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Sample records for abundance community structure

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

    PubMed

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

    2015-04-23

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

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

    PubMed

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

    2016-01-01

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

  3. Influences on the structure of suburban ant (Hymenoptera: Formicidae) communities and the abundance of Tapinoma sessile.

    PubMed

    Toennisson, T A; Sanders, N J; Klingeman, W E; Vail, K M

    2011-12-01

    Urbanization can alter the organization of ant communities and affect populations of urban pest ants. In this study, we sampled ant communities in urban and suburban yards to understand the habitat factors that shape these communities and influence the abundance of a common pest species, Tapinoma sessile (Say). We used pitfall traps to sample ant communities and a combination of pitfall traps and baiting to collect T. sessile at 24 sites in Knoxville, TN. In total, we collected 46 ant species. Ant species richness ranged from seven to 24 species per yard. Ant species richness tended to be lowest near houses, whereas T. sessile abundance was highest near houses. The best predictors of ant species richness in yards were canopy cover and presence of leaf litter: ant species richness peaked at mid-levels of canopy cover and was negatively correlated with the presence of leaf litter. Tapinoma sessile abundance increased with presence of logs, boards, or landscaping timbers and leaf litter in yards. Our results indicate that ant communities and the abundance of particular pest species in these urban and suburban landscapes are shaped by many of the same factors that structure ant communities in less anthropogenically disturbed environments. PMID:22217754

  4. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions. PMID:26184407

  5. Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.

    PubMed

    Tatti, Enrico; Goyer, Claudia; Burton, David L; Wertz, Sophie; Zebarth, Bernie J; Chantigny, Martin; Filion, Martin

    2015-10-01

    Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure. PMID:25851442

  6. Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

    PubMed Central

    Farag, Ibrahim F.; Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S.

    2014-01-01

    We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions. PMID:24637619

  7. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated. PMID:26787774

  8. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  9. Diversity, abundance and community network structure in sporocarp-associated beetle communities of the central Appalachian Mountains.

    PubMed

    Epps, Mary Jane; Arnold, A Elizabeth

    2010-01-01

    Although arthropods are abundant and diverse in and on macrofungal sporocarps, their associations with fungi seldom have been described at a community level. We examined sporocarp-associated beetle communities in two primary sites in the Appalachian Mountains and foothills, assessing beetle diversity and abundance in relation to study site, sampling season (early vs. late summer), and sporocarp characteristics such as taxonomic position, dry mass and age. From 758 sporocarps representing >180 species we recovered 15404 adult beetles representing 72 species and 15 families, primarily Staphylinidae (> 98% of individuals and of 64% morphospecies). The probability of sporocarp colonization by beetles, beetle abundance and diversity differed among fungal species and were positively associated with sporocarp dry mass. Sporocarp age was positively correlated with beetle diversity and abundance (as measured in a focal species, Megacollybia platyphylla, Tricholomataceae), and its effects were independent of dry mass. Many beetle species were generalists, visiting a wide breadth of fungi in both the Agaricales and Polyporales; however, several beetle taxa showed evidence of specialization on particular fungal hosts. Host association data were used to examine the structure underlying sporocarp-beetle associations. Here we present the first evidence of nested community structure in the sporocarp-beetle interaction network. PMID:20648747

  10. Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils.

    PubMed

    Wang, Xiaoyan; Wang, Cui; Bao, Linlin; Xie, Shuguang

    2014-02-01

    Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems. PMID:23949998

  11. Community structure, abundance, and activity of methanotrophs in the Zoige wetland of the Tibetan Plateau.

    PubMed

    Yun, Juanli; Zhuang, Guoqiang; Ma, Anzhou; Guo, Hongguang; Wang, Yanfen; Zhang, Hongxun

    2012-05-01

    The Zoige wetland of the Tibetan Plateau is a high-altitude tundra wetland and one of the biggest methane emission centers in China. In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detected 10(7) to 10(8) of total pmoA gene copies per gram dry weight of soil in the three marshes. Group-specific qPCR and reverse transcriptase qPCR results found that the Methylobacter genus dominates the wetland, and Methylocystis methanotrophs were less abundant, although this group of methanotrophs was estimated to be more active according to mRNA/DNA ratio. Furthermore, EV marsh demonstrated the highest methanotrophs abundance and activity among the three marshes investigated. Our study suggests that both type I and type II methanotrophs contribute to the methane oxidation in the Zoige wetland. PMID:22159497

  12. Picoplankton and virioplankton abundance and community structure in Pearl River Estuary and Daya Bay, South China.

    PubMed

    Ni, Zhixin; Huang, Xiaoping; Zhang, Xia

    2015-06-01

    By using flow cytometry techniques, we investigated the abundance and composition of the heterotrophic prokaryotes, virioplankton and picophytoplankton community in the Pearl River Estuary and Daya Bay in the summer of 2012. We identified two subgroups of prokaryotes, high nucleic acid (HNA) and low nucleic acid (LNA), characterized by different nucleic acid contents. HNA abundance was significantly correlated with larger phytoplankton and Synechococcus (Syn) abundance, which suggested the important role of organic substrates released from primary producers on bacterial growth. Although LNA did not show any association with environmental variables, it was a vital component of the microbial community. In contrast to previous studies, the total virioplankton concentration had a poor relationship with nutrient availability. The positive relationship between large-sized phytoplankton abundance and the V-I population confirmed that V-I was a phytoplankton-infecting viral subgroup. Although the V-II group (bacteriophages) was dominant in the virioplankton community, it was not related with prokaryotic abundance, which indicated factors other than hosts controlling V-II abundance or the uncertainty of virus-host coupling. With respect to the picophytoplankton community, our results implied that river input exerted a strong limitation to Syn distribution in the estuary, while picoeukaryotes (Euk) were numerically less abundant and showed a quite different distribution pattern from that of Syn, and hence presented ecological properties distinct from Syn in our two studied areas. PMID:26040741

  13. Diversity, Abundance and Community Structure of Benthic Macro- and Megafauna on the Beaufort Shelf and Slope

    PubMed Central

    Nephin, Jessica; Juniper, S. Kim; Archambault, Philippe

    2014-01-01

    Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009–2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf ( 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness ( diversity) and diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal diversity across the depth gradient. PMID:25007347

  14. Impact of herbicides on the abundance and structure of indigenous beta-subgroup ammonia-oxidizer communities in soil microcosms.

    PubMed

    Chang, Y J; Hussain, A K; Stephen, J R; Mullen, M D; White, D C; Peacock, A

    2001-11-01

    In this study, mixtures of five herbicide-formulated products (atrazine, dicamba, fluometuron, metolachlor, and sulfentrazone) were applied to soil microcosm columns in increasing concentrations. The toxic impact of herbicides on the indigenous beta-subclass Proteobacteria autotrophic ammonia-oxidizer (beta-AAO) community was assessed. The beta-AAO population abundances were estimated by competitive polymerase chain reaction (PCR) targeting the gene amoA, encoding the alpha-subunit of ammonia monooxygenase. Community structure was examined by PCR and denaturing gradient gel electrophoresis targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA gene fragment clone libraries. The 16S rDNA analyses showed that a single ribotype of Nitrosospira cluster 3 was the dominant beta-AAO in all treatments. At a finer scale, amoA clone library analysis suggested a shift in community structure corresponding to the 100-ppm application. Competitive PCR indicated significant differences between treatments. The control exhibited relatively stable population abundance over the time period examined. The 10-ppm treatment induced a population increase, but a significant decrease was induced by the 100-ppm application. At 1,000 ppm, the ammonia-oxidizer population dropped below the method detection limit by the first sampling point. An impact on ammonia oxidizers resulting from the application of herbicides was observed, both in abundance and community structure. PMID:11699770

  15. Effects of oxytetracycline on the abundance and community structure of nitrogen-fixing bacteria during cattle manure composting.

    PubMed

    Sun, Jiajun; Qian, Xun; Gu, Jie; Wang, Xiaojuan; Gao, Hua

    2016-09-01

    The effects of oxytetracycline (OTC) on nitrogen-fixing bacterial communities were investigated during cattle manure composting. The abundance and community structure of nitrogen-fixing bacteria were determined by qPCR and denaturing gradient gel electrophoresis (DGGE), respectively. The matrix was spiked with OTC at four levels: no OTC, 10mg/kg dry weight (DW) OTC (L), 60mg/kg DW OTC (M), and 200mg/kg DW OTC (H). The high temperature period of composting was shorter with M and H, and the decline in temperature during the cooling stage was accelerated by OTC. OTC had a concentration-dependent inhibitory effect on the nitrogenase activity during early composting, and the nifH gene abundance declined significantly during the later composting stage. The DGGE profile and statistical analysis showed that OTC changed the nitrogen-fixing bacterial community succession and reduced the community richness and dominance. The nitrogen-fixing bacterial community structure was affected greatly by the high level of OTC. PMID:27318157

  16. Nematode diversity, abundance and community structure 50 years after the formation of the volcanic island of Surtsey

    NASA Astrophysics Data System (ADS)

    Ilieva-Makulec, K.; Bjarnadottir, B.; Sigurdsson, B. D.

    2014-10-01

    The soil nematode fauna can give important insights into soil development and other habitat changes that occur during primary succession. We investigated the generic composition, density, distribution and community structure of nematodes 50 years after the formation of a pristine volcanic island, Surtsey, Iceland. Part of the island has received additional nutrient inputs from seagulls breeding there since 1985, while the reminder has been much less affected and is at present found at a different successional sere. In total, 25 genera of nematodes were identified, of which 14 were reported on Surtsey for the first time. Nematode communities were more diverse in the more infertile area outside the gull colony, where 24 genera were found, compared to 18 inside. The trophic structure of the nematode communities showed relatively higher abundance of fungal feeders in the infertile areas, but relatively more bacterial- and plant-feeders inside the colony. Nematode abundance in surface soil was, however, significantly higher within the gull colony, with 16.7 ind. cm-2 compared to 3.6 ind. cm-2 outside. A multivariate analysis indicated that the nematode abundance and distribution on Surtsey were most strongly related to the soil C : N ratio, soil acidity, plant cover and biomass, soil temperature and soil depth.

  17. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    PubMed Central

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  18. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure.

    PubMed

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M B; Bodelier, Paul L E

    2015-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a 'tipping point' where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  19. Variation in abundance and community structure of particle-attached and free-living bacteria in the South China Sea

    NASA Astrophysics Data System (ADS)

    Li, Jiangtao; Wei, Bingbing; Wang, Jiani; Liu, Ying; Dasgupta, Shamik; Zhang, Li; Fang, Jiasong

    2015-12-01

    Bacteria play a crucial role in the biological transfer of carbon in the ocean, especially in the transformation of particulate organic carbon (POC) to dissolved organic carbon (DOC), yet little information is available for their abundance and community structures in mesopelagic and bathypelagic waters. Here we present results of our investigation on the spatial variations of abundance and community composition of the particle-attached (PA) and free-living (FL) bacterial assemblages at different depths (500 m, 800 m, and 1500 m) in the South China Sea (SCS). Our results showed that the abundance of FL bacteria was an order of magnitude higher than that of PA bacteria. The relative abundance of FL bacteria increased from 82% at 500 m to 93% at 1500 m. In all cases, the FL bacteria assemblages were more diverse than the PA fraction. The PA bacterial assemblage was dominated by members of the Rhodobacterales of the α-Proteobacteria and the Alteromonadales of the γ-Proteobacteria. In contrast, the FL bacteria assemblages displayed distinctive spatial heterogeneity and were dominant by different phylotypes at different depths. However, certain bacterial taxa of the α- and γ-Proteobacteria co-occurred in both the FL and PA fractions, with proportions being varied with depth. These results highlight the coexistence of particle-attached and free-living bacteria specialists and generalists, and provide valuable information in understanding the role of different bacterial assemblages in the deep-ocean carbon cycle.

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

    PubMed

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

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community. PMID:27063014

  1. Decreasing Abundance, Increasing Diversity and Changing Structure of the Wild Bee Community (Hymenoptera: Anthophila) along an Urbanization Gradient

    PubMed Central

    Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E.

    2014-01-01

    Background Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient. Methodology/Principal Findings Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size. Conclusions/Significance We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about

  2. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    PubMed

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial

  3. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  4. Vertical changes in abundance, biomass and community structure of copepods down to 3000 m in the southern Bering Sea

    NASA Astrophysics Data System (ADS)

    Homma, Tomoe; Yamaguchi, Atsushi

    2010-08-01

    Vertical changes in abundance, biomass and community structure of copepods down to 3000 m depth were studied at a single station of the Aleutian Basin of the Bering Sea (53°28'N, 177°00'W, depth 3779 m) on the 14th June 2006. Both abundance and biomass of copepods were greatest near the surface layer and decreased with increase in depth. Abundance and biomass of copepods integrated over 0-3000 m were 1,390,000 inds. m -2 and 5056 mg C m -2, respectively. Copepod carcasses occurred throughout the layer, and the carcass:living specimen ratio was the greatest in the oxygen minimum layer (750-100 m, the ratio was 2.3). A total of 72 calanoid copepod species belonging to 34 genera and 15 families occurred in the 0-3000 m water column (Cyclopoida, Harpacticoida and Poecilostomatoida were not identified to species level). Cluster analysis separated calanoid copepod communities into 5 groups (A-E). Each group was separated by depth, and the depth range of each group was at 0-75 m (A), 75-500 m (B), 500-750 m (C), 750-1500 m (D) and 1500-3000 m (E). Copepods were divided into four types based on the feeding pattern: suspension feeders, suspension feeders in diapause, detritivores and carnivores. In terms of abundance the most dominant group was suspension feeders (mainly Cyclopoida) in the epipelagic zone, and detritivores (mainly Poecilostomatoida) were dominant in the meso- and bathypelagic zones. In terms of biomass, suspension feeders in diapause (calanoid copepods Neocalanus spp. and Eucalanus bungii) were the major component (ca. 10-45%), especially in the 250-3000 m depth. These results are compared with the previous studies in the same region and that down to greater depths in the worldwide oceans.

  5. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    PubMed

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil. PMID:27038955

  6. Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

    PubMed

    Merlin, Chloé; Devers, Marion; Béguet, Jérémie; Boggio, Baptiste; Rouard, Nadine; Martin-Laurent, Fabrice

    2016-03-01

    The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil

  7. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

    PubMed

    Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

    2015-09-01

    Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding. PMID:26077223

  8. Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs.

    PubMed

    Rinta-Kanto, J M; Sinkko, H; Rajala, T; Al-Soud, W A; Sørensen, S J; Tamminen, M V; Timonen, S

    2016-07-01

    Prokaryotes colonize decaying wood and contribute to the degradation process, but the dynamics of prokaryotic communities during wood decay is still poorly understood. We studied the abundance and community composition of Bacteria and Archaea inhabiting naturally decaying Picea abies logs and tested the hypothesis that the variations in archaeal and bacterial abundances and community composition are coupled with environmental parameters related to the decay process. The data set comprises >500 logs at different decay stages from five geographical locations in south and central Finland. The results show that Bacteria and Archaea are an integral and dynamic component of decaying wood biota. The abundances of bacterial and archaeal 16S rRNA genes increase as wood decay progresses. Changes in bacterial community composition are clearly linked to the loss of density of wood, while specific fungal-bacterial interactions may also affect the distribution of bacterial taxa in decaying wood. Thaumarchaeota were prominent members of the archaeal populations colonizing decaying wood, providing further evidence of the versatility and cosmopolitan nature of this phylum in the environment. The composition and dynamics of the prokaryotic community suggest that they are an active component of biota that are involved in processing substrates in decaying wood material. PMID:27127195

  9. The Effects of Individual PCB Congeners on the Soil Bacterial Community Structure and the Abundance of Biphenyl Dioxygenase Genes

    PubMed Central

    Correa, Paola A.; Lin, LianShin; Just, Craig L.; Hu, Dingfei; Hornbuckle, Keri C.; Schnoor, Jerald L.; Van Aken, Benoit

    2009-01-01

    -time PCR showed that exposure to all PCB congeners and Aroclor 1242 resulted in a marked increase of two out of the four BPH genes tested, similarly suggesting the selection of PCB-degrading bacteria. This paper showed that exposure to different PCB congeners leads to different structures of the soil bacterial community and BPH genes expression patterns. PMID:19716603

  10. Inconsistent Changes in Microbial Community Structure and Abundance with Biochar Amendment in Rice Paddy Soils from South China

    NASA Astrophysics Data System (ADS)

    Chen, J.; Qu, J.; Liu, X.; Zheng, J.; Li, L.; Pan, G.

    2012-04-01

    Effects of biochar amendment on soil microbiota had not yet been well understood. We conducted a cross site field study on biochar amendment to rice paddies from south China in 2010. The experiment was performed with four treatments including N fertilization only (C0N), N fertilization plus biochar at 20t/ha (C1N) and at 40t/ha (C2N) as well as a control without N fertilization and biochar (C0N0) consistently with three sites. Biochar was spread at soil surface and incorporated into soil and thoroughly mixed to depth of about 12cm before padding for rice seedling transplantation. Rice production was conducted with conventional water and nutrient management practices adapting to local climate and cultivar conditions. Topsoil samples were collected from each treatment plot across sites for chemical properties and molecular analysis after rice harvest in autumn of 2010. Contents of organic carbon, total N as well as soil microbial biomass carbon were determined with recommended methods. Quantitative real-time PCR coupled with 16S rRNA gene and 18S rRNA gene denaturing gradient gel electrophoresis (DGGE) were respectively employed to trace changes in abundance and structure of bacteria and fungi community with biochar amendment. Increase in microbial biomass carbon (SMBC) was not observed in one site but by 10-20% in other two sites while SOC contents were increased by 25-45% in all sites under biochar treatments. Copy numbers of bacterial genes were different between the sites but no changes with biochar treatment in a single site. However, cluster analysis revealed a more or less decreased similarity of bacterial community to the control (ranging from 75% to 85%) by biochar treatment in a single site. Nevertheless, a number of special bands appeared both in bacterial and fungal DGGE patterns under biochar treatments, though varying with site also. While the fungi copy numbers markedly varied both with sites and with biochar treatments, lower similarity and greater

  11. Changes in abundance and community structure of nematodes from the abyssal polymetallic nodule field, Tropical Northeast Pacific

    NASA Astrophysics Data System (ADS)

    Miljutin, Dmitry; Miljutina, Maria; Messié, Monique

    2015-12-01

    Deep-sea fields of polymetallic nodules in the Clarion-Clipperton Zone (CCFZ, tropical NE Pacific) are currently being investigated to assess their potential for commercial mining. During such mining, benthic communities will be inevitably disturbed or destroyed. Therefore, assessments of their standing stock and composition may be helpful for the future evaluation of possible impacts of commercial nodule exploitation. Analysis of nematode communities (at genus level) inhabiting the French license area of the CCFZ were studied based on data from the cruises NODINAUT (2004) and BIONOD (2012). The total nematode density was ca. 1.5-fold higher in 2012 as compared with 2004. This reflected a 2-2.5 times higher density of non-selective deposit-feeders (i.e. possessing a small buccal cavity without armature) in 2012 compared with 2004, whereas no significant differences between sampling periods were observed in the density of the other feeding groups. Consequently, whilst the list of the most abundant genera was identical, their relative abundances changed significantly. The relative abundance of the genus Thalassomonhystera was two times greater in 2012 than in 2004, whereas the relative abundances of the genera Acantholaimus and Theristus were significantly lower in 2012 (10% and 4%, respectively) than in 2004 (28% and 9%). Nematode diversity (including values of diversity indices and total number of recorded genera) was significantly lower in 2012 in comparison with 2004. Although our data do not take into account seasonal and shorter temporal scales of variability in nematode assemblages, we report here that a certain fraction of variations observed between the two sampling periods could be associated with differences in primary production. Future studies should aim to better characterise temporal variability in nematode communities of the CCFZ at seasonal and interannual scales.

  12. Asexual Endophytes and Associated Alkaloids Alter Arthropod Community Structure and Increase Herbivore Abundances on a Native Grass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dispite their minute biomass, microbial symbionts of plants potentially alter herbivory, diversity and community structure. Infection of grasses by asexual endophytic fungi often decreases herbivore loads and alters arthropod diverisy. However, most studies to date have involved agronomic grasses ...

  13. A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments

    NASA Technical Reports Server (NTRS)

    Franklin, Rima B.; Blum, Linda K.; McComb, Alison C.; Mills, Aaron L.

