay of Cladophora, we investigated the prevalence of antibiotic resistance (ABR) in Cladophora-associated bacterial communities up-gradient and down-gradient from a large sewage treatment plant (STP) on Lake Ontario. Although STPs are well-known sources of ABR, we also expected detectable ABR from up-gradient wetland communities, since they receive surface run-off from urban and agricultural sources. Statistically significant differences in aquatic bacterial abundance and ABR were found between down-gradient beach samples and up-gradient coastal wetland samples (ANOVA, Holm-Sidak test, p < 0.05). Decaying and free-floating Cladophora sampled near the STP had the highest bacterial densities overall, including on ampicillin- and vancomycin-treated plates. However, quantitative polymerase chain reaction analysis of the ABR genes ampC, tetA, tetB, and vanA from environmental communities showed a different pattern. Some of the highest ABR gene levels occurred at the 2 coastal wetland sites (vanA). Overall, bacterial ABR profiles from environmental samples were distinguishable between living and decaying Cladophora, inferring that Cladophora may control bacterial ABR depending on its life-cycle stage. Our results also show how spatially and temporally dynamic ABR is in nearshore aquatic bacteria, which warrants further research.

Oceanographic and topographic conditions structure benthic meiofauna communities in the Weddell Sea, Bransfield Strait and Drake Passage (Antarctic)

NASA Astrophysics Data System (ADS)

Veit-Köhler, Gritta; Durst, Stephan; Schuckenbrock, Jan; Hauquier, Freija; Durán Suja, Laura; Dorschel, Boris; Vanreusel, Ann; Martínez Arbizu, Pedro

2018-03-01

The marine environment of the tip of the Antarctic Peninsula is characterised by three oceanographically distinct regions for which we linked continental-slope meiofaunal patterns and environmental drivers on a large scale (100-300 km among ecoregions). Samples for meiofauna communities and sediment analyses were collected with a multicorer, water-column data were derived from water samples and CTD recordings. Meiofauna communities including individuals from 19 higher taxa were compared to a set of 16 environmental variables. We detected significant differences between the communities of Weddell Sea and those of Bransfield Strait and Drake Passage. The amount of phytopigments in the sediment, their freshness and the silt and clay content were driving factors for this separation. The highest meiofauna abundances were found at slopes in the Weddell Sea. Food banks may facilitate high standing stocks. There, the highest ever recorded copepod percentages for the Antarctic were related to the highest phytopigment contents while nematodes were extremely abundant even in deeper sediment layers at stations with fresh organic material. For Bransfield Strait and Drake Passage a sampling scheme of slopes and adjacent troughs was applied. The two regions were divided into three geographical "areas" with the two "habitat" types investigated for each area. Multivariate non-parametric permutational analysis of variance (PERMANOVA) showed that in Bransfield Strait slope and trough meiofauna communities differed significantly in all geographical areas while in Drake Passage this was only the case in the East. These differences were explained best by the regionally and topographically distinct characteristics of 7 out of 11 water-column and sediment-bound factors related to sediment grain size, food quantity and quality, water temperature and salinity. Environmental drivers of the benthic habitat are dependent on large-scale oceanographic conditions and are thus sensitive to changes in water mass characteristics, sea-ice cover and the related primary production.

Plant community succession in modern Yellow River Delta, China*

PubMed Central

Zhang, Gao-sheng; Wang, Ren-qing; Song, Bai-min

2007-01-01

Data were collected in different successional stages using a simultaneous sampling method and analyzed through quantitative classification method. Three large groups and 12 classes were made to represent the community patterns of three succession stages and 12 succession communities. The succession series of plant community in the study area was as follows: saline bare land→community Suaeda salsa→community Tamarix chinensis→grassland. Succession degree and succession process of 12 succession communities were calculated. Most of these communities were in the lower succession stage, however, community Phragmites communis+Glycine soja and community Imperata cylindrica+G. soja were close to the succession stage of grassland climax. Five species diversity indices were used to study the changes in species richness, species evenness and diversity during succession of community. Heterogeneity index and richness index increased gradually during the community succession process, but species evenness tended to decrease with succession development. The relation between succession and environment was studied by ordination technique, and the results showed that the soil salt content was an important factor to halarch succession of the modern Yellow River Delta. It affected community structure, species composition and succession process. PMID:17657854

Romanticism as a function of age, sex, and ethnicity.

PubMed

Regan, Pamela C; Anguiano, Carlos

2010-12-01

This study examined the association between romanticism (operationalized as mean score on the Romantic Beliefs Scale) and age, sex, and ethnicity in a large community sample (N = 436). Age was negatively correlated with romanticism scores; as age increased, romanticism scores decreased. No sex differences were found; men and women had similar, moderate scores. Although ethnicity largely was unrelated to romanticism, Asian/Pacific Islander participants were significantly more romantic than were African-American participants.

Multi-Omics Profiling of Phytoplankton Community Metabolism: Linking Meta-Transcriptomics and Metabolomics to Elucidate Phytoplankton Physiology in a Model Coastal System

NASA Astrophysics Data System (ADS)

Kujawinski, E. B.; Longnecker, K.; Alexander, H.; Dyhrman, S.; Jenkins, B. D.; Rynearson, T. A.

2016-02-01

Phytoplankton blooms in coastal areas contribute a large fraction of primary production to the global oceans. Despite their central importance, there are fundamental unknowns in phytoplankton community metabolism, which limit the development of a more complete understanding of the carbon cycle. Within this complex setting, the tools of systems biology hold immense potential for profiling community metabolism and exploring links to the carbon cycle, but have rarely been applied together in this context. Here we focus on phytoplankton community samples collected from a model coastal system over a three-week period. At each sampling point, we combined two assessments of metabolic function: the meta-transcriptome, or the genes that are expressed by all organisms at each sampling point, and the metabolome, or the intracellular molecules produced during the community's metabolism. These datasets are inherently complementary, with gene expression likely to vary in concert with the concentrations of metabolic intermediates. Indeed, preliminary data show coherence in transcripts and metabolites associated with nutrient stress response and with fixed carbon oxidation. To date, these datasets are rarely integrated across their full complexity but together they provide unequivocal evidence of specific metabolic pathways by individual phytoplankton taxa, allowing a more comprehensive systems view of this dynamic environment. Future application of multi-omic profiling will facilitate a more complete understanding of metabolic reactions at the foundation of the carbon cycle.

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

PubMed Central

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m. PMID:24205246

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

PubMed

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway).

PubMed

Mateos-Rivera, Alejandro; Yde, Jacob C; Wilson, Bryan; Finster, Kai W; Reigstad, Laila J; Øvreås, Lise

2016-04-01

Microbial communities in the glacier forefield of Styggedalsbreen, Norway, were investigated along a chronosequence from newly exposed soil to vegetated soils using next-generation sequencing of the 16S rRNA gene. In order to monitor the short-term effect of temperature on community successions along the soil gradient, the soil samples were incubated at three different temperatures (5°C, 10°C and 22°C). The microbial community composition along the chronosequence differed according to distance from the glacial terminus and incubation temperature. Samples close to the glacier terminus were dominated by Proteobacteria at 5°C and 10°C, while at 22°C members of Chloroflexi, Acidobacteria and Verrucomicrobia in addition to Proteobacteria accounted for most of the diversity, indicating that sites close to the glacier terminus are more closely related to former subglacial environments. Within the Archaea domain, members of the phylum Euryarchaeota dominated in samples closer to the glacier terminus with a shift to members of the phyla Thaumarchaeota-Crenarchaeota with increased soil age. Our data indicate that composition and diversity of the microbial communities along the glacier forefield depend not only on exposure time but are also to a large degree influenced by soil surface temperature and soil maturation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

PubMed Central

Tedjo, Danyta I.; Jonkers, Daisy M. A. E.; Savelkoul, Paul H.; Masclee, Ad A.; van Best, Niels; Pierik, Marieke J.; Penders, John

2015-01-01

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80°C, -20°C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80°C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80°C versus the other methods and -80°C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80°C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4°C or room temperature) or freezing at -20°C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders. PMID:26024217

Assessing sediments from Upper Mississippi River navigational pools using a benthic invertebrate community evaluation and the sediment quality triad approach

USGS Publications Warehouse

Canfield, T.J.; Brunson, E.L.; Dwyer, F.J.; Ingersoll, C.G.; Kemble, N.E.

1998-01-01

Benthic invertebrate samples were collected from 23 pools in the Upper Mississippi River (UMR) and from one station in the Saint Croix River (SCR) as part of a study to assess the effects of the extensive flooding of 1993 on sediment contamination in the UMR system. Sediment contaminants of concern included both organic and inorganic compounds. Oligochaetes and chironomids constituted over 80% of the total abundance in samples from 14 of 23 pools in the UMR and SCR samples. Fingernail clams comprised a large portion of the community in three of 23 UMR pools and exceeded abundances of 1,000/m2 in five of 23 pools. Total abundance ranged from 250/m2 in samples from pool 1 to 22,389/m2 in samples from pool 19. Abundance values are comparable with levels previously reported in the literature for the UMR. Overall frequency of chironomid mouthpart deformities was 3% (range 0-13%), which is comparable to reported incidence of deformities in uncontaminated sediments previously evaluated. Sediment contamination was generally low in the UMR pools and the SCR site. Correlations between benthic measures and sediment chemistry and other abiotic parameters exhibited few significant or strong correlations. The sediment quality triad (Triad) approach was used to evaluate data from laboratory toxicity tests, sediment chemistry, and benthic community analyses; it showed that 88% of the samples were not scored as impacted based on sediment toxicity, chemistry, and benthic measures. Benthic invertebrate distributions and community structure within the UMR in the samples evaluated in the present study were most likely controlled by factors independent of contaminant concentrations in the sediments.

Mindfulness-based stress reduction (MBSR) and distress in a community-based sample.

PubMed

Evans, Susan; Ferrando, Stephen; Carr, Corey; Haglin, Dean

2011-01-01

Numerous studies have found Mindfulness-based stress reduction (MBSR) to be useful for a wide range of problems including anxiety, pain and coping with a medical illness. The primary goal of this study was to evaluate the effectiveness of an 8-week MBSR programme in relieving distress in a community based sample. Subjects (n = 14) were participants in the MBSR programme at a major academic medical center and completed the Profile of Mood States (POMS) and the Mindful Attention Awareness Scale (MAAS) prior to starting the class and at the end of the 8-week course. Means and standard deviations were computed for the pre-and post-POMS total and subscale measures and the MAAS. Wilcoxon Signed Ranks Test was conducted. There were significant reductions on multiple dimensions of distress on the POMS as well as a significant increase in mindful awareness as measured by the MAAS. These results suggest that MBSR appears to be associated with a reduction of distress and increased awareness of everyday life experiences in a sample of residents living in a large urban community.  Copyright © 2010 John Wiley & Sons, Ltd.

Evaluation of tire reefs for enhancing aquatic communities in concrete-lined canals

USGS Publications Warehouse

Mueller, Gordon; Liston, Charles R.

1994-01-01

Large earthen canals in the arid southwest are being lined with concrete to reduce seepage and conserve limited water supplies. Lining reduces habitat and increases operational velocities (relative to unaltered streams), which are detrimental to aquatic communities. Fish communities that become reestablished in these waterways exhibit lower species diversity, densities, and biomass than they did in the former earthen canals. Placement of low-profile tire reefs in the Coachella Canal, California, and the Hayden-Rhodes Aqueduct, Arizona, reversed these trends. Comparative sampling revealed that invertebrate and fish densities were 3 and 20 times higher, respectively, in reef areas than in typical canal sections without reefs. Tire reefs are recommended as an effective means of enhancing aquatic communities in concrete canals.

Sleep habits, insomnia, and daytime sleepiness in a large and healthy community-based sample of New Zealanders.

PubMed

Wilsmore, Bradley R; Grunstein, Ronald R; Fransen, Marlene; Woodward, Mark; Norton, Robyn; Ameratunga, Shanthi

2013-06-15

To determine the relationship between sleep complaints, primary insomnia, excessive daytime sleepiness, and lifestyle factors in a large community-based sample. Cross-sectional study. Blood donor sites in New Zealand. 22,389 individuals aged 16-84 years volunteering to donate blood. N/A. A comprehensive self-administered questionnaire including personal demographics and validated questions assessing sleep disorders (snoring, apnea), sleep complaints (sleep quantity, sleep dissatisfaction), insomnia symptoms, excessive daytime sleepiness, mood, and lifestyle factors such as work patterns, smoking, alcohol, and illicit substance use. Additionally, direct measurements of height and weight were obtained. One in three participants report < 7-8 h sleep, 5 or more nights per week, and 60% would like more sleep. Almost half the participants (45%) report suffering the symptoms of insomnia at least once per week, with one in 5 meeting more stringent criteria for primary insomnia. Excessive daytime sleepiness (evident in 9% of this large, predominantly healthy sample) was associated with insomnia (odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50 to 2.05), depression (OR 2.01, CI 1.74 to 2.32), and sleep disordered breathing (OR 1.92, CI 1.59 to 2.32). Long work hours, alcohol dependence, and rotating work shifts also increase the risk of daytime sleepiness. Even in this relatively young, healthy, non-clinical sample, sleep complaints and primary insomnia with subsequent excess daytime sleepiness were common. There were clear associations between many personal and lifestyle factors-such as depression, long work hours, alcohol dependence, and rotating shift work-and sleep problems or excessive daytime sleepiness.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

PubMed

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

PubMed Central

Campbell, Barbara J.; Polson, Shawn W.; Zeigler Allen, Lisa; Williamson, Shannon J.; Lee, Charles K.; Wommack, K. Eric; Cary, S. Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments. PMID:23898323

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

PubMed

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

2010-08-01

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

When Can Species Abundance Data Reveal Non-neutrality?

PubMed Central

Al Hammal, Omar; Alonso, David; Etienne, Rampal S.; Cornell, Stephen J.

2015-01-01

Species abundance distributions (SAD) are probably ecology’s most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

Is Pubertal Timing Associated with Psychopathology in Young Adulthood?

ERIC Educational Resources Information Center

Graber, Julia A.; Seeley, John R.; Brooks-Gunn, Jeanne; Lewinsohn, Peter M.

2004-01-01

Objective: This investigation tested whether the timing of puberty continued to be associated with experiences of psychopathology (symptoms and disorders) from mid-adolescence into young adulthood. Method: At age 24, 931 participants from a large community sample, who had been interviewed twice during adolescence, completed a telephone interview…

Individualism, Collectivism, and Delinquency in Asian American Adolescents

ERIC Educational Resources Information Center

Le, Thao N.; Stockdale, Gary D.

2005-01-01

Although the study of delinquency has previously focused on identifying individual, family, peer, and social risk and protective factors, little empirical research has studied cultural factors and their relations to delinquency. In a large community sample of 329 Chinese, Cambodian, Laotian/Mien, and Vietnamese youths, individualism was positively…

The Relationship between Father Residency and a Child's ADHD Symptoms

ERIC Educational Resources Information Center

Sulak, Tracey N.; Barnard-Brak, Lucy; Frederick, Karen

2012-01-01

Attention deficit hyperactivity disorder (ADHD) is a commonly diagnosed neuropsychological disorder among school-aged children. The purpose of the current study was to examine the relationship between father residency status and children's symptoms of ADHD using a large, nationally representative and community-based sample. To achieve this…

Effects of small impoundments on downstream crayfish assemblages

Treesearch

Susan B. Adams

2013-01-01

Dams and impoundments, both large and small, affect downstream physicochemical characteristics and up- and downstream biotic communities. I tested whether small dams and their impoundments altered downstream crayfish assemblages in northern Mississippi. I sampled crayfish and measured physicochemical variables at 4 sites downstream of impoundments (outlet sites) and 4...

The relationship between postpartum depression, domestic violence, childhood violence, and substance use: epidemiologic study of a large community sample.

PubMed

Dennis, Cindy-Lee; Vigod, Simone

2013-04-01

The objective of this study was to determine the contribution of interpersonal violence and substance use to the prediction of postpartum depressive symptomatology. A community-based sample of 634 women in British Columbia, Canada was screened for interpersonal violence and substance use using the Antenatal Psychosocial Health Assessment (ALPHA) form. Of these women, 497 (78%) subsequently completed questionnaires at 8 weeks postpartum to assess for depressive symptomatology using the Edinburgh Postnatal Depression Scale (EPDS). A predictive model for postpartum depressive symptomatology (EPDS > 9) was developed using regression analysis. Findings suggest that women who experience past or current interpersonal violence or personal or partner substance use problems should be considered for targeted screening for postpartum depression (PPD).

Detecting selection effects in community implementations of family-based substance abuse prevention programs.

PubMed

Hill, Laura G; Goates, Scott G; Rosenman, Robert

2010-04-01

To calculate valid estimates of the costs and benefits of substance abuse prevention programs, selection effects must be identified and corrected. A supplemental comparison sample is typically used for this purpose, but in community-based program implementations, such a sample is often not available. We present an evaluation design and analytic approach that can be used in program evaluations of real-world implementations to identify selection effects, which in turn can help inform recruitment strategies, pinpoint possible selection influences on measured program outcomes, and refine estimates of program costs and benefits. We illustrate our approach with data from a multisite implementation of a popular substance abuse prevention program. Our results indicate that the program's participants differed significantly from the population at large.

Estimating and comparing microbial diversity in the presence of sequencing errors

PubMed Central

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. PMID:26855872

Field Testing New Plot Designs and Methods for Determining Hydrophytic Vegetation during Wetland Delineations in the United States

DTIC Science & Technology

2014-03-01

Trees and woody vines are sampled in large plots with 9 m (30 ft) radii. Saplings, shrubs , and herbs are sampled in nested smaller plots with 2 m (5 ft... woody vines in 9 m (30 ft) radius plots and saplings, shrubs , and herbaceous species in 2 m (5 ft) radius plots. In herbaceous meadows, only the 2 m (5...suggests stratifying vegetation by growth forms of trees, shrubs , herbs, and vines and sampling plant communities by using nested circular plots

When micro meets macro: microbial lipid analysis and ecosystem ecology

NASA Astrophysics Data System (ADS)

Balser, T.; Gutknecht, J.

2008-12-01

There is growing interest in linking soil microbial community composition and activity with large-scale field studies of nutrient cycling or plant community response to disturbances. And while analysis of microbial communities has moved rapidly in the past decade from culture-based to non-culture based techniques, still it must be asked what have we gained from the move? How well does the necessarily micro-scale of microbial analysis allow us to address questions of interest at the macro-scale? Several challenges exist in bridging the scales, and foremost is the question of methodological feasibility. Past microbiological methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. We describe the use of a modified lipid extraction method to generate microbial community data sets that allow us to match landscape-scale or long-term ecological studies with microbial community data. We briefly discuss the challenges and advantages associated with lipid analysis as an approach to addressing ecosystem ecological studies, and provide examples from our research in ecosystem restoration and recovery following disturbance and climate change.

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates

PubMed Central

2017-01-01

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing. PMID:28981533

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

PubMed

Hesse, Cedar N; Torres-Cruz, Terry J; Tobias, Terri Billingsley; Al-Matruk, Maryam; Porras-Alfaro, Andrea; Kuske, Cheryl R

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO 2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project

PubMed Central

Vecchio-Pagan, Briana; Bewick, Sharon; Mainali, Kumar; Karig, David K.; Fagan, William F.

2017-01-01

Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates. PMID:28769875

Near-bottom pelagic bacteria at a deep-water sewage sludge disposal site.

PubMed

Takizawa, M; Straube, W L; Hill, R T; Colwell, R R

1993-10-01

The epibenthic bacterial community at deep-ocean sewage sludge disposal site DWD-106, located approximately 106 miles (ca. 196 km) off the coast of New Jersey, was assessed for changes associated with the introduction of large amounts of sewage sludge. Mixed cultures and bacterial isolates obtained from water overlying sediment core samples collected at the deep-water (2,500 m) municipal sewage disposal site were tested for the ability to grow under in situ conditions of temperature and pressure. The responses of cultures collected at a DWD-106 station heavily impacted by sewage sludge were compared with those of samples collected from a station at the same depth which was not contaminated by sewage sludge. Significant differences were observed in the ability of mixed bacterial cultures and isolates from the two sites to grow under deep-sea pressure and temperature conditions. The levels of sludge contamination were established by enumerating Clostridium perfringens, a sewage indicator bacterium, in sediment samples from the two sites. The results of hybridization experiments in which DNAs extracted directly from the water overlying sediment core samples were used indicate that the reference site epibenthic community, the disposal site epibenthic community, and the community in a surface sludge plume share many members. Decreased culturability of reference site mixed cultures in the presence of sewage sludge was observed. Thus, the culturable portions of both the autochthonous and allochthonous bacterial communities at the disposal site may be inhibited in situ, the former by sewage sludge and the latter by high pressure and low temperature.

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

DOE PAGES

Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

2014-07-15

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

NASA Astrophysics Data System (ADS)

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-10-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.

PubMed

Jeffries, Thomas C; Ostrowski, Martin; Williams, Rohan B; Xie, Chao; Jensen, Rachelle M; Grzymski, Joseph J; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K; Neches, Russell Y; Drautz-Moses, Daniela I; Chénard, Caroline; Paulsen, Ian T; Lauro, Federico M

2015-10-20

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a 'citizen oceanography' approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

PubMed Central

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-01-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system. PMID:26481089

Spatial distribution of vanadium and microbial community responses in surface soil of Panzhihua mining and smelting area, China.

PubMed

Cao, Xuelong; Diao, Muhe; Zhang, Baogang; Liu, Hui; Wang, Song; Yang, Meng

2017-09-01

Spatial distribution of vanadium in surface soils from different processing stages of vanadium-bearing titanomagnetite in Panzhihua mining and smelting area (China) as well as responses of microbial communities including bacteria and fungi to vanadium were investigated by fieldwork and laboratory incubation experiment. The vanadium contents in this region ranged from 149.3 to 4793.6 mg kg -1 , exceeding the soil background value of vanadium in China (82 mg kg -1 ) largely. High-throughput DNA sequencing results showed bacterial communities from different manufacturing locations were quite diverse, but Bacteroidetes and Proteobacteria were abundant in all samples. The contents of organic matter, available P, available S and vanadium had great influences on the structures of bacterial communities in soils. Bacterial communities converged to similar structure after long-term (240 d) cultivation with vanadium containing medium, dominating by bacteria which can tolerate or reduce toxicities of heavy metals. Fungal diversities decreased after cultivation, but Ascomycota and Ciliophora were still the most abundant phyla as in the original soil samples. Results in this study emphasize the urgency of investigating vanadium contaminations in soils and provide valuable information on how vanadium contamination influences bacterial and fungal communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing.

PubMed

Qian, Pei-Yuan; Wang, Yong; Lee, On On; Lau, Stanley C K; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Wong, Tim Y H

2011-03-01

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (20 [corrected] and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.

Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

PubMed

Li, Jialin; Li, Nan; Li, Fuchao; Zou, Tao; Yu, Shuxian; Wang, Yinchu; Qin, Song; Wang, Guangyi

2014-01-01

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.

Environmental forcing on jellyfish communities in a small temperate estuary.

PubMed

Primo, Ana Lígia; Marques, Sónia C; Falcão, Joana; Crespo, Daniel; Pardal, Miguel A; Azeiteiro, Ulisses M

2012-08-01

The impact of biological, hydrodynamic and large scale climatic variables on the jellyfish community of Mondego estuary was evaluated from 2003 to 2010. Plankton samples were collected at the downstream part of the estuary. Siphonophora Muggiaea atlantica and Diphyes spp. were the main jellyfish species. Jellyfish density was generally higher in summer and since 2005 densities had increased. Summer community analysis pointed out Acartia clausi, estuarine temperature and salinity as the main driven forces for the assemblage's structure. Also, Chl a, estuarine salinity, runoff and SST were identified as the major environmental factors influencing the siphonophores summer interannual variability. Temperature influenced directly and indirectly the community and fluctuation of jellyfish blooms in the Mondego estuary. This study represents a contribution to a better knowledge of the gelatinous plankton communities in small temperate estuaries. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony

PubMed Central

Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M.

2016-01-01

Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample. PMID:27667982

Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach.

PubMed

Durso, Lisa M; Harhay, Gregory P; Bono, James L; Smith, Timothy P L

2011-02-01

The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats. Published by Elsevier B.V.

Anthropogenic and natural disturbances to marine benthic communities in Antarctica

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

Lenihan, H.; Oliver, J.S.

1995-05-01

Sampling and field experiments were conducted from 1975 to 1990 to test how the structure of marine benthic communities around McMurdo Station, Antarctica varied with levels of anthropogenic contaminants in marine sediments. The structure of communities (e.g., infauna density, species composition, and life history characteristics) in contaminated and uncontaminated areas were compared with the structure of communities influenced by two large-scale natural disturbances, anchor ice formation and uplift or iceberg scour. Benthic communities changed radically along a steep spatial gradient of anthropogenic hydrocarbon, metal, and PCB contamination around McMurdo Station. The heavily contaminated end of the gradient, Winter Quarters Bay,more » was low in infaunal and epifaunal abundance and was dominated by a few opportunistic species of polychaete worms. The edge of the heavily contaminated bay, the transition area, contained several motile polychaete species with less opportunistic life histories. Uncontaminated sedimentary habitats harbored dense tube mats of infaunal animals numerically dominated by populations of polychaete worms, crustaceans, and a large suspension feeding bivalve. These species are generally large and relatively sessile, except for several crustacean species living among the tubes. Although the community patterns around anthropogenic and natural disturbances were similar, particularly motile and opportunistic species at heavily disturbed and marginal areas, the natural disturbances cover much greater areas of the sea floor about the entire Antarctic continent. On the other hand, recovery from chemical contamination is likely to take many more decades than recovery from natural disturbances as contaminant degradation is a slow process. 77 refs., 6 figs., 5 tabs.« less

Large-scale experimental landscapes reveal distinctive effects of patch shape and connectivity on arthropod communities.

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

Orrock, John, L.; Curler, Gregory, R.; Danielson, Brent, J.