    2002-01-01

    Small-scale variations in bacterial abundance and community structure were examined in salt marsh sediments from Virginia's eastern shore. Samples were collected at 5 cm intervals (horizontally) along a 50 cm elevation gradient, over a 215 cm horizontal transect. For each sample, bacterial abundance was determined using acridine orange direct counts and community structure was analyzed using randomly amplified polymorphic DNA fingerprinting of whole-community DNA extracts. A geostatistical analysis was used to determine the degree of spatial autocorrelation among the samples, for each variable and each direction (horizontal and vertical). The proportion of variance in bacterial abundance that could be accounted for by the spatial model was quite high (vertical: 60%, horizontal: 73%); significant autocorrelation was found among samples separated by 25 cm in the vertical direction and up to 115 cm horizontally. In contrast, most of the variability in community structure was not accounted for by simply considering the spatial separation of samples (vertical: 11%, horizontal: 22%), and must reflect variability from other parameters (e.g., variation at other spatial scales, experimental error, or environmental heterogeneity). Microbial community patch size based upon overall similarity in community structure varied between 17 cm (vertical) and 35 cm (horizontal). Overall, variability due to horizontal position (distance from the creek bank) was much smaller than that due to vertical position (elevation) for both community properties assayed. This suggests that processes more correlated with elevation (e.g., drainage and redox potential) vary at a smaller scale (therefore producing smaller patch sizes) than processes controlled by distance from the creek bank. c2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

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

    PubMed

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

    2014-02-01

    Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles. PMID:24176706

  15. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    PubMed Central

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  16. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

    PubMed

    Reis, Mariana P; Ávila, Marcelo P; Keijzer, Rosalinde M; Barbosa, Francisco A R; Chartone-Souza, Edmar; Nascimento, Andréa M A; Laanbroek, Hendrikus J

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  17. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of EUVE spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous Advanced Satellite for Cosmology and Astrophysics (ASCA) data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated. With these new models applied to the ASCA spectrum, better fits were obtained. Findings are that: (1) ASCA and EUVE spectra are both dominated by a region at 6 x 10(exp 6) K. (2) The high energy cut-off of the ASCA spectrum is consistent with emission from the highest ionization stages of EUVE, namely Fe XXIV. (3) EUVE requires a continuous emission measure distribution with more than two temperatures. (4) The ASCA spectra are of such high statistical significance that systematic uncertainties dominate, including atomic physics issues and calibration issues. (5) While the ASCA spectral fits achieve lower Chi(exp 2 with two-temperature fits, the EUVE-derived emission measure distribution models are also consistent with the spectra. (6) The Fe/H ratio obtained from the ASCA fit is within 20 % of the Fe/H abundance obtained from the summed spectra of Capella over 5 EUVE pointings, as well as the 1996 EUVE data. This result confirms our claims that quasi-continua composed of weak emission lines in the short wavelength spectrometer of EUVE are not major contributors to the measured Capella continuum. Other abundance ratios are also determined from the ASCA data, using models derived with EUVE. Si, Si, and Mg appear to be close to solar photospheric values, while the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined

  18. Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this report we use Terminal Restriction Fragment Length Polymorphisms (TRFLP) in a tomato production system to “finger printing” the soil microbial community structure with Phylum specific primer sets. Factors influencing the soil microbes are a cover crop of Hairy Vetch (Vicia villosa) or Rye (...

  19. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  20. Age-abundance relationships for neutral communities.

    PubMed

    Danino, Matan; Shnerb, Nadav M

    2015-10-01

    Neutral models for the dynamics of a system of competing species are often used to describe a wide variety of empirical communities. These models are used in many situations, ranging from population genetics and ecological biodiversity to macroevolution and cancer tumors. One of the main issues discussed within this framework is the relationships between the abundance of a species and its age. Here we provide a comprehensive analysis of the age-abundance relationships for fixed-size and growing communities. Explicit formulas for the average and the most likely age of a species with abundance n are given, together with the full probability distribution function. We further discuss the universality of these results and their applicability to the tropical forest community. PMID:26565271

  1. Age-abundance relationships for neutral communities

    NASA Astrophysics Data System (ADS)

    Danino, Matan; Shnerb, Nadav M.

    2015-10-01

    Neutral models for the dynamics of a system of competing species are often used to describe a wide variety of empirical communities. These models are used in many situations, ranging from population genetics and ecological biodiversity to macroevolution and cancer tumors. One of the main issues discussed within this framework is the relationships between the abundance of a species and its age. Here we provide a comprehensive analysis of the age-abundance relationships for fixed-size and growing communities. Explicit formulas for the average and the most likely age of a species with abundance n are given, together with the full probability distribution function. We further discuss the universality of these results and their applicability to the tropical forest community.

  2. Arbuscular mycorrhizal fungi community structure, abundance and species richness changes in soil by different levels of heavy metal and metalloid concentration.

    PubMed

    Krishnamoorthy, Ramasamy; Kim, Chang-Gi; Subramanian, Parthiban; Kim, Ki-Yoon; Selvakumar, Gopal; Sa, Tong-Min

    2015-01-01

    Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity. PMID:26035444

  3. Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration

    PubMed Central

    Krishnamoorthy, Ramasamy; Kim, Chang-Gi; Subramanian, Parthiban; Kim, Ki-Yoon; Selvakumar, Gopal; Sa, Tong-Min

    2015-01-01

    Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity. PMID:26035444

  4. Antifouling Coatings Influence both Abundance and Community Structure of Colonizing Biofilms: a Case Study in the Northwestern Mediterranean Sea

    PubMed Central

    Camps, Mercedes; Barani, Aude; Gregori, Gérald; Bouchez, Agnès; Le Berre, Brigitte; Bressy, Christine; Blache, Yves

    2014-01-01

    When immersed in seawater, substrates are rapidly colonized by both micro- and macroorganisms. This process is responsible for important economic and ecological prejudices, particularly when related to ship hulls or aquaculture nets. Commercial antifouling coatings are supposed to reduce biofouling, i.e., micro- and macrofoulers. In this study, biofilms that primarily settled on seven different coatings (polyvinyl chloride [PVC], a fouling release coating [FRC], and five self-polishing copolymer coatings [SPC], including four commercial ones) were quantitatively studied, after 1 month of immersion in summer in the Toulon Bay (Northwestern Mediterranean Sea, France), by using flow cytometry (FCM), microscopy, and denaturing gradient gel electrophoresis. FCM was used after a pretreatment to separate cells from the biofilm matrix, in order to determine densities of heterotrophic bacteria, picocyanobacteria, and pico- and nanoeukaryotes on these coatings. Among diatoms, the only microphytobenthic class identified by microscopy, Licmophora, Navicula, and Nitzschia were determined to be the dominant taxa. Overall, biocide-free coatings showed higher densities than all other coatings, except for one biocidal coating, whatever the group of microorganisms. Heterotrophic bacteria always showed the highest densities, and diatoms showed the lowest, but the relative abundances of these groups varied depending on the coating. In particular, the copper-free SPC failed to prevent diatom settlement, whereas the pyrithione-free SPC exhibited high picocyanobacterial density. These results highlight the interest in FCM for antifouling coating assessment as well as specific selection among microbial communities by antifouling coatings. PMID:24907329

  5. Antifouling coatings influence both abundance and community structure of colonizing biofilms: a case study in the Northwestern Mediterranean Sea.

    PubMed

    Camps, Mercedes; Barani, Aude; Gregori, Gérald; Bouchez, Agnès; Le Berre, Brigitte; Bressy, Christine; Blache, Yves; Briand, Jean-François

    2014-08-01

    When immersed in seawater, substrates are rapidly colonized by both micro- and macroorganisms. This process is responsible for important economic and ecological prejudices, particularly when related to ship hulls or aquaculture nets. Commercial antifouling coatings are supposed to reduce biofouling, i.e., micro- and macrofoulers. In this study, biofilms that primarily settled on seven different coatings (polyvinyl chloride [PVC], a fouling release coating [FRC], and five self-polishing copolymer coatings [SPC], including four commercial ones) were quantitatively studied, after 1 month of immersion in summer in the Toulon Bay (Northwestern Mediterranean Sea, France), by using flow cytometry (FCM), microscopy, and denaturing gradient gel electrophoresis. FCM was used after a pretreatment to separate cells from the biofilm matrix, in order to determine densities of heterotrophic bacteria, picocyanobacteria, and pico- and nanoeukaryotes on these coatings. Among diatoms, the only microphytobenthic class identified by microscopy, Licmophora, Navicula, and Nitzschia were determined to be the dominant taxa. Overall, biocide-free coatings showed higher densities than all other coatings, except for one biocidal coating, whatever the group of microorganisms. Heterotrophic bacteria always showed the highest densities, and diatoms showed the lowest, but the relative abundances of these groups varied depending on the coating. In particular, the copper-free SPC failed to prevent diatom settlement, whereas the pyrithione-free SPC exhibited high picocyanobacterial density. These results highlight the interest in FCM for antifouling coating assessment as well as specific selection among microbial communities by antifouling coatings. PMID:24907329

  6. Microbial communities on glacier surfaces in Svalbard: impact of physical and chemical properties on abundance and structure of cyanobacteria and algae.

    PubMed

    Stibal, Marek; Sabacká, Marie; Kastovská, Klára

    2006-11-01

    Microbial communities occurring in three types of supraglacial habitats--cryoconite holes, medial moraines, and supraglacial kames--at several glaciers in the Arctic archipelago of Svalbard were investigated. Abundance, biovolume, and community structure were evaluated by using epifluorescence microscopy and culturing methods. Particular emphasis was laid on distinctions in the chemical and physical properties of the supraglacial habitats and their relation to the microbial communities, and quantitative multivariate analyses were used to assess potential relationships. Varying pH (4.8 in cryoconite; 8.5 in a moraine) and texture (the proportion of coarse fraction 2% of dry weight in cryoconite; 99% dw in a kame) were found, and rather low concentrations of organic matter (0.3% of dry weight in a kame; 22% dw in cryoconite) and nutrients (nitrogen up to 0.4% dw, phosphorus up to 0.8% dw) were determined in the samples. In cryoconite sediment, the highest numbers of bacteria, cyanobacteria, and algae were found, whereas relatively low microbial abundances were recorded in moraines and kames. Cyanobacterial cells were significantly more abundant than microalgal ones in cryoconite and supraglacial kames. Different species of the cyanobacterial genus Leptolyngbya were by far the most represented in all samples, and cyanobacteria of the genera Phormidium and Nostoc prevailed in cultures isolated from cryoconite samples. These species are considered opportunistic organisms with wide ecological valency and strong colonizing potential rather than glacial specialists. Statistical analyses suggest that fine sediment with higher water content is the most suitable condition for bacteria, cyanobacteria, and algae. Also, a positive impact of lower pH on microbial growth was found. The fate of a microbial cell deposited on the glacier surface seems therefore predetermined by the physical and chemical factors such as texture of sediment and water content rather than spatial factors

  7. All together now? Sensitivity, dynamics, and predictability of planktonic foraminiferal species abundance versus community structure across Plio-Pleistocene glacial-interglacial cycles

    NASA Astrophysics Data System (ADS)

    Hull, P. M.; Norris, R. D.; Sexton, P.

    2012-12-01

    Most studies to date of biospheric sensitivity to global change have focused on understanding the sensitivity of modern species and communities to recent or experimental environmental change. However, it is unclear how to scale these results towards predicting the response of the biosphere to ongoing global change given that i) similar species often respond individualistically the same perturbation, ii) biotic response often scales nonlinearly with the size and/or duration of environmental change, and iii) many terrestrial and marine community types known from the recent past lack modern analogs. In this context, marine microfossils from deep sea sediments hold enormous promise for furthering our understanding of biotic sensitivity as they capture temporally expanded records of paleoceanographic and biotic response across a range climatic regimes (e.g., icehouse versus greenhouse climates), disturbance types (e.g., from background climate oscillations to mass extinctions), and habitats (e.g., low vs. high latitudes, upwelling vs. gyre ecosystems, etc). Here we use the repeated glacial-interglacial cycles and longer term trend of intensifying Northern Hemisphere glaciation from the Pliocene-Pleistocene to examine issues related to the sensitivity of planktonic foraminiferal species and communities to global change in an icehouse world. More specifically, we quantify the sensitivity and predictability of changes in planktonic foraminiferal species abundance (species specific mass accumulation rates) and community structure (dissimilarity indices and community classification) to glacial-interglacial cycles in the Plio-Pleistocene in two Atlantic sites (ODP Sites 999 and 662). We first examine whether the sensitivity of species and communities to glacial-interglacial cycles in the early Pliocene (~5-3 million years ago) is predictive of i) their sensitivity to the intensification of Northern Hemisphere glaciation (~3-2 million years ago), or ii) their sensitivity to

  8. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    PubMed

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. PMID:25862282

  9. How selection structures species abundance distributions

    PubMed Central

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

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

    PubMed

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

    2015-01-01

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

  11. Heavy-Machinery Traffic Impacts Methane Emissions as Well as Methanogen Abundance and Community Structure in Oxic Forest Soils▿†

    PubMed Central

    Frey, Beat; Niklaus, Pascal A.; Kremer, Johann; Lüscher, Peter; Zimmermann, Stephan

    2011-01-01

    Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH4 consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release. PMID:21742929

  12. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    NASA Astrophysics Data System (ADS)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

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

    PubMed Central

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

    2015-01-01

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

  14. Late-summer zooplankton community structure, abundance, and distribution in the Hudson Bay system (Canada) and their relationships with environmental conditions, 2003-2006

    NASA Astrophysics Data System (ADS)

    Estrada, Rafael; Harvey, Michel; Gosselin, Michel; Starr, Michel; Galbraith, Peter S.; Straneo, Fiammetta

    2012-08-01

    Zooplankton communities were examined for the first time in three different hydrographic regions of the Hudson Bay system (HBS) in early August to early September from 2003 to 2006. Sampling was conducted at 50 stations distributed along different transects located in Hudson Bay (HB), Hudson Strait (HS), and Foxe Basin (FB). Variations in zooplankton biomass, abundance, taxonomic composition, and diversity in relation to environmental variables were studied using multivariate techniques. During all sampling years, the total zooplankton biomass was on average four times lower in HB than in HS and FB. Clustering samples by their relative species compositions revealed no interannual variation in zooplankton community but showed a marked interregional variability between the three regions. Water column stratification explained the greatest proportion (25%) of this spatial variability. According to redundancy analysis (RDA), the zooplankton taxa that contribute most to the separation of the three regions are Microcalanus spp., Oithona similis, Oncaea borealis, Aeginopsis laurentii, Sagitta elegans, Fritillaria sp., and larvae of cnidaria, chaetognatha, and pteropoda in HB; hyperiid amphipods in FB; and Pseudocalanus spp. CI-CV, Calanus glacialis CI-CVI, Calanus finmarchicus CI-CVI, Calanus hyperboreus CV-CVI, Acartia longiremis CI-CV, Metridia longa N3-N6 CI-CIII CVIf, Eukrohnia hamata, larvae of echinodermata, mollusca, cirripedia, appendicularia, and polychaeta in the northwestern and southeastern HS transects. For the HB transect, the RDA analyzed allowed us to distinguish three regions (HB west, central, and east) with different environmental gradients and zooplankton assemblages, in particular higher concentration of Pseudocalanus spp. nauplii and CI-CVI, as well as benthic macrozooplankton and meroplankton larvae in western HB. In HS, Calanoid species (mainly C. finmarchicus and C. glacialis) were mostly observed at the north shore stations associated with the

  15. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  16. Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean

    PubMed Central

    Suzuki, Shotaro; Omori, Yuko; Wong, Shu-Kuan; Ijichi, Minoru; Kaneko, Ryo; Kameyama, Sohiko; Tanimoto, Hiroshi; Hamasaki, Koji

    2015-01-01

    Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean. PMID:25862229

  17. Parasites alter community structure.

    PubMed

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

    2007-05-29

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

  18. Relative resource abundance explains butterfly biodiversity in island communities

    PubMed Central

    Yamamoto, Naoaki; Yokoyama, Jun; Kawata, Masakado

    2007-01-01

    Ecologists have long been intrigued by the factors that control the pattern of biodiversity, i.e., the distribution and abundance of species. Previous studies have demonstrated that coexisting species partition their resources and/or that the compositional similarity between communities is determined by environmental factors, lending support to the niche-assembly model. However, no attempt has been made to test whether the relative amount of resources that reflects relative niche space controls relative species abundance in communities. Here, we demonstrate that the relative abundance of butterfly species in island communities is significantly related to the relative biomasses of their host plants but not to the geographic distance between communities. In the studied communities, the biomass of particular host plant species positively affected the abundance of the butterfly species that used them, and consequently, influenced the relative abundance of the butterfly communities. This indicated that the niche space of butterflies (i.e., the amount of resources) strongly influences butterfly biodiversity patterns. We present this field evidence of the niche-apportionment model that propose that the relative amount of niche space explains the pattern of the relative abundance of the species in communities. PMID:17553963

  19. Effects of habitat structure on the epifaunal community in Mussismilia corals: does coral morphology influence the richness and abundance of associated crustacean fauna?

    NASA Astrophysics Data System (ADS)

    Nogueira, Marcos M.; Neves, Elizabeth; Johnsson, Rodrigo

    2015-06-01

    Coral habitat structures increase abundance and richness of organisms by providing niches, easy access to resources and refuge from predators. Corals harbor a great variety of animals; the variation in coral species morphology contributes to the heterogeneity and complexity of habitat types. In this report, we studied the richness and abundance of crustaceans (Decapoda, Copepoda, Peracarida and Ostracoda) associated with three species of Mussismilia exhibiting different growth morphologies, in two different coral reefs of the Bahia state (Caramuanas and Boipeba-Moreré, Brazil). Mussismilia hispida is a massive coral; M. braziliensis also has a massive growth pattern, but forms a crevice in the basal area of the corallum; M. harttii has a meandroid pattern. PERMANOVA analysis suggests significant differences in associated fauna richness among Mussismilia species, with higher values for M. harttii, followed by M. braziliensis and later by M. hispida. The same trend was observed for density, except that the comparison of M. braziliensis and M. hispida did not show differences. Redundancy and canonical correspondence analysis indicated that almost all of the crustacean species were more associated with the M. harttii colonies that formed a group clearly separated from colonies of M. braziliensis and M. hispida. We also found that the internal volume of interpolyp space, only present in M. harttii, was the most important factor influencing richness and abundance of all analyzed orders of crustaceans.

  20. Abundance and functional diversity of riboswitches in microbial communities

    PubMed Central

    Kazanov, Marat D; Vitreschak, Alexey G; Gelfand, Mikhail S

    2007-01-01

    Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. Results Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198). Conclusion This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes. PMID:17908319

  1. Changes in Arbuscular Mycorrhizal Fungal Abundance and Community Structure in Response to the Long-Term Manipulation of Inorganic Nutrients in a Lowland Tropical Forest

    NASA Astrophysics Data System (ADS)

    Sheldrake, Merlin; Rosenstock, Nicholas; Tanner, Ed

    2014-05-01

    The arbuscular mycorrhizal (AM) symbiosis is considered primarily mutualistic. In exchange for up to 30% of plants' total photosynthate, AM provide improved access to mineral nutrients. While there is evidence that AM fungi provide nitrogen, potassium and other nutrients to their host plants, most research has focused on their effect on plant phosphorus uptake. Pot experiments have shown, and field experiments have provided further support, that nutrient availability (primarily P, but also N) is inversely correlated with mycorrhizal colonization, indicating plant control over carbon losses to AM fungi. Yet pot experiments have also shown that some fungal species are more mutualistic than others and that AM colonization may cause decreased plant growth, suggesting that plant control is not absolute. AMF communities are diverse, and it is poorly understood how factors such as adaptation to local soil environment, fungal-plant compatibility, and plant nutrient status combine to shape AMF community structure. We conducted a study to examine the relative effects of N, P, and K addition on the AMF community in a plant species rich tropical forest, given the long-held belief that AMF are primarily involved in plant P uptake, particularly on weathered tropical soils. Our study site is the Barro Colorado Nature Monument in Panama. It is a 13 year-old factorial N, P, and K addition experiment (40 m x 40m plots; n=4) in an AMF dominated, old (>200 yr), secondary, tropical forest. Previous research has shown co-limitation by N, P, and K, but the strongest plant growth responses were obtained with K additions. We analyzed the AMF community using 454 pyrosequencing of the ribosomal small subunit (SSU) on both soils and the roots of the 6 dominant AMF tree species. Additionally, we used the AMF-specific neutral lipid fatty acid (NLFA) biomarker as a measure of AMF biomass. Both AMF biomass and community structure were altered by nutrient additions. AMF biomass in soil was reduced

  2. Abundance Inequality in Freshwater Communities Has an Ecological Origin.

    PubMed

    Passy, Sophia I

    2016-04-01

    The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)-showing that abundance is unevenly distributed among species-are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the balance between reproduction and immigration, as the ultimate source and species stress tolerance as a proximate factor. Thus, under harsh conditions, only a few tolerant species can reproduce, while some sensitive species can be present in low numbers due to chance immigration. This would lead to high abundance inequality between the two groups of species. Under benign conditions, both groups can reproduce and give rise to higher abundance equality. To test these ideas, I examined the variability in the parameters of a Poisson lognormal fit of the SAD and a square root fit of the RAD in diatom and fish communities across US streams. Indeed, as environmental favorability increased, more sensitive forms were able to establish large populations, diminishing the abundance disparity between locally common and rare species. Finally, it was demonstrated that in diatoms, the RAD belonged to the same family of relationships as those of population density with body size and regional distribution. PMID:27028078

  3. Effects of landscape anthropization on mosquito community composition and abundance

    NASA Astrophysics Data System (ADS)

    Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-07-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

  4. Effects of landscape anthropization on mosquito community composition and abundance

    PubMed Central

    Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-01-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

  5. Effects of landscape anthropization on mosquito community composition and abundance.

    PubMed

    Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-01-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

  6. Remembrance of things past: modelling the relationship between species' abundances in living communities and death assemblages.

    PubMed

    Olszewski, Thomas D

    2012-02-23

    Accumulations of dead skeletal material are a valuable archive of past ecological conditions. However, such assemblages are not equivalent to living communities because they mix the remains of multiple generations and are altered by post-mortem processes. The abundance of a species in a death assemblage can be quantitatively modelled by successively integrating the product of an influx time series and a post-mortem loss function (a decay function with a constant half-life). In such a model, temporal mixing increases expected absolute dead abundance relative to average influx as a linear function of half-life and increases variation in absolute dead abundance values as a square-root function of half-life. Because typical abundance distributions of ecological communities are logarithmically distributed, species' differences in preservational half-life would have to be very large to substantially alter species' abundance ranks (i.e. make rare species common or vice-versa). In addition, expected dead abundances increase at a faster rate than their range of variation with increased time averaging, predicting greater consistency in the relative abundance structure of death assemblages than their parent living community. PMID:21653564

  7. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    PubMed

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence. PMID:25772872

  8. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

    PubMed Central

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-01-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  9. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

    PubMed

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-04-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  10. Making the Case for a Positive Approach to Improving Organizational Performance in Higher Education Institutions: The Community College Abundance Model

    ERIC Educational Resources Information Center

    Shults, Christopher

    2008-01-01

    Increasingly hostile and turbulent environments have rendered top-down, problem-focused management structures inadequate for competing in the ever-changing postsecondary knowledge industry. The community college abundance model (CCAM), a strengths-based approach to performance enhancement in community colleges, is presented as a viable…

  11. Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils

    PubMed Central

    Pereira e Silva, Michele C.; Schloter-Hai, Brigitte; Schloter, Michael; van Elsas, Jan Dirk; Salles, Joana Falcão

    2013-01-01

    Background Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. Methodology/Principal Findings In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. Conclusions Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil. PMID:24058578

  12. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

    PubMed Central

    Chisholm, Ryan A.; Pacala, Stephen W.

    2010-01-01

    A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function. PMID:20733073

  13. Integrating macroecological metrics and community taxonomic structure.

    PubMed

    Harte, John; Rominger, Andrew; Zhang, Wenyu

    2015-10-01

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

  14. Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways.

    PubMed

    Dai, Yu; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2015-11-01

    Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant species and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB abundance and structure in plateau soils with different plant species and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB abundance and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant species, the altitude of sampling site, and soil properties. PMID:26142389

  15. From the Cover: Ecological community description using the food web, species abundance, and body size

    NASA Astrophysics Data System (ADS)

    Cohen, Joel E.; Jonsson, Tomas; Carpenter, Stephen R.

    2003-02-01

    Measuring the numerical abundance and average body size of individuals of each species in an ecological community's food web reveals new patterns and illuminates old ones. This approach is illustrated using data from the pelagic community of a small lake: Tuesday Lake, Michigan, United States. Body mass varies almost 12 orders of magnitude. Numerical abundance varies almost 10 orders of magnitude. Biomass abundance (average body mass times numerical abundance) varies only 5 orders of magnitude. A new food web graph, which plots species and trophic links in the plane spanned by body mass and numerical abundance, illustrates the nearly inverse relationship between body mass and numerical abundance, as well as the pattern of energy flow in the community. Species with small average body mass occur low in the food web of Tuesday Lake and are numerically abundant. Larger-bodied species occur higher in the food web and are numerically rarer. Average body size explains more of the variation in numerical abundance than does trophic height. The trivariate description of an ecological community by using the food web, average body sizes, and numerical abundance includes many well studied bivariate and univariate relationships based on subsets of these three variables. We are not aware of any single community for which all of these relationships have been analyzed simultaneously. Our approach demonstrates the connectedness of ecological patterns traditionally treated as independent. Moreover, knowing the food web gives new insight into the disputed form of the allometric relationship between body mass and abundance.

  16. Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries.

    PubMed

    Frost, Carol M; Peralta, Guadalupe; Rand, Tatyana A; Didham, Raphael K; Varsani, Arvind; Tylianakis, Jason M

    2016-01-01

    Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying of insecticide over 20 hectares. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control. PMID:27577948

  17. Effects of understory structure on the abundance, richness and diversity of Collembola (Arthropoda) in southern Brazil.

    PubMed

    Ribeiro-Troian, Vera R; Baldissera, Ronei; Hartz, Sandra M

    2009-01-01

    The purpose of this study was to investigate the effects of different landscape structures on the understory Collembola community. Four different forest physiognomies were compared: Pinus spp. plantation, Eucalyptus spp. plantation, Araucaria angustifolia plantation, and a remaining native Araucaria forest. Three areas containing two sampling units (25 mx2 m each) were selected in each forest physiognomy. Understory Collembola collection was done with a 1x1 m canvas sheet held horizontally below the vegetation, which was beaten with a 1 m long stick, seasonally from September 2003 to August 2004. We evaluated the influence of forest physiognomies on the abundance, richness and diversity of Collembola communities. It was also verified if the habitat structure of each physiognomy was associated with the composition of the Collembola community. A total number of 4,111 individuals were collected belonging to the families Entomobrydae and Tomocerida (Entomobryomorpha), and Sminthuridae (Symphypleona), and divided in 12 morphospecies. Pinus plantation presented the highest richness, abundance and diversity of Collembola and it was associated to diverse understory vegetation. The abundance of Entomobrydae and Sminthuridae was associated to the presence of bushes, while Tomoceridae abundance was associated to the presence of trees. The habitat structure, measured through understory vegetation density and composition, plays an important role on the determination of the structure and composition of the Collembola community. PMID:19618049

  18. Distribution and abundance of octocoral (Octocorallia, alcyonacea) communities at three Southern Islands of Singapore

    NASA Astrophysics Data System (ADS)

    Seah, Jason Zhi Sheng; Yap, Nicholas Wei Liang; Tan, Lik Tong; Goh, Beverly Pi Lee

    2015-06-01

    Studies concerning subtidal octocoral species from Singapore reefs are few. This study documents the diversity and abundance of octocoral communities from fringing reefs at Singapore's Southern Islands, namely, Pulau Semakau, P. Hantu and Kusu Island. Belt transects of 20 m (× 5) were employed to survey the octocoral communities at these reef sites. Morphology and sclerites of a number of collected octocoral samples were compared with paratypes obtained from the Raffles Museum of Biodiversity Research, National University of Singapore, for species identification. A total of 16 morphotypes, belonging to five octocoral genera, including Cladiella, Lobophytum, Nephthea, Sarcophyton and Sinularia, were identified in this study. Statistical analysis revealed octocoral abundance and diversity at Kusu Island reefs were higher than those around P. Hantu and P. Semakau. Conversely, octocoral community structures encountered along P. Semakau and Kusu Island were more similar than those of P. Hantu. The preliminary data presented in this study could serve as the baseline data for long term biomonitoring programs in assessing the state of coral reefs in Singapore.

  19. Effects of shorebird predation and snail abundance on an intertidal mudflat community

    NASA Astrophysics Data System (ADS)

    Cheverie, Anne V.; Hamilton, Diana J.; Coffin, Michael R. S.; Barbeau, Myriam A.

    2014-09-01

    Top-down effects of predation are well documented in a variety of ecological communities, including marine soft-sediment systems. It has been proposed that intertidal mudflats in the upper Bay of Fundy, Canada, which host a large population of foraging shorebirds each summer, may exhibit this community dynamic. Biofilm (consisting mainly of diatoms) forms the base of the mudflat community food web, which is dominated by the amphipod Corophium volutator. To assess the potential for a trophic cascade, we conducted a manipulative field experiment examining individual and combined effects of the shorebird Calidris pusilla, a primary predator of C. volutator, and the eastern mudsnail (Nassarius obsoletus), an intraguild predator, on community structure (including macrofauna and large meiofauna retained by a 250-μm screen). Snails exhibited density-dependent top-down effects, primarily from strong negative interactions with juvenile and adult C. volutator, likely due to interference, consumption and emigration. Medium and high densities of snails reduced chlorophyll a concentration (a measure of diatom abundance), likely through consumption and disturbance of the sediment. When present at higher densities, snails also increased variability in community structure. Shorebirds were less influential in determining community structure. They reduced C. volutator biomass through consumption, but there was no resulting effect on primary production. Top-down effects of snails and birds were cumulative on C. volutator, but did not generate a trophic cascade. We suggest that a combination of omnivory and intraguild predation by shorebirds and snails, coupled with relatively low grazing pressure by C. volutator, prevented transmission of top-down effects.

  20. Nitrate levels modulate the abundance of Paracoccus sp. in a biofilm community.

    PubMed

    Singh, Shantanu; Nerurkar, Anuradha S; Srinandan, C S

    2015-06-01

    Conditions required to enhance a particular species efficient in degradative capabilities is very useful in wastewater treatment processes. Paracoccus sp. is known to efficiently reduce nitrogen oxides (NOx) due to the branched denitrification pathway. Individual-based simulations showed that the relative fitness of Paracoccus sp. to Pseudomonas sp. increased significantly with nitrate levels above 5 mM. Spatial structure of the biofilm showed substantially less nitrite levels in the areas of Paracoccus sp. dominance. The simulation was validated in a laboratory reactor harboring biofilm community by fluorescent in situ hybridization, which showed that increasing nitrate levels enhanced the abundance of Paracoccus sp. Different levels of NOx did not display any significant effect on biofilm formation of Paracoccus sp., unlike several other bacteria. This study shows that the attribute of Paracoccus sp. to tolerate and efficiently reduce NOx is conferring a fitness payoff to the organism at high concentrations of nitrate in a multispecies biofilm community. PMID:25838197

  1. Microbial abundance and community composition influence production performance in a low-temperature petroleum reservoir.

    PubMed

    Li, Guoqiang; Gao, Peike; Wu, Yunqiang; Tian, Huimei; Dai, Xuecheng; Wang, Yansen; Cui, Qingfeng; Zhang, Hongzuo; Pan, Xiaoxuan; Dong, Hanping; Ma, Ting

    2014-05-01

    Enhanced oil recovery using indigenous microorganisms has been successfully applied in the petroleum industry, but the role of microorganisms remains poorly understood. Here, we investigated the relationship between microbial population dynamics and oil production performance during a water flooding process coupled with nutrient injection in a low-temperature petroleum reservoir. Samples were collected monthly over a two-year period. The microbial composition of samples was determined using 16S rRNA gene pyrosequencing and real-time quantitative polymerase chain reaction analyses. Our results indicated that the microbial community structure in each production well microhabitat was dramatically altered during flooding with eutrophic water. As well as an increase in the density of microorganisms, biosurfactant producers, such as Pseudomonas, Alcaligenes, Rhodococcus, and Rhizobium, were detected in abundance. Furthermore, the density of these microorganisms was closely related to the incremental oil production. Oil emulsification and changes in the fluid-production profile were also observed. In addition, we found that microbial community structure was strongly correlated with environmental factors, such as water content and total nitrogen. These results suggest that injected nutrients increase the abundance of microorganisms, particularly biosurfactant producers. These bacteria and their metabolic products subsequently emulsify oil and alter fluid-production profiles to enhance oil recovery. PMID:24730445

  2. Effects of habitat-forming species richness, evenness, identity, and abundance on benthic intertidal community establishment and productivity.

    PubMed

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS. PMID:25313459

  3. Effects of Habitat-Forming Species Richness, Evenness, Identity, and Abundance on Benthic Intertidal Community Establishment and Productivity

    PubMed Central

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS. PMID:25313459

  4. Zooplankton species composition, abundance and biomass on the eastern Bering Sea shelf during summer: The potential role of water-column stability and nutrients in structuring the zooplankton community

    NASA Astrophysics Data System (ADS)

    Coyle, Kenneth O.; Pinchuk, Alexei I.; Eisner, Lisa B.; Napp, Jeffrey M.

    2008-08-01

    The southeastern Bering Sea sustains one of the largest fisheries in the United States, as well as wildlife resources that support valuable tourist and subsistence economies. The fish and wildlife populations in turn are sustained by a food web linking primary producers to apex predators through the zooplankton community. Recent shifts in climate toward warmer conditions may threaten these resources by altering productivity and trophic relationships in the ecosystem on the southeastern Bering Sea shelf. We examined the zooplankton community near the Pribilof Islands and on the middle shelf of the southeastern Bering Sea in summer of 1999 and 2004 to document differences and similarities in species composition, abundance and biomass by region and year. Between August 1999 and August 2004, the summer zooplankton community of the middle shelf shifted from large to small species. Significant declines were observed in the biomass of large scyphozoans ( Chrysaora melanaster), large copepods ( Calanus marshallae), arrow worms ( Sagitta elegans) and euphausiids ( Thysanoessa raschii, T. inermis) between 1999 and 2004. In contrast, significantly higher densities of the small copepods ( Pseudocalanus spp., Oithona similis) and small hydromedusae ( Euphysa flammea) were observed in 2004 relative to 1999. Stomach analyses of young-of-the-year (age 0) pollock ( Theragra chalcogramma) from the middle shelf indicated a dietary shift from large to small copepods in 2004 relative to 1999. The shift in the zooplankton community was accompanied by a 3-fold increase in water-column stability in 2004 relative to 1999, primarily due to warmer water above the thermocline, with a mean temperature of 7.3 °C in 1999 and 12.6 °C in 2004. The elevated water-column stability and warmer conditions may have influenced the zooplankton composition by lowering summer primary production and selecting for species more tolerant of a warm, oligotrophic environment. A time series of temperature from

  5. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.

    PubMed

    Paula, Fabiana S; Rodrigues, Jorge L M; Zhou, Jizhong; Wu, Liyou; Mueller, Rebecca C; Mirza, Babur S; Bohannan, Brendan J M; Nüsslein, Klaus; Deng, Ye; Tiedje, James M; Pellizari, Vivian H

    2014-06-01

    Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale. PMID:24806276

  6. Indirect effects of predators control herbivore richness and abundance in a benthic eelgrass (Zostera marina) mesograzer community.

    PubMed

    Amundrud, Sarah L; Srivastava, Diane S; O'Connor, Mary I

    2015-07-01

    Herbivore communities can be sensitive to changes in predator pressure (top-down effects) and resource availability (bottom-up effects) in a wide range of systems. However, it remains unclear whether such top-down and bottom-up effects reflect direct impacts of predators and/or resources on herbivores, or are indirect, reflecting altered interactions among herbivore species. We quantified direct and indirect effects of bottom-up and top-down processes on an eelgrass (Zostera marina) herbivore assemblage. In a field experiment, we factorially manipulated water column nutrients (with Osmocote(™) slow-release fertilizer) and predation pressure (with predator exclusion cages) and measured the effects on herbivore abundance, richness and beta diversity. We examined likely mechanisms of community responses by statistically exploring the response of individual herbivore species to trophic manipulations. Predators increased herbivore richness and total abundance, in both cases through indirect shifts in community composition. Increases in richness occurred through predator suppression of common gammarid amphipod species (Monocorophium acherusicum and Photis brevipes), permitting the inclusion of rarer gammarid species (Aoroides columbiae and Pontogeneia rostrata). Increased total herbivore abundance reflected increased abundance of a caprellid amphipod species (Caprella sp.), concurrent with declines in the abundance of other common species. Furthermore, predators decreased beta diversity by decreasing variability in Caprella sp. abundance among habitat patches. Osmocote(™) fertilization increased nutrient concentrations locally, but nutrients dissipated to background levels within 3 m of the fertilizer. Nutrient addition weakly affected the herbivore assemblage, not affecting richness and increasing total abundance by increasing one herbivore species (Caprella sp.). Nutrient addition did not affect beta diversity. We demonstrated that assemblage-level effects of

  7. Fuel breaks affect nonnative species abundance in Californian plant communities

    USGS Publications Warehouse

    Merriam, K.E.; Keeley, J.E.; Beyers, J.L.

    2006-01-01

    We evaluated the abundance of nonnative plants on fuel breaks and in adjacent untreated areas to determine if fuel treatments promote the invasion of nonnative plant species. Understanding the relationship between fuel treatments and nonnative plants is becoming increasingly important as federal and state agencies are currently implementing large fuel treatment programs throughout the United States to reduce the threat of wildland fire. Our study included 24 fuel breaks located across the State of California. We found that nonnative plant abundance was over 200% higher on fuel breaks than in adjacent wildland areas. Relative nonnative cover was greater on fuel breaks constructed by bulldozers (28%) than on fuel breaks constructed by other methods (7%). Canopy cover, litter cover, and duff depth also were significantly lower on fuel breaks constructed by bulldozers, and these fuel breaks had significantly more exposed bare ground than other types of fuel breaks. There was a significant decline in relative nonnative cover with increasing distance from the fuel break, particularly in areas that had experienced more numerous fires during the past 50 years, and in areas that had been grazed. These data suggest that fuel breaks could provide establishment sites for nonnative plants, and that nonnatives may invade surrounding areas, especially after disturbances such as fire or grazing. Fuel break construction and maintenance methods that leave some overstory canopy and minimize exposure of bare ground may be less likely to promote nonnative plants. ?? 2006 by the Ecological Society of America.

  8. Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community

    PubMed Central

    Henderson, Peter A.; Magurran, Anne E.

    2014-01-01

    To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change. PMID:25100702

  9. Composition and abundance of small mammal communities in forest fragments and vegetation corridors in Southern Minas Gerais, Brazil.

    PubMed

    Mesquita, Andréa O; Passamani, Marcelo

    2012-09-01

    Habitat fragmentation leads to isolation and reduce habitat areas, in addition to a series of negative effects on natural populations, affecting richness, abundance and distribution of animal species. In such a context, habitat corridors serve as an alternative for connectivity in fragmented landscapes, minimizing the effects of structural isolation of different habitat areas. This study evaluated the richness, composition and abundance of small mammal communities in forest fragments and in the relevant vegetation corridors that connect these fragments, located in Southern Minas Gerais, Southeastern Brazil. Ten sites were sampled (five forest fragments and five vegetation corridors) using the capture-mark-recapture method, from April 2007-March 2008. A total sampling effort of 6 300 trapnights resulted in 656 captures of 249 individuals. Across the 10 sites sampled, 11 small mammal species were recorded. Multidimensional scaling (MDS) ordinations and ANOSIM based on the composition of small mammal communities within the corridor and fragment revealed a qualitative difference between the two environments. Regarding abundance, there was no significant difference between corridors and fragments. In comparing mean values of abundance per species in each environment, only Cerradomys subflavus showed a significant difference, being more abundant in the corridor environment. Results suggest that the presence of several small mammal species in the corridor environment, in relatively high abundances, could indicate corridors use as habitat, though they might also facilitate and/or allow the movement of individuals using different habitat patches (fragments). PMID:23025102

  10. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  11. Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

    PubMed Central

    Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

    2015-01-01

    Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

  12. Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

    PubMed

    Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

    2015-01-01

    Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

  13. Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

    PubMed

    Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

    2015-10-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. PMID:26257304

  14. The activated sludge ecosystem contains a core community of abundant organisms

    PubMed Central

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

  15. Species abundance in a forest community in South China: A case of poisson lognormal distribution

    USGS Publications Warehouse

    Yin, Z.-Y.; Ren, H.; Zhang, Q.-M.; Peng, S.-L.; Guo, Q.-F.; Zhou, G.-Y.

    2005-01-01

    Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m??20 m, 5 m??5 m, and 1 m??1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (?? and ??) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the ?? and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/?? should be an alternative measure of diversity.

  16. Spatial and temporal variation in enterococcal abundance and its relationship to the microbial community in Hawaii beach sand and water.