2011-09-14

The size, shape, and isolation of habitat patches can affect organism behavior and population dynamics, but little is known about the relative role of shape and connectivity in affecting ecological communities at large spatial scales. Using six sampling sessions from July 2001 until August 2002, we collected 33,685 arthropods throughout seven 12-ha experimental landscapes consisting of clear-cut patches surrounded by a matrix of mature pine forest. Patches were explicitly designed to manipulate connectivity (via habitat corridors) independently of area and edge effects. We found that patch shape, rather than connectivity, affected ground-dwelling arthropod richness and beta diversity (i.e. turnover ofmore » genera among patches). Arthropod communities contained fewer genera and exhibited less turnover in high-edge connected and high-edge unconnected patches relative to low-edge unconnected patches of similar area. Connectivity, rather than patch shape, affected the evenness of ground-dwelling arthropod communities; regardless of patch shape, high-edge connected patches had lower evenness than low- or high-edge unconnected patches. Among the most abundant arthropod orders, increased richness in low-edge unconnected patches was largely due to increased richness of Coleoptera, whereas Hymenoptera played an important role in the lower evenness in connected patches and patterns of turnover. These findings suggest that anthropogenic habitat alteration can have distinct effects on ground-dwelling arthropod communities that arise due to changes in shape and connectivity. Moreover, this work suggests that corridors, which are common conservation tools that change both patch shape and connectivity, can have multiple effects on arthropod communities via different mechanisms, and each effect may alter components of community structure.« less

Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities

PubMed Central

Redding, David W.; Mooers, Arne O.; Şekercioğlu, Çağan H.; Collen, Ben

2015-01-01

Understanding how to prioritize among the most deserving imperilled species has been a focus of biodiversity science for the past three decades. Though global metrics that integrate evolutionary history and likelihood of loss have been successfully implemented, conservation is typically carried out at sub-global scales on communities of species rather than among members of complete taxonomic assemblages. Whether and how global measures map to a local scale has received little scrutiny. At a local scale, conservation-relevant assemblages of species are likely to be made up of relatively few species spread across a large phylogenetic tree, and as a consequence there are potentially relatively large amounts of evolutionary history at stake. We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level by evaluating the extent to which three global measures of evolutionary isolation (evolutionary distinctiveness (ED), average pairwise distance (APD) and the pendant edge or unique phylogenetic diversity (PD) contribution) capture community-level phylogenetic and trait diversity for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most ED species globally safeguards more than twice the total PD of local communities on average, but that this does not translate into increased local trait diversity. By contrast, global APD is strongly related to the APD of those same species at the community level, and prioritizing these species also safeguards local PD and trait diversity. The next step for biologists is to understand the variation in the concordance of global and local level scores and what this means for conservation priorities: we need more directed research on the use of different measures of evolutionary isolation to determine which might best capture desirable aspects of biodiversity. PMID:25561674

Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns

PubMed Central

Millar, Justin J.; Payne, Jason T.; Ochs, Clifford A.

2014-01-01

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with Cyanobacteria were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like Alphaproteobacteria. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages. PMID:25217018

Pliocene large-mammal assemblages from northern Chad: sampling and ecological structure

NASA Astrophysics Data System (ADS)

Fara, Emmanuel; Likius, Andossa; Mackaye, Hassane T.; Vignaud, Patrick; Brunet, Michel

2005-11-01

Numerous Pliocene large-mammal assemblages have been discovered in Chad over the last decade. They offer a unique opportunity to understand the settings in which important chapters of Hominid evolution took place in Central Africa. However, it is crucial to first investigate both sampling and taxonomic homogeneity for these Chadian assemblages because they occur over large sectors in a sandy desert that offers virtually no stratigraphic section. Using cluster analysis and ordination techniques, we show that the three Pliocene sectors from Chad are homogeneous and adequate sampling units. Previous stable isotope analyses on these assemblages have indicated that the environment became richer in C4 plants between approximately 5.3 and 3.5 3 Ma. To test whether this environmental change has affected the structure of palaeo-communities, we assigned body mass, trophic and locomotor eco-variables to mammal species from the three sectors. Statistical analysis shows that the overall ecological structure of the assemblages is not linked with the opening of the plant cover, and eco-variables show no temporal trend from the oldest sector to the youngest. For example, there is no significant change in the relative diversity of grazing and browsing taxa, although mixed feeders are less diversified in the youngest sector than in the preceding one. This pattern apparently does not result from potential biases such as methodological artefacts or taphonomic imprint. Instead, it seems that local heterogeneous environmental factors have played a major role in shaping the ecological spectrum of Chadian mammal palaeo-communities during the Pliocene.

SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

PubMed

Dong, Jun; Shi, Fei; Li, Han; Zhang, Xiaoming; Hu, Xiaozhong; Gong, Jun

2014-01-01

Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs, in the coastal ecosystem in winter.

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides.

PubMed

Chopyk, Jessica; Moore, Ryan M; DiSpirito, Zachary; Stromberg, Zachary R; Lewis, Gentry L; Renter, David G; Cernicchiaro, Natalia; Moxley, Rodney A; Wommack, K Eric

2016-03-22

Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cattle are the major reservoir hosts of these organisms, and while there have been advancements in food safety practices and industry standards, STEC still remains prevalent within beef cattle operations with cattle hides implicated as major sources of carcass contamination. To investigate whether the composition of hide-specific microbial communities are associated with STEC prevalence, 16S ribosomal RNA (rRNA) bacterial community profiles were obtained from hide and fecal samples collected from a large commercial feedlot over a 3-month period. These community data were examined amidst an extensive collection of prevalence data on a subgroup of STEC that cause illness in humans, referred to as enterohemorrhagic E. coli (EHEC). Fecal 16S rRNA gene OTUs (operational taxonomic units) were subtracted from the OTUs found within each hide 16S rRNA amplicon library to identify hide-specific bacterial populations. Comparative analysis of alpha diversity revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups: O26, O111, O103, O121, O45, and O145. This trend occurred regardless of diversity metric or fecal OTU presence. The number of EHEC serogroups present in the samples had a compounding effect on the inverse relationship between pathogen presence and bacterial diversity. Beta diversity data showed differences in bacterial community composition between samples containing O157 and non-O157 populations, with certain OTUs demonstrating significant changes in relative abundance. The cumulative prevalence of the targeted EHEC serogroups was correlated with low bacterial community diversity on pre-harvest cattle hides. Understanding the relationship between indigenous hide bacterial communities and populations may provide strategies to limit EHEC in cattle and provide biomarkers for EHEC risk assessment.

A Survey of Residents' Perceptions of the Effect of Large-Scale Economic Developments on Perceived Safety, Violence, and Economic Benefits

PubMed Central

Geller, Ruth; Bear, Todd M.; Foulds, Abigail L.; Duell, Jessica; Sharma, Ravi

2015-01-01

Background. Emerging research highlights the promise of community- and policy-level strategies in preventing youth violence. Large-scale economic developments, such as sports and entertainment arenas and casinos, may improve the living conditions, economics, public health, and overall wellbeing of area residents and may influence rates of violence within communities. Objective. To assess the effect of community economic development efforts on neighborhood residents' perceptions on violence, safety, and economic benefits. Methods. Telephone survey in 2011 using a listed sample of randomly selected numbers in six Pittsburgh neighborhoods. Descriptive analyses examined measures of perceived violence and safety and economic benefit. Responses were compared across neighborhoods using chi-square tests for multiple comparisons. Survey results were compared to census and police data. Results. Residents in neighborhoods with the large-scale economic developments reported more casino-specific and arena-specific economic benefits. However, 42% of participants in the neighborhood with the entertainment arena felt there was an increase in crime, and 29% of respondents from the neighborhood with the casino felt there was an increase. In contrast, crime decreased in both neighborhoods. Conclusions. Large-scale economic developments have a direct influence on the perception of violence, despite actual violence rates. PMID:26273310

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

Association between community characteristics and implementation of community programmes and policies addressing childhood obesity: the Healthy Communities Study.

PubMed

Schultz, J A; Collie-Akers, V L; Fawcett, S B; Strauss, W J; Nagaraja, J; Landgraf, A J; McIver, K L; Weber, S A; Arteaga, S S; Nebeling, L C; Rauzon, S M

2018-06-19

Little is known about whether characteristics of communities are associated with differential implementation of community programmes and policies to promote physical activity and healthy eating. This study examines associations between community characteristics (e.g. region and race/ethnicity) and the intensity of community programmes and policies implemented to prevent childhood obesity. It explores whether community characteristics moderate the intensity of community efforts to prevent childhood obesity. The objective of this study is to investigate associations between community characteristics and the intensity of community policies and programmes to prevent childhood obesity documented in the Healthy Communities Study that engaged a diverse sample of US communities. Programmes and policies were documented in 130 communities across the USA, reporting over 9000 different community programmes and policies to prevent obesity among children ages 4-15. We examined associations between community characteristics and the intensity of community programmes and policies implemented (i.e. their amount and reach, duration and strength of change strategy). Community characteristics explain 25% of the variability in the intensity of community programmes and policies implemented in communities. Particular characteristics - urbanicity, region, being a large county and the per cent of African-Americans in a community - contributed to more (over 18% of the 25%) of the observed variability. © 2018 World Obesity Federation.

Microbial community analysis using MEGAN.

PubMed

Huson, Daniel H; Weber, Nico

2013-01-01

Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. © 2013 Elsevier Inc. All rights reserved.

Rapid Identification of a Cooling Tower-Associated Legionnaires' Disease Outbreak Supported by Polymerase Chain Reaction Testing of Environmental Samples, New York City, 2014-2015.

PubMed

Benowitz, Isaac; Fitzhenry, Robert; Boyd, Christopher; Dickinson, Michelle; Levy, Michael; Lin, Ying; Nazarian, Elizabeth; Ostrowsky, Belinda; Passaretti, Teresa; Rakeman, Jennifer; Saylors, Amy; Shamoonian, Elena; Smith, Terry-Ann; Balter, Sharon

2018-04-01

We investigated an outbreak of eight Legionnaires' disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings) <1 km from patient residences, a market misting system, a community-wide water system used for heating and cooling, and potable water. To support a timely public health response, we used real-time polymerase chain reaction (PCR) to identify Legionella DNA in environmental samples within hours of specimen collection. We detected L. pneumophila serogroup 1 DNA only at a power plant cooling tower, supporting the decision to order remediation before culture results were available. An isolate from a power plant cooling tower sample was indistinguishable from a patient isolate by pulsed-field gel electrophoresis, suggesting the cooling tower was the outbreak source. PCR results were available <1 day after sample collection, and culture results were available as early as 5 days after plating. PCR is a valuable tool for identifying Legionella DNA in environmental samples in outbreak settings.

A comparison of confidence interval methods for the intraclass correlation coefficient in community-based cluster randomization trials with a binary outcome.

PubMed

Braschel, Melissa C; Svec, Ivana; Darlington, Gerarda A; Donner, Allan

2016-04-01

Many investigators rely on previously published point estimates of the intraclass correlation coefficient rather than on their associated confidence intervals to determine the required size of a newly planned cluster randomized trial. Although confidence interval methods for the intraclass correlation coefficient that can be applied to community-based trials have been developed for a continuous outcome variable, fewer methods exist for a binary outcome variable. The aim of this study is to evaluate confidence interval methods for the intraclass correlation coefficient applied to binary outcomes in community intervention trials enrolling a small number of large clusters. Existing methods for confidence interval construction are examined and compared to a new ad hoc approach based on dividing clusters into a large number of smaller sub-clusters and subsequently applying existing methods to the resulting data. Monte Carlo simulation is used to assess the width and coverage of confidence intervals for the intraclass correlation coefficient based on Smith's large sample approximation of the standard error of the one-way analysis of variance estimator, an inverted modified Wald test for the Fleiss-Cuzick estimator, and intervals constructed using a bootstrap-t applied to a variance-stabilizing transformation of the intraclass correlation coefficient estimate. In addition, a new approach is applied in which clusters are randomly divided into a large number of smaller sub-clusters with the same methods applied to these data (with the exception of the bootstrap-t interval, which assumes large cluster sizes). These methods are also applied to a cluster randomized trial on adolescent tobacco use for illustration. When applied to a binary outcome variable in a small number of large clusters, existing confidence interval methods for the intraclass correlation coefficient provide poor coverage. However, confidence intervals constructed using the new approach combined with Smith's method provide nominal or close to nominal coverage when the intraclass correlation coefficient is small (<0.05), as is the case in most community intervention trials. This study concludes that when a binary outcome variable is measured in a small number of large clusters, confidence intervals for the intraclass correlation coefficient may be constructed by dividing existing clusters into sub-clusters (e.g. groups of 5) and using Smith's method. The resulting confidence intervals provide nominal or close to nominal coverage across a wide range of parameters when the intraclass correlation coefficient is small (<0.05). Application of this method should provide investigators with a better understanding of the uncertainty associated with a point estimator of the intraclass correlation coefficient used for determining the sample size needed for a newly designed community-based trial. © The Author(s) 2015.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Marketing activities of vape shops across racial/ethnic communities

PubMed Central

Garcίa, Robert; Sidhu, Anupreet; Allem, Jon-Patrick; Baezconde-Garbanati, Lourdes; Unger, Jennifer B.; Sussman, Steve

2017-01-01

INTRODUCTION There has been a surge in the number of vape shops in the USA. Research on the marketing practices of e-cigarette manufacturers is scarce and even less known are the practices of vape shop retailers. Past research on tobacco marketing has shown differences in the amount and content of marketing material, based on a community’s demographic profile. This study examined marketing strategies in vape shops and explored differences among vape shops located in communities that differ by ethnic composition. METHODS Data was gathered in 2014 from a pilot-study on vape shops (n=77) in Los Angeles, which documented the characteristics of shops through employee interviews and in-store observations. Data were collected from shops located in communities that were predominantly, African-American (n=20), Hispanic (n=17), Korean (n=18), or non-Hispanic White (n=22). RESULTS Sixty-one percent of vape shops had advertisements (print ads and posters) for e-cigarettes and 84% offered discounts. Vape shops in Hispanic communities were more likely to have ethnic specific marketing material compared to shops in other communities. All the shops provided customers with free samples, however those in Korean and non-Hispanic White communities had a significantly higher prevalence of customer accessible free samples. CONCLUSIONS Vape shop marketing practices differed by ethnic community. A large majority of shops provided free samples to their customers, a practice which is now banned by the FDA. It will be important to monitor how vape shops will adjust their marketing strategy because of this ban. Future research should expand on the findings presented here to provide regulators with further crucial information. PMID:29046899

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

PubMed Central

Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A.; Shouche, Yogesh S.; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity. PMID:26066038

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

PubMed

Kumbhare, Shreyas V; Dhotre, Dhiraj P; Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A; Shouche, Yogesh S; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

Language Attitudes in Catalan Multilingual Classrooms: Educational Implications

ERIC Educational Resources Information Center

Madariaga, José-María; Huguet, Ángel; Janés, Judit

2016-01-01

Catalonia is the Autonomous Community of Spain with the highest proportion of immigrant students. This study analyses the language attitudes of Catalan, as well as the possible explanatory variables for such attitudes, for a large sample with a high proportion of immigrant students and a great linguistic diversity. A questionnaire was given to…

Precursors and Correlates of Anxiety Trajectories from Late Childhood to Late Adolescence

ERIC Educational Resources Information Center

Letcher, Primrose; Sanson, Ann; Smart, Diana; Toumbourou, John W.

2012-01-01

The present research employed a prospective, multi-informant design to examine precursors and correlates of differing anxiety profiles from late childhood to late adolescence. The sample consisted of 626 boys and 667 girls who are participants in the Australian Temperament Project, a large, longitudinal, community-based study that has followed…

Adolescents' Sociopolitical Values in the Context of Organized Activity Involvement

ERIC Educational Resources Information Center

Oosterhoff, Benjamin; Ferris, Kaitlyn A.; Metzger, Aaron

2017-01-01

Sociopolitical values are hypothesized to form during adolescence, but the developmental and contextual origins of these values have been largely unexplored. A sample of 846 adolescents (M[subscript age] = 15.96, SD = 1.22, range = 13-20 years) reported on their organized activity involvement (volunteering, sports, church, community clubs,…

The Kindness of Strangers Revisited: A Comparison of 24 US Cities

ERIC Educational Resources Information Center

Levine, Robert V.; Reysen, Stephen; Ganz, Ellen

2008-01-01

Three field studies compared helping behavior across a sample of 24 small, medium and large cities across the United States. The relationship of helping to statistics reflecting the demographic, social, and economic characteristics of these communities was then examined. The strongest predictors of city differences in helping were population size,…

Stability and Change in Positive Development during Young Adulthood

ERIC Educational Resources Information Center

Hawkins, Mary T.; Letcher, Primrose; Sanson, Ann; O'Connor, Meredith; Toumbourou, John W.; Olsson, Craig

2011-01-01

Calls have been made for a greater focus on successful development and how positive functioning can be conceptualized in theory and empirical research. Drawing on a large Australian community sample (N = 890; 61.7% female), this article examines the structure and stability of positive development at two time points during young adulthood.…

Are There Stable Factors in Preadolescent Girls' Externalizing Behaviors?

ERIC Educational Resources Information Center

Loeber, Rolf; Pardini, Dustin A.; Hipwell, Alison; Stouthamer-Loeber, Magda; Keenan, Kate; Sembower, Mark A.

2009-01-01

Relatively little is known about the factor structure of disruptive behavior among preadolescent girls. The present study reports on exploratory and confirmatory factor analyses of disruptive girl behavior over four successive data waves as rated by parents and teachers in a large, representative community sample of girls (N = 2,451). Five factors…

Eyes on Cognitive Styles and the Processing of Visual Information.

ERIC Educational Resources Information Center

Sitz, Robert

A simulated art history textbook reading assignment was designed to examine the effects of visual information on student learning and understanding. A sample of 234 students was taken from a population of freshman/sophomore English students in a large metropolitan community college district. In phase one of the study, students took the Group…

Accommodation Decision Making for Postsecondary Students with Learning Disabilities: Individually Tailored or One Size Fits All?

ERIC Educational Resources Information Center

Weis, Robert; Dean, Emily L.; Osborne, Karen J.

2016-01-01

Clinicians uniformly recommend accommodations for college students with learning disabilities; however, we know very little about which accommodations they select and the validity of their recommendations. We examined the assessment documentation of a large sample of community college students receiving academic accommodations for learning…

Application-Specific Graph Sampling for Frequent Subgraph Mining and Community Detection

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

Purohit, Sumit; Choudhury, Sutanay; Holder, Lawrence B.

Graph mining is an important data analysis methodology, but struggles as the input graph size increases. The scalability and usability challenges posed by such large graphs make it imperative to sample the input graph and reduce its size. The critical challenge in sampling is to identify the appropriate algorithm to insure the resulting analysis does not suffer heavily from the data reduction. Predicting the expected performance degradation for a given graph and sampling algorithm is also useful. In this paper, we present different sampling approaches for graph mining applications such as Frequent Subgrpah Mining (FSM), and Community Detection (CD). Wemore » explore graph metrics such as PageRank, Triangles, and Diversity to sample a graph and conclude that for heterogeneous graphs Triangles and Diversity perform better than degree based metrics. We also present two new sampling variations for targeted graph mining applications. We present empirical results to show that knowledge of the target application, along with input graph properties can be used to select the best sampling algorithm. We also conclude that performance degradation is an abrupt, rather than gradual phenomena, as the sample size decreases. We present the empirical results to show that the performance degradation follows a logistic function.« less

Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

PubMed Central

Leung, Marcus H. Y.; Wilkins, David; Li, Ellen K. T.; Kong, Fred K. F.

2014-01-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. PMID:25172855

Validation of Rapid Radiochemical Method for Californium ...

EPA Pesticide Factsheets

Technical Brief In the event of a radiological/nuclear contamination event, the response community would need tools and methodologies to rapidly assess the nature and the extent of contamination. To characterize a radiologically contaminated outdoor area and to inform risk assessment, large numbers of environmental samples would be collected and analyzed over a short period of time. To address the challenge of quickly providing analytical results to the field, the U.S. EPA developed a robust analytical method. This method allows response officials to characterize contaminated areas and to assess the effectiveness of remediation efforts, both rapidly and accurately, in the intermediate and late phases of environmental cleanup. Improvement in sample processing and analysis leads to increased laboratory capacity to handle the analysis of a large number of samples following the intentional or unintentional release of a radiological/nuclear contaminant.

Utilizing Big Data and Twitter to Discover Emergent Online Communities of Cannabis Users

PubMed Central

Baumgartner, Peter; Peiper, Nicholas

2017-01-01

Large shifts in medical, recreational, and illicit cannabis consumption in the United States have implications for personalizing treatment and prevention programs to a wide variety of populations. As such, considerable research has investigated clinical presentations of cannabis users in clinical and population-based samples. Studies leveraging big data, social media, and social network analysis have emerged as a promising mechanism to generate timely insights that can inform treatment and prevention research. This study extends a novel method called stochastic block modeling to derive communities of cannabis consumers as part of a complex social network on Twitter. A set of examples illustrate how this method can ascertain candidate samples of medical, recreational, and illicit cannabis users. Implications for research planning, intervention design, and public health surveillance are discussed. PMID:28615950

Taenia solium Infection in Peru: A Collaboration between Peace Corps Volunteers and Researchers in a Community Based Study

PubMed Central

Watts, Nathaniel S.; Pajuelo, Monica; Clark, Taryn; Loader, Maria-Cristina I.; Verastegui, Manuela R.; Sterling, Charles; Friedland, Jon S.; Garcia, Hector H.; Gilman, Robert H.

2014-01-01

Background Neurocysticercosis is a leading cause of seizures and epilepsy in most of the world, and it occurs when Taenia solium larval cysts infect the central nervous system. T. solium tapeworm infection is endemic in much of Peru, but there are scarce data on the prevalence in many rural highland communities where it is likely to be hyper-endemic. Peace Corps Volunteers live and work in these communities; however, to our knowledge, they have not been used to facilitate public health research. Materials and Methods We utilized Peace Corps Volunteers to estimate the prevalence of T. solium tapeworm infection in seven rural communities in northern Peru. A convenience non-random sampling frame was used. Peace Corps Volunteers facilitated the collection of stool samples (N = 2,328), which were analyzed by sedimentation and microscopy. Niclosamide treatment and purgation preceded species identification, which was done by PCR-REA. Results Taenia sp. egg-positive stool samples were found in three of the seven communities we surveyed. The overall prevalence of Taenia sp. egg positivity was 2.1% (49/2,328) (95% CI = 1.6–2.8%) with prevalence up to 4.3% (42/977) (95% CI = 3.1–5.8%) by community. All 34 of the specimens tested by PCR-REA were T. solium. The overall prevalence of T. solium tapeworm infection was 1.5% (34/2,328) (95% CI = 1.0–2.0%). Prevalence up to 2.9% (28/977) (95% CI = 1.9–4.1%) by community was observed. Conclusion/Significance This study recorded high T. solium tapeworm prevalence, and identified hyper-endemic rural communities. It demonstrates that synergy between researchers and Peace Corps Volunteers can be an effective means to conducting large-scale, community-based studies in remote areas of Peru. PMID:25469506

Sampling benthic macroinvertebrates in a large flood-plain river: Considerations of study design, sample size, and cost

USGS Publications Warehouse

Bartsch, L.A.; Richardson, W.B.; Naimo, T.J.

1998-01-01

Estimation of benthic macroinvertebrate populations over large spatial scales is difficult due to the high variability in abundance and the cost of sample processing and taxonomic analysis. To determine a cost-effective, statistically powerful sample design, we conducted an exploratory study of the spatial variation of benthic macroinvertebrates in a 37 km reach of the Upper Mississippi River. We sampled benthos at 36 sites within each of two strata, contiguous backwater and channel border. Three standard ponar (525 cm(2)) grab samples were obtained at each site ('Original Design'). Analysis of variance and sampling cost of strata-wide estimates for abundance of Oligochaeta, Chironomidae, and total invertebrates showed that only one ponar sample per site ('Reduced Design') yielded essentially the same abundance estimates as the Original Design, while reducing the overall cost by 63%. A posteriori statistical power analysis (alpha = 0.05, beta = 0.20) on the Reduced Design estimated that at least 18 sites per stratum were needed to detect differences in mean abundance between contiguous backwater and channel border areas for Oligochaeta, Chironomidae, and total invertebrates. Statistical power was nearly identical for the three taxonomic groups. The abundances of several taxa of concern (e.g., Hexagenia mayflies and Musculium fingernail clams) were too spatially variable to estimate power with our method. Resampling simulations indicated that to achieve adequate sampling precision for Oligochaeta, at least 36 sample sites per stratum would be required, whereas a sampling precision of 0.2 would not be attained with any sample size for Hexagenia in channel border areas, or Chironomidae and Musculium in both strata given the variance structure of the original samples. Community-wide diversity indices (Brillouin and 1-Simpsons) increased as sample area per site increased. The backwater area had higher diversity than the channel border area. The number of sampling sites required to sample benthic macroinvertebrates during our sampling period depended on the study objective and ranged from 18 to more than 40 sites per stratum. No single sampling regime would efficiently and adequately sample all components of the macroinvertebrate community.

Greatest soil microbial diversity found in micro-habitats

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

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

A Study of the Antecedents and Consequences of Members' Helping Behaviors in Online Community

NASA Astrophysics Data System (ADS)

Chu, Kuo-Ming

Despite the growing popularity of online communities, there are a major gap between practitioners and academicians as to how to share information and knowledge among members of these groups. However, none of the previous studies have integrated these variables into a more comprehensive framework. Thus more validations are required the aim of this paper is to develop a theoretical model that enables us to examine the antecedents and consequences effects of members’ helping behavior in online communities. The moderating effects of the sense of community on the relationships between members’ helping behaviors on information sharing and knowledge contribution are also evaluated. A complete model is developed for empirical testing. Using Yahoo’s members as the samples of this study, the empirical results suggested that online communities members’ helping behavior represents a large pool of product know-how. They seem to be a promising source of innovation capabilities for new product development.

Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline▿†

PubMed Central

Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W.; Caffrey, Sean M.; Jack, Thomas R.; Boivin, Joe; Voordouw, Gerrit

2011-01-01

Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

Native Perennial Forb Variation Between Mountain Big Sagebrush and Wyoming Big Sagebrush Plant Communities

NASA Astrophysics Data System (ADS)

Davies, Kirk W.; Bates, Jon D.

2010-09-01

Big sagebrush ( Artemisia tridentata Nutt.) occupies large portions of the western United States and provides valuable wildlife habitat. However, information is lacking quantifying differences in native perennial forb characteristics between mountain big sagebrush [ A. tridentata spp. vaseyana (Rydb.) Beetle] and Wyoming big sagebrush [ A. tridentata spp. wyomingensis (Beetle & A. Young) S.L. Welsh] plant communities. This information is critical to accurately evaluate the quality of habitat and forage that these communities can produce because many wildlife species consume large quantities of native perennial forbs and depend on them for hiding cover. To compare native perennial forb characteristics on sites dominated by these two subspecies of big sagebrush, we sampled 106 intact big sagebrush plant communities. Mountain big sagebrush plant communities produced almost 4.5-fold more native perennial forb biomass and had greater native perennial forb species richness and diversity compared to Wyoming big sagebrush plant communities ( P < 0.001). Nonmetric multidimensional scaling (NMS) and the multiple-response permutation procedure (MRPP) demonstrated that native perennial forb composition varied between these plant communities ( P < 0.001). Native perennial forb composition was more similar within plant communities grouped by big sagebrush subspecies than expected by chance ( A = 0.112) and composition varied between community groups ( P < 0.001). Indicator analysis did not identify any perennial forbs that were completely exclusive and faithful, but did identify several perennial forbs that were relatively good indicators of either mountain big sagebrush or Wyoming big sagebrush plant communities. Our results suggest that management plans and habitat guidelines should recognize differences in native perennial forb characteristics between mountain and Wyoming big sagebrush plant communities.

A comparison of shoreline seines with fyke nets for sampling littoral fish communities in floodplain lakes

USGS Publications Warehouse

Clark, S.J.; Jackson, J.R.; Lochmann, S.E.

2007-01-01

We compared shoreline seines with fyke nets in terms of their ability to sample fish species in the littoral zone of 22 floodplain lakes of the White River, Arkansas. Lakes ranged in size from less than 0.5 to 51.0 ha. Most contained large amounts of coarse woody debris within the littoral zone, thus making seining in shallow areas difficult. We sampled large lakes (>2 ha) using three fyke nets; small lakes (<2 ha) were sampled using two fyke nets. Fyke nets were set for 24 h. Large lakes were sampled with an average of 11 seine hauls/ lake and small lakes were sampled with an average of 3 seine hauls/lake, but exact shoreline seining effort varied among lakes depending on the amount of open shoreline. Fyke nets collected more fish and produced greater species richness and diversity measures than did seining. Species evenness was similar for the two gear types. Two species were unique to seine samples, whereas 13 species and 3 families were unique to fyke-net samples. Although fyke nets collected more fish and more species than did shoreline seines, neither gear collected all the species present in the littoral zone of floodplain lakes. These results confirm the need for a multiple-gear approach to fully characterize the littoral fish assemblages in floodplain lakes. ?? Copyright by the American Fisheries Society 2007.

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

PubMed

Wearn, Oliver R; Carbone, Chris; Rowcliffe, J Marcus; Bernard, Henry; Ewers, Robert M

2016-07-01

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. © 2016 by the Ecological Society of America.

Evaluation of HIV/AIDS prevention intervention messages on a rural sam- ple of South African youth's knowledge, attitudes, beliefs and behaviours over a period of 15 months.

PubMed

Peltzer, Karl; Seoka, Phillip

2004-10-01

The aim of this study is to evaluate HIV/AIDS prevention intervention messages in a large rural youth population (15-24 years) in South Africa over a period of 15 months. A representative community sample of 421 youth at time one and 416 at time two participated in the study using a three-stage cluster sampling method for a household survey. Results show that over a period of 15 months sexual risk behaviour reduced (multiple partners) and the number of sexually transmitted symptoms reduced. Attitudes towards persons living with HIV/AIDS improved partly due to mass media and to a lesser extent through community interventions and partly determined by the high level of mortality experienced in the studied communities. Peer educators had a significant impact on HIV/AIDS knowledge and favourable attitude towards people living with HIV/AIDS, magazines on lower HIV risk behaviour and exposure to HIV/AIDS radio messages on consistent condom use. In this African sample of youth the reduction of sexual partners seem to be more feasible than (consistent) condom use to prevent STD and HIV infection.

Determinants of Aggression Toward Sexual Minorities in a Community Sample

PubMed Central

Parrott, Dominic J.; Peterson, John L.; Bakeman, Roger

2011-01-01

Objective Sexual prejudice and masculine gender role stress were examined as mediators of the associations between adherence to different male gender norms and aggression toward sexual minorities. This study also sought to extend past research to a community sample and employ multiple methods to assess aggression. Method Participants were 199 heterosexual men between the ages of 18–30 who were recruited from a large southeastern United States city. Participants completed measures of adherence to male gender role norms, sexual prejudice, masculine gender role stress, and aggression toward sexual minorities. Results Associations between adherence to the status and antifemininity norms and aggression toward sexual minorities were mediated by sexual prejudice, but not masculine gender role stress. The portion of unique association between adherence to the antifemininity norm and aggression toward sexual minorities was about three times larger than the portion mediated by sexual prejudice and masculine gender role stress. Conclusions Findings provide the first multivariate evidence from a community-based sample for determinants of aggression toward sexual minorities motivated by gender role enforcement. These data support intervention programming and preventative intervention studies aimed at reducing sexual prejudice and facilitating less stereotypic attitudes about the male gender role, particularly surrounding the antifemininity norm. PMID:21479161

Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

PubMed Central

Rappé, Michael S.

2013-01-01

In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

Data for Program Management: An Accuracy Assessment of Data Collected in Household Registers by Community Health Workers in Southern Kayonza, Rwanda.

PubMed

Mitsunaga, Tisha; Hedt-Gauthier, Bethany L; Ngizwenayo, Elias; Farmer, Didi Bertrand; Gaju, Erick; Drobac, Peter; Basinga, Paulin; Hirschhorn, Lisa; Rich, Michael L; Winch, Peter J; Ngabo, Fidele; Mugeni, Cathy

2015-08-01

Community health workers (CHWs) collect data for routine services, surveys and research in their communities. However, quality of these data is largely unknown. Utilizing poor quality data can result in inefficient resource use, misinformation about system gaps, and poor program management and effectiveness. This study aims to measure CHW data accuracy, defined as agreement between household registers compared to household member interview and client records in one district in Eastern province, Rwanda. We used cluster-lot quality assurance sampling to randomly sample six CHWs per cell and six households per CHW. We classified cells as having 'poor' or 'good' accuracy for household registers for five indicators, calculating point estimates of percent of households with accurate data by health center. We evaluated 204 CHW registers and 1,224 households for accuracy across 34 cells in southern Kayonza. Point estimates across health centers ranged from 79 to 100% for individual indicators and 61 to 72% for the composite indicator. Recording error appeared random for all but the widely under-reported number of women on modern family planning method. Overall, accuracy was largely 'good' across cells, with varying results by indicator. Program managers should identify optimum thresholds for 'good' data quality and interventions to reach them according to data use. Decreasing variability and improving quality will facilitate potential of these routinely-collected data to be more meaningful for community health program management. We encourage further studies assessing CHW data quality and the impact training, supervision and other strategies have on improving it.

Large-Angular-Scale Clustering as a Clue to the Source of UHECRs

NASA Astrophysics Data System (ADS)

Berlind, Andreas A.; Farrar, Glennys R.

We explore what can be learned about the sources of UHECRs from their large-angular-scale clustering (referred to as their "bias" by the cosmology community). Exploiting the clustering on large scales has the advantage over small-scale correlations of being insensitive to uncertainties in source direction from magnetic smearing or measurement error. In a Cold Dark Matter cosmology, the amplitude of large-scale clustering depends on the mass of the system, with more massive systems such as galaxy clusters clustering more strongly than less massive systems such as ordinary galaxies or AGN. Therefore, studying the large-scale clustering of UHECRs can help determine a mass scale for their sources, given the assumption that their redshift depth is as expected from the GZK cutoff. We investigate the constraining power of a given UHECR sample as a function of its cutoff energy and number of events. We show that current and future samples should be able to distinguish between the cases of their sources being galaxy clusters, ordinary galaxies, or sources that are uncorrelated with the large-scale structure of the universe.

Fish stomach contents in benthic macroinvertebrate assemblage assessments.

PubMed

Tupinambás, T H; Pompeu, P S; Gandini, C V; Hughes, R M; Callisto, M

2015-01-01

The choice of sampling gears to assess benthic macroinvertebrate communities depends on environmental characteristics, study objectives, and cost effectiveness. Because of the high foraging capacity and diverse habitats and behaviors of benthophagous fishes, their stomach contents may offer a useful sampling tool in studies of benthic macroinvertebrates, especially in large, deep, fast rivers that are difficult to sample with traditional sediment sampling gear. Our objective was to compare the benthic macroinvertebrate communities sampled from sediments with those sampled from fish stomachs. We collected benthic macroinvertebrates and fish from three different habitat types (backwater, beach, riffle) in the wet season, drying season, and dry season along a single reach of the Grande River (Paraná River Basin, southeast Brazil). We sampled sediments through use of a Petersen dredge (total of 216 grabs) and used gill nets to sample fish (total of 36 samples). We analyzed the stomach contents of three commonly occurring benthophagous fish species (Eigenmannia virescens, Iheringichthys labrosus, Leporinus amblyrhynchus). Chironomids dominated in both sampling methods. Macroinvertebrate taxonomic composition and abundances from fish stomachs differed from those from sediment samples, but less so from riffles than from backwater and beach habitats. Macroinvertebrate taxa from E. virescens stomachs were more strongly correlated with sediment samples from all three habitats than were those from the other two species. The species accumulation curves and higher mean dispersion values, compared with with sediment samples suggest that E. virescens is more efficient than sediment samples and the other fish studied at collecting benthic taxa. We conclude that by analyzing the stomach contents of benthophagous fishes it is possible to assess important characteristics of benthic communities (dispersion, taxonomic composition and diversity). This is especially true for studies that only sample fish assemblages to evaluate aquatic ecosystem impacts. Therefore, this approach can be useful to amplify assessments of human impacts, and to incorporate additional bioindicators.

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

PubMed

Kantor, Rose S; van Zyl, A Wynand; van Hille, Robert P; Thomas, Brian C; Harrison, Susan T L; Banfield, Jillian F

2015-12-01

Gold ore processing uses cyanide (CN(-) ), which often results in large volumes of thiocyanate- (SCN(-) ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN(-) and CN(-) , but little is known about their membership and metabolic potential. Microbial-based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN(-) and CN(-) into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN(-) and CN(-) degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN(-) degradation. Genome-based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN(-) degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes.

PubMed

Toulza, Eve; Tagliabue, Alessandro; Blain, Stéphane; Piganeau, Gwenael

2012-01-01

Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil.

PubMed

Jousset, Alexandre; Lara, Enrique; Nikolausz, Marcell; Harms, Hauke; Chatzinotas, Antonis

2010-02-01

Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats. Copyright 2009 Elsevier B.V. All rights reserved.

Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs.

PubMed

McKay, Robert M L; Prášil, Ondrej; Pechar, Libor; Lawrenz, Evelyn; Rozmarynowycz, Mark J; Bullerjahn, George S

2015-12-01

Abundant phytoplankton and bacteria were identified by high-throughput 16S rRNA tag Illumina sequencing of samples from water and ice phases collected during winter at commercial fish ponds and a sand pit lake within the UNESCO Třeboň Basin Biosphere Reserve, Czech Republic. Bacterial reads were dominated by Proteobacteria and Bacteroidetes. Despite dominance by members of just two phyla, UniFrac principal coordinates analysis of the bacterial community separated the water community of Klec fish pond, as well as the ice-associated community of Klec-Sand Pit from other samples. Both phytoplankton and cyanobacteria were represented with hundreds of sequence reads per sample, a finding corroborated by microscopy. In particular, ice from Klec-Sand Pit contained high contributions from photoautotrophs accounting for 25% of total reads with reads dominated by single operational taxonomic units (OTUs) of the cyanobacterium Planktothrix sp. and two filamentous diatoms. Dominant OTUs recovered from ice were largely absent (< 0.01%) from underlying water suggestive of low floristic similarity of phytoplankton partitioned between these phases. Photosynthetic characterization of phototrophs resident in water and ice analysed by variable chlorophyll a fluorescence showed that communities from both phases were photosynthetically active, thus supporting ice as viable habitat for phytoplankton in freshwater lakes and reservoirs. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Building from within: pastoral insights into community resources and assets.

PubMed

Ford, Cassandra D

2013-01-01

To explore perceptions of community pastors regarding the extent of community resources and assets in a rural, Southern, African American community. Utilizing a qualitative, descriptive design, interviews were conducted with six African American pastors. Interviews were conducted using a semi-structured interview guide based on an assets-oriented approach. Pastors discussed various resources and assets, probable within the community that may be considered as support for program development. Key themes included: (1) community strengths, (2) community support, and (3) resources for a healthy lifestyle. The church was identified, throughout the interviews, as a primary source of strength and support for community members. In this study of African American pastors, various perceptions of community resources were identified. Findings indicate that a sample, rural, Southern, African American community has a wealth of resources and assets, but additional resources related to health promotion are still necessary to produce optimal results. Specific programs to prevent chronic conditions such as cardiovascular disease can provide an effective means for addressing related health disparities. Programs implemented through churches can reach large numbers of individuals in the community and provide an important source of sustainable efforts to improve the health of African Americans. © 2013 Wiley Periodicals, Inc.

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

PubMed Central

Pereira, Letícia Bianca; Vicentini, Renato; Ottoboni, Laura M. M.

2014-01-01

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. PMID:24796430

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

DOE PAGES

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

2017-07-28

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

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

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

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

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

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

PubMed

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

2017-01-01

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

A Lactobacillus-Deficient Vaginal Microbiota Dominates Postpartum Women in Rural Malawi

PubMed Central

2018-01-01

ABSTRACT The bacterial community found in the vagina is an important determinant of a woman's health and disease status. A healthy vaginal microbiota is associated with low species richness and a high proportion of one of a number of different Lactobacillus spp. When disrupted, the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations that may not capture the full complexity of the community or adequately predict what constitutes a healthy microbiota in all populations. In this study, we sampled and characterized the vaginal microbiota found on vaginal swabs taken postpartum from a cohort of 1,107 women in rural Malawi. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year postpartum. This Lactobacillus-deficient anaerobic community, commonly labeled community state type (CST) 4, could be subdivided into four further communities. A Lactobacillus iners-dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal postpartum vaginal microbiota is. Previous identification of community state types and associations among bacterial species, bacterial vaginosis, and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. (This study has been registered at ClinicalTrials.gov as NCT01239693.) IMPORTANCE A bacterial community in the vaginal tract is dominated by a small number of Lactobacillus species, and when not present there is an increased incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study, we characterized the postpartum vaginal bacterial community of a large group of women from a resource-poor, undersampled population in rural Malawi. The majority of women were found to have a Lactobacillus-deficient community, and even when sampled a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus-dominant community is unknown, and this could suggest that not all Lactobacillus-deficient community structures are adverse. A better understanding of this complex community state type is needed. PMID:29305501

Weak and Habitat-Dependent Effects of Nutrient Pollution on Macrofaunal Communities of Southeast Australian Estuaries

PubMed Central

Nicastro, Andrea; Bishop, Melanie J.

2013-01-01

Among the impacts of coastal settlements to estuaries, nutrient pollution is often singled out as a leading cause of modification to the ecological communities of soft sediments. Through sampling of 48 sites, distributed among 16 estuaries of New South Wales, Australia, we tested the hypotheses that (1) anthropogenic nutrient loads would be a better predictor of macrofaunal communities than estuarine geomorphology or local sediment characteristics; and (2) local environmental context, as determined largely by sediment characteristics, would modify the relationship between nutrient loading and community composition. Contrary to the hypothesis, multivariate multiple regression analyses revealed that sediment grain size was the best predictor of macrofaunal assemblage composition. When samples were stratified according to median grain size, relationships between faunal communities and nitrogen loading and latitude emerged, but only among estuaries with sandier sediments. In these estuaries, capitellid and nereid polychaetes and chironomid larvae were the taxa that showed the strongest correlations with nutrient loading. Overall, this study failed to provide evidence of a differential relationship between diffuse nutrient enrichment and benthic macrofauna across a gradient of 7° of latitude and 4°C temperature. Nevertheless, as human population growth continues to place increasing pressure on southeast Australian estuaries, manipulative field studies examining when and where nutrient loading will lead to significant changes in estuarine community structure are needed. PMID:23799037

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Carbon utilization profiles of river bacterial strains facing sole carbon sources suggest metabolic interactions.

PubMed

Goetghebuer, Lise; Servais, Pierre; George, Isabelle F

2017-05-01

Microbial communities play a key role in water self-purification. They are primary drivers of biogenic element cycles and ecosystem processes. However, these communities remain largely uncharacterized. In order to understand the diversity-heterotrophic activity relationship facing sole carbon sources, we assembled a synthetic community composed of 20 'typical' freshwater bacterial species mainly isolated from the Zenne River (Belgium). The carbon source utilization profiles of each individual strain and of the mixed community were measured in Biolog Phenotype MicroArrays PM1 and PM2A microplates that allowed testing 190 different carbon sources. Our results strongly suggest interactions occurring between our planktonic strains as our synthetic community showed metabolic properties that were not displayed by its single components. Finally, the catabolic performances of the synthetic community and a natural community from the same sampling site were compared. The synthetic community behaved like the natural one and was therefore representative of the latter in regard to carbon source consumption. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metaproteome analysis of endodontic infections in association with different clinical conditions.

PubMed

Provenzano, José Claudio; Siqueira, José F; Rôças, Isabela N; Domingues, Romênia R; Paes Leme, Adriana F; Silva, Márcia R S

2013-01-01

Analysis of the metaproteome of microbial communities is important to provide an insight of community physiology and pathogenicity. This study evaluated the metaproteome of endodontic infections associated with acute apical abscesses and asymptomatic apical periodontitis lesions. Proteins persisting or expressed after root canal treatment were also evaluated. Finally, human proteins associated with these infections were identified. Samples were taken from root canals of teeth with asymptomatic apical periodontitis before and after chemomechanical treatment using either NaOCl or chlorhexidine as the irrigant. Samples from abscesses were taken by aspiration of the purulent exudate. Clinical samples were processed for analysis of the exoproteome by using two complementary mass spectrometry platforms: nanoflow liquid chromatography coupled with linear ion trap quadrupole Velos Orbitrap and liquid chromatography-quadrupole time-of-flight. A total of 308 proteins of microbial origin were identified. The number of proteins in abscesses was higher than in asymptomatic cases. In canals irrigated with chlorhexidine, the number of identified proteins decreased substantially, while in the NaOCl group the number of proteins increased. The large majority of microbial proteins found in endodontic samples were related to metabolic and housekeeping processes, including protein synthesis, energy metabolism and DNA processes. Moreover, several other proteins related to pathogenicity and resistance/survival were found, including proteins involved with adhesion, biofilm formation and antibiotic resistance, stress proteins, exotoxins, invasins, proteases and endopeptidases (mostly in abscesses), and an archaeal protein linked to methane production. The majority of human proteins detected were related to cellular processes and metabolism, as well as immune defense. Interrogation of the metaproteome of endodontic microbial communities provides information on the physiology and pathogenicity of the community at the time of sampling. There is a growing need for expanded and more curated protein databases that permit more accurate identifications of proteins in metaproteomic studies.

Application of the new keystone-species concept to prairie dogs: How well does it work?

USGS Publications Warehouse

Kotliar, N.B.

2000-01-01

It has been suggested that the keystone-species concept should be dropped from ecology and conservation, primarily because the concept is poorly defined. This prompted Power et al. (1996) to refine the definition: keystone species have large effects on community structure or ecosystem function (i.e., high overall importance), and this effect should be large relative to abundance (i.e., high community importance). Using prairie dogs (Cynomys spp.) as an example, I review operational and conceptual difficulties encountered in applying this definition. As applied to prairie dogs, the implicit assumption that overall importance is a linear function of abundance is invalid. In addition, community importance is sensitive to abundance levels, the definition of community, and sampling scale. These problems arise largely from the equation for community importance, as used in conjunction with removal experiments at single abundance levels. I suggest that we shift from the current emphasis on the dualism between keystone and nonkeystone species and instead examine how overall and community importance vary (1) with abundance, (2) across spatial and temporal scales, and (3) under diverse ecological conditions. In addition, I propose that a third criterion be incorporated into the definition: keystone species perform roles not performed by other species or processes. Examination of how these factors vary among populations of keystone species should help identify the factors contributing to, or limiting, keystone-level functions, thereby increasing the usefulness of the keystone-species concept in ecology and conservation. Although the quantitative framework of Power et al. falls short of being fully operational, my conceptual guidelines may improve the usefulness of the keystone-species concept. Careful attention to the factors that limit keystone function will help avoid misplaced emphasis on keystone species at the expense of other species.

Biotic homogenization of three insect groups due to urbanization.

PubMed

Knop, Eva

2016-01-01

Cities are growing rapidly, thereby expected to cause a large-scale global biotic homogenization. Evidence for the homogenization hypothesis is mostly derived from plants and birds, whereas arthropods have so far been neglected. Here, I tested the homogenization hypothesis with three insect indicator groups, namely true bugs, leafhoppers, and beetles. In particular, I was interested whether insect species community composition differs between urban and rural areas, whether they are more similar between cities than between rural areas, and whether the found pattern is explained by true species turnover, species diversity gradients and geographic distance, by non-native or specialist species, respectively. I analyzed insect species communities sampled on birch trees in a total of six Swiss cities and six rural areas nearby. In all indicator groups, urban and rural community composition was significantly dissimilar due to native species turnover. Further, for bug and leafhopper communities, I found evidence for large-scale homogenization due to urbanization, which was driven by reduced species turnover of specialist species in cities. Species turnover of beetle communities was similar between cities and rural areas. Interestingly, when specialist species of beetles were excluded from the analyses, cities were more dissimilar than rural areas, suggesting biotic differentiation of beetle communities in cities. Non-native species did not affect species turnover of the insect groups. However, given non-native arthropod species are increasing rapidly, their homogenizing effect might be detected more often in future. Overall, the results show that urbanization has a negative large-scale impact on the diversity specialist species of the investigated insect groups. Specific measures in cities targeted at increasing the persistence of specialist species typical for the respective biogeographic region could help to stop the loss of biodiversity. © 2015 John Wiley & Sons Ltd.

Callous-Unemotional Behaviors in Young Girls: Shared and Unique Effects Relative to Conduct Problems

ERIC Educational Resources Information Center

Hipwell, Alison E.; Pardini, Dustin A.; Loeber, Rolf; Sembower, Mark; Keenan, Kate; Stouthamer-Loeber, Magda

2007-01-01

Among girls, little is known about the shared and unique associations that callous-unemotional (CU) behaviors and conduct problems have with aspects of emotional and behavioral dysregulation and with parenting practices. This study examined these associations using a large community-based sample of young girls (N = 990). The findings revealed that…

Balancing Healthy Meals and Busy Lives: Associations between Work, School, and Family Responsibilities and Perceived Time Constraints among Young Adults

ERIC Educational Resources Information Center

Pelletier, Jennifer E.; Laska, Melissa N.

2012-01-01

Objective: To characterize associations between perceived time constraints for healthy eating and work, school, and family responsibilities among young adults. Design: Cross-sectional survey. Setting: A large, Midwestern metropolitan region. Participants: A diverse sample of community college (n = 598) and public university (n = 603) students.…

Mapping ecological systems with a random foret model: tradeoffs between errors and bias

Treesearch

Emilie Grossmann; Janet Ohmann; James Kagan; Heather May; Matthew Gregory

2010-01-01

New methods for predictive vegetation mapping allow improved estimations of plant community composition across large regions. Random Forest (RF) models limit over-fitting problems of other methods, and are known for making accurate classification predictions from noisy, nonnormal data, but can be biased when plot samples are unbalanced. We developed two contrasting...

Mothers' and Fathers' Personality and Parenting: The Mediating Role of Sense of Competence

ERIC Educational Resources Information Center

De Haan, Amaranta D.; Prinzie, Peter; Dekoviv, Maja

2009-01-01

This prospective longitudinal study addressed 3 key questions regarding the processes of parenting in a large community sample of mothers (n = 589) and fathers (n = 518). First, the collective impact of parental Big Five personality dimensions on overreactive and warm parenting, assessed 6 years later by adolescents, was examined. Second,…

Developing a large-scale model to predict the effects of land use and climatic variation on the biological condition of USA streams and rivers

EPA Science Inventory

The US EPA’s National Rivers and Streams Assessment (NRSA) uses spatially balanced sampling to estimate the proportion of streams within the continental US (CONUS) that fail to support healthy biological communities. However, to manage these systems, we also must understand...

Sex and Age Differences in Attention-Deficit/Hyperactivity Disorder Symptoms and Diagnoses: Implications for DSM-V and ICD-11

ERIC Educational Resources Information Center

Ramtekkar, Ujjwal P.; Reiersen, Angela M.; Todorov, Alexandre A.; Todd, Richard D.

2010-01-01

Objective: To examine gender and age differences in attention-deficit/hyperactivity disorder (ADHD) symptom endorsement in a large community-based sample. Method: Families with four or more full siblings ascertained from Missouri birth records completed telephone interviews regarding lifetime DSM-IV ADHD symptoms and the Strengths and Weaknesses…

Reptile and amphibian responses to large-scale wildfires in southern California

USGS Publications Warehouse

Rochester, C.J.; Brehme, C.S.; Clark, D.R.; Stokes, D.C.; Hathaway, S.A.; Fisher, R.N.

2010-01-01

In 2003, southern California experienced several large fires that burned thousands of hectares of wildlife habitats and conserved lands. To investigate the effects of these fires on the reptile and amphibian communities, we compared the results from prefire herpetofauna and vegetation sampling to two years of postfire sampling across 38 burned and 17 unburned plots. The sampling plots were spread over four vegetation types and four open space areas within San Diego County. Our capture results indicated that burned chaparral and coastal sage scrub plots lost herpetofaunal species diversity after the fires and displayed a significant shift in overall community structure. Shrub and tree cover at the burned plots, averaged across the second and third postfire years, had decreased by 53 in chaparral and 75 in coastal sage scrub. Additionally, postfire herpetofauna community structure at burned plots was more similar to that found in unburned grasslands. In grassland and woodland/riparian vegetation plots, where shrub and tree cover was not significantly affected by fires, we found no differences in the herpetofaunal species diversity or community composition. At the individual species level, Sceloporus occidentalis was the most abundant reptile in these areas both before and after the fires. We saw increases in the net capture rates for several lizard species, including Aspidoscelis tigris, Phrynosoma coronatum, and Uta stansburiana in burned chaparral plots and Aspidoscelis hyperythra and U. stansburiana in burned coastal sage scrub plots. The toad, Bufo boreas, was detected at significantly fewer burned plots in chaparral after the fires. Additionally, we documented decreases in the number of plots occupied by lizards (Elgaria multicarinata), salamanders (Batrachoseps major), and snakes (Coluber constrictor, Lampropeltis getula, Pituophis catenifer, and Masticophis lateralis) in coastal sage scrub and chaparral after the fires. We discuss the individual species results as they relate to such life-history traits as the susceptibility to initial mortality, the response to the altered postfire habitat, and shifts in the availability of potential prey. We foresee that a continued unnatural fire regime will result in a simplification of the southern California reptile and amphibian communities. ?? 2010 Society for the Study of Amphibians and Reptiles.

Study protocol for a cluster randomized trial of the Community of Voices choir intervention to promote the health and well-being of diverse older adults.

PubMed

Johnson, Julene K; Nápoles, Anna M; Stewart, Anita L; Max, Wendy B; Santoyo-Olsson, Jasmine; Freyre, Rachel; Allison, Theresa A; Gregorich, Steven E

2015-10-13

Older adults are the fastest growing segment of the United States population. There is an immediate need to identify novel, cost-effective community-based approaches that promote health and well-being for older adults, particularly those from diverse racial/ethnic and socioeconomic backgrounds. Because choral singing is multi-modal (requires cognitive, physical, and psychosocial engagement), it has the potential to improve health outcomes across several dimensions to help older adults remain active and independent. The purpose of this study is to examine the effect of a community choir program (Community of Voices) on health and well-being and to examine its costs and cost-effectiveness in a large sample of diverse, community-dwelling older adults. In this cluster randomized controlled trial, diverse adults age 60 and older were enrolled at Administration on Aging-supported senior centers and completed baseline assessments. The senior centers were randomly assigned to either start the choir immediately (intervention group) or wait 6 months to start (control). Community of Voices is a culturally tailored choir program delivered at the senior centers by professional music conductors that reflects three components of engagement (cognitive, physical, and psychosocial). We describe the nature of the study including the cluster randomized trial study design, sampling frame, sample size calculation, methods of recruitment and assessment, and primary and secondary outcomes. The study involves conducting a randomized trial of an intervention as delivered in "real-world" settings. The choir program was designed using a novel translational approach that integrated evidence-based research on the benefits of singing for older adults, community best practices related to community choirs for older adults, and the perspective of the participating communities. The practicality and relatively low cost of the choir intervention means it can be incorporated into a variety of community settings and adapted to diverse cultures and languages. If successful, this program will be a practical and acceptable community-based approach for promoting health and well-being of older adults. ClinicalTrials.gov NCT01869179 registered 9 January 2013.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

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

PubMed

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

2016-01-01

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

Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure.