    PubMed

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn; Yan, Tao

    2013-06-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

  17. Voluntary Associations and Community Structure.

    ERIC Educational Resources Information Center

    Dillman, Don A.; And Others

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

  18. Species abundance distribution and population dynamics in a two-community model of neutral ecology

    NASA Astrophysics Data System (ADS)

    Vallade, M.; Houchmandzadeh, B.

    2006-11-01

    Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

  19. LogCauchy, log-sech and lognormal distributions of species abundances in forest communities

    USGS Publications Warehouse

    Yin, Z.-Y.; Peng, S.-L.; Ren, H.; Guo, Q.; Chen, Z.-H.

    2005-01-01

    Species-abundance (SA) pattern is one of the most fundamental aspects of biological community structure, providing important information regarding species richness, species-area relation and succession. To better describe the SA distribution (SAD) in a community, based on the widely used lognormal (LN) distribution model with exp(-x2) roll-off on Preston's octave scale, this study proposed two additional models, logCauchy (LC) and log-sech (LS), respectively with roll-offs of simple x-2 and e-x. The estimation of the theoretical total number of species in the whole community, S*, including very rare species not yet collected in sample, was derived from the left-truncation of each distribution. We fitted these three models by Levenberg-Marquardt nonlinear regression and measured the model fit to the data using coefficient of determination of regression, parameters' t-test and distribution's Kolmogorov-Smirnov (KS) test. Examining the SA data from six forest communities (five in lower subtropics and one in tropics), we found that: (1) on a log scale, all three models that are bell-shaped and left-truncated statistically adequately fitted the observed SADs, and the LC and LS did better than the LN; (2) from each model and for each community the S* values estimated by the integral and summation methods were almost equal, allowing us to estimate S* using a simple integral formula and to estimate its asymptotic confidence internals by regression of a transformed model containing it; (3) following the order of LC, LS, and LN, the fitted distributions became lower in the peak, less concave in the side, and shorter in the tail, and overall the LC tended to overestimate, the LN tended to underestimate, while the LS was intermediate but slightly tended to underestimate, the observed SADs (particularly the number of common species in the right tail); (4) the six communities had some similar structural properties such as following similar distribution models, having a common

  20. Predators alter community organization of coral reef cryptofauna and reduce abundance of coral mutualists

    NASA Astrophysics Data System (ADS)

    Stier, A. C.; Leray, M.

    2014-03-01

    Coral reefs are the most diverse marine systems in the world, yet our understanding of the processes that maintain such extraordinary diversity remains limited and taxonomically biased toward the most conspicuous species. Cryptofauna that live deeply embedded within the interstitial spaces of coral reefs make up the majority of reef diversity, and many of these species provide important protective services to their coral hosts. However, we know very little about the processes governing the diversity and composition of these less conspicuous but functionally important species. Here, we experimentally quantify the role of predation in driving the community organization of small fishes and decapods that live embedded within Pocillopora eydouxi, a structurally complex, reef-building coral found widely across the Indo-Pacific. We use surveys to describe the natural distribution of predators, and then, factorially manipulate two focal predator species to quantify the independent and combined effects of predator density and identity on P. eydouxi-dwelling cryptofauna. Predators reduced abundance (34 %), species richness (20 %), and modified species composition. Rarefaction revealed that observed reductions in species richness were primarily driven by changes in abundance. Additionally, the two predator species uniquely affected the beta diversity and composition of the prey assemblage. Predators reduced the abundance and modified the composition of a number of mutualist fishes and decapods, whose benefit to the coral is known to be both diversity- and density-dependent. We predict that the density and identity of predators present within P. eydouxi may substantially alter coral performance in the face of an increased frequency and intensity of natural and anthropogenic stressors.

  1. Species-abundance--seed-size patterns within a plant community affected by grazing disturbance.

    PubMed

    Wu, Gao-lin; Shang, Zhan-huan; Zhu, Yuan-jun; Ding, Lu-ming; Wang, Dong

    2015-04-01

    Seed size has been advanced as a key factor that influences the dynamics of plant communities, but there are few empirical or theoretical predictions of how community dynamics progress based on seed size patterns. Information on the abundance of adults, seedlings, soil seed banks, seed rains, and the seed mass of 96 species was collected in alpine meadows of the Qinghai-Tibetan Plateau (China), which had different levels of grazing disturbance. The relationships between seed-mass-abundance patterns for adults, seedlings, the soil seed bank, and seed rain in the plant community were evaluated using regression models. Results showed that grazing levels affected the relationship between seed size and abundance properties of adult species, seedlings, and the soil seed bank, suggesting that there is a shift in seed-size--species-abundance relationships as a response to the grazing gradient. Grazing had no effect on the pattern of seed-size-seed-rain-abundance at four grazing levels. Grazing also had little effect on the pattern of seed-size--species-abundance and pattern of seed-size--soil-seed-bank-abundance in meadows with no grazing, light grazing, and moderate grazing), but there was a significant negative effect in meadows with heavy grazing. Grazing had little effect on the pattern of seed-size--seedling-abundance with no grazing, but had significant negative effects with light, moderate, and heavy grazing, and the |r| values increased with grazing levels. This indicated that increasing grazing pressure enhanced the advantage of smaller-seeded species in terms of the abundances of adult species, seedlings, and soil seed banks, whereas only the light grazing level promoted the seed rain abundance of larger-seeded species in the plant communities. This study suggests that grazing disturbances are favorable for increasing the species abundance for smaller-seeded species but not for the larger-seeded species in an alpine meadow community. Hence, there is a clear

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

    USGS Publications Warehouse

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

    2007-01-01

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

  3. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities.

    PubMed

    Smith, Renee J; Paterson, James S; Sibley, Cally A; Hutson, John L; Mitchell, James G

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  4. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

    PubMed Central

    Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  5. Experimental simulation of pollinator decline causes community-wide reductions in seedling diversity and abundance.

    PubMed

    Lundgren, Rebekka; Totland, Ørjan; Lázaro, Amparo

    2016-06-01

    Pollinator decline can disrupt the mutualistic interactions between plants and pollinators and potentially affect the maintenance of plant populations. However, there is still little knowledge on how changes in pollinator abundance can affect seedling recruitment, which is essential for population persistence. We experimentally simulated a community-wide reduction in pollinator availability during four years to examine its effects on seedling recruitment in 10 perennial herbs in a Norwegian hay meadow. Our experimental reduction in pollinator availability significantly reduced community-wide seedling diversity. Overall seedling abundance was also consistently lower under reduced pollinator availability, although this effect was only significant when the most abundant plant species in the community was excluded from the analysis. Despite an overall negative effect on seedling abundance, the experimental reduction in pollinator availability had contrasting effects on individual plant species. This tended to cause a larger change in seedling species composition in the experimental than in the control plots after the four study years. Our study demonstrates for the first time a direct causal link between reduced pollinator availability and reduced plant diversity and abundance. PMID:27459773

  6. Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils.

    PubMed

    Jung, Jaejoon; Yeom, Jinki; Han, Jiwon; Kim, Jisun; Park, Woojun

    2012-06-01

    The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change. PMID:22752898

  7. Motor abundance and control structure in the golf swing.

    PubMed

    Morrison, A; McGrath, D; Wallace, E S

    2016-04-01

    Variability and control structure are under-represented areas of golf swing research. This study investigated the use of the abundant degrees of freedom in the golf swing of high and intermediate skilled golfers using uncontrolled manifold (UCM) analysis. The variance parallel to (VUCM) and orthogonal to (VOrth) the UCM with respect to the orientation and location of the clubhead were calculated. The higher skilled golfers had proportionally higher values of VUCM than lower skilled players for all measured outcome variables. Motor synergy was found in the control of the orientation of the clubhead and the combined outcome variables but not for clubhead location. Clubhead location variance zeroed-in on impact as has been previously shown, whereas clubhead orientation variance increased near impact. Both skill levels increased their control over the clubhead location leading up to impact, with more control exerted over the clubhead orientation in the early downswing. The results suggest that to achieve higher skill levels in golf may not lie simply in optimal technique, but may lie more in developing control over the abundant degrees of freedom in the body. PMID:26784706

  8. Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.

    PubMed

    Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R

    2016-04-01

    We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O. PMID:26983553

  9. Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System.

    PubMed

    Jin, Di; Zhao, Shengguo; Wang, Pengpeng; Zheng, Nan; Bu, Dengpan; Beckers, Yves; Wang, Jiaqi

    2016-01-01

    Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. PMID:27446045

  10. Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System

    PubMed Central

    Jin, Di; Zhao, Shengguo; Wang, Pengpeng; Zheng, Nan; Bu, Dengpan; Beckers, Yves; Wang, Jiaqi

    2016-01-01

    Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. PMID:27446045

  11. Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

    PubMed

    Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

    2016-05-01

    Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed. PMID:26742616

  12. Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

    2014-01-01

    While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

  13. Megafaunal communities in rapidly warming fjords along the West Antarctic Peninsula: hotspots of abundance and beta diversity.

    PubMed

    Grange, Laura J; Smith, Craig R

    2013-01-01

    Glacio-marine fjords occur widely at high latitudes and have been extensively studied in the Arctic, where heavy meltwater inputs and sedimentation yield low benthic faunal abundance and biodiversity in inner-middle fjords. Fjord benthic ecosystems remain poorly studied in the subpolar Antarctic, including those in extensive fjords along the West Antarctic Peninsula (WAP). Here we test ecosystem predictions from Arctic fjords on three subpolar, glacio-marine fjords along the WAP. With seafloor photographic surveys we evaluate benthic megafaunal abundance, community structure, and species diversity, as well as the abundance of demersal nekton and macroalgal detritus, in soft-sediment basins of Andvord, Flandres and Barilari Bays at depths of 436-725 m. We then contrast these fjord sites with three open shelf stations of similar depths. Contrary to Arctic predictions, WAP fjord basins exhibited 3 to 38-fold greater benthic megafaunal abundance than the open shelf, and local species diversity and trophic complexity remained high from outer to inner fjord basins. Furthermore, WAP fjords contained distinct species composition, substantially contributing to beta and gamma diversity at 400-700 m depths along the WAP. The abundance of demersal nekton and macroalgal detritus was also substantially higher in WAP fjords compared to the open shelf. We conclude that WAP fjords are important hotspots of benthic abundance and biodiversity as a consequence of weak meltwater influences, low sedimentation disturbance, and high, varied food inputs. We postulate that WAP fjords differ markedly from their Arctic counterparts because they are in earlier stages of climate warming, and that rapid warming along the WAP will increase meltwater and sediment inputs, deleteriously impacting these biodiversity hotspots. Because WAP fjords also provide important habitat and foraging areas for Antarctic krill and baleen whales, there is an urgent need to develop better understanding of the

  14. Megafaunal Communities in Rapidly Warming Fjords along the West Antarctic Peninsula: Hotspots of Abundance and Beta Diversity

    PubMed Central

    Grange, Laura J.; Smith, Craig R.

    2013-01-01

    Glacio-marine fjords occur widely at high latitudes and have been extensively studied in the Arctic, where heavy meltwater inputs and sedimentation yield low benthic faunal abundance and biodiversity in inner-middle fjords. Fjord benthic ecosystems remain poorly studied in the subpolar Antarctic, including those in extensive fjords along the West Antarctic Peninsula (WAP). Here we test ecosystem predictions from Arctic fjords on three subpolar, glacio-marine fjords along the WAP. With seafloor photographic surveys we evaluate benthic megafaunal abundance, community structure, and species diversity, as well as the abundance of demersal nekton and macroalgal detritus, in soft-sediment basins of Andvord, Flandres and Barilari Bays at depths of 436–725 m. We then contrast these fjord sites with three open shelf stations of similar depths. Contrary to Arctic predictions, WAP fjord basins exhibited 3 to 38-fold greater benthic megafaunal abundance than the open shelf, and local species diversity and trophic complexity remained high from outer to inner fjord basins. Furthermore, WAP fjords contained distinct species composition, substantially contributing to beta and gamma diversity at 400–700 m depths along the WAP. The abundance of demersal nekton and macroalgal detritus was also substantially higher in WAP fjords compared to the open shelf. We conclude that WAP fjords are important hotspots of benthic abundance and biodiversity as a consequence of weak meltwater influences, low sedimentation disturbance, and high, varied food inputs. We postulate that WAP fjords differ markedly from their Arctic counterparts because they are in earlier stages of climate warming, and that rapid warming along the WAP will increase meltwater and sediment inputs, deleteriously impacting these biodiversity hotspots. Because WAP fjords also provide important habitat and foraging areas for Antarctic krill and baleen whales, there is an urgent need to develop better understanding of the

  15. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    PubMed

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  16. The rainy season increases the abundance and richness of the aquatic insect community in a Neotropical reservoir.

    PubMed

    Santana, H S; Silva, L C F; Pereira, C L; Simião-Ferreira, J; Angelini, R

    2015-01-01

    Alterations in aquatic systems and changes in water levels, whether due to rains or dam-mediated control can cause changes in community structure, forcing the community to readjust to the new environment. This study tested the hypothesis that there is an increase in the richness and abundance of aquatic insects during the rainy season in the Serra da Mesa Reservoir, with the premise that increasing the reservoir level provides greater external material input and habitat diversity, and, therefore, conditions that promote colonization by more species. We used the paired t test to test the differences in richness, beta diversity, and abundance, and a Non-metric Multidimensional Scaling (NMDS) was performed to identify patterns in the community under study. Additionally, Pearson correlations were analyzed between the richness, abundance, and beta diversity and the level of the reservoir. We collected 35,028 aquatic insect larvae (9,513 in dry period and 25,515 in the rainy season), predominantly of the Chironomidae family, followed by orders Ephemeroptera, Trichoptera, and Odonata. Among the 33 families collected, only 12 occurred in the dry season, while all occurred in the rainy season. These families are common in lentic environments, and the dominance of Chironomidae was associated with its fast colonization, their behavior of living at high densities and the great tolerance to low levels of oxygen in the environment. The hypothesis was confirmed, as the richness, beta diversity, and abundance were positively affected by the increase in water levels due to the rainy season, which most likely led to greater external material input, greater heterogeneity of habitat, and better conditions for colonization by several families. PMID:25945631

  17. Effects of subinhibitory ciprofloxacin concentrations on the abundance of qnrS and composition of bacterial communities from water supply reservoirs.

    PubMed

    Marti, Elisabet; Huerta, Belinda; Rodríguez-Mozaz, Sara; Barceló, Damià; Balcázar, Jose Luis; Marcé, Rafael

    2016-10-01

    We used a short-term microcosm approach to investigate the influence of two different subinhibitory concentrations of ciprofloxacin (0.01 and 0.1 μg/ml) on both the abundance of a plasmid-mediated quinolone resistance determinant (qnrS) and the structure and composition of bacterial communities from impaired and pristine water supply reservoirs. The results showed that the abundance of the qnrS gene increases in water samples exposed to both subinhibitory concentrations of ciprofloxacin, especially in water samples from La Llosa del Cavall, which represents the pristine system. Subinhibitory ciprofloxacin concentrations also induced changes in bacterial community composition as indicated by the relative abundances of each operational taxonomic unit (OTU) across treatments. Therefore, our findings may be of significant importance because subinhibitory ciprofloxacin concentrations may promote antibiotic resistance and affect bacterial community composition in environmental settings. PMID:27459158

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

    NASA Astrophysics Data System (ADS)

    Lu, Hu; Wei, Hui

    2012-12-01

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

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

    PubMed

    Chertoprud, M V

    2007-01-01

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

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

    PubMed

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

    2005-05-01

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

  1. Abundance, diversity and community characterization of aquatic Coleoptera in a rice field of Northeastern Argentina.

    PubMed

    Gómez Lutz, María Constanza; Kehr, Arturo I; Fernández, Liliana A

    2015-09-01

    Rice fields occupy large areas in Northeastern Argentina, and in Corrientes this widespead activity has become a feature in the landscape, as it is one of the main producing provinces. The aquatic Coleoptera is part of the fauna inhabiting these artificial environments but little is known about this group in irrigated rice fields. The aims of this study were to determine the diversity and species richness of coleopterans in a typical rice field, and to characterize the community of water beetles through different abundance models. For this, samples were collected from an active rice field located in "El Sombrero" town, in Corrientes Province, between November 2011 and April 2012. An entomological net of 30 cm diameter was used, and species richness, diversity and equitability were calculated monthly; besides, the community composition was characterized by means of rank-abundance models. A total of 74 species of aquatic coleopterans were identified. January and February resulted the months with the highest diversity. The aquatic Coleoptera species found in most of the sampled months were adjusted to the logarithmic rank-abundance model. The data suggests that, if it is properly managed, rice cropping in Northeastern Argentina can support a diverse aquatic coleopteran fauna. PMID:26666120

  2. Change in Fish Community Structure in the Barents Sea

    PubMed Central

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

    2013-01-01

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

  3. Ecological niche structure and rangewide abundance patterns of species

    PubMed Central

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

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

    PubMed Central

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

    1994-01-01

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

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

    USGS Publications Warehouse

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

    1994-01-01

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

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

    PubMed

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

    1994-10-11

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

  7. Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

    PubMed Central

    Liu, Xing; Zhang, Junlian; Gu, Tianyu; Zhang, Wenming; Shen, Qirong; Yin, Shixue; Qiu, Huizhen

    2014-01-01

    Background Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Methodology/Principal Findings Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (HShannon) and richness (SChao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Conclusions Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait

  8. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area.

    PubMed

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area. PMID:26902649

  9. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

    PubMed Central

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area. PMID:26902649

  10. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

    PubMed

    Qiu, Yu-Qing; Tian, Xue; Zhang, Shihua

    2015-01-01

    Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes. PMID:26451823

  11. Temporal variations in the abundance and composition of biofilm communities colonizing drinking water distribution pipes.

    PubMed

    Kelly, John J; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

    2014-01-01

    Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter. PMID:24858562

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

    PubMed Central

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

    2014-01-01

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

  13. Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes

    PubMed Central

    Kelly, John J.; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

    2014-01-01

    Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter. PMID:24858562

  14. Discovering Network Structure Beyond Communities

    PubMed Central

    Nishikawa, Takashi; Motter, Adilson E.

    2011-01-01

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

  15. Forest Structure and Roe Deer Abundance Predict Tick-Borne Encephalitis Risk in Italy

    PubMed Central

    Rizzoli, Annapaola; Hauffe, Heidi C.; Tagliapietra, Valentina; Neteler, Markus; Rosà, Roberto

    2009-01-01

    Background The Western Tick-borne encephalitis (TBE) virus often causes devastating or lethal disease. In Europe, the number of human TBE cases has increased dramatically over the last decade, risk areas are expanding and new foci are being discovered every year. The early localisation of new TBE foci and the identification of the main risk factors associated with disease emergence represent a priority for the public health community. Although a number of socio-economic parameters have been suggested to explain TBE upsurges in eastern Europe, the principal driving factors in relatively stable western European countries have not been identified. Methodology/Principal Findings In this paper, we analyse the correlation between the upsurge of TBE in 17 alpine provinces in northern Italy from 1992 to 2006 with climatic variables, forest structure (as a proxy for small mammal reservoir host abundance), and abundance of the principal large vertebrate tick host (roe deer), using datasets available for the last 40 years. No significant differences between the pattern of changes in climatic variables in provinces where TBE has emerged compared to provinces were no clinical TBE cases have been observed to date. Instead, the best model for explaining the increase in TBE incidence in humans in this area include changes in forest structure, in particular the ratio of coppice to high stand forest, and the density of roe deer. Conclusion/Significance Substantial changes in vegetation structure that improve habitat suitability for the main TBE reservoir hosts (small mammals), as well as an increase in roe deer abundance due to changes in land and wildlife management practices, are likely to be among the most crucial factors affecting the circulation potential of Western TBE virus and, consequently, the risk of TBE emergence in humans in western Europe. We believe our approach will be useful in predicting TBE risk on a wider scale. PMID:19183811

  16. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities

    SciTech Connect

    Podar, Mircea; Abulencia, Carl; Walcher, Marion; Hutchinson, Don; Zengler, Karsten; Garcia, Joseph; Holland, Trevin; Cotton, Dave; Hauser, Loren John; Keller, Martin

    2007-01-01

    Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.

  17. Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas.

    PubMed

    Yang, Yuyin; Wang, Jie; Liao, Jingqiu; Xie, Shuguang; Huang, Yi

    2015-02-01

    Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems. PMID:25236802

  18. Protozoan community structure in a fractal soil environment.

    PubMed

    Finlay, B J; Fenchel, T

    2001-09-01

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

  19. Significant Scales in Community Structure

    PubMed Central

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

    2013-01-01

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

  20. Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR.