PubMed

Keiblinger, Katharina M; Schneider, Martin; Gorfer, Markus; Paumann, Melanie; Deltedesco, Evi; Berger, Harald; Jöchlinger, Lisa; Mentler, Axel; Zechmeister-Boltenstern, Sophie; Soja, Gerhard; Zehetner, Franz

2018-03-01

Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg -1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC 50 ranging from 76 to 187 mg EDTA-extractable Cu kg -1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC 50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg -1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.

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

PubMed Central

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

2016-01-01

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

Plant epiphytism in semiarid conditions revealed the influence of habitat and climate variables on AM fungi communities distribution

NASA Astrophysics Data System (ADS)

Torrecillas, Emma; Torres, Pilar; Díaz, Gisela; del Mar Alguacil, Maria; Querejeta, Jose Ignacio; García, Fuensanta; Roldán, Antonio

2014-05-01

In semiarid Mediterranean ecosystems epiphytic plant species are practically absent and only some species of palm-trees can support epiphytes growing in their lower crown area, such as Phoenix dactylifera L. (date palm). In this study we focused in Sonchus tenerrimus L. plants growing as facultative epiphytes in P. dactylifera and its terrestrial forms growing in adjacent soils, Our aim was to determine the possible presence of AMF in these peculiar habitats and to relate AMF communities with climatic variations. We investigated the AMF community composition of epiphytic and terrestrial S. tenerrimus plants along a temperature and precipitation gradient across 12 localities. Epiphytic roots were colonized by AM fungi as determined by microscopic observation, all epiphytic and terrestrial samples analysed showed AMF sequences from taxa belonging to the phylum Glomeromycota, which were grouped in 30 AMF OTUs. The AMF community composition was clearly different between epiphytic and terrestrial root samples and this could be attributable to dispersal constraints and/or the contrasting environmental and ecophysiological conditions prevailing in each habitat. Across sites, the richness and diversity of terrestrial AMF communities was positively correlated with rainfall amount during the most recent growing season. In contrast, there was no significant correlation between climate variables and AMF richness and diversity for epiphytic AMF communities, which suggests that the composition of AMF communities in epiphytic habitats appears to be largely determined by the availability and dispersion of fungal propagules from adjacent terrestrial habitats.

Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure

USGS Publications Warehouse

Meador, M.R.; McIntyre, J.P.; Pollock, K.H.

2003-01-01

Two-pass backpack electrofishing data collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program were analyzed to assess the efficacy of single-pass backpack electrofishing. A two-capture removal model was used to estimate, within 10 river basins across the United States, proportional fish species richness from one-pass electrofishing and probabilities of detection for individual fish species. Mean estimated species richness from first-pass sampling (ps1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, ps1 values for individual sites ranged from 40% to 100% of estimated total species richness. Additional species unique to the second pass were collected in 50.3% of the samples. Of these, cyprinids and centrarchids were collected most frequently. Proportional fish species richness estimated for the first pass increased significantly with decreasing stream width for 1 of the 10 river basins. When used to calculate probabilities of detection of individual fish species, the removal model failed 48% of the time because the number of individuals of a species was greater in the second pass than in the first pass. Single-pass backpack electrofishing data alone may make it difficult to determine whether characterized fish community structure data are real or spurious. The two-pass removal model can be used to assess the effectiveness of sampling species richness with a single electrofishing pass. However, the two-pass removal model may have limited utility to determine probabilities of detection of individual species and, thus, limit the ability to assess the effectiveness of single-pass sampling to characterize species relative abundances. Multiple-pass (at least three passes) backpack electrofishing at a large number of sites may not be cost-effective as part of a standardized sampling protocol for large-geographic-scale studies. However, multiple-pass electrofishing at some sites may be necessary to better evaluate the adequacy of single-pass electrofishing and to help make meaningful interpretations of fish community structure.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

The Biogeography of Endorheic Soda Lakes in the Western United States

NASA Astrophysics Data System (ADS)

Stamps, B. W.; Petryshyn, V.; Johnson, H.; Berelson, W.; Nunn, H. S.; Stevenson, B. S.; Loyd, S. J.; Oremland, R. S.; Miller, L. G.; Rosen, M. R.; Corsetti, F. A.; Spear, J. R.

2016-12-01

Closed-basin (endorheic) soda lakes are of economic, social, and ecological importance. Shifts in global climate, which in turn affects local climate, significantly impact the distribution and diversity of microbial communities and lake ecologies. In California, the Mono Lake Basin (MLB) is especially fragile, as it has undergone a significant decline in lake level beginning in the early twentieth century due to both climatic effects and water diversion. The result is a lake with elevated salinity (60-90 g/L) and pH (9.8). The diversion of MLB water has created a unique lake environment dominated by a single macroeukaryote (Artemia monica) in which primary production is controlled at all depths by the microalgae Picocystis sp. In order to better understand the microbial diversity and functional potential of Mono Lake during an on-going drought and climatic upheaval, a combined geochemical, metagenomic, and metatranscriptomic study was undertaken. Members of The International GeoBiology course sampled the water column at multiple depths in the summer of 2016, during a large bloom of Picocystis. A mud spring from a volcanic island (Paoha) near the center of the lake was also sampled. The spring was recently submerged and interacts intermittently with Mono Lake, which may allow for mixing of microbial communities as lake levels fluctuate. Surface sediment samples were also taken from 7 m water depth. Finally, via SSU rRNA gene sequence analyses, the microbial communities of nearby soda lakes were compared in an attempt to place the Mono Lake community in the context of the overall regional biodiversity of endorheic soda lakes. Overall the microbial communities at Mono Lake were distinct both in the bacterial community composition and the abundance of Picocystis from those found at other sampled soda lakes or the surrounding rivers and springs. Our results reveal diverse microbial ecosystems at multiple lakes potentially at risk to continued climate change.

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers

PubMed Central

Llewellyn, Anna C.; Lucas, Claressa E.; Roberts, Sarah E.; Brown, Ellen W.; Nayak, Bina S.; Winchell, Jonas M.

2017-01-01

Cooling towers (CTs) are a leading source of outbreaks of Legionnaires’ disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US. PMID:29261791

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers.

PubMed

Llewellyn, Anna C; Lucas, Claressa E; Roberts, Sarah E; Brown, Ellen W; Nayak, Bina S; Raphael, Brian H; Winchell, Jonas M

2017-01-01

Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

PubMed

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO 2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO 2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO 2 levels (sample groups I and II) and one control site with low CO 2 content (group III). Samples from sites with elevated CO 2 had pH ranging from 6.2 to 4.5 and samples from the low-CO 2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO 2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae , and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO 2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO 2 leakage from geologic storage sites.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

PubMed Central

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F.; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites. PMID:29170659

Multiscale spatial and small-scale temporal variation in the composition of Riverine fish communities.

PubMed

Growns, Ivor; Astles, Karen; Gehrke, Peter

2006-03-01

We studied the multiscale (sites, river reaches and rivers) and short-term temporal (monthly) variability in a freshwater fish assemblage. We found that small-scale spatial variation and short-term temporal variability significantly influenced fish community structure in the Macquarie and Namoi Rivers. However, larger scale spatial differences between rivers were the largest source of variation in the data. The interaction between temporal change and spatial variation in fish community structure, whilst statistically significant, was smaller than the variation between rivers. This suggests that although the fish communities within each river changed between sampling occasions, the underlying differences between rivers were maintained. In contrast, the strongest interaction between temporal and spatial effects occurred at the smallest spatial scale, at the level of individual sites. This means whilst the composition of the fish assemblage at a given site may fluctuate, the magnitude of these changes is unlikely to affect larger scale differences between reaches within rivers or between rivers. These results suggest that sampling at any time within a single season will be sufficient to show spatial differences that occur over large spatial scales, such as comparisons between rivers or between biogeographical regions.

Promotion of Civic Engagement with the Family Leadership Training Institute.

PubMed

MacPhee, David; Forlenza, Eileen; Christensen, Kyle; Prendergast, Sarah

2017-12-01

In this efficacy study, both quantitative and qualitative data were used to gauge the effects of the Family Leadership Training Institute (FLTI) on civic knowledge and empowerment, civic engagement, and community health. The sample of 847 FLTI participants and 166 comparison adults completed pretest and posttest surveys. Medium to very large short-term effects were observed in civic literacy, empowerment, and engagement. Results mapping interviews were conducted with a stratified random sample of FLTI graduates (n = 52) to assess long-term (M = 2.73 years) program impact. Most FLTI graduates (86%) sustained meaningful, sometimes transformative, levels of civic engagement after program completion. This engagement involved multiple forms of leadership, most often advocacy, program implementation, and media campaigns; 63% of graduates directed at least some of their activities to marginalized populations. Content analyses of graduates' civic (capstone) projects and results mapping story maps indicated that 81-90% of community activities aligned with public health priorities. Thus, one promising means to promote community health is to empower families to develop leadership skills, become engaged in civic life, and forge connections with diverse constituents. © Society for Community Research and Action 2017.

Natural trophic variability in a large, oligotrophic, near-pristine lake

USGS Publications Warehouse

Young, Talia; Jensen, Olaf P.; Weidel, Brian C.; Chandra, Sudeep

2015-01-01

Conclusions drawn from stable isotope data can be limited by an incomplete understanding of natural isotopic variability over time and space. We quantified spatial and temporal variability in fish carbon and nitrogen stable isotopes in Lake Hövsgöl, Mongolia, a large, remote, oligotrophic lake with an unusually species-poor fish community. The fish community demonstrated a high degree of trophic level overlap. Variability in δ13C was inversely related to littoral-benthic dependence, with pelagic species demonstrating more δ13C variability than littoral-benthic species. A mixed effects model suggested that space (sampling location) had a greater impact than time (collection year) on both δ13C and δ15N variability. The observed variability in Lake Hövsgöl was generally greater than isotopic variability documented in other large, oligotrophic lakes, similar to isotopic shifts attributed to introduced species, and less than isotopic shifts attributed to anthropogenic chemical changes such as eutrophication. This work complements studies on isotopic variability and changes in other lakes around the world.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

PubMed Central

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer. PMID:29099490

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

PubMed Central

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2013-01-01

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample. PMID:24098498

Influence of manure age and sunlight on the community structure of cattle fecal bacteria as revealed by Illumina sequencing

NASA Astrophysics Data System (ADS)

Wong, K.; Shaw, T. I.; Oladeinde, A.; Molina, M.

2013-12-01

Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. Stream and river impairment due to fecal pollution is largely the result of agricultural activities in the United States. In the last few years, numerous metagenomic studies utilized next generation sequencing to develop microbial community profiles by massively sequencing the 16sRNA hypervariable region. This technology supports the application of water quality assessment such as pathogen detection and fecal source tracking. The bacteria communities of samples in these studies were determined when they were freshly collected; therefore, little is known about how feces age or how environmental stress influences the microbial ecology of fecal materials. In this study we monitored bacteria community changes in cattle feces for 57 days after excretion (day 0, 2, 4 8, 15, 22, 29, 43, 57) by sequencing the 16s variable region 4, using Illumnia MiSeq. Twelve cattle feces were studied; half of the samples were directly exposed to sunlight (unshaded) and half were shaded. Results indicate that the relative abundance (RA) profile in both shaded and unshaded samples rapidly changed from day 0 to 15, but stabilized from day 22 to 57. Firmcutes were the most abundant phylum (~40%) at day 0, but were reduced to <10% by day 57. The RA of Proteobacteria was only 1% at day 0, but increased to ~50% by day 57in both shaded and unshaded samples. By the end of the study, shaded and unshaded samples had a similar RA of Firmcutes and Proteobacteria but the RA of Bacteroidetes and Actinobacteria was, respectively, about 7% lower and 10% higher for unshaded samples. UV intensity, moisture, and temperature were significantly different between shaded and unshaded plots, indicating that these environmental stresses could influence the structure of fecal bacteria community in the natural environment. According to the rarefaction curve analysis, richness of bacteria diversity in feces decreased as time progressed. Some pathogens such as Campylobacter were detected only at the beginning, meaning they substantially decayed during the course of our study. Overall, this study indicated: (1) sunlight can influence the community structure and (2) after excretion the fecal bacteria diversity can be significantly changed over time. Future studies should therefore use not only the microbial signature of fresh but also moderately aged fecal samples to develop more accurate community profiles for fecal source tracking.

Fish abundances in shoreline habitats and submerged aquatic vegetation in a tidal freshwater embayment of the Potomac River.

PubMed

Kraus, Richard T; Jones, R Christian

2012-05-01

Submerged aquatic vegetation (SAV) is considered an important habitat for juvenile and small forage fish species, but many long-term recruitment surveys do not effectively monitor fish communities in SAV. To better understand the impact of recent large increases of SAV on the fish community in tidal freshwater reaches of the Potomac River, we compared traditional seine sampling from shore with drop ring sampling of SAV beds (primarily Hydrilla) in a shallow water (depths, <1.5 m) embayment, Gunston Cove. To accomplish this, we developed species-specific catch efficiency values for the seine gear and calculated area-based density in both shoreline and SAV habitats in late summer of three different years (2007, 2008, and 2009). For the dominant species (Fundulus diaphanus, Lepomis macrochirus, Etheostoma olmstedi, Morone americana, Lepomis gibbosus, and Fundulus heteroclitus), density was nearly always higher in SAV, but overall, species richness was highest in shoreline habitats sampled with seines. Although historical monitoring of fish in Gunston Cove (and throughout Chesapeake Bay) is based upon seine sampling (and trawl sampling in deeper areas), the high densities of fish and larger areal extent of SAV indicated that complementary sampling of SAV habitats would produce more accurate trends in abundances of common species. Because drop ring samples cover much less area than seines and may miss rare species, a combination of methods that includes seine sampling is needed for biodiversity assessment. The resurgence of SAV in tidal freshwater signifies improving water quality, and methods we evaluated here support improved inferences about population trends and fish community structure as indicators of ecosystem condition.

Bacterial assemblages differ between compartments within the coral holobiont

NASA Astrophysics Data System (ADS)

Sweet, M. J.; Croquer, A.; Bythell, J. C.

2011-03-01

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the `snot sucker') was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the `snot sucker' and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay.

PubMed

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

2016-06-01

Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community. Copyright © 2016. Published by Elsevier B.V.

The role of stabilizing and communicating symptoms given overlapping communities in psychopathology networks.

PubMed

Blanken, Tessa F; Deserno, Marie K; Dalege, Jonas; Borsboom, Denny; Blanken, Peter; Kerkhof, Gerard A; Cramer, Angélique O J

2018-04-11

Network theory, as a theoretical and methodological framework, is energizing many research fields, among which clinical psychology and psychiatry. Fundamental to the network theory of psychopathology is the role of specific symptoms and their interactions. Current statistical tools, however, fail to fully capture this constitutional property. We propose community detection tools as a means to evaluate the complex network structure of psychopathology, free from its original boundaries of distinct disorders. Unique to this approach is that symptoms can belong to multiple communities. Using a large community sample and spanning a broad range of symptoms (Symptom Checklist-90-Revised), we identified 18 communities of interconnected symptoms. The differential role of symptoms within and between communities offers a framework to study the clinical concepts of comorbidity, heterogeneity and hallmark symptoms. Symptoms with many and strong connections within a community, defined as stabilizing symptoms, could be thought of as the core of a community, whereas symptoms that belong to multiple communities, defined as communicating symptoms, facilitate the communication between problem areas. We propose that defining symptoms on their stabilizing and/or communicating role within and across communities accelerates our understanding of these clinical phenomena, central to research and treatment of psychopathology.

Preparing for community violence: mood and behavioral correlates of the second Rodney King verdicts.

PubMed

Swendsen, J D; Norman, S

1998-01-01

This prospective investigation applied the Experience Sampling Method to examine the mood and behavioral responses of individuals facing the risk of community violence (in anticipation of the second Rodney King verdicts). Threatened participants experienced more negative affect and were less stable in behavioral involvement than individuals not under threat. Threatened participants also avoided social contact except for well-known individuals, and were more likely to be traveling than nonthreatened participants. Social contact with family or close friends and being at home (one's own home or the home of familiar individuals) were associated with large reductions in negative affect for those at risk for urban violence. The findings are discussed in terms of risk factors for trauma following community-wide stressors.

Do recreational activities affect coastal biodiversity?

NASA Astrophysics Data System (ADS)

Riera, Rodrigo; Menci, Cristiano; Sanabria-Fernández, José Antonio; Becerro, Mikel A.

2016-09-01

Human activities are largely affecting coastal communities worldwide. Recreational perturbations have been overlooked in comparison to other perturbations, yet they are potential threats to marine biodiversity. They affect coastal communities in different ways, underpinning consistent shifts in fish and invertebrates assemblages. Several sites were sampled subjected to varying effects by recreational fishermen (low and high pressure) and scuba divers (low and high) in an overpopulated Atlantic island. Non-consistent differences in ecological, trophic and functional diversity were found in coastal communities, considering both factors (;diving; and ;fishing;). Multivariate analyses only showed significant differences in benthic invertebrates between intensively-dived and non-dived sites. The lack of clear trends may be explained by the depletion of coastal resources in the study area, an extensively-affected island by overfishing.

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

PubMed

Lan, Freeman; Demaree, Benjamin; Ahmed, Noorsher; Abate, Adam R

2017-07-01

The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape

PubMed Central

Miller, Joshua H.

2011-01-01

Natural accumulations of skeletal material (death assemblages) have the potential to provide historical data on species diversity and population structure for regions lacking decades of wildlife monitoring, thereby contributing valuable baseline data for conservation and management strategies. Previous studies of the ecological and temporal resolutions of death assemblages from terrestrial large-mammal communities, however, have largely focused on broad patterns of community composition in tropical settings. Here, I expand the environmental sampling of large-mammal death assemblages into a temperate biome and explore more demanding assessments of ecological fidelity by testing their capacity to record past population fluctuations of individual species in the well-studied ungulate community of Yellowstone National Park (Yellowstone). Despite dramatic ecological changes following the 1988 wildfires and 1995 wolf re-introduction, the Yellowstone death assemblage is highly faithful to the living community in species richness and community structure. These results agree with studies of tropical death assemblages and establish the broad capability of vertebrate remains to provide high-quality ecological data from disparate ecosystems and biomes. Importantly, the Yellowstone death assemblage also correctly identifies species that changed significantly in abundance over the last 20 to ∼80 years and the directions of those shifts (including local invasions and extinctions). The relative frequency of fresh versus weathered bones for individual species is also consistent with documented trends in living population sizes. Radiocarbon dating verifies the historical source of bones from Equus caballus (horse): a functionally extinct species. Bone surveys are a broadly valuable tool for obtaining population trends and baseline shifts over decadal-to-centennial timescales. PMID:21464921

Synergistic interactions between edge and area effects in a heavily fragmented landscape.

PubMed

Ewers, Robert M; Thorpe, Stephen; Didham, Raphael K

2007-01-01

Both area and edge effects have a strong influence on ecological processes in fragmented landscapes, but there is little understanding of how these two factors might interact to exacerbate local species declines. To test for synergistic interactions between area and edge effects, we sampled a diverse beetle community in a heavily fragmented landscape in New Zealand. More than 35,000 beetles of approximately 900 species were sampled over large gradients in habitat area (10(-2) 10(6) ha) and distance from patch edge (2(0)-2(10) m from the forest edge into both the forest and adjacent matrix). Using a new approach to partition variance following an ordination analysis, we found that a synergistic interaction between habitat area and distance to edge was a more important determinant of patterns in beetle community composition than direct edge or area effects alone. The strength of edge effects in beetle-species composition increased nonlinearly with increasing fragment area. One important consequence of the synergy is that the slopes of species area (SA) curves constructed from habitat islands depend sensitively on the distance from edge at which sampling is conducted. Surprisingly, we found negative SA curves for communities sampled at intermediate distances from habitat edges, caused by differential edge responses of matrix- vs. forest-specialist species in fragments of increasing area. Our data indicate that distance to habitat edge has a consistently greater impact on beetle community composition than habitat area and that variation in the strength of edge effects may underlie many patterns that are superficially related to habitat area.

Archean Microbial Mat Communities

NASA Astrophysics Data System (ADS)

Tice, Michael M.; Thornton, Daniel C. O.; Pope, Michael C.; Olszewski, Thomas D.; Gong, Jian

2011-05-01

Much of the Archean record of microbial communities consists of fossil mats and stromatolites. Critical physical emergent properties governing the evolution of large-scale (centimeters to meters) topographic relief on the mat landscape are (a) mat surface roughness relative to the laminar sublayer and (b) cohesion. These properties can be estimated for fossil samples under many circumstances. A preliminary analysis of Archean mat cohesion suggests that mats growing in shallow marine environments from throughout this time had cohesions similar to those of modern shallow marine mats. There may have been a significant increase in mat strength at the end of the Archean.

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi.

PubMed

Doyle, Ronan; Gondwe, Austridia; Fan, Yue-Mei; Maleta, Kenneth; Ashorn, Per; Klein, Nigel; Harris, Kathryn

2018-01-05

The bacterial community found in the vagina is an important determinant of a woman's health and disease. A healthy vaginal microbiota is associated with a lower species richness and high proportions of one of a number of different Lactobacillus spp.. When disrupted the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations which may not capture the full complexity of the community, nor adequately predict what constitutes a healthy microbiota in all populations. In this study we sampled and characterised the vaginal microbiota from a cohort of 1107 women in rural Malawi found on vaginal swabs taken post-partum. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year post-partum. The Lactobacillus -deficient anaerobic community commonly labelled community state type (CST) 4 could be sub-divided into four further communities. A Lactobacillus iners dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal vaginal microbiota is post-partum. Previous identification of community state types and associations between bacterial species, bacterial vaginosis and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. Importance A bacterial community in the vaginal tract that is dominated by small number of bacterial Lactobacillus species and when they are not present, there is a greater incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study we characterised the vaginal microbiota after delivery of a large group of women from a resource poor, under-sampled population in rural Malawi. The majority of women were found to have a Lactobacillus -deficient community and even after a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus dominant community is unknown and could suggest that not all Lactobacillus -deficient community structures are adverse. A better understanding is needed of this complex community state type. Copyright © 2018 Doyle et al.

Results of preliminary reconnaissance trip to determine the presence of wetlands in wet forest habitats on the Island of Hawaii as part of the Hawaii Geothermal Project, October 1993

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

Wakeley, J.S.; Sprecher, S.W.; Lichvar, R.

1994-02-25

In October 1993, the authors sampled soils, vegetation, and hydrology at eight sites representing a range of substrates, elevations, soil types, and plant community types within rainforest habitats on the Island of Hawaii. Their purpose was to determine whether any of these habitats were wetlands according to the 1987 Corps of Engineers Wetlands Delineation Manual. None of the rainforest habitats they sampled was wetland in its entirety. However, communities established on pahoehoe lava flows contained scattered wetlands in depressions and folds in the lava, where water could accumulate. Therefore, large construction projects, such as that associated with proposed geothermal energymore » development in the area, have the potential to impact a significant number and/or area of wetlands. To estimate those impacts more accurately, they present a supplementary scope of work and cost estimate for additional sampling in the proposed geothermal project area.« less

An investigation of the measurement properties of the Spot-the-Word test in a community sample.

PubMed

Mackinnon, Andrew; Christensen, Helen

2007-12-01

Intellectual ability is assessed with the Spot-the-Word (STW) test (A. Baddeley, H. Emslie, & I. Nimmo Smith, 1993) by asking respondents to identify a word in a word-nonword item pair. Results in moderate-sized samples suggest this ability is resistant to decline due to dementia. The authors used a 3-parameter item response theory model to investigate the measurement properties of the STW in a large community-dwelling sample (n=2,480) 60 to 64 years of age. A number of poorly performing items were identified. Substantial guessing was present; however, the number of words correctly identified was found to be an accurate index of ability. Performance was moderately related to a number of tests of cognitive performance and was effectively unrelated to visual acuity and to physical or mental health status. The STW is a promising test of ability that, in the future, may be refined by the deletion or replacement of poorly functioning items.

Primary and secondary exercise dependence in a community-based sample of road race runners.

PubMed

Cook, Brian; Karr, Trisha M; Zunker, Christie; Mitchell, James E; Thompson, Ron; Sherman, Roberta; Crosby, Ross D; Cao, Li; Erickson, Ann; Wonderlich, Stephen A

2013-10-01

The purpose of our study was to examine exercise dependence (EXD) in a large community-based sample of runners. The secondary purpose of this study was to examine differences in EXD symptoms between primary and secondary EXD. Our sample included 2660 runners recruited from a local road race (M age = 38.78 years, SD = 10.80; 66.39% women; 91.62% Caucasian) who completed all study measures online within 3 weeks of the race. In this study, EXD prevalence was lower than most previously reported rates (gamma = .248, p < .001) and individuals in the at-risk for EXD category participated in longer distance races, F(8,1) = 14.13, p = .01, partial eta squared = .05. Group differences were found for gender, F(1,1921) 8.08, p = .01, partial eta squared = .004, and primary or secondary group status, F(1,1921) 159.53, p = .01, partial eta squared = .077. Implications of primary and secondary EXD differences and future research are discussed.

Screening for Binge Eating Disorders Using the Patient Health Questionnaire in a Community Sample

PubMed Central

Striegel-Moore, Ruth H.; Perrin, Nancy; DeBar, Lynn; Wilson, G. Terence; Rosselli, Francine; Kraemer, Helena C.

2009-01-01

Objective To examine the operating characteristics of the Patient Health Questionnaire eating disorder module (PHQ-ED) for identifying bulimia nervosa/binge eating disorder (BN/BED) or recurrent binge eating (RBE) in a community sample, and to compare true positive (TP) versus false positive (FP) cases on clinical validators. Method 259 screen positive individuals and a random sample of 89 screen negative cases completed a diagnostic interview. Sensitivity, specificity, and Positive Predictive Value (PPV) were calculated. TP and FP cases were compared using t-tests and Chi-Square tests. Results The PHQ-ED had high sensitivity (100%) and specificity (92%) for detecting BN/BED or RBE, but PPV was low (15% or 19%). TP and FP cases did not differ significantly on frequency of subjective bulimic episodes, objective overeating, restraint, on BMI, and on self-rated health. Conclusions The PHQ-ED is recommended for use in large populations only in conjunction with follow-up questions to rule out cases without objective bulimic episodes. PMID:19424976

The Community Integration Questionnaire - Revised: Australian normative data and measurement of electronic social networking.

PubMed

Callaway, Libby; Winkler, Dianne; Tippett, Alice; Herd, Natalie; Migliorini, Christine; Willer, Barry

2016-06-01

Consideration of the relationship between meaningful participation, health and wellbeing underpins occupational therapy intervention, and drives measurement of community integration following acquired brain injury (ABI). However, utility of community integration measures has been limited to date by lack of normative data against which to compare outcomes, and none examine the growing use of electronic social networking (ESN) for social participation. This research had four aims: (i) develop and pilot items assessing ESN to add to the Community Integration Questionnaire, producing the Community Integration Questionnaire-Revised (CIQ-R); (ii) examine factor structure of the CIQ-R; (iii) collect Australian CIQ-R normative data; and (iv) assess test-retest reliability of the revised measure. Australia. A convenience sample of adults without ABI (N = 124) was used to develop and pilot ESN items. A representative general population sample of adults without ABI aged 18-64 years (N = 1973) was recruited to gather normative CIQ-R data. Cross-sectional survey. Demographic items and the CIQ-R. The CIQ-R demonstrated acceptable psychometric properties, with minor modification to the original scoring based on the factor analyses provided. Large representative general population CIQ-R normative data have been established, detailing contribution of a range of independent demographic variables to community integration. The addition of electronic social networking items to the CIQ-R offers a contemporary method of assessing community integration following ABI. Normative CIQ-R data enhance the understanding of community integration in the general population, allowing occupational therapists and other clinicians to make more meaningful comparisons between groups. © 2016 Occupational Therapy Australia.

The NKI-Rockland Sample: A Model for Accelerating the Pace of Discovery Science in Psychiatry

PubMed Central

Nooner, Kate Brody; Colcombe, Stanley J.; Tobe, Russell H.; Mennes, Maarten; Benedict, Melissa M.; Moreno, Alexis L.; Panek, Laura J.; Brown, Shaquanna; Zavitz, Stephen T.; Li, Qingyang; Sikka, Sharad; Gutman, David; Bangaru, Saroja; Schlachter, Rochelle Tziona; Kamiel, Stephanie M.; Anwar, Ayesha R.; Hinz, Caitlin M.; Kaplan, Michelle S.; Rachlin, Anna B.; Adelsberg, Samantha; Cheung, Brian; Khanuja, Ranjit; Yan, Chaogan; Craddock, Cameron C.; Calhoun, Vincent; Courtney, William; King, Margaret; Wood, Dylan; Cox, Christine L.; Kelly, A. M. Clare; Di Martino, Adriana; Petkova, Eva; Reiss, Philip T.; Duan, Nancy; Thomsen, Dawn; Biswal, Bharat; Coffey, Barbara; Hoptman, Matthew J.; Javitt, Daniel C.; Pomara, Nunzio; Sidtis, John J.; Koplewicz, Harold S.; Castellanos, Francisco Xavier; Leventhal, Bennett L.; Milham, Michael P.

2012-01-01

The National Institute of Mental Health strategic plan for advancing psychiatric neuroscience calls for an acceleration of discovery and the delineation of developmental trajectories for risk and resilience across the lifespan. To attain these objectives, sufficiently powered datasets with broad and deep phenotypic characterization, state-of-the-art neuroimaging, and genetic samples must be generated and made openly available to the scientific community. The enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) is a response to this need. NKI-RS is an ongoing, institutionally centered endeavor aimed at creating a large-scale (N > 1000), deeply phenotyped, community-ascertained, lifespan sample (ages 6–85 years old) with advanced neuroimaging and genetics. These data will be publically shared, openly, and prospectively (i.e., on a weekly basis). Herein, we describe the conceptual basis of the NKI-RS, including study design, sampling considerations, and steps to synchronize phenotypic and neuroimaging assessment. Additionally, we describe our process for sharing the data with the scientific community while protecting participant confidentiality, maintaining an adequate database, and certifying data integrity. The pilot phase of the NKI-RS, including challenges in recruiting, characterizing, imaging, and sharing data, is discussed while also explaining how this experience informed the final design of the enhanced NKI-RS. It is our hope that familiarity with the conceptual underpinnings of the enhanced NKI-RS will facilitate harmonization with future data collection efforts aimed at advancing psychiatric neuroscience and nosology. PMID:23087608

Indoor-air microbiome in an urban subway network: diversity and dynamics.

PubMed

Leung, Marcus H Y; Wilkins, David; Li, Ellen K T; Kong, Fred K F; Lee, Patrick K H

2014-11-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

PubMed

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R; Vincent, Warwick F

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

Rapid Identification of a Cooling Tower-Associated Legionnaires’ Disease Outbreak Supported by Polymerase Chain Reaction Testing of Environmental Samples, New York City, 2014–2015

PubMed Central

Benowitz, Isaac; Fitzhenry, Robert; Boyd, Christopher; Dickinson, Michelle; Levy, Michael; Lin, Ying; Nazarian, Elizabeth; Ostrowsky, Belinda; Passaretti, Teresa; Rakeman, Jennifer; Saylors, Amy; Shamoonian, Elena; Smith, Terry-Ann; Balter, Sharon

2018-01-01

We investigated an outbreak of eight Legionnaires’ disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings) <1 km from patient residences, a market misting system, a community-wide water system used for heating and cooling, and potable water. To support a timely public health response, we used real-time polymerase chain reaction (PCR) to identify Legionella DNA in environmental samples within hours of specimen collection. We detected L. pneumophila serogroup 1 DNA only at a power plant cooling tower, supporting the decision to order remediation before culture results were available. An isolate from a power plant cooling tower sample was indistinguishable from a patient isolate by pulsed-field gel electrophoresis, suggesting the cooling tower was the outbreak source. PCR results were available <1 day after sample collection, and culture results were available as early as 5 days after plating. PCR is a valuable tool for identifying Legionella DNA in environmental samples in outbreak settings. PMID:29780175

Metabarcoding of environmental DNA samples to explore the use of uranium mine containment ponds as a water source for wildlife

USGS Publications Warehouse

Klymus, Katy E.; Richter, Cathy; Thompson, Nathan; Hinck, Jo E.

2017-01-01

Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area’s overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work.

Comparing two basic subtypes in OCD across three large community samples: a pure compulsive versus a mixed obsessive-compulsive subtype.

PubMed

Rodgers, Stephanie; Ajdacic-Gross, Vladeta; Kawohl, Wolfram; Müller, Mario; Rössler, Wulf; Hengartner, Michael P; Castelao, Enrique; Vandeleur, Caroline; Angst, Jules; Preisig, Martin

2015-12-01

Due to its heterogeneous phenomenology, obsessive-compulsive disorder (OCD) has been subtyped. However, these subtypes are not mutually exclusive. This study presents an alternative subtyping approach by deriving non-overlapping OCD subtypes. A pure compulsive and a mixed obsessive-compulsive subtype (including subjects manifesting obsessions with/without compulsions) were analyzed with respect to a broad pattern of psychosocial risk factors and comorbid syndromes/diagnoses in three representative Swiss community samples: the Zurich Study (n = 591), the ZInEP sample (n = 1500), and the PsyCoLaus sample (n = 3720). A selection of comorbidities was examined in a pooled database. Odds ratios were derived from logistic regressions and, in the analysis of pooled data, multilevel models. The pure compulsive subtype showed a lower age of onset and was characterized by few associations with psychosocial risk factors. The higher social popularity of the pure compulsive subjects and their families was remarkable. Comorbidities within the pure compulsive subtype were mainly restricted to phobias. In contrast, the mixed obsessive-compulsive subtype had a higher prevalence and was associated with various childhood adversities, more familial burden, and numerous comorbid disorders, including disorders characterized by high impulsivity. The current comparison study across three representative community surveys presented two basic, distinct OCD subtypes associated with differing psychosocial impairment. Such highly specific subtypes offer the opportunity to learn about pathophysiological mechanisms specifically involved in OCD.

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing.

PubMed

O'Connell, Lauren; Gao, Song; McCorquodale, Donald; Fleisher, Jay; Lopez, Jose V

2018-01-01

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus . However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014-16 El Niño event.

Elemental carbon and PM(2.5 )levels in an urban community heavily impacted by truck traffic.

PubMed Central

Lena, T Suvendrini; Ochieng, Victor; Carter, Majora; Holguín-Veras, José; Kinney, Patrick L

2002-01-01

Hunts Point, a 690-acre peninsula in the South Bronx, New York City, is a hub in the tristate (New York, New Jersey, and Connecticut) freight transportation system. This study was carried out in response to community concerns about potential health effects of exposure to diesel exhaust particulate (DEP). We measured particulate matter < 2.5 microm in aerodynamic diameter (PM(2.5)) and elemental carbon (EC) on sidewalks and tested whether spatial variations in concentrations were related to local truck traffic density. Ten-hour integrated air samples for EC and PM(2.5) were collected for 9 days over a 3-week period in the summer of 1999 at seven geographically distinct intersections. Simultaneous traffic counts were carried out for each sampling event. Traffic was classified into three classes: passenger cars, small trucks, and large trucks (diesel vehicles). Mean diesel vehicle volumes ranged from 9.3 to 276.5 vehicles/hr across sites. Mean EC concentrations by site ranged from 2.6 microg/m(3) at the control site to 7.3 microg/m(3) along a designated truck route. Linear regression of site-specific mean EC concentration on mean large truck counts predicted an increase of 1.69 microg/m(3) EC per 100 large trucks/hr (SE = 0.37; p = 0.01; R(2) = 0.84). Average PM(2.5) concentrations by site ranged 1.6-fold (19.0-29.9 microg/m(3)) and were more weakly associated with local traffic. Variations over time for PM(2.5 )were more pronounced, ranging almost 4-fold (8.9-34.4 microg/m(3)). These results show that airborne EC concentrations, an important component of DEP, are elevated in Hunts Point and that the impact varies across the community as a function of large truck traffic. PMID:12361926

Comparison of breeding bird and vegetation communities in primary and secondary forests of Great Smoky Mountains National Park

USGS Publications Warehouse

Simons, Theodore R.; Shriner, Susan A.; Farnsworth, George L.

2006-01-01

We compared breeding bird communities and vegetation characteristics at paired point locations in primary (undisturbed) and mature secondary forest (70-100 years old) sites in Great Smoky Mountains National Park, USA to understand how sites logged prior to creation of the park compare to undisturbed sites following 70 years of protection from human disturbance. We found that bird and vegetation communities are currently similar, but retain some differences in species composition. Rank abundance curves for primary and secondary forest bird communities showed very similar patterns of species dominance. Species composition was also similar on the two sites which shared 24 of the 25 most frequently recorded species. Nonetheless, comparisons of density estimates derived from distance sampling showed three bird species were more abundant on primary forest sites and that one bird species was significantly more abundant on secondary forest sites. Notably, comparisons based on raw counts (unadjusted for potential differences in detectability) produced somewhat different results. Analyses of vegetation samples for the paired sites also showed relative similarity, but with some differences between primary and secondary forests. Primary forest sites had more large trees (trees greater than 50 cm diameter at breast height) and late successional species. Primary forest sites had a denser tall shrub layer while secondary forest sites had a denser canopy layer. Nonetheless, tree species richness, basal area of live trees and number of standing snags did not differ between primary and secondary forest sites. Results indicate that breeding bird communities on sites within the park that were logged commercially 70 years ago are currently quite similar to bird communities on sites with no history of human disturbance. Similarities between the bird communities on previously disturbed and undisturbed sites in Great Smoky Mountains National Park may exceed those on more fragmented landscapes because large patches of primary forest, adjacent to commercially logged sites, remained in the park when it was established in 1935. These patches of primary forest may have served as source areas for commercially logged sites.

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets

PubMed Central

Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W.; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S.; Brodie, Eoin L.; Nelson, Karen E.

2014-01-01

ABSTRACT Human papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects. IMPORTANCE This nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections. PMID:24522917

Large-Scale Operations Management Test of Use of the White Amur for Control of Problem Aquatic Plants. Report 1. Baseline Studies. Volume VIII. Summary of Baseline Studies and Data.

DTIC Science & Technology

1982-05-01

in May 1976, and, by July 1976, all sampling techniques were employed. In addition to routine displays of data analysis such as frequency tables and...amphibian and reptile communities in large aquatic habitats in Florida, comparison with similar herpetofaunal assemblages or populations is not possible... field environment was initiated at Lake Conway near Orlando, Fla., to study the effectiveness of the fish as a biological macrophyte control agent. A

Social networks and community prevention coalitions.

PubMed

Feinberg, Mark E; Riggs, Nathaniel R; Greenberg, Mark T

2005-07-01

This study investigates the links between community readiness and the social networks among participants in Communities That Care (CTC), community-based prevention coalitions. The coalitions targeted adolescent behavior problems through community risk factor assessments, prioritization of risk factors, and selection/implementation of corresponding evidence-based family, school, and community programs. Key leaders (n = 219) in 23 new CTC sites completed questionnaires focusing on community readiness to implement CTC and the respondents' personal, work, and social organization links to other key leaders in the community. Outside technical assistants also completed ratings of each community's readiness and early CTC functioning. Measures of network cohesion/integration were positively associated with readiness, while centralization was negatively associated. These results suggest that non-centralized networks in which ties between members are close and direct may be an indicator of community readiness. In addition, we found different associations between readiness and different domains of social relations. EDITORS' STRATEGIC IMPLICATIONS: The authors present the promising practice of using social network analysis to characterize the functioning of local prevention coalitions and their readiness to implement a community-based prevention initiative. Researchers and community planners will benefit from the lessons in this article, which capitalizes on a large sample and multiple informants. This work raises interesting questions about how to combine the promotion of coalition functioning while simultaneously encouraging diversity of coalition membership.

Negative Effects of an Exotic Grass Invasion on Small-Mammal Communities

PubMed Central

Freeman, Eric D.; Sharp, Tiffanny R.; Larsen, Randy T.; Knight, Robert N.; Slater, Steven J.; McMillan, Brock R.

2014-01-01

Exotic invasive species can directly and indirectly influence natural ecological communities. Cheatgrass (Bromus tectorum) is non-native to the western United States and has invaded large areas of the Great Basin. Changes to the structure and composition of plant communities invaded by cheatgrass likely have effects at higher trophic levels. As a keystone guild in North American deserts, granivorous small mammals drive and maintain plant diversity. Our objective was to assess potential effects of invasion by cheatgrass on small-mammal communities. We sampled small-mammal and plant communities at 70 sites (Great Basin, Utah). We assessed abundance and diversity of the small-mammal community, diversity of the plant community, and the percentage of cheatgrass cover and shrub species. Abundance and diversity of the small-mammal community decreased with increasing abundance of cheatgrass. Similarly, cover of cheatgrass remained a significant predictor of small-mammal abundance even after accounting for the loss of the shrub layer and plant diversity, suggesting that there are direct and indirect effects of cheatgrass. The change in the small-mammal communities associated with invasion of cheatgrass likely has effects through higher and lower trophic levels and has the potential to cause major changes in ecosystem structure and function. PMID:25269073

Associations of Personality with Body Mass Index and Obesity in a Large Late Midlife Community Sample

PubMed Central

Wimmelmann, Cathrine Lawaetz; Lund, Rikke; Flensborg-Madsen, Trine; Christensen, Ulla; Osler, Merete; Lykke Mortensen, Erik

2018-01-01

Objective The study examined cross-sectional associations of personality with BMI and obesity among men and women in a large late midlife community sample. Methods The sample comprised 5,286 Danish individuals aged 49–63 years from the Copenhagen Ageing and Midlife Biobank (CAMB) with complete information on measured BMI, personality assessed by the NEO Five Factor Inventory (NEO FFI), and sociodemographic factors including sex, age and educational length. Analysis of variance and logistic regression models were used to investigate associations between personality and BMI as well as obesity. Personality traits were analyzed separately and combined in the same model. Results All personality traits except for neuroticism were significantly associated with BMI, with extraversion (p value ranged from <0.001 to 0.012) and agreeableness (p value ranged from 0.001 to 0.002) being the most consistent predictors of BMI among men and women, respectively. Furthermore, extraversion among men (high scores) (p = 0.016) and agreeableness among women (low scores) (p = 0.026) were the only personality traits significantly associated with obesity when adjusting for duration of education. Conclusion Personality was significantly associated with BMI and to a lesser extent with obesity, and these associations differed between men and women. Also, it was suggested that the interrelations of the five personality traits should be considered in future research of personality and health outcomes. PMID:29631276

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Physiological Response and Childhood Anxiety: Association With Symptoms of Anxiety Disorders and Cognitive Bias

ERIC Educational Resources Information Center

Weems, Carl F.; Zakem, Alan H.; Costa, Natalie M.; Cannon, Melinda F.; Watts, Sarah E.

2005-01-01

This study examined the physiological response (skin conductance and heart rate [HR]) of youth exposed to a mildly phobic stimulus (video of a large dog) and its relation to child- and parent-reported anxiety symptoms and cognitive bias in a community-recruited sample of youth (n = 49). The results of this study indicated that HR and…

Understanding Violence in Contemporary and Earlier Gangs: An Exploratory Application of the Theory of Reasoned Action.

ERIC Educational Resources Information Center

Evans, Judy P.; Taylor, Jerome

1995-01-01

Reviews the theory of reasoned action to demonstrate how it can be applied to understanding gang violence, and illustrates its potential applicability to a pilot sample of 30 contemporary and 18 earlier gangs living in a large metropolitan community. Results indicate this theory has been helpful in explaining higher levels of violence in…

Developmental Trajectories in Adolescents and Adults With Autism: The Case of Daily Living Skills

ERIC Educational Resources Information Center

Smith, Leann E.; Maenner, Matthew J.; Seltzer, Marsha Mailick

2012-01-01

Objective: This study aimed to investigate the longitudinal course of daily living skills in a large, community-based sample of adolescents and adults with autism spectrum disorders (ASD) over a 10-year period. Method: Adolescents and adults with ASD (n = 397) were drawn from an ongoing, longitudinal study of individuals with ASD and their…

Psychosocial Factors in Adolescent and Young Adult Self-Reported Depressive Symptoms: Causal or Correlational Associations?

ERIC Educational Resources Information Center

Steinhausen, Hans-Christoph; Haslimeier, Claudia; Metzke, Christa Winkler

2007-01-01

Using a large longitudinal representative community sample, this study identified three groups of subjects who were depressed either in pre-adolescence, late adolescence or early adulthood, and matched by age and gender to controls without depression. The 90th percentile on one or two self-reported symptom scales [i. e. the Center for…

The Impact of the Developmental Timing of Trauma Exposure on PTSD Symptoms and Psychosocial Functioning among Older Adults

ERIC Educational Resources Information Center

Ogle, Christin M.; Rubin, David C.; Siegler, Ilene C.

2013-01-01

The present study examined the impact of the developmental timing of trauma exposure on posttraumatic stress disorder (PTSD) symptoms and psychosocial functioning in a large sample of community-dwelling older adults (N = 1,995). Specifically, we investigated whether the negative consequences of exposure to traumatic events were greater for traumas…

Body Dissatisfaction and Eating Disturbances in Early Adolescence: A Structural Modeling Investigation Examining Negative Affect and Peer Factors

ERIC Educational Resources Information Center

Hutchinson, Delyse M.; Rapee, Ronald M.; Taylor, Alan

2010-01-01

This study tested five proposed models of the relationship of negative affect and peer factors in early adolescent body dissatisfaction, dieting, and bulimic behaviors. A large community sample of girls in early adolescence was assessed via questionnaire (X[overbar] age = 12.3 years). Structural equation modeling (SEM) indicated that negative…

A Systems View of Mother-Infant Face-to-Face Communication

ERIC Educational Resources Information Center

Beebe, Beatrice; Messinger, Daniel; Bahrick, Lorraine E.; Margolis, Amy; Buck, Karen A.; Chen, Henian

2016-01-01

Principles of a dynamic, dyadic systems view of mother-infant face-to-face communication, which considers self- and interactive processes in relation to one another, were tested. The process of interaction across time in a large low-risk community sample at infant age 4 months was examined. Split-screen videotape was coded on a 1-s time base for…

High-Risk Sexual Behavior among Students of a Minority-Serving University in a Community with a High HIV/AIDS Prevalence

ERIC Educational Resources Information Center

Trepka, Mary Jo; Kim, Sunny; Pekovic, Vukosava; Zamor, Peggy; Velez, Elvira; Gabaroni, Mariela V.

2008-01-01

Objective: The authors used a stratified cluster sampling design to inform campus sexually transmitted diseases prevention programs. Participants and Methods: They conducted a cross-sectional study of students (N = 1,130) at a large, urban, minority-serving university in South Florida using the 2004 National College Health Assessment Survey…

Adolescent Internet Abuse: A Study on the Role of Attachment to Parents and Peers in a Large Community Sample

PubMed Central

Volpi, Barbara; Marzilli, Eleonora; Tambelli, Renata

2018-01-01

Adolescents are the main users of new technologies and their main purpose of use is social interaction. Although new technologies are useful to teenagers, in addressing their developmental tasks, recent studies have shown that they may be an obstacle in their growth. Research shows that teenagers with Internet addiction experience lower quality in their relationships with parents and more individual difficulties. However, limited research is available on the role played by adolescents' attachment to parents and peers, considering their psychological profiles. We evaluated in a large community sample of adolescents (N = 1105) the Internet use/abuse, the adolescents' attachment to parents and peers, and their psychological profiles. Hierarchical regression analyses were conducted to verify the influence of parental and peer attachment on Internet use/abuse, considering the moderating effect of adolescents' psychopathological risk. Results showed that adolescents' attachment to parents had a significant effect on Internet use. Adolescents' psychopathological risk had a moderating effect on the relationship between attachment to mothers and Internet use. Our study shows that further research is needed, taking into account both individual and family variables. PMID:29707572

Gender Differences in Cognition in China and Reasons for Change over Time: Evidence from CHARLS.

PubMed

Lei, Xiaoyan; Smith, James P; Sun, Xiaoting; Zhao, Yaohui

2014-12-01

In this paper, we model gender differences in cognitive ability in China using a new sample of middle-aged and older Chinese respondents. Modeled after the American Health and Retirement Survey (HRS), CHARLS respondents are 45 years and older and are nationally representative of the Chinese population in this age span. Our measures of cognition in CHARLS rely on two measures that proxy for different dimensions of adult cognition-episodic memory and intact mental status. We relate these cognitive measures to adult health and SES outcomes during the adult years. We find large cognitive differences to the detriment of women that were mitigated by large gender differences in education among these generations of Chinese people. These gender differences in cognition are especially concentrated in the older age groups and poorer communities within the sample. We also investigated historical, geographical, and cultural characteristics of communities to understand how they impact cognition. Economic development and environmental improvement such as having electricity, increases in wage per capita and green coverage ratio generally contribute to higher cognition ability. Women benefit more from the fruits of development -electricity and growth of green coverage ratio are conducive to lessening female disadvantage in cognition.

HIV testing among at-risk adolescents and young adults: a prospective analysis of a community sample.

PubMed

Tolou-Shams, Marina; Payne, Nanetta; Houck, Christopher; Pugatch, David; Beausoleil, Nancy; Brown, Larry K

2007-12-01

Little is known about predictors of human immunodeficiency virus (HIV) testing among sexually active adolescents, who account for a large proportion of new HIV infections. This study sought to determine predictors of HIV testing among a large community-based sample of adolescents in three cities who had recent unprotected sexual intercourse. Sexually active adolescents (N = 1222) completed baseline and 3-month assessments of sexual behavior, substance use and HIV testing behaviors as part of a larger, multi-site, brief HIV prevention program. Approximately half of the adolescents reported having previously been tested for HIV, and of those one third were tested in the next 3 months without a specific intervention. Adolescents who received HIV testing were more likely at baseline to have ever been tested, to have a STI diagnosis, to have not used substances during sex and to have been assertive about condom use with a partner. Health care models encouraging more widespread, universal testing may be an important public health initiative to curb the spread of HIV. Regular HIV screenings provide an opportunity to enhance awareness of behavioral risk and HIV status, as well as provide opportunities for early detection and care.

Gender Differences in Cognition in China and Reasons for Change over Time: Evidence from CHARLS

PubMed Central

Lei, Xiaoyan; Sun, Xiaoting; Zhao, Yaohui

2014-01-01

In this paper, we model gender differences in cognitive ability in China using a new sample of middle-aged and older Chinese respondents. Modeled after the American Health and Retirement Survey (HRS), CHARLS respondents are 45 years and older and are nationally representative of the Chinese population in this age span. Our measures of cognition in CHARLS rely on two measures that proxy for different dimensions of adult cognition—episodic memory and intact mental status. We relate these cognitive measures to adult health and SES outcomes during the adult years. We find large cognitive differences to the detriment of women that were mitigated by large gender differences in education among these generations of Chinese people. These gender differences in cognition are especially concentrated in the older age groups and poorer communities within the sample. We also investigated historical, geographical, and cultural characteristics of communities to understand how they impact cognition. Economic development and environmental improvement such as having electricity, increases in wage per capita and green coverage ratio generally contribute to higher cognition ability. Women benefit more from the fruits of development –electricity and growth of green coverage ratio are conducive to lessening female disadvantage in cognition. PMID:25530942

Impacts of changing rainfall regime on the demography of tropical birds

NASA Astrophysics Data System (ADS)

Brawn, Jeffrey D.; Benson, Thomas J.; Stager, Maria; Sly, Nicholas D.; Tarwater, Corey E.

2017-02-01

Biodiversity in tropical regions is particularly high and may be highly sensitive to climate change. Unfortunately, a lack of long-term data hampers understanding of how tropical species, especially animals, may react to projected environmental changes. The amount and timing of rainfall is key to the function of tropical ecosystems and, although specific model predictions differ, there is general agreement that rainfall regimes will change over large areas of the tropics. Here, we estimate associations between dry season length (DSL) and the population biology of 20 bird species sampled in central Panama over a 33-year period. Longer dry seasons decreased the population growth rates and viability of nearly one-third of the species sampled. Simulations with modest increases in DSL suggest that consistently longer dry seasons will change the structure of tropical bird communities. Such change may occur even without direct loss of habitat--a finding with fundamental implications for conservation planning. Systematic changes in rainfall regime may threaten some populations and communities of tropical animals even in large tracts of protected habitat. These findings suggest the need for collaboration between climate scientists and conservation biologists to identify areas where rainfall regimes will be able to plausibly maintain wildlife populations.

The Airplane Cabin Microbiome.

PubMed

Weiss, Howard; Hertzberg, Vicki Stover; Dupont, Chris; Espinoza, Josh L; Levy, Shawn; Nelson, Karen; Norris, Sharon

2018-06-06

Serving over three billion passengers annually, air travel serves as a conduit for infectious disease spread, including emerging infections and pandemics. Over two dozen cases of in-flight transmissions have been documented. To understand these risks, a characterization of the airplane cabin microbiome is necessary. Our study team collected 229 environmental samples on ten transcontinental US flights with subsequent 16S rRNA sequencing. We found that bacterial communities were largely derived from human skin and oral commensals, as well as environmental generalist bacteria. We identified clear signatures for air versus touch surface microbiome, but not for individual types of touch surfaces. We also found large flight-to-flight beta diversity variations with no distinguishing signatures of individual flights, rather a high between-flight diversity for all touch surfaces and particularly for air samples. There was no systematic pattern of microbial community change from pre- to post-flight. Our findings are similar to those of other recent studies of the microbiome of built environments. In summary, the airplane cabin microbiome has immense airplane to airplane variability. The vast majority of airplane-associated microbes are human commensals or non-pathogenic, and the results provide a baseline for non-crisis-level airplane microbiome conditions.

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy.

PubMed

Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Shedden, Kerby A; Neiswanger, Katherine; Trumble, Erika; Li, Jiean J; McNeil, Daniel W; Crout, Richard J; Weyant, Robert J; Marazita, Mary L; Foxman, Betsy

2016-09-15

Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition. Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy

PubMed Central

Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Shedden, Kerby A.; Neiswanger, Katherine; Trumble, Erika; Li, Jiean J.; McNeil, Daniel W.; Crout, Richard J.; Weyant, Robert J.; Marazita, Mary L.

2016-01-01

ABSTRACT Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition. IMPORTANCE Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work. PMID:27371581

Community turnover of wood-inhabiting fungi across hierarchical spatial scales.