    PubMed

    Stokell, Joshua R; Hamp, Timothy J; Steck, Todd R

    2016-08-01

    Changes in the composition of microbial communities are often examined using high-throughput sequencing (HTS). Here we analyzed bar-coded Illumina sequencing data from a previous work describing the microbial community found in the sputum of a cystic fibrosis patient by itself or in combination with qPCR to measure the absolute abundance of Pseudomonas aeruginosa and Burkholderia multivorans. Through this comparison we were able to determine the computational analysis accuracy of sequencing data to measure the relative abundance of specific taxa. While no correlation was found between relative abundance and absolute abundance of P. aeruginosa or B. multivorans, we did find conclusions derived from HTS data alone differed from those derived from a combination of HTS and qPCR. Our results highlight the importance of using qPCR with HTS when characterizing organisms in microbial communities having a dominant taxon. PMID:27160743

  1. Community- Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance

    PubMed Central

    Jeltsch, Florian; Wurst, Susanne

    2015-01-01

    Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root

  2. Community-Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance.

    PubMed

    Sonnemann, Ilja; Pfestorf, Hans; Jeltsch, Florian; Wurst, Susanne

    2015-01-01

    Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root

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

    PubMed

    Mouritsen, K N; Poulin, R

    2002-01-01

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

  4. Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

    PubMed

    Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

    2013-09-01

    Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for

  5. [Diversity and abundance of mollusks in the sublittoral epifaunal community of Punta Patilla, Venezuela].

    PubMed

    Prieto, Antulio; Ruiz, Lilia J; García, Natividad

    2005-01-01

    The diversity of a sublittoral epifaunal mollusk community of Punta Patilla, Sucre State, Venezuela, was studied from September 1990 to September 1991. We identified 25 species (14 bivalves and 11 gastropods) of mollusks that inhabit gravel, soft sand and bottoms covered by Thalassia testudinum. Total diversity indices were H' = 3.42. J' = 0.74 and 1-D = 0.85. Monthly diversity reached its maximum in March 1991 (3.12 bits/ ind.), June 1991 (2.88 bits/ind.) and September 1991 (2.95 bits/ind.); minimum diversity was recorded in August 1991 (1.20 bits/ind.). A log series model showed a diversity index alpha = 4.56 for species abundance data and alpha = 3.11 for biomass data. The more abundant species were Chione cancellata, Anigona listeri, Chione granulata and Area zebra among the bivalves, and Chicoreus brevifrons, Turritella variegata and Phllonotus pomum among the gastropods (which present maximum biomass). The average total biomass (56.80 g/m2) is low when compared to reports from other tropical zones. PMID:17354426

  6. The plankton community in Norwegian coastal waters—abundance, composition, spatial distribution and diel variation

    NASA Astrophysics Data System (ADS)

    Bratbak, Gunnar; Jacquet, Stéphan; Larsen, Aud; Pettersson, Lasse H.; Sazhin, Andrey F.; Thyrhaug, Runar

    2011-09-01

    The purpose of the present study was to explore the composition and variation of the pico-, nano- and micro-plankton communities in Norwegian coastal waters and Skagerrak, and the co-occurrence of bacteria and viruses. Samples were collected along three cruise transects from Jæren, Lista and Oksøy on the south coast of Norway and into the North Sea and Skagerrak. We also followed a drifting buoy for 55 h in Skagerrak in order to observe diel variations. Satellite ocean color images (SeaWiFS) of the chlorophyll a (chl a) distribution compared favorably to in situ measurements in open waters, while closer to the shore remote sensing chl a data was overestimated compared to the in situ data. Using light microscopy, we identified 49 micro- and 15 nanoplankton sized phototrophic forms as well as 40 micro- and 12 nanoplankton sized heterotrophic forms. The only picoeukaryote (0.2-2.0 μm) we identified was Resultor micron (Pedinophyceae ). Along the transects a significant variation in the distribution and abundance of different plankton forms were observed, with Synechococcus spp and autotrophic picoeukaryotes as the most notable examples. There was no correlation between viruses and chl a, but between viruses and bacteria, and between viruses and some of the phytoplankton groups, especially the picoeukaryotes. Moreover, there was a negative correlation between nutrients and small viruses (Low Fluorescent Viruses) but a positive correlation between nutrients and large viruses (High Fluorescent Viruses). The abundance of autotrophic picoplankton, bacteria and viruses showed a diel variation in surface waters with higher values around noon and late at night and lower values in the evening. Synechococcus spp were found at 20 m depth 25-45 nautical miles from shore apparently forming a bloom that stretched out for more than 100 nautical miles from Skagerrak and up the south west coast of Norway. The different methods used for assessing abundance, distribution and

  7. Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions

    USGS Publications Warehouse

    Angermeier, Paul L.; Smogor, Roy A.

    1995-01-01

    We sampled fishes and measured microhabitat in series of contiguous habitat units (riffles, runs, pools) in three Virginia streams. We used Monte Carlo simulations to construct hypothetical series of habitat units, then examined how number of species, similarity in relative abundances, and number of microhabitats accumulated with increasing number of habitat units (i.e., sampling effort). Proportions of all species and microhabitats represented were relatively low and variable at low sampling effort, but increased asymptotically and became less variable with greater sampling effort. To facilitate comparisons among streams, we fitted simulation results to negative exponential curves. The curves indicated that 90% of the species present were usually found by sampling 5 to 14 habitat units (stream length of 22–67 stream widths). Estimates of species relative abundances required less sampling effort for a given accuracy than estimates of number of species. Rates of species accumulation (with effort) varied among streams and reflected discontinuity in species distributions among habitat units. Most discontinuity seemed to be due to low population density rather than to habitat selectivity. Results from an Illinois stream corroborated our findings from Virginia, and suggested that greater sampling effort is needed to characterize fish community structure in more homogeneous stream reaches.

  8. Spatiotemporal Changes in the Structure and Composition of a Less-Abundant Bacterial Phylum (Planctomycetes) in Two Perialpine Lakes ▿ †

    PubMed Central

    Pollet, Thomas; Tadonléké, Rémy D.; Humbert, Jean François

    2011-01-01

    We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of “abundant or core” and “rare” bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column. PMID:21602381

  9. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  10. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.

  11. Cell abundance and microbial community composition along a complete oil sand mining and reclamation process

    NASA Astrophysics Data System (ADS)

    Lappé, M.; Schneider, B.; Kallmeyer, J.

    2012-12-01

    (~0.37 mmol/L), whereas in the MFTs nitrate concentrations are much lower (~0.04 mmol/L). In some MFT samples sulphate appears to be the most abundant electron acceptor (up to 94 mmol/L) but no hydrogen sulphide could be detected. High cell counts in root-bearing layers might be related to a supply with otherwise unavailable nutrients, especially phosphorus. Another plausible explanation is that the cells are brought in the sand with the peat-mineral mix, because it seems that the mix contains a significant amount of roots. Samples with low amounts or no roots showed lower cell abundances. Sand and MFTs also differ in the microbial community composition. Molecular analysis of bacterial isolates of samples with different oil content show that β-Proteobacteria dominate the cultivable bacterial population in substrates with a high residual content of oil, whereas in the low oil content sand they play a minor role. The data of corresponding metagenomic analyses confirm these results. In MFTs β-Proteobacteria make up about 80% of the total bacterial population. The surprisingly stable cell abundance indicates that microbial processes take place throughout the entire production process. Rising cell numbers in root-bearing horizons show that a plant cover fosters microbial abundance and diversity, helping to restore full ecosystem functionality.

  12. Simple probabilistic algorithm for detecting community structure

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  13. Community Structure in Directed Networks

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  14. Diatom community structure on in-service cruise ship hulls.

    PubMed

    Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

    2014-10-01

    Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm. PMID

  15. Community structure in the phonological network

    PubMed Central

    Siew, Cynthia S. Q.

    2013-01-01

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

  16. Linking DNRA community structure and activity in a shallow lagoonal estuarine system

    PubMed Central

    Song, Bongkeun; Lisa, Jessica A.; Tobias, Craig R.

    2014-01-01

    Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between the structure and activity of DNRA communities has yet to be discovered. We examined the composition, diversity, abundance, and activities of DNRA communities at five sites along a salinity gradient in the New River Estuary, North Carolina, USA, a shallow temporal/lagoonal estuarine system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates, while the abundance of DNRA communities was calculated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, commonly found in DNRA bacteria. A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine the diversity and composition of DNRA communities within the estuarine sediment community. We found higher levels of nrfA gene abundance and DNRA activities in sediments with higher percent organic content. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the salinity gradient of the New River Estuary. Percent abundance of dominant populations was found to have significant influence on overall activities of DNRA communities. Abundance of dominant DNRA bacteria and organic carbon availability are important regulators of DNRA activities in the eutrophic New River Estuary. PMID:25232351

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

    PubMed

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

    2013-06-01

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

  18. A global perspective on marine photosynthetic picoeukaryote community structure

    PubMed Central

    Kirkham, Amy R; Lepère, Cécile; Jardillier, Ludwig E; Not, Fabrice; Bouman, Heather; Mead, Andrew; Scanlan, David J

    2013-01-01

    A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change. PMID:23364354

  19. Social significance of community structure: Statistical view

    NASA Astrophysics Data System (ADS)

    Li, Hui-Jia; Daniels, Jasmine J.

    2015-01-01

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

  20. Social significance of community structure: statistical view.

    PubMed

    Li, Hui-Jia; Daniels, Jasmine J

    2015-01-01

    Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a framework to analyze the significance of a social community. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of the nodes and their corresponding leaders. Then, using a log-likelihood score, the tightness of the community can be derived. Based on the distribution of community tightness, we establish a connection between p-value theory and network analysis, and then we obtain a significance measure of statistical form . Finally, the framework is applied to both benchmark networks and real social networks. Experimental results show that our work can be used in many fields, such as determining the optimal number of communities, analyzing the social significance of a given community, comparing the performance among various algorithms, etc. PMID:25679651

  1. Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods.

    PubMed

    Burbrink, Frank T; McKelvy, Alexander D; Pyron, R Alexander; Myers, Edward A

    2015-11-22

    Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities. PMID:26609083

  2. RANGELAND COMMUNITIES: STRUCTURE, FUNCTION, AND CLASSIFICATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  4. Structurally Resolved Abundances and Depletions in the Rho OPH Cloud

    NASA Astrophysics Data System (ADS)

    Seab, C.

    1995-07-01

    The mechanism that determines the pattern of depletion ofelements in the interstellar medium has been a problem for along time. It is clear that some of the most refractoryelements such as Si, Fe, and Mg, are heavily depleted onto theinterstellar grains. On the other hand, some elements such asS and Zn are normally either undepleted or very lightlydepleted. The difference between the two cases is notunderstood. We propose to address this question with adetailed study of the depletion patterns in the Rho Ophiuchicloud. This study is strongly based on a combination of thecapabilities of two modern instruments: the GHRS for high-resolution UV data, and the Ultra High Resolution Facility(UHRF) of the AAT. This instrument has been used to obtain NaI line profiles in the Rho Oph cloud with a resolution ofR=1,000,000. The combination of these two types of data willbe used to resolve the velocity structure of the elementdepletions in the cloud.

  5. Relating methanogen community structure and anaerobic digester function.

    PubMed

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

    2015-03-01

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

  6. Physical and biological control of protistan community composition, distribution and abundance in the seasonal ice zone of the Southern Ocean between 30 and 80°E

    NASA Astrophysics Data System (ADS)

    Davidson, Andrew T.; Scott, Fiona J.; Nash, Geraldine V.; Wright, Simon W.; Raymond, Ben

    2010-05-01

    trophic structure and function of the microbial community was frequently typical of nanoflagellate-dominated systems in high-nutrient low-chlorophyll waters. Nanoflagellate abundances were low during the survey and were either poorly resolved by our study or limited by microheterotrophic grazing. We propose that protistan abundance and composition in the sea-ice zone of the Indian Sector were determined by synoptic-scale oceanographic features, meso-scale changes caused by sea-ice retreat and meso- to nano- scale interactions between grazers and the composition and abundance of their protistan prey.

  7. Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments.

    PubMed

    Besaury, Ludovic; Ghiglione, Jean-François; Quillet, Laurent

    2014-04-01

    We analyzed the impact of copper mine tailing discharges on benthic Archaea and Bacteria around the city of Chanaral in northern Chile. Quantitative PCR (Q-PCR) showed that the bacteria dominated the prokaryotic community at both sites, but only the bacteria showed a decrease in abundance in the copper-contaminated site. Q-PCR on reverse transcripts indicated a higher activity of both bacterial and archaeal communities in the contaminated site, suggesting an adaptation of the two communities to copper. This hypothesis was reinforced by the concomitant augmentation of the copper-resistant copA gene coding for a P-type ATP-ase pump in the contaminated site. The metabolically active bacterial community of the contaminated site was dominated by Gammaproteobacteria related to Ectothiorhodospiraceae and Chromatiaceae and by Alphaproteobacteria phylum related to Rhodobacteraceae. The metabolically active archaeal community was dominated by one lineage belonging to unclassified Euryarchaeota and to methanogenic Archaea. PMID:24072336

  8. Experimental Manipulation of Soil Moisture Regime Impacts Soil Microbial Community Abundance, Diversity, and Function in a Semi-Arid Sagebrush Steppe

    NASA Astrophysics Data System (ADS)

    Sorensen, P. O.; Feris, K. P.; Germino, M. J.

    2010-12-01

    Rising global temperatures are predicted to alter regional climate regimes, including the spatial and temporal distribution of precipitation. In water-limited (e.g. arid and semi-arid) ecosystems annual precipitation is low and shows a high degree of variability. In these environments, soil microbes occupy a pivotal seat coupling the effects of water availability and plant productivity to biogeochemical cycling and ecosystem function. Using a long running ecological field experiment (>15 years) sited in Idaho’s sagebrush steppe, effects of experimentally manipulated precipitation regime on microbial diversity, abundance, and terrestrial carbon cycling are being explored. Soils were sampled in January (winter) of 2009. Replicate cores collected at 15-20cm and 95-100cm, were taken from field plots planted with native vegetation under three different precipitation amendments; Ambient, Summer (+200mm in June), or Fall/Spring (+200mm in April or October). Bacterial and Fungal community structure was analyzed by high-resolution 454 pyrosequencing. Edaphic properties (soil moisture, pH, total C, total N, organic C, inorganic N, ortho P) were measured and used as factors for general linear modeling of Bacterial and Fungal community structure against field treatments. Labile soil carbon pools were measured as C mineralization rates by gas chromatography using long term soil incubations. Pyrosequencing analysis of soil Bacterial communities has revealed greater Bacterial community abundance and diversity across all treatments relative to Archaeal and Fungal communities. General linear modeling of sequences obtained from 454 pyrosequencing showed significant interactions of phyla-level Bacterial and Fungal abundance with experimental precipitation regime and depth of sampling. Edaphic properties such as soil moisture and pH also showed significant interactions with phyla-level Bacterial and Fungal abundance. Long-term soil incubation studies revealed treatment effects on

  9. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

    PubMed

    Robertson, Gail S; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  10. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance

    PubMed Central

    Robertson, Gail S.; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  11. Deciphering Network Community Structure by Surprise

    PubMed Central

    Aldecoa, Rodrigo; Marín, Ignacio

    2011-01-01

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

  12. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera

    NASA Astrophysics Data System (ADS)

    Ulrich, Werner

    2005-09-01

    Recent investigations about the relationship between the number of species of taxonomic lineages and regional patterns of species abundances gave indecisive results. Here, it is shown that mean densities of species of a species-rich community of forest Hymenoptera (673 species out of 25 families) were positively related to the number of European species per family. The fraction of abundant species per family declined and the fraction of rare species increased with species richness. Species rich families contained relatively more species, which were present in only one study year (occasional species), and relatively fewer species present during the whole study period (frequent species).

  13. Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

    NASA Astrophysics Data System (ADS)

    Balasooriya, W. K.; Denef, K.; Peters, J.; Verhoest, N. E. C.; Boeckx, P.

    2007-10-01

    Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; textit{Caricetum gracilis} at the wet depression and textit{Arrhenatherum elatioris} at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria was significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

  14. Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

    NASA Astrophysics Data System (ADS)

    Balasooriya, W. K.; Denef, K.; Peters, J.; Verhoest, N. E. C.; Boeckx, P.

    2008-02-01

    Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

  15. Diversity and Abundance of the Bacterial Community of the Red Macroalga Porphyra umbilicalis: Did Bacterial Farmers Produce Macroalgae?

    PubMed Central

    Miranda, Lilibeth N.; Hutchison, Keith; Grossman, Arthur R.; Brawley, Susan H.

    2013-01-01

    Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1) to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2) determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3) to determine how the microbial community associated with a laboratory strain (P.um.1) established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1) were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5–V6 and V8; 147,880 total reads). The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7). The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria) were also abundant. Sphingobacteria (Bacteroidetes) and Flavobacteria (Bacteroidetes) had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes), was abundant. Lewinella (as 66 OTUs) was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had unexpected

  16. Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses

    PubMed Central

    Warshan, Denis; Bay, Guillaume; Nahar, Nurun; Wardle, David A; Nilsson, Marie-Charlotte; Rasmussen, Ulla

    2016-01-01

    Dinitrogen (N2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, Pleurozium schreberi and Hylocomium splendens) represents the main pathway of biological N input into N-depleted boreal forests. Little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of N2-fixation. Using specific nifH primers targeting four major cyanobacterial clusters and quantitative PCR, we investigated how community composition, abundance and nifH expression varied by moss species and over the growing seasons. We evaluated N2-fixation rates across nine forest sites in June and September and explored the abundance and nifH expression of individual cyanobacterial clusters when N2-fixation is highest. Our results showed temporal and host-dependent variations of cyanobacterial community composition, nifH gene abundance and expression. N2-fixation was higher in September than June for both moss species, explained by higher nifH gene expression of individual clusters rather than higher nifH gene abundance or differences in cyanobacterial community composition. In most cases, ‘Stigonema cluster' made up less than 29% of the total cyanobacterial community, but accounted for the majority of nifH gene expression (82–94% of total nifH expression), irrespective of sampling date or moss species. Stepwise multiple regressions showed temporal variations in N2-fixation being greatly explained by variations in nifH expression of the ‘Stigonema cluster'. These results suggest that Stigonema is potentially the most influential N2-fixer in symbiosis with boreal forest feather mosses. PMID:26918665

  17. Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses.

    PubMed

    Warshan, Denis; Bay, Guillaume; Nahar, Nurun; Wardle, David A; Nilsson, Marie-Charlotte; Rasmussen, Ulla

    2016-09-01

    Dinitrogen (N2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, Pleurozium schreberi and Hylocomium splendens) represents the main pathway of biological N input into N-depleted boreal forests. Little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of N2-fixation. Using specific nifH primers targeting four major cyanobacterial clusters and quantitative PCR, we investigated how community composition, abundance and nifH expression varied by moss species and over the growing seasons. We evaluated N2-fixation rates across nine forest sites in June and September and explored the abundance and nifH expression of individual cyanobacterial clusters when N2-fixation is highest. Our results showed temporal and host-dependent variations of cyanobacterial community composition, nifH gene abundance and expression. N2-fixation was higher in September than June for both moss species, explained by higher nifH gene expression of individual clusters rather than higher nifH gene abundance or differences in cyanobacterial community composition. In most cases, 'Stigonema cluster' made up less than 29% of the total cyanobacterial community, but accounted for the majority of nifH gene expression (82-94% of total nifH expression), irrespective of sampling date or moss species. Stepwise multiple regressions showed temporal variations in N2-fixation being greatly explained by variations in nifH expression of the 'Stigonema cluster'. These results suggest that Stigonema is potentially the most influential N2-fixer in symbiosis with boreal forest feather mosses. PMID:26918665

  18. Fine-scale community and genetic structure are tightly linked in species-rich grasslands

    PubMed Central

    Whitlock, Raj; Bilton, Mark C.; Grime, J. Phil; Burke, Terry

    2011-01-01

    Recent evidence indicates that grassland community structure and species diversity are influenced by genetic variation within species. We review what is known regarding the impact of intraspecific diversity on grassland community structure, using an ancient limestone pasture as a focal example. Two genotype-dependent effects appear to modify community structure in this system. First, the abundance of individual constituent species can depend upon the combined influence of direct genetic effects stemming from individuals within the population. Second, the outcome of localized interspecific interactions occurring within the community can depend on the genotypes of participating individuals (indicating indirect genetic effects). Only genotypic interactions are thought to be capable of allowing the long-term coexistence of both genotypes and species. We discuss the implications of these effects for the maintenance of diversity in grasslands. Next, we present new observations indicating that losses of genotypic diversity from each of two species can be predicted by the abundance of other coexisting species within experimental grassland communities. These results suggest genotype-specific responses to abundance in other coexisting species. We conclude that both direct and indirect genetic effects are likely to shape community structure and species coexistence in grasslands, implying tight linkage between fine-scale genetic and community structure. PMID:21444309

  19. Resources Alter the Structure and Increase Stochasticity in Bromeliad Microfauna Communities

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  1. Fingerprints of anomalous primordial Universe on the abundance of large scale structures

    SciTech Connect

    Baghram, Shant; Abolhasani, Ali Akbar; Firouzjahi, Hassan; Namjoo, Mohammad Hossein E-mail: abolhasani@ipm.ir E-mail: MohammadHossein.Namjoo@utdallas.edu

    2014-12-01

    We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that the abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures. Using the quasars data and adopting the power-law scaling k{sup n{sub A}-1} for the amplitude of dipole we find the upper bound n{sub A} < 0.6 for the spectral index of the dipole asymmetry. In all cases there is a critical mass scale M{sub c} in which for M M{sub c}) the enhancement in variance induced from anomalous feature decreases (increases) the abundance of dark matter structures in Universe.