PubMed

Abrego, Nerea; García-Baquero, Gonzalo; Halme, Panu; Ovaskainen, Otso; Salcedo, Isabel

2014-01-01

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

PubMed Central

Abrego, Nerea; García-Baquero, Gonzalo; Halme, Panu; Ovaskainen, Otso; Salcedo, Isabel

2014-01-01

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence. PMID:25058128

The Specific Level of Functioning Scale: construct validity, internal consistency and factor structure in a large Italian sample of people with schizophrenia living in the community.

PubMed

Mucci, Armida; Rucci, Paola; Rocca, Paola; Bucci, Paola; Gibertoni, Dino; Merlotti, Eleonora; Galderisi, Silvana; Maj, Mario

2014-10-01

The study aimed to assess the construct validity, internal consistency and factor structure of the Specific Levels of Functioning Scale (SLOF), a multidimensional instrument assessing real life functioning. The study was carried out in 895 Italian people with schizophrenia, all living in the community and attending the outpatient units of 26 university psychiatric clinics and/or community mental health departments. The construct validity of the SLOF was analyzed by means of the multitrait-multimethod approach, using the Personal and Social Performance (PSP) Scale as the gold standard. The factor structure of the SLOF was examined using both an exploratory principal component analysis and a confirmatory factor analysis. The six factors identified using exploratory principal component analysis explained 57.1% of the item variance. The examination of the multitrait-multimethod matrix revealed that the SLOF factors had high correlations with PSP factors measuring the same constructs and low correlations with PSP factors measuring different constructs. The confirmatory factor analysis (CFA) corroborated the 6-factor structure reported in the original validation study. Loadings were all significant and ranged from a minimum of 0.299 to a maximum of 0.803. The CFA model was adequately powered and had satisfactory goodness of fit indices (comparative fit index=0.927, Tucker-Lewis index=0.920 and root mean square error of approximation=0.047, 95% CI 0.045-0.049). The present study confirms, in a large sample of Italian people with schizophrenia living in the community, that the SLOF is a reliable and valid instrument for the assessment of social functioning. It has good construct validity and internal consistency, and a well-defined factor structure. Copyright © 2014 Elsevier B.V. All rights reserved.

A community outbreak of Legionnaires' disease associated with a cooling tower in Vic and Gurb, Catalonia (Spain) in 2005.

PubMed

Ferré, M R Sala; Arias, C; Oliva, J M; Pedrol, A; García, M; Pellicer, T; Roura, P; Domínguez, A

2009-02-01

We report the investigation of a community-acquired outbreak of Legionnaires' disease. An epidemiological, environmental, and meteorological investigation was undertaken. Fifty-five cases were reported in October and November 2005. The exposure occurred in a large area, with 12 cases (21.8%) located between 1,800 and 3,400 metres from the source. Water sample cultures showed that Legionella pneumophila serogroup 1 (Lp-1) was present in five cooling towers in two industrial locations in Gurb (plants A and B). Two Lp-1 strains were recovered from plants A and B, but only Lp-1 strains from plant A showed a pulsed-field gel electrophoresis (PFGE) profile identical to those obtained from three of the cases. Inspection of the cooling towers in plant A revealed inadequate maintenance. Weather conditions in October 2005, with mostly high temperatures and high humidity, together with the flat terrain could have been favouring factors. This study showed a community outbreak from a cooling tower as a common source in a large area. Climate and terrain could explain the dissemination of contaminated aerosols.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes.

PubMed

Docherty, Kathryn M; Borton, Hannah M; Espinosa, Noelle; Gebhardt, Martha; Gil-Loaiza, Juliana; Gutknecht, Jessica L M; Maes, Patrick W; Mott, Brendon M; Parnell, John Jacob; Purdy, Gayle; Rodrigues, Pedro A P; Stanish, Lee F; Walser, Olivia N; Gallery, Rachel E

2015-01-01

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

PubMed Central

Borton, Hannah M.; Espinosa, Noelle; Gebhardt, Martha; Gil-Loaiza, Juliana; Gutknecht, Jessica L. M.; Maes, Patrick W.; Mott, Brendon M.; Parnell, John Jacob; Purdy, Gayle; Rodrigues, Pedro A. P.; Stanish, Lee F.; Walser, Olivia N.

2015-01-01

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers. PMID:26536666

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

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

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptualmore » model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.« less

Change in attitudes and knowledge of problem drug use and harm reduction among a community cohort in Kabul, Afghanistan.

PubMed

Todd, C S; Stanekzai, M R; Nasir, A; Fiekert, K; Orr, M G; Strathdee, S A; Vlahov, D

2016-06-15

This pre-post evaluation aimed to measure changes in knowledge and attitudes towards drug users among community representatives in Kabul, Afghanistan, over a period of expansion of harm reduction and drug dependence programming. A convenience sample of 160 professionals aged 18+ years completed interview questionnaires in 2007 and 2009. Views endorsing programme quality and the provision of condoms, infection counselling/testing and needle/syringe distribution increased significantly over the 2-year period. In 13 of 38 statements, there was a substantial (> 10%) change in agreement level, most commonly among men and medical professionals. Attitudes concerning support of drug users remained largely positive, with substantial attitude changes in some subgroups of the population. Further community education through the media and a more cohesive government drug policy may be needed to strengthen community support for harm reduction/drug treatment in Afghanistan.

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes.

PubMed

Videvall, Elin; Strandh, Maria; Engelbrecht, Anel; Cloete, Schalk; Cornwallis, Charlie K

2017-01-01

The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples ( r s > 0.7) but had low repeatability for cloacal ( r s = 0.39) and ileal ( r s = -0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.

Community stability within the St. Marys River fish community: Evidence from trawl surveys

USGS Publications Warehouse

Schaeffer, Jeffrey S.; Bowen, Anjanette K.; Fielder, David G.

2017-01-01

A trawl survey was conducted in the Saint Marys River during 2010–2011 and we compared our results to a prior trawl survey conducted during 1979–1983 to look for long-term changes in the fish community, especially in terms of changes induced by invasive species. We found no substantive temporal differences in fish density, fish biomass, or fish diversity; lower trawl biomass during 2010–2011 was likely a result of day versus night trawling. The Saint Marys River remains a center of high fish diversity, invasive species remain rare, and the system continues to exhibit overall long-term stability. Trawling captured a wide range of fish species, but was likely not an effective stock assessment tool for managed game fish because catch rates were low or variable for all game species except yellow perch. Trawling appeared to be an effective tool for sampling connecting channel diversity, especially when large numbers of individuals are needed for directed studies, but annual sampling would be needed to use data to assess recruitment.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

Decrease in fungal biodiversity along an available phosphorous gradient in arable Andosol soils in Japan.

PubMed

Bao, Zhihua; Matsushita, Yuko; Morimoto, Sho; Hoshino, Yuko Takada; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Murakami, Hiroharu; Kuroyanagi, Yukiko; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2013-06-01

Andosols comprise one of the most important soil groups for agricultural activities in Japan because they cover about 46.5% of arable upland fields. In this soil group, available phosphorus (P) is accumulated by application of excessive fertilizer, but little is known about the influence of increasing P availability on microbial community diversity at large scales. We collected soil samples from 9 agro-geographical sites with Andosol soils across an available P gradient (2048.1-59.1 mg P2O5·kg(-1)) to examine the influence of P availability on the fungal community diversity. We used polymerase chain reaction - denaturing gradient gel electrophoresis to analyze the fungal communities based on 18S rRNA genes. Statistical analyses revealed a high negative correlation between available P and fungal diversity (H'). Fungal diversity across all sites exhibited a significant hump-shaped relationship with available P (R(2) = 0.38, P < 0.001). In addition, the composition of the fungal community was strongly correlated with the available P gradient. The ribotype F6, which was positively correlated with available P, was closely related to Mortierella. The results show that both the diversity and the composition of the fungal community were influenced by available P concentrations in Andosols, at a large scale. This represents an important step toward understanding the processes responsible for the maintenance of fungal diversity in Andosolic soils.

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

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

Howe, Adina; Ringus, Daina L.; Williams, Ryan J.

To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showedmore » significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.« less

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

DOE PAGES

Howe, Adina; Ringus, Daina L.; Williams, Ryan J.; ...

2015-10-16

To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showedmore » significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.« less

Contrasting clonal structure among Pocillopora (Scleractinia) communities at two environmentally distinct sites in the Gulf of California

NASA Astrophysics Data System (ADS)

Pinzón, J. H.; Reyes-Bonilla, H.; Baums, I. B.; LaJeunesse, T. C.

2012-09-01

The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10 km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9 m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples = 0.35; observed Genotypic diversity/expected Genotypic diversity = 0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity ( N g / N = 0.85; G o / G e = 0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will advance ecological research and aid in the conservation of these corals.

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench.

PubMed

Tarn, Jonathan; Peoples, Logan M; Hardy, Kevin; Cameron, James; Bartlett, Douglas H

2016-01-01

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

PubMed

Gravuer, Kelly; Eskelinen, Anu

2017-01-01

Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

PubMed

Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench

PubMed Central

Tarn, Jonathan; Peoples, Logan M.; Hardy, Kevin; Cameron, James; Bartlett, Douglas H.

2016-01-01

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats. PMID:27242695

The Koori Growing Old Well Study: investigating aging and dementia in urban Aboriginal Australians.

PubMed

Radford, Kylie; Mack, Holly A; Robertson, Hamish; Draper, Brian; Chalkley, Simon; Daylight, Gail; Cumming, Robert; Bennett, Hayley; Jackson Pulver, Lisa; Broe, Gerald A

2014-06-01

Dementia is an emerging health priority in Australian Aboriginal communities, but substantial gaps remain in our understanding of this issue, particularly for the large urban section of the population. In remote Aboriginal communities, high prevalence rates of dementia at relatively young ages have been reported. The current study is investigating aging, cognitive decline, and dementia in older urban/regional Aboriginal Australians. We partnered with five Aboriginal communities across the eastern Australian state of New South Wales, to undertake a census of all Aboriginal men and women aged 60 years and over residing in these communities. This was followed by a survey of the health, well-being, and life history of all consenting participants. Participants were also screened using three cognitive instruments. Those scoring below designated cut-offs, and a 20% random sample of those scoring above (i.e. "normal" range), completed a contact person interview (with a nominated family member) and medical assessment (blind to initial screening results), which formed the basis of "gold standard" clinical consensus determinations of cognitive impairment and dementia. This paper details our protocol for a population-based study in collaboration with local Aboriginal community organizations. The study will provide the first available prevalence rates for dementia and cognitive impairment in a representative sample of urban Aboriginal people, across city and rural communities, where the majority of Aboriginal Australians live. It will also contribute to improved assessment of dementia and cognitive impairment and to the understanding of social determinants of successful aging, of international significance.

Diversity of the benthic macrofauna off northern Namibia from the shelf to the deep sea

NASA Astrophysics Data System (ADS)

Eisenbarth, Simone; Zettler, Michael L.

2016-03-01

In late summer 2011, shortly after an upwelling event, 17 stations ranging from 30 to 2513 m water depth have been sampled at 20° south in the northern part of the Benguela Current Large Marine Ecosystem (BCLME) for the investigation of the benthic macrofauna. Sediments of this area are dominated by silt. At the time of sampling, oxygen conditions on the shelf were poor (between 0.42 and 0.68 ml l- 1) but not hypoxic. Below 400 m, however, concentrations rose steadily up to 5.28 ml l- 1. Macrozoobenthic communities along this depth gradient are described, revealing among others the community structure for the continental margin area and the deep sea off northern Namibia for the first time. Cluster analysis revealed 5 different communities along the depth gradient with three shelf communities, one continental margin community and one deep-sea community. All in all, 314 different taxa were found with polychaetes being the most abundant group. Diversity index (Shannon) was lowest for the shallow water community with 2.21 and highest for the deep-sea community with 4.79, showing a clear trend with increasing water depth. Species richness, however, reached its maximum with 187 taxa along the continental margin between 400 and 1300 m water depth. Dominant species for each community are named with the two Cumacea, Iphinoeafricana and Upselaspis caparti, being characteristic for the shallow water community. On the shelf, we found surprisingly high biomass values (23-123 g m- 2), mainly caused by polychaetes, the bivalve Sinupharus galatheae and the gastropod Nassarius vinctus. In terms of composition, the remaining communities were dominated by polychaetes with members of the Paraonidae dominating along the continental margin where we also found surprisingly high abundances of the bivalves Pecten sp. and Dosinia sp. Spionid polychaetes and some representatives of the genus Paraonis were the most common organisms for the deep-sea community.

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

PubMed

Erwin, Patrick M; Olson, Julie B; Thacker, Robert W

2011-01-01

Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.

A menu with prices: Annual per person costs of programs addressing community integration.

PubMed

Leff, H Stephen; Cichocki, Ben; Chow, Clifton; Salzer, Mark; Wieman, Dow

2016-02-01

Information on costs of programs addressing community integration for persons with serious mental illness in the United States, essential for program planning and evaluation, is largely lacking. To address this knowledge gap, community integration programs identified through directories and snowball sampling were sent an online survey addressing program costs and organizational attributes. 64 Responses were received for which annual per person costs (APPC) could be computed. Programs were categorized by type of services provided. Program types differed in median APPCs, though median APPCs identified were consistent with the ranges identified in the limited literature available. Multiple regression was used to identify organizational variables underlying APPCs such as psychosocial rehabilitation program type, provision of EBPs, number of volunteers, and percentage of budget spent on direct care staff, though effects sizes were moderate at best. This study adds tentative prices to the menu of community integration programs, and the implications of these findings for choosing, designing and evaluating programs addressing community integration are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Clinical signs and bacterial communities of deciduous necrotic root canals detected by PCR-DGGE analysis: research association.

PubMed

de Paula, Viviane Andrade Cancio; de Carvalho Ferreira, Dennis; Cavalcante, Fernanda Sampaio; do Carmo, Flávia Lima; Rosado, Alexandre Soares; Primo, Laura Guimarães; dos Santos, Kátia Regina Netto

2014-08-01

This study sought to investigate the possible association between clinical and radiographic data of the patients with the bacterial community profiles involved in cases of necrosis in primary root canals. Microbial community profiles for 25 samples from necrotic deciduous root canals were analyzed using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting approach. These results were related to the clinical and radiographic data of these patients. The analysis showed a large diversity of microbial communities in necrotic deciduous root canals. The statistical results pointed out that posterior and anterior teeth were associated with <20 bands and >20 bands in PCR-DGGE method, respectively. A relationship was verified between ages >4 years old and posterior teeth and, ages ≤4 years old and anterior teeth. The data showed a polymicrobial community and pointed out the association of age with necrosis in anterior and posterior teeth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation.

PubMed

Sun, Weimin; Li, Jiwei; Jiang, Lei; Sun, Zhilei; Fu, Meiyan; Peng, Xiaotong

2015-10-01

Successful bioremediation of oil pollution is based on a comprehensive understanding of the in situ physicochemical conditions and indigenous microbial communities as well as the interaction between microorganisms and geochemical variables. Nineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. Phylogenetic analysis indicated that the vast majority of sequences were related to the genera Arthrobacter, Dietzia, Pseudomonas, Rhodococcus, and Marinobacter, many of which contain known oil-degrading or oil-emulsifying species. Remarkably, a number of archaeal genera including Halalkalicoccus, Natronomonas, Haloterrigena, and Natrinema were found in relatively high abundance in some of the oil-contaminated soil samples, indicating that these Euryarchaeota may play an important ecological role in some oil-contaminated soils. This study offers a direct and reliable reference of the diversity of the microbial community in various oil-contaminated soils and may influence strategies for in situ bioremediation of oil pollution.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

PubMed

Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M; Cutter, Lynda S; Fuhrman, Jed A; Sañudo-Wilhelmy, Sergio A; Moran, Mary Ann

2018-04-16

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B 12 synthesis, but not of vitamin-B 7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B 1 synthesis transcripts. Furthermore, ambient vitamin-B 1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission.

PubMed

Kohl, Kevin D; Brun, Antonio; Magallanes, Melisa; Brinkerhoff, Joshua; Laspiur, Alejandro; Acosta, Juan Carlos; Caviedes-Vidal, Enrique; Bordenstein, Seth R

2017-02-01

Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts. © 2016 John Wiley & Sons Ltd.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Hazardous alcohol use and intimate partner violence in the military: understanding protective factors.

PubMed

Foran, Heather M; Heyman, Richard E; Smith Slep, Amy M; Snarr, Jeffery D

2012-09-01

Hazardous alcohol use is a well-established risk factor for men's intimate partner violence (IPV), with dozens of studies demonstrating the association. The current study extends understanding of the hazardous alcohol use-IPV link by examining what factors moderate this association in a more systematic and broader way that has been done in past studies. Individual, family, workplace, community, and developmental factors were tested as moderators of the hazardous alcohol use and IPV link in a large, representative sample of active duty service members (the 2006 Community Assessment), and the results were tested for replicability in a hold-out sample. Two family variables (relationship satisfaction and parent-child satisfaction), 1 community variable (community safety), and 3 developmental variables (years in the military, marital length, and family income/pay grade) cross-validated as significant moderators of the association between men's hazardous alcohol use and IPV. Across the significant moderators, the association between hazardous alcohol use and men's IPV was weakened by maturation/development, improved community safety, and better relationship functioning. No individual or workplace variables were significant moderators for men, and there were no significant moderators found for women. The results support the importance of a developmental and relational perspective to understanding the hazardous alcohol use-IPV link, rather than solely an individual coping perspective. PsycINFO Database Record (c) 2012 APA, all rights reserved.

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

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Global Diversity of Desert Hypolithic Cyanobacteria.

PubMed

Lacap-Bugler, Donnabella C; Lee, Kevin K; Archer, Stephen; Gillman, Len N; Lau, Maggie C Y; Leuzinger, Sebastian; Lee, Charles K; Maki, Teruya; McKay, Christopher P; Perrott, John K; de Los Rios-Murillo, Asunción; Warren-Rhodes, Kimberley A; Hopkins, David W; Pointing, Stephen B

2017-01-01

Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nif H genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts.

Global Diversity of Desert Hypolithic Cyanobacteria

PubMed Central

Lacap-Bugler, Donnabella C.; Lee, Kevin K.; Archer, Stephen; Gillman, Len N.; Lau, Maggie C.Y.; Leuzinger, Sebastian; Lee, Charles K.; Maki, Teruya; McKay, Christopher P.; Perrott, John K.; de los Rios-Murillo, Asunción; Warren-Rhodes, Kimberley A.; Hopkins, David W.; Pointing, Stephen B.

2017-01-01

Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts. PMID:28559886

Generalizability of Pharmacologic and Psychotherapy Clinical Trial Results for Posttraumatic Stress Disorder to Community Samples.

PubMed

Franco, Silvia; Hoertel, Nicolas; McMahon, Kibby; Wang, Shuai; Rodríguez-Fernández, Jorge Mario; Peyre, Hugo; Limosin, Frédéric; Blanco, Carlos

2016-08-01

The present study sought to quantify the generalizability of pharmacologic and psychotherapy clinical trial results in individuals with a DSM-IV diagnosis of posttraumatic stress disorder (PTSD) to a large representative community sample. Data were derived from the 2004-2005 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), a large nationally representative sample of the adult US population. We applied a standard set of exclusion criteria representative of pharmacologic and psychotherapy clinical trials to all adults with a DSM-IV diagnosis of PTSD in the previous 12 months (n = 1,715) and then to a subsample of participants seeking treatment (n = 366). Our aim was to assess how many participants with PTSD would fulfill typical eligibility criteria. We found that more than 6 of 10 respondents from the overall PTSD sample and more than 7 of 10 respondents seeking treatment for PTSD would have been excluded by 1 exclusion criterion or more in a typical pharmacologic trial. In contrast, about 2 of 10 participants in the full sample and about 3 of 10 participants seeking treatment for PTSD would have been excluded in a typical psychotherapy efficacy trial. We found that psychotherapy trial results may be applied to most patients with PTSD in routine clinical practice. The designers of pharmacologic clinical trials should carefully consider the trade-offs between the application of each exclusion criterion and its impact on representativeness. Specification a priori of the goals of the study, better justification for each exclusion criterion, and estimation of the proportion of individuals ineligible for the trial would assist study design. Developing integrated forms of pharmacotherapy and psychotherapy that simultaneously target commonly overlapping psychiatric disorders may yield more informative results for mental health care providers and research funding agencies. © Copyright 2016 Physicians Postgraduate Press, Inc.

Sensual, erotic, and sexual behaviors of women from the "kink" community.

PubMed

Rehor, Jennifer Eve

2015-05-01

Unconventional sensual, erotic, and sexual behaviors (herein referred to as kink behaviors) investigated by academia are based largely on clinical and criminal cases, and most published, peer-reviewed, quantitative research on these behaviors is based almost exclusively on male participants. For this study, information was collected and analyzed from 1580 female participants recruited from the kink community, using a non-clinical and non-criminal sample. We explored and described the preferences and diversity of more than 126 sensual, erotic, and sexual behaviors found among these participants, along with recommendations for continued research. Gaining a better understanding of the breadth and depth of activities engaged in by female kink practitioners could benefit educators, counselors, therapists, medical doctors, and other professionals when interacting with members of the kink community.

Nondestructive Analysis of Apollo Samples by Micro-CT and Micro-XRF Analysis: A PET Style Examination

NASA Technical Reports Server (NTRS)

Zeigler, Ryan A.

2014-01-01

An integral part of any sample return mission is the initial description and classification of returned samples by the preliminary examination team (PET). The goal of a PET is to characterize and classify the returned samples, making this information available to the general research community who can then conduct more in-depth studies on the samples. A PET strives to minimize the impact their work has on the sample suite, which often limits the PET work to largely visual measurements and observations like optical microscopy. More modern techniques can also be utilized by future PET to nondestructively characterize astromaterials in a more rigorous way. Here we present our recent analyses of Apollo samples 14321 and 14305 by micro-CT and micro-XRF (respectively), assess the potential for discovery of "new" Apollo samples for scientific study, and evaluate the usefulness of these techniques in future PET efforts.

Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses.

PubMed

Chai, Zhao Yang; He, Zhi Li; Deng, Yun Yan; Yang, Yu Feng; Tang, Ying Zhong

2018-02-01

Plankton diversity reflects the quality and health of waters and should be monitored as a critical feature of marine ecosystems. This study applied a pair of 28S rRNA gene-specific primers and pyrosequencing to assess the effects of large-scale cultivation of the seaweed Gracilaria lemaneiformis on the biodiversity of eukaryotic plankton community in the coastal water of Guangdong, China. With 1 million sequences (2,221 operational taxonomic units [OTUs]) obtained from 51 samples, we found that the biodiversity of eukaryotic plankton community was significantly higher in the seaweed cultivation area than that in the nearby control area as reflected in OTU richness, evenness (Shannon-Wiener index) and dominance (Simpson index) for total plankton community and its four subcategories when Gracilaria biomass reached the maximum, while no such a significant difference was observed before seaweed inoculation. Our laboratory experiment using an artificial phytoplankton community of nine species observed the same effects of Gracilaria exposure. Principal component analysis and principal coordinates analysis showed the plankton community structure in cultivation area markedly differed from the control area when Gracilaria biomass reached its maximum. Redundancy analysis showed that G. lemaneiformis was the critical factor in controlling the dynamics of eukaryotic plankton communities in the studied coastal ecosystem. Our results explicitly demonstrated G. lemaneiformis cultivation could enhance biodiversity of plankton community via allelopathy, which prevents one or several plankton species from blooming and consequently maintains a relatively higher biodiversity. Our study provided further support for using large-scale G. lemaneiformis cultivation as an effective approach for improving costal ecosystem health. © 2018 John Wiley & Sons Ltd.

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

PubMed Central

Heath, Allison P; Greenway, Matthew; Powell, Raymond; Spring, Jonathan; Suarez, Rafael; Hanley, David; Bandlamudi, Chai; McNerney, Megan E; White, Kevin P; Grossman, Robert L

2014-01-01

Background As large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, and analyze them. One possible approach is to provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along with tools and resources to analyze it. Methods Bionimbus is an open source cloud-computing platform that is based primarily upon OpenStack, which manages on-demand virtual machines that provide the required computational resources, and GlusterFS, which is a high-performance clustered file system. Bionimbus also includes Tukey, which is a portal, and associated middleware that provides a single entry point and a single sign on for the various Bionimbus resources; and Yates, which automates the installation, configuration, and maintenance of the software infrastructure required. Results Bionimbus is used by a variety of projects to process genomics and phenotypic data. For example, it is used by an acute myeloid leukemia resequencing project at the University of Chicago. The project requires several computational pipelines, including pipelines for quality control, alignment, variant calling, and annotation. For each sample, the alignment step requires eight CPUs for about 12 h. BAM file sizes ranged from 5 GB to 10 GB for each sample. Conclusions Most members of the research community have difficulty downloading large genomics datasets and obtaining sufficient storage and computer resources to manage and analyze the data. Cloud computing platforms, such as Bionimbus, with data commons that contain large genomics datasets, are one choice for broadening access to research data in genomics. PMID:24464852

Relationship of demographic and health factors to cognition in older adults in the ACTIVE study.

PubMed

Rexroth, Daniel F; Tennstedt, Sharon L; Jones, Richard N; Guey, Lin T; Rebok, George W; Marsiske, Michael M; Xu, Yan; Unverzagt, Frederick W

2013-12-01

Examine the relationship of demographics and health conditions, alone and in combination, on objective measures of cognitive function in a large sample of community-dwelling older adults. Baseline data from 2,782 participants in the Advanced Cognitive Training in Independent and Vital Elderly (ACTIVE) study were used to examine relationships of demographics and health conditions with composite scores of memory, reasoning, and speed of processing. Younger age, increased education, and White race were independently associated with better performance in each cognitive domain after adjusting for gender and health conditions. Male gender, diabetes, and suspected clinical depression were associated with poorer cognitive functioning; suspected clinical depression was associated with lower reasoning and diabetes and history of stroke with slower speed of processing. Age, education, and race are consistently associated with cognitive performance in this sample of older community-dwelling adults. Diabetes, stroke, and suspected clinical depression had independent but weaker effects on cognition.

Parental divorce and adjustment in adulthood: findings from a community sample. The ALSPAC Study Team. Avon Longitudinal Study of Pregnancy and Childhood.

PubMed

O'Connor, T G; Thorpe, K; Dunn, J; Golding, J

1999-07-01

The current study examines the link between the experience of divorce in childhood and several indices of adjustment in adulthood in a large community sample of women. Results replicated previous research on the long-term correlation between parental divorce and depression and divorce in adulthood. Results further suggested that parental divorce was associated with a wide range of early risk factors, life course patterns, and several indices of adult adjustment. Regression analyses indicated that the long-term correlation between parental divorce and depression in adulthood is explained by quality of parent-child and parental marital relations (in childhood), concurrent levels of stressful life events and social support, and cohabitation. The long-term association between parental divorce and experiencing a divorce in adulthood was partly mediated through quality of parent-child relations, teenage pregnancy, leaving home before 18 years, and educational attainment.

Space Radiation Program Element Tissue Sharing Initiative

NASA Technical Reports Server (NTRS)

Wu, H.; Huff, J. L.; Simonsen, L. C.

2014-01-01

Over the years, a large number of animal experiments have been conducted at the NASA Space Radiation Laboratory and other facilities under the support of the NASA Space Radiation Program Element (SRPE). Studies using rodents and other animal species to address the space radiation risks will remain a significant portion of the research portfolio of the Element. In order to maximize scientific return of the animal studies, SRPE is taking the initiative to promote tissue sharing among the scientists in the space radiation research community. This initiative is enthusiastically supported by the community members as voiced in the responses to a recent survey. For retrospective tissue samples, an online platform will be established for the PIs to post a list of the available samples, and to exchange information with the potential recipients. For future animal experiments, a tissue sharing policy is being developed by SRPE.

Examining the DSM-5 Section III Criteria for Obsessive-Compulsive Personality Disorder in a Community Sample.

PubMed

Liggett, Jacqueline; Sellbom, Martin; Carmichael, Kieran L C

2017-12-01

The current study examined the extent to which the trait-based operationalization of obsessive-compulsive personality disorder (OCPD) in Section III of the DSM-5 describes the same construct as the one described in Section II. A community sample of 313 adults completed a series of personality inventories indexing the DSM-5 Sections II and III diagnostic criteria for OCPD, in addition to a measure of functional impairment modelled after the criteria in Section III. Results indicated that latent constructs representing Section II and Section III OCPD overlapped substantially (r = .75, p < .001). Hierarchical latent regression models revealed that at least three of the four DSM-5 Section III facets (Rigid Perfectionism, Perseveration, and Intimacy Avoidance) uniquely accounted for a large proportion of variance (53%) in a latent Section II OCPD variable. Further, Anxiousness and (low) Impulsivity, as well as self and interpersonal impairment, augmented the prediction of latent OCPD scores.

The Relationship Between Adverse Childhood Experiences and Recidivism in a Sample of Juvenile Offenders in Community-Based Treatment.

PubMed

Wolff, Kevin T; Baglivio, Michael T; Piquero, Alex R

2017-08-01

Adverse childhood experiences (ACEs) have been identified as a key risk factor for a range of negative life outcomes, including delinquency. Much less is known about how exposure to negative experiences relates to continued offending among juvenile offenders. In this study, we examine the effect of ACEs on recidivism in a large sample of previously referred youth from the State of Florida who were followed for 1 year after participation in community-based treatment. Results from a series of Cox hazard models suggest that ACEs increase the risk of subsequent arrest, with a higher prevalence of ACEs leading to a shorter time to recidivism. The relationship between ACEs and recidivism held quite well in demographic-specific analyses. Implications for empirical research on the long-term effects of traumatic childhood events and juvenile justice policy are discussed.

Diverse Applications of Environmental DNA Methods in Parasitology.

PubMed

Bass, David; Stentiford, Grant D; Littlewood, D T J; Hartikainen, Hanna

2015-10-01

Nucleic acid extraction and sequencing of genes from organisms within environmental samples encompasses a variety of techniques collectively referred to as environmental DNA or 'eDNA'. The key advantages of eDNA analysis include the detection of cryptic or otherwise elusive organisms, large-scale sampling with fewer biases than specimen-based methods, and generation of data for molecular systematics. These are particularly relevant for parasitology because parasites can be difficult to locate and are morphologically intractable and genetically divergent. However, parasites have rarely been the focus of eDNA studies. Focusing on eukaryote parasites, we review the increasing diversity of the 'eDNA toolbox'. Combining eDNA methods with complementary tools offers much potential to understand parasite communities, disease risk, and parasite roles in broader ecosystem processes such as food web structuring and community assembly. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Geography and Location Are the Primary Drivers of Office Microbiome Composition

PubMed Central

Chase, John; Fouquier, Jennifer; Zare, Mahnaz; Sonderegger, Derek L.; Knight, Rob; Kelley, Scott T.; Siegel, Jeffrey

2016-01-01

ABSTRACT In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities. PMID:27822521

Large herbivores affect forest ecosystem functions by altering the structure of dung beetle communities

NASA Astrophysics Data System (ADS)

Iida, Taichi; Soga, Masashi; Koike, Shinsuke

2018-04-01

Dramatic increases in populations of large mammalian herbivores have become a major ecological issue, particularly in the northern hemisphere, due to their substantial impacts on both animal and plant communities through processes such as grazing, browsing, and trampling. However, little is known about the consequences of these population explosions on ecosystem functions. Here, we experimentally investigated how the population density of sika deer (Cervus nippon) in temperate deciduous forest areas in Japan affected the decomposition of mammal dung by dung beetles, which is a key process in forest ecosystems. We measured a range of environmental variables (e.g., vegetation cover, soil hardness) and the dung decomposition rate, measured as the amount of deer dung decomposed during one week, and sampled dung beetles at 16 study sites with three different deer densities (high/intermediate/low). We then used structural equation modeling to investigate the relationships between deer density, environmental variables, the biomass of dung beetles (classified into small or large species), and the dung decomposition rate. We found that the biomass of small species increased with increasing deer density, whereas that of large species was not related to deer density. Furthermore, the dung decomposition rate was positively related to the biomass of small species but unrelated to that of large species. Overall, our results showed that an increase in deer density affects the decomposition rate of mammal dung by changing the structure of dung beetle communities (i.e., increasing the number of small dung beetles). Such an understanding of how increases in large herbivore populations affect ecosystem functions is important for accurately evaluating the ecological consequences of their overabundance and ultimately managing their populations appropriately.

Using facebook to recruit young adult veterans: online mental health research.

PubMed

Pedersen, Eric R; Helmuth, Eric D; Marshall, Grant N; Schell, Terry L; PunKay, Marc; Kurz, Jeremy

2015-06-01

Veteran research has primarily been conducted with clinical samples and those already involved in health care systems, but much is to be learned about veterans in the community. Facebook is a novel yet largely unexplored avenue for recruiting veteran participants for epidemiological and clinical studies. In this study, we utilized Facebook to recruit a sample of young adult veterans for the first phase of an online alcohol intervention study. We describe the successful Facebook recruitment process, including data collection from over 1000 veteran participants in approximately 3 weeks, procedures to verify participation eligibility, and comparison of our sample with nationally available norms. Participants were young adult veterans aged 18-34 recruited through Facebook as part of a large study to document normative drinking behavior among a large community sample of veterans. Facebook ads were targeted toward young veterans to collect information on demographics and military characteristics, health behaviors, mental health, and health care utilization. We obtained a sample of 1023 verified veteran participants over a period of 24 days for the advertising price of approximately US $7.05 per verified veteran participant. Our recruitment strategy yielded a sample similar to the US population of young adult veterans in most demographic areas except for race/ethnicity and previous branch of service, which when we weighted the sample on race/ethnicity and branch a sample better matched with the population data was obtained. The Facebook sample recruited veterans who were engaged in a variety of risky health behaviors such as binge drinking and marijuana use. One fourth of veterans had never since discharge been to an appointment for physical health care and about half had attended an appointment for service compensation review. Only half had attended any appointment for a mental health concern at any clinic or hospital. Despite more than half screening positive for current probable mental health disorders such as post-traumatic stress disorder, depression, anxiety, only about 1 in 3 received mental health care in the past year and only 1 in 50 received such care within the past month. This work expands on the work of other studies that have examined clinical samples of veterans only and suggests Facebook can be an adequate method of obtaining samples of veterans in need of care. Clinicaltrials.gov NCT02187887; http://clinicaltrials.gov/ct2/show/NCT02187887 (Archived by WebCite at http://www.webcitation.org/6YiUKRsXY).

Using Facebook to Recruit Young Adult Veterans: Online Mental Health Research

PubMed Central

2015-01-01

Background Veteran research has primarily been conducted with clinical samples and those already involved in health care systems, but much is to be learned about veterans in the community. Facebook is a novel yet largely unexplored avenue for recruiting veteran participants for epidemiological and clinical studies. Objective In this study, we utilized Facebook to recruit a sample of young adult veterans for the first phase of an online alcohol intervention study. We describe the successful Facebook recruitment process, including data collection from over 1000 veteran participants in approximately 3 weeks, procedures to verify participation eligibility, and comparison of our sample with nationally available norms. Methods Participants were young adult veterans aged 18-34 recruited through Facebook as part of a large study to document normative drinking behavior among a large community sample of veterans. Facebook ads were targeted toward young veterans to collect information on demographics and military characteristics, health behaviors, mental health, and health care utilization. Results We obtained a sample of 1023 verified veteran participants over a period of 24 days for the advertising price of approximately US $7.05 per verified veteran participant. Our recruitment strategy yielded a sample similar to the US population of young adult veterans in most demographic areas except for race/ethnicity and previous branch of service, which when we weighted the sample on race/ethnicity and branch a sample better matched with the population data was obtained. The Facebook sample recruited veterans who were engaged in a variety of risky health behaviors such as binge drinking and marijuana use. One fourth of veterans had never since discharge been to an appointment for physical health care and about half had attended an appointment for service compensation review. Only half had attended any appointment for a mental health concern at any clinic or hospital. Despite more than half screening positive for current probable mental health disorders such as post-traumatic stress disorder, depression, anxiety, only about 1 in 3 received mental health care in the past year and only 1 in 50 received such care within the past month. Conclusions This work expands on the work of other studies that have examined clinical samples of veterans only and suggests Facebook can be an adequate method of obtaining samples of veterans in need of care. Trial Registration Clinicaltrials.gov NCT02187887; http://clinicaltrials.gov/ct2/show/NCT02187887 (Archived by WebCite at http://www.webcitation.org/6YiUKRsXY). PMID:26033209

Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge

PubMed Central

Meyer, Julie L.; Akerman, Nancy H.; Proskurowski, Giora; Huber, Julie A.

2013-01-01

Microbial processes within the subseafloor can be examined during the ephemeral and uncommonly observed phenomena known as snowblower venting. Snowblowers are characterized by the large quantity of white floc that is expelled from the seafloor following mid-ocean ridge eruptions. During these eruptions, rapidly cooling lava entrains seawater and hydrothermal fluids enriched in geochemical reactants, creating a natural bioreactor that supports a subseafloor microbial “bloom.” Previous studies hypothesized that the eruption-associated floc was made by sulfide-oxidizing bacteria; however, the microbes involved were never identified. Here we present the first molecular analysis combined with microscopy of microbial communities in snowblower vents from samples collected shortly after the 2011 eruption at Axial Seamount, an active volcano on the Juan de Fuca Ridge. We obtained fluid samples and white flocculent material from active snowblower vents as well as orange flocculent material found on top of newly formed lava flows. Both flocculent types revealed diverse cell types and particulates when examined by phase contrast and scanning electron microscopy (SEM). Distinct archaeal and bacterial communities were detected in each sample type through Illumina tag sequencing of 16S rRNA genes and through sequencing of the sulfide oxidation gene, soxB. In fluids and white floc, the dominant bacteria were sulfur-oxidizing Epsilonproteobacteria and the dominant archaea were thermophilic Methanococcales. In contrast, the dominant organisms in the orange floc were Gammaproteobacteria and Thaumarchaeota Marine Group I. In all samples, bacteria greatly outnumbered archaea. The presence of anaerobic methanogens and microaerobic Epsilonproteobacteria in snowblower communities provides evidence that these blooms are seeded by subseafloor microbes, rather than from microbes in bottom seawater. These eruptive events thus provide a unique opportunity to observe subseafloor microbial communities. PMID:23785361

Identification of Fungal Communities Associated with the Biodeterioration of Waterlogged Archeological Wood in a Han Dynasty Tomb in China

PubMed Central

Liu, Zijun; Wang, Yu; Pan, Xiaoxuan; Ge, Qinya; Ma, Qinglin; Li, Qiang; Fu, Tongtong; Hu, Cuiting; Zhu, Xudong; Pan, Jiao

2017-01-01

The Mausoleum of the Dingtao King (termed ‘M2’) is a large-scale huangchang ticou tomb that dates to the Western Han Dynasty (206 B.C.–25 A.D.). It is the highest-ranking Han Dynasty tomb discovered to date. However, biodeterioration on the surface of the tomb M2 is causing severe damage to its wooden materials. The aim of the present study was to give insight into the fungal communities colonized the wooden tomb. For this purpose, seven samples were collected from different sections of the tomb M2 which exhibited obvious biodeterioration in the form of white spots. Microbial structures associated with the white spots were observed with scanning electron microscopy. Fungal community structures were assessed for seven samples via a combination of high-throughput sequencing and culture-dependent techniques. Sequencing analyses identified 114 total genera that belonged to five fungal phyla. Hypochnicium was the most abundant genus across all samples and accounted for 98.61–99.45% of the total community composition. Further, Hypochnicium sp. and Mortierella sp. cultures were successfully isolated from the tomb samples, and were distinguished as Hypochnicium sp. WY-DT1 and Mortierella sp. NK-DT1, respectively. Cultivation-dependent experiments indicated that the dominant member, Hypochnicium sp. WY- DT1, could grow at low temperatures and significantly degraded cellulose and lignin. Thus, our results taken together suggest that this fungal strain must be regarded as a serious threat to the preservation of the wooden tomb M2. The results reported here are useful for informing future contamination mitigation efforts for the tomb M2 as well as other similar cultural artifacts. PMID:28890715

Characterizing the diversity of coral reef habitats and fish communities found in a UNESCO World Heritage Site: the strategy developed for Lagoons of New Caledonia.

PubMed

Andréfouët, S; Wantiez, L

2010-01-01

Since 1972, the UNESCO "World Heritage Convention" offers an international canvas for conservation and management that targets areas of high cultural and environmental significance. To support the designation of areas within the 36.000 km(2) of New Caledonia coral reefs and lagoons as a World Heritage Site, the natural value and diversity of the proposed zones needed to be demonstrated. To exhaustively identify each configuration of shallow habitats, high resolution remote sensing images were used to select the sampling sites. This optimal scheme resulted in the selection of nearly 1300 sampling sites, and was then simplified to render its application realistic. In the final sampling plan, only the most common or the most remarkable coral zones were selected. Following this selection, in situ habitat and fish surveys were conducted in 2006-2008 in five large areas spanning a 600 km-long latitudinal gradient. Habitats were described using line-intercept transects in parallel with underwater visual census of indicator and commercial coral reef fish species. We report here on the results achieved in terms of: (i) the actual diversity of coral habitats captured by the remote sensing based sampling strategy, (ii) the different reef fish communities captured from the different sites, and (iii) how well they represent New Caledonia diversity. We discuss the possible generalization of this scheme to other sites, in the context of World Heritage Site selection and for other large-scale conservation planning activities. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Effects of large-scale wildfire on ground foraging ants (Hymenoptera: Formicidae) in southern California

USGS Publications Warehouse

Matsuda, Tritia; Turschak, Greta; Brehme, Cheryl; Rochester, Carlton; Mitrovich, Milan; Fisher, Robert

2011-01-01

We investigated the effect of broad-scale wildfire on ground foraging ants within southern California. In October and November of 2003, two wildfires burned large portions of the wildlands within San Diego County. Between January 2005 and September 2006, we surveyed 63 plots across four sites to measure the effect of the fires on the ant assemblages present in four vegetation types: 1) coastal sage scrub, 2) chaparral, 3) grassland, and 4) woodland riparian. Thirty-six of the 63 plots were sampled before the fires between March 2001 and June 2003. Mixed model regression analyses, accounting for the burn history of each plot and our pre- and postfire sampling efforts, revealed that fire had a negative effect on ant species diversity. Multivariate analyses showed that ant community structure varied significantly among the four vegetation types, and only the ant assemblage associated with coastal sage scrub exhibited a significant difference between burned and unburned samples. The most notable change detected at the individual species level involved Messor andrei (Mayr), which increased from <1% of prefire coastal sage scrub ant samples to 32.1% in burned plots postfire. We theorize that M. andrei responded to the increase of bare ground and postfire seed production, leading to an increase in the detection rate for this species. Collectively, our results suggest that wildfires can have short-term impacts on the diversity and community structure of ground foraging ants in coastal sage scrub. We discuss these findings in relation to management implications and directions for future research.

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1

PubMed Central

Villandre, Luc; Günthard, Huldrych F.; Kouyos, Roger; Stadler, Tanja

2016-01-01

Background Transmission patterns of sexually-transmitted infections (STIs) could relate to the structure of the underlying sexual contact network, whose features are therefore of interest to clinicians. Conventionally, we represent sexual contacts in a population with a graph, that can reveal the existence of communities. Phylogenetic methods help infer the history of an epidemic and incidentally, may help detecting communities. In particular, phylogenetic analyses of HIV-1 epidemics among men who have sex with men (MSM) have revealed the existence of large transmission clusters, possibly resulting from within-community transmissions. Past studies have explored the association between contact networks and phylogenies, including transmission clusters, producing conflicting conclusions about whether network features significantly affect observed transmission history. As far as we know however, none of them thoroughly investigated the role of communities, defined with respect to the network graph, in the observation of clusters. Methods The present study investigates, through simulations, community detection from phylogenies. We simulate a large number of epidemics over both unweighted and weighted, undirected random interconnected-islands networks, with islands corresponding to communities. We use weighting to modulate distance between islands. We translate each epidemic into a phylogeny, that lets us partition our samples of infected subjects into transmission clusters, based on several common definitions from the literature. We measure similarity between subjects’ island membership indices and transmission cluster membership indices with the adjusted Rand index. Results and Conclusion Analyses reveal modest mean correspondence between communities in graphs and phylogenetic transmission clusters. We conclude that common methods often have limited success in detecting contact network communities from phylogenies. The rarely-fulfilled requirement that network communities correspond to clades in the phylogeny is their main drawback. Understanding the link between transmission clusters and communities in sexual contact networks could help inform policymaking to curb HIV incidence in MSMs. PMID:26863322

Integration of NASA/GSFC and USGS Rock Magnetic Databases.

NASA Astrophysics Data System (ADS)

Nazarova, K. A.; Glen, J. M.

2004-05-01

A global Magnetic Petrology Database (MPDB) was developed and continues to be updated at NASA/Goddard Space Flight Center. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via the Internet for a more realistic interpretation of satellite (as well as aeromagnetic and ground) lithospheric magnetic anomalies. The MPDB contains data on rocks from localities around the world (about 19,000 samples) including the Ukranian and Baltic Shields, Kamchatka, Iceland, Urals Mountains, etc. The MPDB is designed, managed and presented on the web as a research oriented database. Several database applications have been specifically developed for data manipulation and analysis of the MPDB. The geophysics unit at the USGS in Menlo Park has over 17,000 rock-property data, largely from sites within the western U.S. This database contains rock-density and rock-magnetic parameters collected for use in gravity and magnetic field modeling, and paleomagnetic studies. Most of these data were taken from surface outcrops and together they span a broad range of rock types. Measurements were made either in-situ at the outcrop, or in the laboratory on hand samples and paleomagnetic cores acquired in the field. The USGS and NASA/GSFC data will be integrated as part of an effort to provide public access to a single, uniformly maintained database. Due to the large number of data and the very large area sampled, the database can yield rock-property statistics on a broad range of rock types; it is thus applicable to study areas beyond the geographic scope of the database. The intent of this effort is to provide incentive for others to further contribute to the database, and a tool with which the geophysical community can entertain studies formerly precluded.

Soil microbial abundance, activity and diversity response in two different altitude-adapted plant communities affected by wildfire in Sierra Nevada National Park (Granada, Spain)

NASA Astrophysics Data System (ADS)

Bárcenas-Moreno, Gema; Zavala, Lorena; Jordan, Antonio; Bååth, Erland; Mataix-Beneyto, Jorge

2013-04-01

Plant communities can play an important role in fire severity and post-fire ecosystem recovery due to their role as combustible and different plant-soil microorganisms interactions. Possible differences induced by plant and microorganisms response after fire could affect the general ecosystem short and long-term response and its sustainability. The main objective of this work was the evaluation of the effect of wildfire on soil microbial abundance, activity and diversity in two different plant communities associated to different altitudes in Sierra Nevada National Park (Granada, Spain). Samples were collected in two areas located on the Sierra Nevada Mountain between 1700 and 2000 m above sea level which were affected by a large wildfire in 2005. Two samplings were carried out 8 and 20 months after fire and samples were collected in both burned and unburned (control) zones in each plant community area. Area A is located at 1700m and it is formed by Quercus rotundifolia forest while area B is located at 2000 m altitude and is composed of alpine vegetation formed by creeping bearing shrubs. Microbial biomass measured by Fumigation-Extraction method followed the same trend in both areas showing slight and no significant differences between burned and unburned area during the study period while viable and cultivable bacteria abundance were markedly higher in fire affected samples than in the control ones in both samplings. Viable and cultivable filamentous fungi had different behavior depending of plant vegetation community studied showing no differences between burned and unburned area in area A while was significantly higher in burned samples than in the control ones in area B. Microbial activity monitoring with soil microbial respiration appears to had been affected immediately after fire since microbial respiration was lower in burned samples from area A than in unburned one only 8 months after fire and no significant differences were observed between burned and unburned samples in area B. Soil microbial community composition studied by Principal Component Analyses (PCA) of the PLFA pattern revealed both fire and seasonal effects. General overview of the results could lead to think in a slight negative or even positive effect of fire on soil microbial parameters studied, mainly in zone B. Nevertheless if we calculate the ratio between C-biomass and organic-C we find lower ratio in fire-affected samples than in the control ones in both areas, showing the most marked effect on area B which remain with this tendency 20 months after fire. Acknowledgements: This research was supported by the CICYT co-financed FEDER project CGL2006-11107-C02-01/BOS. We are grateful for the Sierra Nevada National Park support during the study.

Community Engagement and Data Disclosure in Environmental Health Research

PubMed Central

Haynes, Erin N.; Elam, Sarah; Burns, Roxanne; Spencer, Alonzo; Yancey, Elissa; Kuhnell, Pierce; Alden, Jody; Walton, Mike; Reynolds, Virgil; Newman, Nicholas; Wright, Robert O.; Parsons, Patrick J.; Praamsma, Meredith L.; Palmer, Christopher D.; Dietrich, Kim N.

2016-01-01

Summary: Federal funding agencies increasingly support stakeholder participation in environmental health studies, and yet there is very little published research on engagement of community members in the development of data disclosure (DD) strategies. The Ohio Environmental Protection Agency reported airborne manganese (Mn) concentrations in East Liverpool, Ohio, 30 times higher than the reference concentration, which led to an academic–community research partnership to address community concern about Mn exposure, particularly among children. Children and their families were recruited to participate in a pilot study. Samples of blood and hair were collected from the children and analyzed for metals. DD mechanisms were developed using an iterative approach between community and academic partners. Individual DD letters were mailed to each participating family, and a community meeting was held. A post-meeting survey was administered to gauge community perception of the DD strategies. The purpose of this article is to demonstrate the effectiveness of engaging community partners in the conduct of environmental health research and in the development of DD strategies for individuals and the community at large. Scientists should include community partners in the development of DD strategies to enhance translation of the research findings and support the right of study participants to know their individual results. PMID:26829152

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

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

PubMed

Boucher, Delphine; Jardillier, Ludwig; Debroas, Didier

2006-01-01

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

Perception of Community Pharmacists towards Dispensing Errors in Community Pharmacy Setting in Gondar Town, Northwest Ethiopia

PubMed Central

2017-01-01

Background Dispensing errors are inevitable occurrences in community pharmacies across the world. Objective This study aimed to identify the community pharmacists' perception towards dispensing errors in the community pharmacies in Gondar town, Northwest Ethiopia. Methods A cross-sectional study was conducted among 47 community pharmacists selected through convenience sampling. Data were analyzed using SPSS version 20. Descriptive statistics, Mann–Whitney U test, and Pearson's Chi-square test of independence were conducted with P ≤ 0.05 considered statistically significant. Result The majority of respondents were in the 23–28-year age group (N = 26, 55.3%) and with at least B.Pharm degree (N = 25, 53.2%). Poor prescription handwriting and similar/confusing names were perceived to be the main contributing factors while all the strategies and types of dispensing errors were highly acknowledged by the respondents. Group differences (P < 0.05) in opinions were largely due to educational level and age. Conclusion Dispensing errors were associated with prescribing quality and design of dispensary as well as dispensing procedures. Opinion differences relate to age and educational status of the respondents. PMID:28612023

Perception of Community Pharmacists towards Dispensing Errors in Community Pharmacy Setting in Gondar Town, Northwest Ethiopia.

PubMed

Asmelashe Gelayee, Dessalegn; Binega Mekonnen, Gashaw

2017-01-01

Dispensing errors are inevitable occurrences in community pharmacies across the world. This study aimed to identify the community pharmacists' perception towards dispensing errors in the community pharmacies in Gondar town, Northwest Ethiopia. A cross-sectional study was conducted among 47 community pharmacists selected through convenience sampling. Data were analyzed using SPSS version 20. Descriptive statistics, Mann-Whitney U test, and Pearson's Chi-square test of independence were conducted with P ≤ 0.05 considered statistically significant. The majority of respondents were in the 23-28-year age group ( N = 26, 55.3%) and with at least B.Pharm degree ( N = 25, 53.2%). Poor prescription handwriting and similar/confusing names were perceived to be the main contributing factors while all the strategies and types of dispensing errors were highly acknowledged by the respondents. Group differences ( P < 0.05) in opinions were largely due to educational level and age. Dispensing errors were associated with prescribing quality and design of dispensary as well as dispensing procedures. Opinion differences relate to age and educational status of the respondents.

Epistemological Issues in Astronomy Education Research: How Big of a Sample is "Big Enough"?

NASA Astrophysics Data System (ADS)

Slater, Stephanie; Slater, T. F.; Souri, Z.

2012-01-01

As astronomy education research (AER) continues to evolve into a sophisticated enterprise, we must begin to grapple with defining our epistemological parameters. Moreover, as we attempt to make pragmatic use of our findings, we must make a concerted effort to communicate those parameters in a sensible way to the larger astronomical community. One area of much current discussion involves a basic discussion of methodologies, and subsequent sample sizes, that should be considered appropriate for generating knowledge in the field. To address this question, we completed a meta-analysis of nearly 1,000 peer-reviewed studies published in top tier professional journals. Data related to methodologies and sample sizes were collected from "hard science” and "human science” journals to compare the epistemological systems of these two bodies of knowledge. Working back in time from August 2011, the 100 most recent studies reported in each journal were used as a data source: Icarus, ApJ and AJ, NARST, IJSE and SciEd. In addition, data was collected from the 10 most recent AER dissertations, a set of articles determined by the science education community to be the most influential in the field, and the nearly 400 articles used as reference materials for the NRC's Taking Science to School. Analysis indicates these bodies of knowledge have a great deal in common; each relying on a large variety of methodologies, and each building its knowledge through studies that proceed from surprisingly low sample sizes. While both fields publish a small percentage of studies with large sample sizes, the vast majority of top tier publications consist of rich studies of a small number of objects. We conclude that rigor in each field is determined not by a circumscription of methodologies and sample sizes, but by peer judgments that the methods and sample sizes are appropriate to the research question.

Counting on β-Diversity to Safeguard the Resilience of Estuaries

PubMed Central

de Juan, Silvia; Thrush, Simon F.; Hewitt, Judi E.