  2. Environmental factors influencing cyanobacteria community structure in Dongping Lake, China.

    PubMed

    Lu, Xuetang; Tian, Chang; Pei, Haiyan; Hu, Wenrong; Xie, Jun

    2013-11-01

    The present study was conducted to provide a detailed understanding of the variation in cyanobacterial communities of Dongping Lake, which is the final water volume adjusting and storing lake in the east route of the South-to-North Water Diversion Project in China. The spatial and temporal distribution of cyanobacteria was assessed from May 2010 to October 2012 based on monthly samples collected from three stations. Over the 30-month survey, 15 genera and 25 species of cyanobacteria were identified, with cyanobacterial abundance at each monitoring station ranging from undetected to 3.04x10(7) cells/L, average of 4.27x10(6) cells/L. The dominant cyanobacterial species were Pseudanabaena limnetica and Aphanizomenon issatschenkoi and not the usual bloom-forming genera such as Microcystis and Anabaena. Cyanobacterial community structure and water quality variables exhibited substantial changes over the period of survey. Redundancy analysis, Pearson correlations, and regression analysis were applied to analyze the relationships among the variables. The results suggested that temperature and chemical oxygen demand were key drivers of the cyanobacterial community composition in Dongping Lake. In addition, the concentration of inorganic nitrogen in the lake had a profound effect on the cyanobacterial abundance as a non-limiting factor in warm periods. PMID:24552047

  3. Centrality measures for networks with community structure

    NASA Astrophysics Data System (ADS)

    Gupta, Naveen; Singh, Anurag; Cherifi, Hocine

    2016-06-01

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

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

    PubMed Central

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

    2014-01-01

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

  5. Environmental Regulation of Microbial Community Structure

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  6. Using counts to simultaneously estimate abundance and detection probabilities in a salamander community

    USGS Publications Warehouse

    Dodd, C.K., Jr.; Dorazio, R.M.

    2004-01-01

    A critical variable in both ecological and conservation field studies is determining how many individuals of a species are present within a defined sampling area. Labor intensive techniques such as capture-mark-recapture and removal sampling may provide estimates of abundance, but there are many logistical constraints to their widespread application. Many studies on terrestrial and aquatic salamanders use counts as an index of abundance, assuming that detection remains constant while sampling. If this constancy is violated, determination of detection probabilities is critical to the accurate estimation of abundance. Recently, a model was developed that provides a statistical approach that allows abundance and detection to be estimated simultaneously from spatially and temporally replicated counts. We adapted this model to estimate these parameters for salamanders sampled over a six vear period in area-constrained plots in Great Smoky Mountains National Park. Estimates of salamander abundance varied among years, but annual changes in abundance did not vary uniformly among species. Except for one species, abundance estimates were not correlated with site covariates (elevation/soil and water pH, conductivity, air and water temperature). The uncertainty in the estimates was so large as to make correlations ineffectual in predicting which covariates might influence abundance. Detection probabilities also varied among species and sometimes among years for the six species examined. We found such a high degree of variation in our counts and in estimates of detection among species, sites, and years as to cast doubt upon the appropriateness of using count data to monitor population trends using a small number of area-constrained survey plots. Still, the model provided reasonable estimates of abundance that could make it useful in estimating population size from count surveys.

  7. Closed benchmarks for network community structure characterization

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2012-02-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-11-01

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

  10. Effects of climate and land-use change on species abundance in a Central European bird community.

    PubMed

    Lemoine, Nicole; Bauer, Hans-Günther; Peintinger, Markus; Böhning-Gaese, Katrin

    2007-04-01

    Although it is known that changes in land use and climate have an impact on ecological communities, it is unclear which of these factors is currently most important. We sought to determine the influence of land-use and climate alteration on changes in the abundance of Central European birds. We examined the impact of these factors by contrasting abundance changes of birds of different breeding habitat, latitudinal distribution, and migratory behavior. We examined data from the semiquantitative Breeding Bird Atlas of Lake Constance, which borders Germany, Switzerland, and Austria. Changes in the regional abundance of the 159 coexisting bird species from 1980-1981 to 2000-2002 were influenced by all three factors. Farmland birds, species with northerly ranges, and long-distance migrants declined, and wetland birds and species with southerly ranges increased in abundance. A separate analysis of the two decades between 1980-1981 and 1990-1992 and between 1990-1992 and 2000-2002 showed that the impact of climate change increased significantly over time. Latitudinal distribution was not significant in the first decade and became the most significant predictor of abundance changes in the second decade. Although the spatial scale and temporal resolution of our study is limited, this is the first study that suggests that climate change has overtaken land-use modification in determining population trends of Central European birds. PMID:17391199

  11. Abundance inhomogeneities and atmospheric structure in CN-bimodal globular cluster giants

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy J.; Plez, Bertrand; Smith, Verne V.

    1993-01-01

    It has been suggested by several authors that the sodium and aluminum abundance variations correlating with CN-band strength, frequently observed in CN-bimodal globular cluster giants, could be spurious manifestations of different temperature structures in the 'CN-strong' and 'CN-weak' stars, caused by different molecular line blanketing related to the C, N, and O trio. For stellar parameters generally appropriate to giants in the intermediate metallicity CN-bimodal cluster M4, we demonstrate through new model atmosphere calculations, employing opacity sampling and spherical geometry, that the observed abundance anomalies cannot be the result of atmospheric temperature structure. Our results using spherical geometry are compared to identical calculations performed with plane-parallel geometry: the effects of atmospheric extension on derived abundances for all lines considered amount to less than 0.1 dex.

  12. Hydrographic structure and zooplankton abundance and diversity off Paita, northern Peru (1994 to 2004) — ENSO effects, trends and changes

    NASA Astrophysics Data System (ADS)

    Aronés, Katia; Ayón, Patricia; Hirche, Hans-Jürgen; Schwamborn, Ralf

    2009-11-01

    The objective of the present study was to verify possible spatial, seasonal, and inter-annual changes in the zooplankton off Paita (northern Peru), an upwelling area located closely to the limits of cold Humboldt Current and warm Equatorial Surface Waters. Zooplankton was sampled at subsurface on 53 occasions from August 1994 to December 2004 at four stations located 2 to 30 km offshore with a WP-2 net (300 µm). Extremely high surface water temperatures combined with low salinities were observed during the 1997/98 El Niño up to 29.0 °C) and in April 2002 (up to 25.0 °C). Temperatures more than 2 °C above monthly average were also observed in October 1994, in April 2000, and in November 2004. Significant trends were observed for oxygen concentration (increase) and several horizontal and vertical gradients. Among the copepods (72% of all individuals), the most abundant species were Paracalanus parvus (28%), Acartia tonsa (26%), and Calanus sp. (10%). The strong 1997-98 El Niño (EN) event led to drastic changes in species composition that were reversed during the 1998-99 La Niña (LN) event. Community parameters such as total abundance, diversity, equitability and species richness displayed marked variations associated with the 1997-98 EN and long-term trends. Long-term trends were significant for several vertical and horizontal temperature and oxygen gradients, indicating an increase in upwelling intensity at the shelf during the study period. 10-year-trends were also significant for total zooplankton abundance (increase) and community evenness ( J, decline). Our data confirmed the importance of the weak EN in 2002/03 for the study region. Within the trend of increasing zooplankton abundance, a sharp step or shift was observed from 1999 to 2000. When using sequential t-tests to detect shifts in ( x + 1) transformed abundance data, a significant rupture was found between the last sampling in 1999 and the first sampling in 2000. Also, a substantial decrease in

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  14. Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure.

    PubMed

    Qian, Xun; Sun, Wei; Gu, Jie; Wang, Xiao-Juan; Sun, Jia-Jun; Yin, Ya-Nan; Duan, Man-Li

    2016-09-01

    Livestock manure is often subjected to aerobic composting but little is known about the variation in antibiotic resistance genes (ARGs) during the composting process under different concentrations of antibiotics. This study compared the effects of three concentrations of oxytetracycline (OTC; 10, 60, and 200mg/kg) on ARGs and the succession of the bacterial community during composting. Very similar trends were observed in the relative abundances (RAs) of each ARG among the OTC treatments and the control during composting. After composting, the RAs of tetC, tetX, sul1, sul2, and intI1 increased 2-43 times, whereas those of tetQ, tetM, and tetW declined by 44-99%. OTC addition significantly increased the absolute abundances and RAs of tetC and intI1, while 200mg/kg OTC also enhanced those of tetM, tetQ, and drfA7. The bacterial community could be grouped according to the composting time under different treatments. The highest concentration of OTC had a more persistent effect on the bacterial community. In the present study, the succession of the bacterial community appeared to have a greater influence on the variation of ARGs during composting than the presence of antibiotics. Aerobic composting was not effective in reducing most of the ARGs, and thus the compost product should be considered as an important reservoir for ARGs. PMID:27179201

  15. Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget?

    PubMed

    Meunier, Antony; Jacquet, Stéphan

    2015-01-01

    Phages are the most abundant and diversified biological entities in aquatic ecosystems. Understanding their functional role requires laboratory experiments on a short time-scale. Using samples of surface waters of Lake Bourget, we studied whether viruses impact (i) the abundance patterns of the bacterial and phytoplankton communities, (ii) a part of the prokaryotic community composition (both for Eubacteria and Archaea), and (iii) the recycling of nutrients and/or organic matter. Three experiments were performed (one each in February, March and April) at the transition between winter and spring in 2013. The experiment reduced or increased the abundance of virus-like particles in samples containing only the picoplanktonic fraction. Viral and cellular abundances, bacterial and archaeal community structures as well as nutrient concentrations were analysed every 24 h for 3 days. Some of the results reveal that increasing the phage abundance increased the diversity of the eubacterial community. Consistent with the 'killing the winner' concept, viruses are thus likely to significantly change the composition of the bacterial community. This suggests a positive association between viral abundance and bacterial diversity. In contrast, the composition of the archaeal community did not seem to be affected by phage abundance, suggesting the absence of viral control on this community or the inability to observe it at this period of year, either based on the time scale of the investigation or because the archaeal virus titre was too low to induce a significant and visible effect. Lastly, we were unable to demonstrate viruses driving the cycling of nutrients or the response of plankton to nutrient concentration changes in a significant way, suggesting that the role of viruses may be subtle or difficult to assess through the use of such experimental procedures. PMID:26500223

  16. Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget?

    PubMed Central

    Meunier, Antony; Jacquet, Stéphan

    2015-01-01

    ABSTRACT Phages are the most abundant and diversified biological entities in aquatic ecosystems. Understanding their functional role requires laboratory experiments on a short time-scale. Using samples of surface waters of Lake Bourget, we studied whether viruses impact (i) the abundance patterns of the bacterial and phytoplankton communities, (ii) a part of the prokaryotic community composition (both for Eubacteria and Archaea), and (iii) the recycling of nutrients and/or organic matter. Three experiments were performed (one each in February, March and April) at the transition between winter and spring in 2013. The experiment reduced or increased the abundance of virus-like particles in samples containing only the picoplanktonic fraction. Viral and cellular abundances, bacterial and archaeal community structures as well as nutrient concentrations were analysed every 24 h for 3 days. Some of the results reveal that increasing the phage abundance increased the diversity of the eubacterial community. Consistent with the ‘killing the winner’ concept, viruses are thus likely to significantly change the composition of the bacterial community. This suggests a positive association between viral abundance and bacterial diversity. In contrast, the composition of the archaeal community did not seem to be affected by phage abundance, suggesting the absence of viral control on this community or the inability to observe it at this period of year, either based on the time scale of the investigation or because the archaeal virus titre was too low to induce a significant and visible effect. Lastly, we were unable to demonstrate viruses driving the cycling of nutrients or the response of plankton to nutrient concentration changes in a significant way, suggesting that the role of viruses may be subtle or difficult to assess through the use of such experimental procedures. PMID:26500223

  17. Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P.M.; Paxton, Eben

    2015-01-01

    Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

  18. School, Community Leadership, and Election Structure

    ERIC Educational Resources Information Center

    Allen, Ann

    2008-01-01

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

  19. Emergence of structured communities through evolutionary dynamics.

    PubMed

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

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. PMID:26231415

  20. Phylogenetic structure in tropical hummingbird communities

    PubMed Central

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

    2009-01-01

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

  1. Phylogenetic structure in tropical hummingbird communities.

    PubMed

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

    2009-11-17

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

  2. The nested structure of a scavenger community

    PubMed Central

    Selva, Nuria; Fortuna, Miguel A

    2007-01-01

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

  3. Distribution and abundance of sea urchins in Singapore reefs and their potential ecological impacts on macroalgae and coral communities

    NASA Astrophysics Data System (ADS)

    Goh, Beverly P. L.; Lim, Dawn Y. F.

    2015-06-01

    The sea urchin Diadema setosum is often encountered in the coral reefs in the Southern Islands of Singapore. While sea urchins have been known to play a role in regulating algal communities and influencing coral recruitment in other parts of the world, their role in Singapore reefs has not been determined. This study was conducted to determine the distribution and abundance of sea urchins in Singapore reefs, to examine algal cover, algal biomass, algal species and live coral cover, and to determine any interactions between urchin density and algal communities that may impact coral cover. Several reefs in Singapore were surveyed using belt transects measuring 20 m by 2 m, laid down on the reef crest. Abundance of urchins, algal species, biomass, and live coral cover were determined by the use of quadrats within each belt transect. This study revealed an increasing abundance of the sea urchin Diadema setosum in reefs progressing southwards away from mainland Singapore with low density of urchins occurring in Sisters' Island, St John's Island, Pulau Tekukor, and Kusu Island, and the highest density observed at Raffles Lighthouse. A significant negative linear relationship between algal cover and live coral cover (P < 0.05) was established. The results of this study indicate that sea urchins may not be an important component of the herbivore guild in Singapore.

  4. Heterogeneity of macrozoobenthic assemblages within a Zostera noltii seagrass bed: diversity, abundance, biomass and structuring factors

    NASA Astrophysics Data System (ADS)

    Blanchet, Hugues; de Montaudouin, Xavier; Lucas, Aurélien; Chardy, Pierre

    2004-09-01

    The macrobenthic fauna community of a 70-km 2Zostera noltii seagrass bed (Arcachon bay, France) was studied by sampling 49 stations systematically. A total of 126 taxa were identified. Cluster Analysis based on χ2 distance showed that in this apparently homogeneous habitat, four distinct macrobenthic communities could be identified. Multiple Discriminant Analysis highlighted the major contribution of the overlying water mass as a forcing variable, and, to a lesser extent, of tidal level and Z. noltii's below-ground parts. Seven stations did not constitute any conspicuous group, and were characterized by a low biomass of leaf (<28 g DW m -2), considered as the lowest value to constitute a Z. noltii community. Less than 24% of the seagrass bed was situated in more oceanic waters and at a quite low tidal level. In this relatively stable environment, the macrofauna community was characterized by a high species richness (mean = 39) and a moderate density and high biomass (12 638 individuals m -2 and 25 g AFDW m -2, respectively). Annelids dominated, particularly the oligochaetes. When physical constraints increased (emersion or brackish water conditions), diversity decreased, abundance and biomass increased. The seagrass bed (55%) was flooded with highly fluctuating waters in term of temperature and salinity, here species richness was low (mean = 27) but abundance and biomass were high (24 384 individuals m -2 and 28 g AFDW m -2, respectively), with a dominance of molluscs. The meadow (7%) was in external waters but at a higher tidal level (2.4 m vs 1.8 m above medium low tide level). This community was characterized by the particularly high density (41 826 individuals m -2) and dominance of oligochaetes (79% of total abundance). Species richness was high (mean = 37) here. A fourth community, extending over 12% of the meadow was dominated by the gastropod Hydrobia ulvae but could not be linked to a specific forcing variable. This study confirmed the almost

  5. Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake.

    PubMed

    Zhao, Da-yong; Luo, Juan; Zeng, Jin; Wang, Meng; Yan, Wen-ming; Huang, Rui; Wu, Qinglong L

    2014-01-01

    Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56 × 10(6) copies to 1.06 × 10(7) copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13 × 10(5) to 3.21 × 10(6) copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems. PMID:23784056

  6. Community structure and dynamics in social systems

    NASA Astrophysics Data System (ADS)

    Wilkinson, Dennis M.

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

  7. Information transfer in community structured multiplex networks

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  8. Scale-dependence of processes structuring dung beetle metacommunities using functional diversity and community deconstruction approaches.

    PubMed

    Silva, Pedro Giovâni da; 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

  9. 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

  10. The structure and function of microbial communities in recirculating hydroponic systems.

    PubMed

    Garland, J L

    1994-11-01

    Strategies to control the microbial community associated with plant growth systems need to be based on a fundamental understanding of the factors which structure and regulate the community. Spatial and temporal patterns in the abundance and production rate of microorganisms in hydroponic systems containing wheat were examined to evaluate how root-derived carbon is processed. The relevance of results to monitoring and control strategies is discussed. PMID:11540209

  11. The structure and function of microbial communities in recirculating hydroponic systems

    NASA Astrophysics Data System (ADS)

    Garland, J. L.

    1994-11-01

    Strategies to control the microbial community associated with plant growth systems need to be based on a fundamental understanding of the factors which structure and regulate the community. Spatial and temporal patterns in the abundance and production rate of microorganisms in hydroponic systems containing wheat were examined to evaluate how root-derived carbon is processed. The relevance of results to monitoring and control strategies is discussed.

  12. Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays

    PubMed Central

    Fierer, Noah; Jackson, Jason A.; Vilgalys, Rytas; Jackson, Robert B.

    2005-01-01

    Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure. PMID:16000830

  13. Benthic infaunal community structuring in an acidified tropical estuarine system

    PubMed Central

    2014-01-01

    Background Recent studies suggest that increasing ocean acidification (OA) should have strong direct and indirect influences on marine invertebrates. While most theory and application for OA is based on relatively physically-stable oceanic ecological systems, less is known about the effects of acidification on nearshore and estuarine systems. Here, we investigated the structuring of a benthic infaunal community in a tropical estuarine system, along a steep salinity and pH gradient, arising largely from acid-sulphate groundwater inflows (Sungai Brunei Estuary, Borneo, July 2011- June 2012). Results Preliminary data indicate that sediment pore-water salinity (range: 8.07 - 29.6 psu) declined towards the mainland in correspondence with the above-sediment estuarine water salinity (range: 3.58 – 31.2 psu), whereas the pore-water pH (range: 6.47- 7.72) was generally lower and less variable than the estuarine water pH (range: 5.78- 8.3), along the estuary. Of the thirty six species (taxa) recorded, the polychaetes Neanthes sp., Onuphis conchylega, Nereididae sp. and the amphipod Corophiidae sp., were numerically dominant. Calcified microcrustaceans (e.g., Cyclopoida sp. and Corophiidae sp.) were abundant at all stations and there was no clear distinction in distribution pattern along the estuarine between calcified and non-calcified groups. Species richness increased seawards, though abundance (density) showed no distinct directional trend. Diversity indices were generally positively correlated (Spearman’s rank correlation) with salinity and pH (p <0.05) and negatively with clay and organic matter, except for evenness values (p >0.05). Three faunistic assemblages were distinguished: (1) nereid-cyclopoid-sabellid, (2) corophiid-capitellid and (3) onuphid- nereid-capitellid. These respectively associated with lower salinity/pH and a muddy bottom, low salinity/pH and a sandy bottom, and high salinity/pH and a sandy bottom. However, CCA suggested that species distribution

  14. Diversity, abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant.

    PubMed

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-09-01

    The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment. PMID:24818690

  15. Identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Chenxi; Duan, Yubing

    2015-07-01

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

  16. Modularity and community structure in networks.

    PubMed

    Newman, M E J

    2006-06-01

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

  17. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    PubMed

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. PMID:24937356

  18. Coronal Thermal Structure and Abundance of Super-Metal-Rich Late-Type Stars

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy; Mushotzky, Richard F. (Technical Monitor)

    2002-01-01

    This report covers the NASA grant NAG5-9943 for Cycle 1 XMM Guest Observer Program. The project is entitled 'Coronal Thermal Structure and Abundances of Super-Metal-Rich Late-Type Stars.' This observation is for grating spectroscopy of 30 Ari, a late-type star with very high metallicity (about twice solar). The goal is to use extreme cases to help understand how abundances change from the photosphere to the corona. The target was obtained by XMM-Newton on 2001 January 16 for 28000 sec. Data processing could not proceed until last fall because the SAS RGS software did not work. A poster was presented at the conference 'New Visions of the X-ray Universe in the XMM-Newton and Chandra Era,' held in Noordwijk 26-30 November 2001. The paper was entitled,'Coronal Abundances and Thermal Structure of the Super-Metal-Rich Star 30 Ari,'. The poster presented analysis of EPIC and RGS data to determine the individual abundances from the star and the emission measure distribution as a function of temperature. Results were compared with previous results on this star by our team using ASCA data.