2013-01-01

Coastal ecosystems are often stressed by non-point source and cumulative effects that can lead to local-scale community homogenisation and a concomitant loss of large-scale ecological connectivity. Here we investigate the use of β-diversity as a measure of both community heterogeneity and ecological connectivity. To understand the consequences of different environmental scenarios on heterogeneity and connectivity, it is necessary to understand the scale at which different environmental factors affect β-diversity. We sampled macrofauna from intertidal sites in nine estuaries from New Zealand’s North Island that represented different degrees of stress derived from land-use. We used multiple regression models to identify relationships between β-diversity and local sediment variables, factors related to the estuarine and catchment hydrodynamics and morphology and land-based stressors. At local scales, we found higher β-diversity at sites with a relatively high total richness. At larger scales, β-diversity was positively related to γ-diversity, suggesting that a large regional species pool was linked with large-scale heterogeneity in these systems. Local environmental heterogeneity influenced β-diversity at both local and regional scales, although variables at the estuarine and catchment scales were both needed to explain large scale connectivity. The estuaries expected a priori to be the most stressed exhibited higher variance in community dissimilarity between sites and connectivity to the estuary species pool. This suggests that connectivity and heterogeneity metrics could be used to generate early warning signals of cumulative stress. PMID:23755252

Effects of clothianidin on aquatic communities: Evaluating the impacts of lethal and sublethal exposure to neonicotinoids

PubMed Central

Miles, Jesse C.; Hua, Jessica; Sepulveda, Maria S.; Krupke, Christian H.

2017-01-01

The widespread usage of neonicotinoid insecticides has sparked concern over their effects on non-target organisms. While research has largely focused on terrestrial systems, the low soil binding and high water solubility of neonicotinoids, paired with their extensive use on the landscape, puts aquatic environments at high risk for contamination via runoff events. We assessed the potential threat of these compounds to wetland communities using a combination of field surveys and experimental exposures including concentrations that are representative of what invertebrates experience in the field. In laboratory toxicity experiments, LC50 values ranged from 0.002 ppm to 1.2 ppm for aquatic invertebrates exposed to clothianidin. However, freshwater snails and amphibian larvae showed high tolerance to the chemical with no mortality observed at the highest dissolvable concentration of the insecticide. We also observed behavioral effects of clothianidin. Water bugs, Belostoma flumineum, displayed a dose-dependent reduction in feeding rate following exposure to clothianidin. Similarly, crayfish, Orconectes propinquus, exhibited reduced responsiveness to stimulus with increasing clothianidin concentration. Using a semi-natural mesocosm experiment, we manipulated clothianidin concentration (0.6, 5, and 352 ppb) and the presence of predatory invertebrates to explore community-level effects. We observed high invertebrate predator mortality with increases in clothianidin concentration. With increased predator mortality, prey survival increased by 50% at the highest clothianidin concentration. Thus, clothianidin contamination can result in a top-down trophic cascade in a community dominated by invertebrate predators. In our Indiana field study, we detected clothianidin (max = 176 ppb), imidacloprid (max = 141 ppb), and acetamiprid (max = 7 ppb) in soil samples. In water samples, we detected clothianidin (max = 0.67 ppb), imidacloprid (max = 0.18 ppb), and thiamethoxam (max = 2,568 ppb). Neonicotinoids were detected in >56% of soil samples and >90% of the water samples, which reflects a growing understanding that neonicotinoids are ubiquitous environmental contaminants. Collectively, our results underscore the need for additional research into the effects of neonicotinoids on aquatic communities and ecosystems. PMID:28334022

Bacterial succession across seasonal transitions in the coastal waters of the western Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Luria, C.; Rich, J. J.; Amaral-Zettler, L. A.; Ducklow, H. W.

2016-02-01

The marine ecosystem west of the Antarctic Peninsula (WAP) undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including the intense phytoplankton blooms that support a highly productive food web. Despite having important implications for the microbial loop and the biological carbon pump, the degree of trophic coupling between phytoplankton and bacteria is unclear. In particular, due to the difficulties inherent in sampling this remote system during the Antarctic winter and spring, little is known about how phytoplankton blooms may or may not drive bacterial seasonal succession. Using 16S rRNA gene amplicon sequencing, we assessed bacterial community composition in 68 samples from 24 dates that spanned the cold, dark winter, spring transitional period, and summer phytoplankton bloom. Our analysis resulted in 15 million sequences and 12,000 Operational Taxonomic Units (OTUs). We found that mid-winter bacterial communities had the highest richness ( 1,800 observed OTUs in rarefied libraries) and a greater abundance of oligotrophic and potentially chemoautolithotrophic taxa. The bacterial community changed only gradually up until the onset of a mid-summer phytoplankton bloom, which coincided with a 100-fold increase in bacterial production, a rapid decline in richness to 700 OTUs, and a shift in community composition toward copiotrophic taxa. This period lasted only a few weeks, at the end of which the bacterial community had largely reverted to its mid-winter state. Our findings provide new evidence of trophic coupling between bacteria and phytoplankton and highlight the importance of higher-resolution time series sampling in order to capture rapid seasonal changes.

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

DOE PAGES

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; ...

2013-08-13

In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relativemore » abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.« less

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

PubMed Central

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost. PMID:23967218

Biophysical Factors Affecting the Distribution of Demersal Fish around the Head of a Submarine Canyon Off the Bonney Coast, South Australia

PubMed Central

Currie, David R.; McClatchie, Sam; Middleton, John F.; Nayar, Sasi

2012-01-01

We sampled the demersal fish community of the Bonney Canyon, South Australia at depths (100–1,500 m) and locations that are poorly known. Seventy-eight species of demersal fish were obtained from 12 depth-stratified trawls along, and to either side, of the central canyon axis. Distributional patterns in species richness and biomass were highly correlated. Three fish assemblage groupings, characterised by small suites of species with narrow depth distributions, were identified on the shelf, upper slope and mid slope. The assemblage groupings were largely explained by depth (ρw = 0.78). Compared to the depth gradient, canyon-related effects are weak or occur at spatial or temporal scales not sampled in this study. A conceptual physical model displayed features consistent with the depth zonational patterns in fish, and also indicated that canyon upwelling can occur. The depth zonation of the fish assemblage was associated with the depth distribution of water masses in the area. Notably, the mid-slope community (1,000 m) coincided with a layer of Antarctic Intermediate Water, the upper slope community (500 m) resided within the core of the Flinders Current, and the shelf community was located in a well-mixed layer of surface water (<450 m depth). PMID:22253907

Evaluation of the impact of 2 years of a dosing intervention on canine echinococcosis in the Alay Valley, Kyrgyzstan.

PubMed

VAN Kesteren, F; Mastin, A; Torgerson, P R; Mytynova, Bermet; Craig, P S

2017-09-01

Echinococcosis is a re-emerging zoonotic disease in Kyrgyzstan. In 2012, an echinococcosis control scheme was started that included dosing owned dogs in the Alay Valley, Kyrgyzstan with praziquantel. Control programmes require large investments of money and resources; as such it is important to evaluate how well these are meeting their targets. However, problems associated with echinococcosis control schemes include remoteness and semi-nomadic customs of affected communities, and lack of resources. These same problems apply to control scheme evaluations, and quick and easy assessment tools are highly desirable. Lot quality assurance sampling was used to assess the impact of approximately 2 years of echinococcosis control in the Alay valley. A pre-intervention coproELISA prevalence was established, and a 75% threshold for dosing compliance was set based on previous studies. Ten communities were visited in 2013 and 2014, with 18-21 dogs sampled per community, and questionnaires administered to dog owners. After 21 months of control efforts, 8/10 communities showed evidence of reaching the 75% praziquantel dosing target, although only 3/10 showed evidence of a reduction in coproELISA prevalence. This is understandable, since years of sustained control are required to effectively control echinococcosis, and efforts in the Alay valley should be and are being continued.

What shapes edaphic communities in mineral and ornithogenic soils of Cierva Point, Antarctic Peninsula?

NASA Astrophysics Data System (ADS)

Mataloni, G.; Garraza, G. González; Bölter, M.; Convey, P.; Fermani, P.

2010-08-01

Three mineral soil and four ornithogenic soil sites were sampled during summer 2006 at Cierva Point (Antarctic Peninsula) to study their bacterial, microalgal and faunal communities in relation to abiotic and biotic features. Soil moisture, pH, conductivity, organic matter and nutrient contents were consistently lower and more homogeneous in mineral soils. Ornithogenic soils supported larger and more variable bacterial abundances than mineral ones. Algal communities from mineral soils were more diverse than those from ornithogenic soils, although chlorophyll- a concentrations were significantly higher in the latter. This parameter and bacterial abundance were correlated with nutrient and organic matter contents. The meiofauna obtained from mineral soils was homogeneous, with one nematode species dominating all samples. The fauna of ornithogenic soils varied widely in composition and abundance. Tardigrades and rotifers dominated the meiofauna at eutrophic O2, where they supported a large population of the predatory nematode Coomansus gerlachei. At site O3, high bacterial abundance was consistent with high densities of the bacterivorous nematodes Plectus spp. This study provides evidence that Antarctic soils are complex and diverse systems, and suggests that biotic interactions (e.g. competition and predation) may have a stronger and more direct influence on community variability in space and time than previously thought.

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

PubMed Central

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E.; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data. PMID:21045053

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.

PubMed

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.

Temporal patterns in the distribution, biomass and community structure of macrozooplankton and micronekton within Port Foster, Deception Island, Antarctica

NASA Astrophysics Data System (ADS)

Kaufmann, Ronald S.; Fisher, Erin C.; Gill, Walthus H.; King, Andrew L.; Laubacher, Matthew; Sullivan, Brian

2003-06-01

The pelagic community within the flooded caldera of Deception Island, Antarctica, was sampled with a 10-m 2 opening-closing MOCNESS trawl on five cruises between March 1999 and November 2000. Collections were made in 50 m strata from the surface to 150 m depth in an area with a bottom depth of 155-160 m. From March 1999 through February 2000 the pelagic community was dominated by krill, primarily Euphausia crystallorophias and E. superba, which made up >94% of total pelagic biomass on a dry-weight basis. Community composition shifted during early 2000, and samples from May and November 2000 contained a more diverse assemblage and large numbers of cydippid ctenophores, comprising ca. 30-35% of pelagic biomass on a dry weight basis. E. crystallorophias, which made up nearly 85% of the pelagic biomass in November 1999, declined to 5.8% during November 2000. The change in composition was accompanied by displacement of the biomass mode to greater depths, due to the deeper occurrence and lack of diel vertical migration in ctenophores, compared to krill. Integrated water-column biomass increased substantially from 1999 to 2000, primarily because of elevated abundances of gelatinous zooplankton and the presence of significantly larger krill during 2000.

Meltwater export of prokaryotic cells from the Greenland ice sheet.

PubMed

Cameron, Karen A; Stibal, Marek; Hawkings, Jon R; Mikkelsen, Andreas B; Telling, Jon; Kohler, Tyler J; Gözdereliler, Erkin; Zarsky, Jakub D; Wadham, Jemma L; Jacobsen, Carsten S

2017-02-01

Microorganisms are flushed from the Greenland Ice Sheet (GrIS) where they may contribute towards the nutrient cycling and community compositions of downstream ecosystems. We investigate meltwater microbial assemblages as they exit the GrIS from a large outlet glacier, and as they enter a downstream river delta during the record melt year of 2012. Prokaryotic abundance, flux and community composition was studied, and factors affecting community structures were statistically considered. The mean concentration of cells exiting the ice sheet was 8.30 × 10 4 cells mL -1 and we estimate that ∼1.02 × 10 21 cells were transported to the downstream fjord in 2012, equivalent to 30.95 Mg of carbon. Prokaryotic microbial assemblages were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Cell concentrations and community compositions were stable throughout the sample period, and were statistically similar at both sample sites. Based on our observations, we argue that the subglacial environment is the primary source of the river-transported microbiota, and that cell export from the GrIS is dependent on discharge. We hypothesise that the release of subglacial microbiota to downstream ecosystems will increase as freshwater flux from the GrIS rises in a warming world. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gambling harms and gambling help-seeking amongst indigenous Australians.

PubMed

Hing, Nerilee; Breen, Helen; Gordon, Ashley; Russell, Alex

2014-09-01

This paper aimed to analyze the harms arising from gambling and gambling-related help-seeking behaviour within a large sample of Indigenous Australians. A self-selected sample of 1,259 Indigenous Australian adults completed a gambling survey at three Indigenous sports and cultural events, in several communities and online. Based on responses to the problem gambling severity index (PGSI), the proportions of the sample in the moderate risk and problem gambler groups were higher than those for the population of New South Wales. Many in our sample appeared to face higher risks with their gambling and experience severe gambling harms. From PGSI responses, notable harms include financial difficulties and feelings of guilt and regret about gambling. Further harms, including personal, relationship, family, community, legal and housing impacts, were shown to be significantly higher for problem gamblers than for the other PGSI groups. Most problem gamblers relied on family, extended family and friends for financial help or went without due to gambling losses. Nearly half the sample did not think they had a problem with gambling but the results show that the majority (57.7 %) faced some risk with their gambling. Of those who sought gambling help, family, extended family, friends and respected community members were consulted, demonstrating the reciprocal obligations underpinning traditional Aboriginal culture. The strength of this finding is that these people are potentially the greatest source of gambling help, but need knowledge and resources to provide that help effectively. Local Aboriginal services were preferred as the main sources of professional help for gambling-related problems.

A Review of the Services Offered by English Sure Start Children's Centres in 2011 and 2012

ERIC Educational Resources Information Center

Hall, James; Eisenstadt, Naomi; Sylva, Kathy; Smith, Teresa; Sammons, Pamela; Smith, George; Evangelou, Maria; Goff, Jenny; Tanner, Emily; Agur, Maya; Hussey, David

2015-01-01

This paper presents a review of the family services that were offered by a sample of 121 English Sure Start Children's Centres in 2011 and 2012. Children's Centres are community based facilities that aim to improve outcomes for at-risk families and children through the delivery of a range of services largely aimed at families with young children.…

Using Modern Statistical Methods to Analyze Demographics of Kansas ABE/GED Students Who Transition to Community or Technical College Programs

ERIC Educational Resources Information Center

Zacharakis, Jeff; Wang, Haiyan; Patterson, Margaret Becker; Andersen, Lori

2015-01-01

This research analyzed linked high-quality state data from K-12, adult education, and postsecondary state datasets in order to better understand the association between student demographics and successful completion of a postsecondary program. Due to the relatively small sample size compared to the large number of features, we analyzed the data…

The Role of Enrollment Choice in Online Education: Course Selection Rationale and Course Difficulty as Factors Affecting Retention

ERIC Educational Resources Information Center

Wladis, Claire; Wladis, Katherine; Hachey, Alyse C.

2014-01-01

There is well-documented evidence that online retention rates are lower than face-to-face retention rates. However, most past research on online retention focuses on student characteristics, with little knowledge existing on the impact of course type. This study uses a matched sample of 2,330 students at a large urban community college to analyze…

Results of Macroinvertebrate Sampling Conducted at 33 SRS Stream Locations, July--August 1993

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

Specht, W.L.

1994-12-01

In order to assess the health of the macroinvertebrate communities of SRS streams, the macroinvertebrate communities at 30 stream locations on SRS were sampled during the summer of 1993, using Hester-Dendy multiplate samplers. In addition, three off-site locations in the Upper Three Runs drainage were sampled in order to assess the potential for impact from off-site activities. In interpreting the data, it is important to recognize that these data were from a single set of collections. Macroinvertebrate communities often undergo considerable temporal variation, and are also greatly influenced by such factors as water depth, water velocity, and available habitat. Thesemore » stations were selected with the intent of developing an on-going sampling program at a smaller number of stations, with the selection of the stations to be based largely upon the results of this preliminary sampling program. When stations within a given stream showed similar results, fewer stations would be sampled in the future. Similarly, if a stream appeared to be perturbed, additional stations or chemical analyses might be added so that the source of the perturbation could be identified. In general, unperturbed streams will contain more taxa than perturbed streams, and the distribution of taxa among orders or families will differ. Some groups of macroinvertebrates, such as Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddisflies), which are collectively called EPT taxa, are considered to be relatively sensitive to most kinds of stream perturbation; therefore a reduced number of EPT taxa generally indicates that the stream has been subject to chemical or physical stressors. In coastal plain streams, EPT taxa are generally less dominant than in streams with rocky substrates, while Chironomidae (midges) are more abundant. (Abstract Truncated)« less

Couples with Intimate Partner Violence Seeking Relationship Help: Associations and Implications for Self-Help and Online Interventions.

PubMed

Roddy, McKenzie K; Georgia, Emily J; Doss, Brian D

2017-04-20

In-person conjoint treatments for relationship distress are effective at increasing relationship satisfaction, and newly developed online programs are showing promising results. However, couples reporting even low levels intimate partner violence (IPV) are traditionally excluded from these interventions. To improve the availability of couple-based treatment for couples with IPV, the present study sought to determine whether associations with IPV found in community samples generalized to couples seeking help for their relationship and whether web-based interventions for relationship distressed worked equally well for couples with IPV. In the first aim, in a sample of 2,797 individuals who were seeking online help for their relationship, the levels and correlates of both low-intensity and clinically significant IPV largely matched what is found in community samples. In the second aim, in a sample of 300 couples who were randomly assigned to a web-based intervention or a waitlist control group, low-impact IPV did not moderate the effects of the intervention for relationship distress. Therefore, web-based interventions may be an effective (and easily accessible) intervention for relationship distress for couples with low-intensity IPV. © 2017 Family Process Institute.

Prevalence and correlates of body dysmorphic disorder in a community sample of adolescents.

PubMed

Schneider, Sophie C; Turner, Cynthia M; Mond, Jonathan; Hudson, Jennifer L

2017-06-01

Body dysmorphic disorder typically begins in adolescence, yet little is known about the prevalence and correlates of the disorder in this age group. The current study aimed to explore the presenting features of adolescents meeting probable criteria for body dysmorphic disorder in a large community sample, and compare levels of comorbid psychopathology, quality of life and mental health service use between adolescents with probable body dysmorphic disorder and those without. Questionnaires were completed at school by 3149 adolescents: 63% male, aged 12-18 years ( M = 14.58). These assessed Diagnostic and Statistical Manual of Mental Disorders (4th ed.) body dysmorphic disorder criteria, past mental health service use and symptoms of body dysmorphic disorder, anxiety, depression, obsessive-compulsive disorder and eating disorders. In male participants, additional measures assessed quality of life, muscularity concerns, emotional symptoms, peer problems, conduct problems and hyperactivity. The prevalence of probable body dysmorphic disorder was 1.7%; there was no sex difference in prevalence, but older adolescents reported higher prevalence than younger adolescents. Probable body dysmorphic disorder participants reported substantially elevated levels of psychopathology, quality of life impairment and mental health service use compared to non-body dysmorphic disorder participants. The prevalence of body dysmorphic disorder in adolescents is similar to adult samples, and probable body dysmorphic disorder is associated with comorbidity, distress and functional impairment in a community sample. Further research is required to better understand the presentation of body dysmorphic disorder in adolescents, and to improve diagnosis and treatment.

Exploring Arabidopsis thaliana Root Endophytes via Single-Cell Genomics

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

Lundberg, Derek; Woyke, Tanja; Tringe, Susannah

2014-03-19

Land plants grow in association with microbial communities both on their surfaces and inside the plant (endophytes). The relationships between microbes and their host can vary from pathogenic to mutualistic. Colonization of the endophyte compartment occurs in the presence of a sophisticated plant immune system, implying finely tuned discrimination of pathogens from mutualists and commensals. Despite the importance of the microbiome to the plant, relatively little is known about the specific interactions between plants and microbes, especially in the case of endophytes. The vast majority of microbes have not been grown in the lab, and thus one of the fewmore » ways of studying them is by examining their DNA. Although metagenomics is a powerful tool for examining microbial communities, its application to endophyte samples is technically difficult due to the presence of large amounts of host plant DNA in the sample. One method to address these difficulties is single-cell genomics where a single microbial cell is isolated from a sample, lysed, and its genome amplified by multiple displacement amplification (MDA) to produce enough DNA for genome sequencing. This produces a single-cell amplified genome (SAG). We have applied this technology to study the endophytic microbes in Arabidopsis thaliana roots. Extensive 16S gene profiling of the microbial communities in the roots of multiple inbred A. thaliana strains has identified 164 OTUs as being significantly enriched in all the root endophyte samples compared to their presence in bulk soil.« less

How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities

PubMed Central

Sini, Maria; Vatikiotis, Konstantinos; Katsoupis, Christos

2018-01-01

Background Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. Methods The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. Results Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. Discussion Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility. PMID:29942703

Community Extreme Tonnage User Service (CETUS): A 5000 Ton Open Research Facility in the United States

NASA Technical Reports Server (NTRS)

Danielson, L.; Righter, K.; McCubbin, F.

2016-01-01

Large sample volume 5000 ton multi-anvil presses have contributed to the exploration of deep Earth and planetary interiors, synthesis of ultra-hard and other novel materials, and serve as a sample complement to pressure and temperature regimes already attainable by diamond anvil cell experiments. However, no such facility exists on the North American continent. We propose the establishment of an open user facility for COMPRES members and the entire research community, with the unique capability of a 5000 ton (or more) press, supported by a host of extant co-located experimental and analytical laboratories and research staff. We offer wide range of complementary and/or preparatory experimental options. Any required synthesis of materials or follow up experiments can be carried out controlled atmosphere furnaces, piston cylinders, multi-anvil, or experimental impact apparatus. Additionally, our division houses two machine shops that would facilitate any modification or custom work necessary for development of CETUS, one for general fabrication and one located specifically within our experimental facilities. We also have a general sample preparation laboratory, specifically for experimental samples, that allows users to quickly and easily prepare samples for ebeam analyses and more. A service we can offer to COMPRES community members in general, and CETUS visiting users specifically, is a multitude of analytical instrumentation literally steps away from the experimental laboratories. This year we will be pursuing site funding of our laboratories through NASA's Planetary Science Directorate, which should result in substantial cost savings to all visiting users, and supports our mission of interagency cooperation for the enhancement of science for all (see companion PSAMS abstract). The PI is in a unique position as an employee of Jacobs Technology to draw funding from multiple sources, including those from industry and commerce. We submitted a Planetary Major Equipment proposal to the NASA Emerging Worlds solicitation for the full cost of a press, with competitive bids submitted from Sumitomo, Rockland Research, and Voggenreiter. Additional funding is currently being sought from industry sources through the Strategic Partnerships Office at NASA JSC, External Pursuits Program Office on the JETS contract, and Jacobs corporate in the United States. Internal funding is available for JETS contract personnel to travel to large press locations worldwide to study set-up and operations. We also anticipate a fortuitous cost savings in installation of the large press because plans are already underway for major renovations to the entire experimental petrology suite within the next 2 years in order to accommodate our growing user base. Our focus as contract staff is on serving the scientific needs of our users and collaborators. We are seeking community expert input on multiple aspects of this proposed facility, such as the press type and design, access management, immediate projects, and future innovation initiatives.

Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

PubMed Central

Vivien, Régis; Lejzerowicz, Franck; Pawlowski, Jan

2016-01-01

Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities. PMID:26866802

Achieving cultural congruency in weight loss interventions: can a spirituality-based program attract and retain an inner-city community sample?

PubMed

Davis, Chad; Dutton, William Blake; Durant, Taryn; Annunziato, Rachel A; Marcotte, David

2014-01-01

Ethnic minorities continue to be disproportionately affected by obesity and are less likely to access healthcare than Caucasians. It is therefore imperative that researchers develop novel methods that will attract these difficult-to-reach groups. The purpose of the present study is to describe characteristics of an urban community sample attracted to a spiritually based, weight loss intervention. METHODS. Thirteen participants enrolled in a pilot version of Spiritual Self-Schema Therapy (3S) applied to disordered eating behavior and obesity. Treatment consisted of 12 one-hour sessions in a group therapy format. At baseline, participants were measured for height and weight and completed a battery of self-report measures. The sample was predominantly African-American and Hispanic and a large percentage of the sample was male. Mean baseline scores of the EDE-Q, YFAS, and the CES-D revealed clinically meaningful levels of eating disordered pathology and depression, respectively. The overall attrition rate was quite low for interventions targeting obesity. This application of a spiritually centered intervention seemed to attract and retain a predominantly African-American and Hispanic sample. By incorporating a culturally congruent focus, this approach may have been acceptable to individuals who are traditionally more difficult to reach.

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

PubMed Central

Ng, Terry Fei Fan; Willner, Dana L.; Lim, Yan Wei; Schmieder, Robert; Chau, Betty; Nilsson, Christina; Anthony, Simon; Ruan, Yijun; Rohwer, Forest; Breitbart, Mya

2011-01-01

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes. PMID:21674005

Biodiversity in canopy-forming algae: Structure and spatial variability of the Mediterranean Cystoseira assemblages

NASA Astrophysics Data System (ADS)

Piazzi, L.; Bonaviri, C.; Castelli, A.; Ceccherelli, G.; Costa, G.; Curini-Galletti, M.; Langeneck, J.; Manconi, R.; Montefalcone, M.; Pipitone, C.; Rosso, A.; Pinna, S.

2018-07-01

In the Mediterranean Sea, Cystoseira species are the most important canopy-forming algae in shallow rocky bottoms, hosting high biodiverse sessile and mobile communities. A large-scale study has been carried out to investigate the structure of the Cystoseira-dominated assemblages at different spatial scales and to test the hypotheses that alpha and beta diversity of the assemblages, the abundance and the structure of epiphytic macroalgae, epilithic macroalgae, sessile macroinvertebrates and mobile macroinvertebrates associated to Cystoseira beds changed among scales. A hierarchical sampling design in a total of five sites across the Mediterranean Sea (Croatia, Montenegro, Sardinia, Tuscany and Balearic Islands) was used. A total of 597 taxa associated to Cystoseira beds were identified with a mean number per sample ranging between 141.1 ± 6.6 (Tuscany) and 173.9 ± 8.5(Sardinia). A high variability at small (among samples) and large (among sites) scale was generally highlighted, but the studied assemblages showed different patterns of spatial variability. The relative importance of the different scales of spatial variability should be considered to optimize sampling designs and propose monitoring plans of this habitat.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants.

PubMed

Vályi, Kriszta; Rillig, Matthias C; Hempel, Stefan

2015-03-01

We studied the effect of host plant identity and land-use intensity (LUI) on arbuscular mycorrhizal fungi (AMF, Glomeromycota) communities in roots of grassland plants. These are relevant factors for intraradical AMF communities in temperate grasslands, which are habitats where AMF are present in high abundance and diversity. In order to focus on fungi that directly interact with the plant at the time, we investigated root-colonizing communities. Our study sites represent an LUI gradient with different combinations of grazing, mowing, and fertilization. We used massively parallel multitag pyrosequencing to investigate AMF communities in a large number of root samples, while being able to track the identity of the host. We showed that host plants significantly differed in AMF community composition, while land use modified this effect in a plant species-specific manner. Communities in medium and low land-use sites were subsets of high land-use communities, suggesting a differential effect of land use on the dispersal of AMF species with different abundances and competitive abilities. We demonstrate that in these grasslands, there is a small group of highly abundant, generalist fungi which represent the dominating species in the AMF community. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome.

PubMed

Lupatini, Manoeli; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Suleiman, Afnan Khalil Ahmad; Fulthorpe, Roberta R; Roesch, Luiz Fernando Würdig

2013-02-01

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

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

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

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

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

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

DOE PAGES

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

2017-03-13

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