  19. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes

    PubMed Central

    Yang, Jian; Ma, Li’an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-01-01

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions. PMID:27113678

  20. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    PubMed

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-01-01

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions. PMID:27113678

  1. A cheating limit for structured communities

    SciTech Connect

    Perelson, Alan S; Gerrish, Philip J

    2008-01-01

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

  2. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community

    PubMed Central

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  3. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community.

    PubMed

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  4. Jellyfish modulate bacterial dynamic and community structure.

    PubMed

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

    2012-01-01

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

  5. Jellyfish Modulate Bacterial Dynamic and Community Structure

    PubMed Central

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

    2012-01-01

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

  6. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture.

    PubMed Central

    González, J M; Whitman, W B; Hodson, R E; Moran, M A

    1996-01-01

    Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the alpha-subclass of Proteobacteria, and the other two were in the gamma-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented. PMID:8953714

  7. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity

    PubMed Central

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of

  8. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

    PubMed

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen-fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha

  9. Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers.

    PubMed

    Drury, Bradley; Rosi-Marshall, Emma; Kelly, John J

    2013-03-01

    In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization. PMID:23315724

  10. How does abundance scale with body size in coupled size-structured food webs?

    PubMed

    Blanchard, Julia L; Jennings, Simon; Law, Richard; Castle, Matthew D; McCloghrie, Paul; Rochet, Marie-Joëlle; Benoît, Eric

    2009-01-01

    1. Widely observed macro-ecological patterns in log abundance vs. log body mass of organisms can be explained by simple scaling theory based on food (energy) availability across a spectrum of body sizes. The theory predicts that when food availability falls with body size (as in most aquatic food webs where larger predators eat smaller prey), the scaling between log N vs. log m is steeper than when organisms of different sizes compete for a shared unstructured resource (e.g. autotrophs, herbivores and detritivores; hereafter dubbed 'detritivores'). 2. In real communities, the mix of feeding characteristics gives rise to complex food webs. Such complexities make empirical tests of scaling predictions prone to error if: (i) the data are not disaggregated in accordance with the assumptions of the theory being tested, or (ii) the theory does not account for all of the trophic interactions within and across the communities sampled. 3. We disaggregated whole community data collected in the North Sea into predator and detritivore components and report slopes of log abundance vs. log body mass relationships. Observed slopes for fish and epifaunal predator communities (-1.2 to -2.25) were significantly steeper than those for infaunal detritivore communities (-0.56 to -0.87). 4. We present a model describing the dynamics of coupled size spectra, to explain how coupling of predator and detritivore communities affects the scaling of log N vs. log m. The model captures the trophic interactions and recycling of material that occur in many aquatic ecosystems. 5. Our simulations demonstrate that the biological processes underlying growth and mortality in the two distinct size spectra lead to patterns consistent with data. Slopes of log N vs. log m were steeper and growth rates faster for predators compared to detritivores. Size spectra were truncated when primary production was too low for predators and when detritivores experienced predation pressure. 6. The approach also allows

  11. Taxonomies of networks from community structure

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  12. Taxonomies of networks from community structure

    PubMed Central

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

    2014-01-01

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

  13. Microbial diversity and community structure in an antimony-rich tailings dump.

    PubMed

    Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

    2016-09-01

    To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities. PMID:27188777

  14. Changes in the bacterial community structure in stored wormbed leachate.

    PubMed

    Romero-Tepal, Elda M; Contreras-Blancas, Eduardo; Navarro-Noya, Yendi E; Ruíz-Valdiviezo, Víctor M; Luna-Guido, Marco; Gutiérrez-Miceli, Federico A; Dendooven, Luc

    2014-01-01

    Organic wastes, such as cow manure, are often composted with earthworms (vermicomposting) while excess water is drained and collected. This wormbed leachate is nutrient-rich and it has been extensively used to fertilize plants. However, it is derived partially from a not yet finished compost process and could exhibit phytotoxicity or contain potentially hazardous microorganisms. The bacterial community in wormbed leachate derived from vermicomposting of cow manure was studied by pyrosequencing the 16S rRNA gene. The fresh wormbed leachate was rich in Mollicutes, particularly the genus Acholeplasma which contain phytopathogen species. The abundance of the Mollicutes decreased when the leachate was stored, while that of the Rhizobiales and the genus Pseudomonas increased. The bacterial communities changed rapidly in the leachate during storage. The changes in ammonium, nitrate and inorganic carbon content of the wormbed leachate when stored were correlated to changes in the bacterial community structure. It was found that storage of the wormbed leachate might be required before it can be applied to crops as large proportions of potentially plant pathogens were found in the fresh leachate. PMID:24577291

  15. Abundance and diversity of sedimentary bacterial communities in a coastal productive setting in the Western Irish Sea

    NASA Astrophysics Data System (ADS)

    O'Reilly, S. S.; Pentlavalli, P.; Flanagan, P. V.; Allen, C. C. R.; Monteys, X.; Szpak, M. T.; Murphy, B. T.; Jordan, S. F.; Kelleher, B. P.

    2016-02-01

    The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12-111 m), organic carbon content (0.09-1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal polyunsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclopropyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavobacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.

  16. THE SPATIAL STRUCTURE OF MONO-ABUNDANCE SUB-POPULATIONS OF THE MILKY WAY DISK

    SciTech Connect

    Bovy, Jo; Rix, Hans-Walter; Liu Chao; Hogg, David W.; Beers, Timothy C.; Lee, Young Sun

    2012-07-10

    The spatial, kinematic, and elemental-abundance structure of the Milky Way's stellar disk is complex, and has been difficult to dissect with local spectroscopic or global photometric data. Here, we develop and apply a rigorous density modeling approach for Galactic spectroscopic surveys that enables investigation of the global spatial structure of stellar sub-populations in narrow bins of [{alpha}/Fe] and [Fe/H], using 23,767 G-type dwarfs from SDSS/SEGUE, which effectively sample 5 kpc < R{sub GC} < 12 kpc and 0.3 kpc {approx}< |Z| {approx}< 3 kpc. We fit models for the number density of each such ([{alpha}/Fe] and [Fe/H]) mono-abundance component, properly accounting for the complex spectroscopic SEGUE sampling of the underlying stellar population, as well as for the metallicity and color distributions of the samples. We find that each mono-abundance sub-population has a simple spatial structure that can be described by a single exponential in both the vertical and radial directions, with continuously increasing scale heights ( Almost-Equal-To 200 pc to 1 kpc) and decreasing scale lengths (>4.5 kpc to 2 kpc) for increasingly older sub-populations, as indicated by their lower metallicities and [{alpha}/Fe] enhancements. That the abundance-selected sub-components with the largest scale heights have the shortest scale lengths is in sharp contrast with purely geometric 'thick-thin disk' decompositions. To the extent that [{alpha}/Fe] is an adequate proxy for age, our results directly show that older disk sub-populations are more centrally concentrated, which implies inside-out formation of galactic disks. The fact that the largest scale-height sub-components are most centrally concentrated in the Milky Way is an almost inevitable consequence of explaining the vertical structure of the disk through internal evolution. Whether the simple spatial structure of the mono-abundance sub-components and the striking correlations between age, scale length, and scale height can

  17. Distance from a fishing community explains fish abundance in a no-take zone with weak compliance.

    PubMed

    Advani, Sahir; Rix, Laura N; Aherne, Danielle M; Alwany, Magdy A; Bailey, David M

    2015-01-01

    There are numerous examples of no-take marine reserves effectively conserving fish stocks within their boundaries. However, no-take reserves can be rendered ineffective and turned into 'paper parks' through poor compliance and weak enforcement of reserve regulations. Long-term monitoring is thus essential to assess the effectiveness of marine reserves in meeting conservation and management objectives. This study documents the present state of the 15-year old no-take zone (NTZ) of South El Ghargana within the Nabq Managed Resource Protected Area, South Sinai, Egyptian Red Sea. Previous studies credited willing compliance by the local fishing community for the increased abundances of targeted fish within the designated NTZ boundaries compared to adjacent fished or take-zones. We compared benthic habitat and fish abundance within the NTZ and the adjacent take sites open to fishing, but found no significant effect of the reserve. Instead, the strongest evidence was for a simple negative relationship between fishing pressure and distance from the closest fishing village. The abundance of targeted piscivorous fish increased significantly with increasing distance from the village, while herbivorous fish showed the opposite trend. This gradient was supported by a corresponding negative correlation between the amount of discarded fishing gear observed on the reef and increasing distance from the village. Discarded fishing gear within the NTZ suggested decreased compliance with the no-take regulations. Our findings indicate that due to non-compliance the no-take reserve is no longer functioning effectively, despite its apparent initial successes and instead a gradient of fishing pressure exists with distance from the nearest fishing community. PMID:25950815

  18. Distance from a Fishing Community Explains Fish Abundance in a No-Take Zone with Weak Compliance

    PubMed Central

    Alwany, Magdy A.; Bailey, David M.

    2015-01-01

    There are numerous examples of no-take marine reserves effectively conserving fish stocks within their boundaries. However, no-take reserves can be rendered ineffective and turned into ‘paper parks’ through poor compliance and weak enforcement of reserve regulations. Long-term monitoring is thus essential to assess the effectiveness of marine reserves in meeting conservation and management objectives. This study documents the present state of the 15-year old no-take zone (NTZ) of South El Ghargana within the Nabq Managed Resource Protected Area, South Sinai, Egyptian Red Sea. Previous studies credited willing compliance by the local fishing community for the increased abundances of targeted fish within the designated NTZ boundaries compared to adjacent fished or take-zones. We compared benthic habitat and fish abundance within the NTZ and the adjacent take sites open to fishing, but found no significant effect of the reserve. Instead, the strongest evidence was for a simple negative relationship between fishing pressure and distance from the closest fishing village. The abundance of targeted piscivorous fish increased significantly with increasing distance from the village, while herbivorous fish showed the opposite trend. This gradient was supported by a corresponding negative correlation between the amount of discarded fishing gear observed on the reef and increasing distance from the village. Discarded fishing gear within the NTZ suggested decreased compliance with the no-take regulations. Our findings indicate that due to non-compliance the no-take reserve is no longer functioning effectively, despite its apparent initial successes and instead a gradient of fishing pressure exists with distance from the nearest fishing community. PMID:25950815

  19. Epidemic spreading on complex networks with community structures

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  20. Epidemic spreading on complex networks with community structures

    PubMed Central

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

    2016-01-01

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

  1. Epidemic spreading on complex networks with community structures.

    PubMed

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

    2016-01-01

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

  2. Patterns of spatio-temporal distribution, abundance, and diversity in a mosquito community from the eastern Smoky Hills of Kansas.

    PubMed

    Ganser, Claudia; Wisely, Samantha M

    2013-12-01

    Nearly 30% of emerging infectious disease events are caused by vector-borne pathogens with wildlife origins. Their transmission involves a complex interplay among pathogens, arthropod vectors, the environment and host species, and they pose a risk for public health, livestock and wildlife species. Examining habitat associations of vector species known to transmit infectious diseases, and quantifying spatio-temporal dynamics of mosquito vector communities is one aspect of the holistic One Health approach that is necessary to develop effective control measures. A survey was conducted from May to August, 2010 of the abundance and diversity of mosquito species occurring in the mixed-grass prairie habitat of the Smoky Hills of Kansas. This region is an important breeding ground for North America's grassland nesting birds and, as such, it could represent an important habitat for the enzootic amplification cycle of avian malaria and infectious encephalitides, as well as spill-over events to humans and livestock. A total of 11 species, belonging to the three genera Aedes, Anopheles, and Culex, was collected during this study. Aedes nigromaculis, Ae. sollicitans, Ae. taeniorhynchus, Culex salinarius, and Cx. tarsalis accounted for 98% of the collected species. Multiple linear regression models suggested that mosquito abundances in the grasslands of the central Great Plains were explained by meteorological and environmental variables. Temporal dynamics in mosquito abundances were well supported by models that included maximum and minimum temperature indices (adjusted R(2) = 0.73). Spatial dynamics of mosquito abundances were best explained by a model containing the following environmental variables (adjusted R(2) =0.37): ground curvature, topographic wetness index, distance to woodland, and distance to road. The mosquito species we detected are known vectors for infectious encephalitides, including West Nile virus. Understanding the microhabitat characteristics of these

  3. Opposing resonses to ecological gradients structure amphibian and reptile communities across a temperate grassland-savanna-forest landscape

    USGS Publications Warehouse

    Grundel, Ralph; Beamer, David; Glowacki, Gary A.; Frohnapple, Krystal; Pavlovic, Noel B.

    2014-01-01

    Temperate savannas are threatened across the globe. If we prioritize savanna restoration, we should ask how savanna animal communities differ from communities in related open habitats and forests. We documented distribution of amphibian and reptile species across an open-savanna–forest gradient in the Midwest U.S. to determine how fire history and habitat structure affected herpetofaunal community composition. The transition from open habitats to forests was a transition from higher reptile abundance to higher amphibian abundance and the intermediate savanna landscape supported the most species overall. These differences warn against assuming that amphibian and reptile communities will have similar ecological responses to habitat structure. Richness and abundance also often responded in opposite directions to some habitat characteristics, such as cover of bare ground or litter. Herpetofaunal community species composition changed along a fire gradient from infrequent and recent fires to frequent but less recent fires. Nearby (200-m) wetland cover was relatively unimportant in predicting overall herpetofaunal community composition while fire history and fire-related canopy and ground cover were more important predictors of composition, diversity, and abundance. Increased developed cover was negatively related to richness and abundance. This indicates the importance of fire history and fire related landscape characteristics, and the negative effects of development, in shaping the upland herpetofaunal community along the native grassland–forest continuum.

  4. Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments

    PubMed Central

    Webster, Gordon; O'Sullivan, Louise A.; Meng, Yiyu; Williams, Angharad S.; Sass, Andrea M.; Watkins, Andrew J.; Parkes, R. John; Weightman, Andrew J.

    2014-01-01

    Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2–8 × 107 16S rRNA gene copies cm−3) than the high-salinity marine sites from BR and AR (2 × 104–2 × 107 and 4 × 106–2 × 107 16S rRNA gene copies cm−3, respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the ‘Bathyarchaeota’ (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only ‘marine’ group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments. PMID:25764553

  5. Community structure, population structure and topographical specialisation of Gyrodactylus (monogenea) ectoparasites living on sympatric stickleback species.

    PubMed

    Raeymaekers, Joost A M; Huyse, Tine; Maelfait, Hannelore; Hellemans, Bart; Volckaert, Filip A M

    2008-09-01

    In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living on sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitius pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITS1). Each stickleback species hosted a characteristic gill- and fin-parasitic Gyrodactylus: G. arcuatus Bychowsky, 1933 and G. gasterostei Gläser, 1974 respectively infecting the three-spined stickleback, with G. rarus Wegener, 1910 and G. pungitii Malmberg, 1964 infecting the nine-spined stickleback. Host size and seasonal dynamics were strong determinants of parasite abundance. A strong interaction between host and parasite species determined infection levels and affected three levels of parasite organisation: community structure, population structure and topographical specialisation. Community and population structure were shaped by asymmetric cross-infections, resulting in a net transmission of the Gyro-dactylus species typical of the nine-spined stickleback towards the three-spined stickleback. Host density was not a major determinant of parasite exchange. Aggregation and topographical specialisation of the Gyrodactylus species of the three-spined stickleback were more pronounced than that of the nine-spined stickleback. PMID:19202677

  6. Bottom-up regulation of plant community structure in an aridland ecosystem.

    PubMed

    Báez, Selene; Collins, Scott L; Lightfoot, David; Koontz, Terri L

    2006-11-01

    We conducted a long-term rodent exclosure experiment in native grass- and shrub-dominated vegetation to evaluate the importance of top-down and bottom-up controls on plant community structure in a low-productivity aridland ecosystem. Using multiple regressions and analysis of covariance, we assessed how bottom-up precipitation pulses cascade through vegetation to affect rodent populations, how rodent populations affect plant community structure, and how rodents alter rates of plant community change over time. Our findings showed that bottom-up pulses cascade through the system, increasing the abundances of plants and rodents, and that rodents exerted no control on plant community structure and rate of change in grass-dominated vegetation, and only limited control in shrub-dominated vegetation. These results were discussed in the context of top-down effects on plant communities across broad gradients of primary productivity. We conclude that bottom-up regulation maintains this ecosystem in a state of low primary productivity that constrains the abundance of consumers such that they exert limited influence on plant community structure and dynamics. PMID:17168019

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

    NASA Astrophysics Data System (ADS)

    Webb, A. E.

    2012-12-01

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

  8. High abundance of small zoobenthos around biogenic structures in tidal sediments of the Wadden Sea

    NASA Astrophysics Data System (ADS)

    Reise, K.

    1981-12-01

    On the tidal flats of the island of Sylt (eastern part of the North Sea) the quantity of micro- and meiofauna associated with shoots of seagrass (Zostera noltii), with infaunal bivalves (Macoma balthica), and with tubes and burrows of polychaetes (Pygospio elegans, Pectinaria koreni, Nereis diversicolor, Nereis virens, Arenicola marina) was found to add up to 5 to 33 % of the overall abundance. These structures, taken together, account for 10 to 50 % of the faunal abundance on an average tidal flat at Sylt. The quantitative effect of biogenic structures at the sediment surface (casts and funnels) is small compared to that of tubes and burrows penetrating the anaerobic subsurface layer. In providing stable oxic microenvironments these elite structures frequently bring together more individuals than occur in the entire reducing sediment below surface. Faunal composition of irrigated dwellings of large infauna is different from that of the oxic surface sediment. The common denominator of all elite structures of the subsurface is an oxic halo. Burrows without such a halo are unattractive. There is no evidence that owners of burrows prey on their smaller inmates.

  9. Seasonal changes in the intertidal and subtidal macrobenthic invertebrate community structure in Baker Bay, lower Columbia River estuary. Technical memo

    SciTech Connect

    Furota, T.; Emmett, R.L.

    1993-01-01

    Macrobenthic invertebrates and sediments at 1 subtidal and 10 intertidal stations along a transect in Baker Bay of the lower Columbia River estuary were sampled monthly from November 1980 to October 1981. Water column temperatures and salinities were also recorded at the subtidal station. The intertidal community consisted primarily of estuarine species, whereas the subtidal community had additional marine species. Marine species declined in abundance after the interstitial salinity minimum (June), indicating the important role of salinity in determining benthic community structure.

  10. Community-oriented support and research structures

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  11. Effects of ocean acidification on population dynamics and community structure of crustose coralline algae.

    PubMed

    Ordoñez, Alexandra; Doropoulos, Christopher; Diaz-Pulido, Guillermo

    2014-06-01

    Calcification and growth of crustose coralline algae (CCA) are affected by elevated seawater pCO2 and associated changes in carbonate chemistry. However, the effects of ocean acidification (OA) on population and community-level responses of CCA have barely been investigated. We explored changes in community structure and population dynamics (size structure and reproduction) of CCA in response to OA. Recruited from an experimental flow-through system, CCA settled onto the walls of plastic aquaria and developed under exposure to one of three pCO2 treatments (control [present day, 389±6 ppm CO2], medium [753±11 ppm], and high [1267±19 ppm]). Elevated pCO2 reduced total CCA abundance and affected community structure, in particular the density of the dominant species Pneophyllum sp. and Porolithon onkodes. Meanwhile, the relative abundance of P. onkodes declined from 24% under control CO2 to 8.3% in high CO2 (65% change), while the relative abundance of Pneophyllum sp. remained constant. Population size structure of P. onkodes differed significantly across treatments, with fewer larger individuals under high CO2. In contrast, the population size structure and number of reproductive structures (conceptacles) per crust of Pneophyllum sp. was similar across treatments. The difference in the magnitude of the response of species abundance and population size structure between species may have the potential to induce species composition changes in the future. These results demonstrate that the impacts of OA on key coral reef builders go beyond declines in calcification and growth, and suggest important changes to aspects of population dynamics and community ecology. PMID:25070869

  12. Interlinking backscatter, grain size and benthic community structure

    NASA Astrophysics Data System (ADS)

    McGonigle, Chris; Collier, Jenny S.

    2014-06-01

    The relationship between acoustic backscatter, sediment grain size and benthic community structure is examined using three different quantitative methods, covering image- and angular response-based approaches. Multibeam time-series backscatter (300 kHz) data acquired in 2008 off the coast of East Anglia (UK) are compared with grain size properties, macrofaunal abundance and biomass from 130 Hamon and 16 Clamshell grab samples. Three predictive methods are used: 1) image-based (mean backscatter intensity); 2) angular response-based (predicted mean grain size), and 3) image-based (1st principal component and classification) from Quester Tangent Corporation Multiview software. Relationships between grain size and backscatter are explored using linear regression. Differences in grain size and benthic community structure between acoustically defined groups are examined using ANOVA and PERMANOVA+. Results for the Hamon grab stations indicate significant correlations between measured mean grain size and mean backscatter intensity, angular response predicted mean grain size, and 1st principal component of QTC analysis (all p < 0.001). Results for the Clamshell grab for two of the methods have stronger positive correlations; mean backscatter intensity (r2 = 0.619; p < 0.001) and angular response predicted mean grain size (r2 = 0.692; p < 0.001). ANOVA reveals significant differences in mean grain size (Hamon) within acoustic groups for all methods: mean backscatter (p < 0.001), angular response predicted grain size (p < 0.001), and QTC class (p = 0.009). Mean grain size (Clamshell) shows a significant difference between groups for mean backscatter (p = 0.001); other methods were not significant. PERMANOVA for the Hamon abundance shows benthic community structure was significantly different between acoustic groups for all methods (p ≤ 0.001). Overall these results show considerable promise in that more than 60% of the variance in the mean grain size of the Clamshell grab

  13. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects

    PubMed Central

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

    Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930–2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., NH4+-N, SO42−-S, PO43−-P) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a pronounced annual cycle. PMID:26635785

  14. Kelp forest size alters microbial community structure and function on Vancouver Island, Canada.

    PubMed

    Clasen, J L; Shurin, J B

    2015-03-01

    Bacteria are ubiquitous and important components of marine ecosystems, yet the interaction between bacteria and higher trophic levels remain poorly understood. The trophic cascade involving sea otters, urchins, and kelp in the North Pacific is a classic case of altered ecosystem states; however, its impacts on microbial communities are unknown. We investigated the response of microbial communities to variation in kelp abundance between regions with and without sea otter populations along the west coast of Vancouver Island, British Columbia, Canada. We compared bacterial community structure and function between regions with large and small kelp forests, including an subset of the bacterial community that produces alginate lyase, which allows direct utilization of kelp carbon. The abundance and activity of alginate-lyase-producing bacteria were 3.2 and 1.4 times higher, respectively, in the region with large kelp forests, and declined rapidly with increasing distance from kelp. Total bacterial abundance was 2.7 times greater, and bacteria grew faster and experienced more zooplankton grazing and viral-mediated mortality in the presence of large kelp forests. These patterns suggest that larger kelp forests produce more detritus and dissolved organic matter, which stimulate microbial activity. Our results indicate that variation in kelp forest size alters the community structure and productivity of microbes and contributes to the growing evidence that top predators interact with microbes and ecosystem processes through a cascade of indirect effects. PMID:26236881

  15. Meiobenthic and Macrobenthic Community Structure in Carbonate Sediments of Rocas Atoll (North-east, Brazil)

    NASA Astrophysics Data System (ADS)

    Netto, S. A.; Warwick, R. M.; Attrill, M. J.

    1999-01-01

    Rocas is the only atoll of the South Atlantic and it is built almost exclusively by coralline red algae, vermetid gastropods and encrusting foraminiferans. Patterns in the community structure of meiofauna and macrofauna, particularly nematodes and polychaetes, at Rocas Atoll, north-east Brazil, are determined and compared for different habitats: sublittoral, tidal flat, reef pools and lagoon. Nematodes and copepods were the most abundant meiofaunal taxa. In all studied habitats at Rocas Atoll, oligochaetes, nematodes and polychaetes numerically dominate the macrofauna. Univariate and multivariate analyses reveal clear differences in community structure between the habitats of the atoll, especially between the sublittoral and the inner habitats. The number of species, total density, diversity (H') and trophic structure vary significantly between the habitats, but the differences are dependent on which faunistic category (meiobenthic or macrobenthic) is analysed. Nematodes belonging to the Epsilonematidae and Draconematidae, together with a diverse community of meiobenthic polychaetes, characterize the sublittoral habitat of Rocas Atoll. Both meiofauna and macrofauna are depressed in the tidal flat, and the local sediment instability particularly affects the polychaete abundance. Reef pools and lagoons support a very dense aggregation of invertebrates, particularly the macrofauna, when compared with other carbonate reef sediments. However, differences in the structure of meiofauna and macrofauna communities between reef pools and lagoons are not significant. Changes in meiobenthic and macrobenthic community structure are related to the gradation in the physical environment of the atoll.

  16. Riparian Ficus Tree Communities: The Distribution and Abundance of Riparian Fig Trees in Northern Thailand

    PubMed Central

    Pothasin, Pornwiwan; Compton, Stephen G.; Wangpakapattanawong, Prasit

    2014-01-01

    Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010–2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance. PMID:25310189

  17. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis.

    PubMed

    Tout, Jessica; Siboni, Nachshon; Messer, Lauren F; Garren, Melissa; Stocker, Roman; Webster, Nicole S; Ralph, Peter J; Seymour, Justin R

    2015-01-01

    Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems. PMID:26042096

  18. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis

    PubMed Central

    Tout, Jessica; Siboni, Nachshon; Messer, Lauren F.; Garren, Melissa; Stocker, Roman; Webster, Nicole S.; Ralph, Peter J.; Seymour, Justin R.

    2015-01-01

    Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems. PMID:26042096

  19. Variability of Prokaryotic Community Structure in a Drinking Water Reservoir (Marathonas, Greece)

    PubMed Central

    Lymperopoulou, Despoina S.; Kormas, Konstantinos Ar.; Karagouni, Amalia D.

    2012-01-01

    The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H′ 0.81–3.28 and 1.36–1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning. PMID:21971081

  20. Submesoscale dynamics and planktonic community structure

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    ERIC Educational Resources Information Center

    Crowe, Jessica

    2010-01-01

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

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

    PubMed

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

    2011-04-01

    The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies. PMID:21261797

  3. Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

    PubMed

    Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

    2010-12-01

    Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing

  4. Common community structure in time-varying networks

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  5. Virioplankton Community Structure in Tunisian Solar Salterns

    PubMed Central

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

    2012-01-01

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

  6. Identification of Low Abundant Isomeric N-Glycan Structures in Biological Therapeutics by LC/MS.

    PubMed

    Zhao, Jia; Li, Siyang; Li, Chen; Wu, Shiaw-Lin; Xu, Wei; Chen, Yuetian; Shameem, Mohammed; Richardson, Douglas; Li, Huijuan

    2016-07-19

    An effective LC-MS based method for online characterization of low abundant structural isomers of N-linked glycans in biological therapeutics was developed. N-linked glycans of a recombinant monoclonal antibody were released by PNGase F and labeled with 2-aminobenzamide (2-AB) fluorescent tag. The labeled glycans were analyzed by online ultraperformance liquid chromatography-hydrophilic interaction liquid chromatography (UPLC-HILIC) coupled with mass spectrometry (MS). The glycan structure was characterized by MS(n) fragmentation in negative ion mode followed by identification of the signature D ions. The assignment included monosaccharide sequence and linkage information. The developed method successfully characterized structural isomers of A1G1F (assigned as terminal sialic acid attached in the 1,6 branch at 2,3 position), and A1G1F' (assigned as terminal sialic acid attached in the 1,3 branch at 2,3 position). Moreover, using the same approach, previously unknown low abundant species were identified unambiguously. One such structural isomer at low level, terminal GlcNAc of G1F+GlcNAc, was identified to be linked at the 1,6 branch. Additionally, another low level structural isomer, previously assigned as Man8 glycan, was found to be Man7+Glc glycan as its 1,3 branch containing three mannoses and one terminal glucose. The identification was further confirmed by a purified α-1,2-endomannosidase enzyme to generate the cleavage of α-1,3 linked terminal disaccharides (Man+glucose). Using this approach, different lots or different CHO produced mAbs was thoroughly examined and found that the newly identified "Man8" (Man7+Glc) was also present in different batches and in some commercially available therapeutic mAbs. PMID:27291648

  7. Binning of shallowly sampled metagenomic sequence fragments reveals that low abundance bacteria play important roles in sulfur cycling and degradation of complex organic polymers in an acid mine drainage community

    NASA Astrophysics Data System (ADS)

    Dick, G. J.; Andersson, A.; Banfield, J. F.

    2007-12-01

    Our understanding of environmental microbiology has been greatly enhanced by community genome sequencing of DNA recovered directly the environment. Community genomics provides insights into the diversity, community structure, metabolic function, and evolution of natural populations of uncultivated microbes, thereby revealing dynamics of how microorganisms interact with each other and their environment. Recent studies have demonstrated the potential for reconstructing near-complete genomes from natural environments while highlighting the challenges of analyzing community genomic sequence, especially from diverse environments. A major challenge of shotgun community genome sequencing is identification of DNA fragments from minor community members for which only low coverage of genomic sequence is present. We analyzed community genome sequence retrieved from biofilms in an acid mine drainage (AMD) system in the Richmond Mine at Iron Mountain, CA, with an emphasis on identification and assembly of DNA fragments from low-abundance community members. The Richmond mine hosts an extensive, relatively low diversity subterranean chemolithoautotrophic community that is sustained entirely by oxidative dissolution of pyrite. The activity of these microorganisms greatly accelerates the generation of AMD. Previous and ongoing work in our laboratory has focused on reconstrucing genomes of dominant community members, including several bacteria and archaea. We binned contigs from several samples (including one new sample and two that had been previously analyzed) by tetranucleotide frequency with clustering by Self-Organizing Maps (SOM). The binning, evaluated by comparison with information from the manually curated assembly of the dominant organisms, was found to be very effective: fragments were correctly assigned with 95% accuracy. Improperly assigned fragments often contained sequences that are either evolutionarily constrained (e.g. 16S rRNA genes) or mobile elements that are

  8. Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

    PubMed

    Liu, Biao; Wu, Chundu; Zhou, Xiaohong

    2014-01-01

    In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment. PMID:25259486

  9. [Effects of Perfluoroalkyl Substances on the Microbial Community Structure in Surface Sediments of Typical River, China].

    PubMed

    Sun, Ya-jun; Wang, Tie-yu; Peng, Xia-wei; Wang, Pei

    2015-07-01

    In order to reveal the relationship between Perfluoroalkyl substances (PFASs) contamination and the bacterial community composition, surface sediment samples were collected along the Xiaoqing River in Shandong Province in April and July 2014 (XQ1-XQ10), where many PFASs manufacturers were located. PFASs were quantified by HPLC/MS-MS, related environmental factors affecting the microbial community structure were measured, and the microbial community structure in surface sediments was measured by the second-generation sequencing technology Illumina MiSeq. The results not only revealed the degree of PFASs pollution in the sediments of Xiaoqing River, but also illustrated the relationship between PFASs pollution and the microbial community structure. Among the twelve kinds of PFASs detected in this study, PFOA was the predominant compound, and the highest PFOA concentrations were detected in the sample of XQ5 (April: 456. 2 ng. g-1; July: 748.7 ng . g-1) located at the downstream of Xiaoqing River with many fluoropolymer producing facilities. PFOA contamination was the main factor affecting the microbial community structure in April, accordingly community richness and evenness were significantly negatively correlated with PFOA levels. The abundance of Thiobacillus increased with the increasing PFOA concentration in the sediment PFOA. This suggested that Thiobacillus was sensitive to PFOA pollution and might be the potential indicator to reveal the degree of PFOA pollution in sediment. When the concentrations of PFOA were below 100 ng . g-1, no significant effects on the microbial community structure were observed. PMID:26489317

  10. Simultaneous mapping of chemical abundances and magnetic field structure in Ap stars

    NASA Astrophysics Data System (ADS)

    Lueftinger, T.

    2014-11-01

    Magnetic A stars represent about 5 highly ordered, very stable and often very strong magnetic fields. They frequently show variations in both brightness and spectral line profiles that are synchronised to stellar rotation. Those variations are believed to be produced by atomic diffusion operating in the stellar atmospheres which have become stabilized by multi-kG magnetic fields. In recent years, with the development and application of the Doppler and magnetic-Doppler imaging techniques and the availability of high-precision spectroscopic and spectropolarimetric data, it has became possible to map the chemical abundances and magnetic field structures of Ap stars simultaneously and in increasing detail, based on full Stokes vector observations. I review the state-of-the-art understanding pf Ap star spots and their relation to magnetic fields, the development of Doppler and magnetic-Doppler imaging into one of the most powerful remote sensing methods for astrophysics, and the physics of Ap stars atmospheres that we can deduce from simultaneous mapping of magnetic field structure and chemical abundances.

  11. Influence of Land Use, Nutrients, and Geography on Microbial Communities and Fecal Indicator Abundance at Lake Michigan Beaches

    PubMed Central

    Cloutier, Danielle D.; Alm, Elizabeth W.

    2015-01-01

    Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, fine-scale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress. PMID:25979888

  12. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.

    PubMed

    Lozupone, Catherine A; Hamady, Micah; Kelley, Scott T; Knight, Rob

    2007-03-01

    The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny. PMID:17220268

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

    ERIC Educational Resources Information Center

    Starr, Paul D.; Roberts, Alden E.

    1982-01-01

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

  14. Bipartite Community Structure of eQTLs.

    PubMed

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

    2016-09-01

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

  15. Community Structure in Online Collegiate Social Networks

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Smith, Reginald D.

    2006-02-01

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

  17. Composition and structure of bird communities in vegetational gradients of Bodoquena Mountains, western Brazil.

    PubMed

    Godoi, Mauricio N; Souza, Franco L; Laps, Rudi R; Ribeiro, Danilo B

    2016-03-01

    The informations of bird species distribution in different habitats and the structure of their communities are crucial for bird conservation. We tested the differences in composition, richness and abundance of birds in different phytophysiognomies at Bodoquena Mountains, western Brazil, and we demonstrated the variations in richness and abundance of birds between different trophic groups. Sampling was conducted between July 2011 and June 2012 in 200 point counts arranged in the study area. A total of 3350 contacts were obtained belonging to 156 bird species. Woodland savannas, seasonal forests and arboreal savannas had higher bird abundance and richness, while riparian forests, clean pastures and dirty pastures had smaller values of these parameters. The bird community was organized according to local vegetational gradient, with communities of forests, open areas and savannas, although many species occurred in more than one vegetation type. The insectivorous, omnivorous, frugivorous and gramnivorous birds composed most of the community. These data showed how important environmental heterogeneity is to bird communities. Furthermore, the presence of extensive patches of natural habitats, the small distance between these patches and the permeability of pastures, with high arboreal and shrubby cover, are indicated as important factors to maintain the bird diversity. PMID:26959319

  18. [Phytoplankton pigment patterns and community structure in the Yangtze Estuary and its adjacent areas].

    PubMed

    Lai, Jun-xiang; Yu, Zhi-ming; Song, Xiu-xian; Han, Xiao-tian; Cao, Xi-hua; Yuan, Yong-quan

    2013-09-01

    Three cruises were carried out in the Yangtze Estuary and its adjacent areas in May, November, June during 2009-2010. The spatial variations of phytoplankton community structure were investigated based on RP-HPLC analysis of pigments and CHEMTAX processing of the pigment data. 21 kinds of pigments were detected, among which chlorophyll a, peridinin, fucoxanthin, 19'-butanoyloxyfucoxanthin, 19'-hexanoyloxyfucoxanthin, chlorophyll b, diadinoxanthin, alloxanthin and zeaxanthin were the major pigments in the Yangtze Estuary and its adjacent areas. Chlorophyll a was the most abundant in all pigments, followed by fuxoxanthin. Other pigments generally contributed a minor proportion to the total pigments. High concentrations of fucoxanthin and peridinin were observed in May 2009 and June 2010, indicating blooms of diatoms and dinoflagellates. The results showed that the composition and distribution of phytoplankton pigments were influenced by environmental factors. The phytoplankton community, as determined by biomarker pigment concentration using HPLC and CHEMTAX, was composed mainly of diatoms, dinoflagellates, cryptophytes, chlorophytes, cyanobacteria, prymnesiophytes, chrysophytes and prasinophytes. The dominant algal groups were diatoms, dinoflagellates and chlorophytes in May 2009. The phytoplankton community was characterized by high contribution of diatoms in November 2009. Diatoms, dinoflagellates and cryptophytes accounted for 62.5% of chlorophyll a in June 2010, and the relative abundance of cyanobacteria was higher in this cruise. The spatial variations of phytoplankton community structure featured distinct regionality. Diatoms, chlorophytes and cryptophytes were the main groups in the inshore waters, and the abundances of prymnesiophytes, chrysophytes and cyanobacteria were increasing from inshore to the open sea. PMID:24288983

  19. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

    USGS Publications Warehouse

    Hamdan, L.J.; Gillevet, P.M.; Pohlman, J.W.; Sikaroodi, M.; Greinert, J.; Coffin, R.B.

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and the community was dominated by uncultured members of the Burkholderiales. Chloroflexi/GNS and Deltaproteobacteria were abundant in sediments from a methane seep located landward of the ridge. Gas-charged and organic-rich sediments further landward had the highest overall diversity. Surface sediments, with the exception of those from the basin, were dominated by Rhodobacterales sequences associated with organic matter deposition. Taxa related to the Desulfosarcina/Desulfococcus and the JS1 candidates were highly abundant at the sulfate-methane transition zone (SMTZ) at three sites. To determine how community structure was influenced by terrestrial, pelagic and in situ substrates, sequence data were statistically analyzed against geochemical data (e.g. sulfate, chloride, nitrogen, phosphorous, methane, bulk inorganic and organic carbon pools) using the Biota-Environmental matching procedure. Landward of the ridge, sulfate was among the most significant structuring factors. Seaward of the ridge, silica and ammonium were important structuring factors. Regardless of the transect location, methane was the principal structuring factor on SMTZ communities. FEMS Microbiology Ecology ?? 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

  20. Partitioning the effects of an ecosystem engineer: kangaroo rats control community structure via multiple pathways.

    PubMed

    Prugh, Laura R; Brashares, Justin S

    2012-05-01

    1. Ecosystem engineers impact communities by altering habitat conditions, but they can also have strong effects through consumptive, competitive and other non-engineering pathways. 2. Engineering effects can lead to fundamentally different community dynamics than non-engineering effects, but the relative strengths of these interactions are seldom quantified. 3. We combined structural equation modelling and exclosure experiments to partition the effects of a keystone engineer, the giant kangaroo rat (Dipodomys ingens), on plants, invertebrates and vertebrates in a semi-arid California grassland. 4. We separated the effects of burrow creation from kangaroo rat density and found that kangaroo rats increased the diversity and abundance of other species via both engineering and non-engineering pathways. 5. Engineering was the primary factor structuring plant and small mammal communities, whereas non-engineering effects structured invertebrate communities and increased lizard abundance. 6. These results highlight the importance of the non-engineering effects of ecosystem engineers and shed new light on the multiple pathways by which strong-interactors shape communities. PMID:22098534

  1. Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

    PubMed

    You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

    2014-03-01

    Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations. PMID

  2. The Effect of Dilution on the Structure of Microbial Communities

    NASA Technical Reports Server (NTRS)

    Mills, Aaron L.

    2000-01-01

    To determine how dilution of microbial communities affects the diversity of the diluted assemblage a series of numerical simulations were conducted that determined the theoretical change in diversity, richness, and evenness of the community with serial dilution. The results of the simulation suggested that the effects are non linear with a high degree of dependence on the initial evenness of the community being diluted. A series of incubation experiments using a range of dilutions of raw sewage as an inoculum into sterile sewage was used for comparison to the simulations. The diluted communities were maintained in batch fed reactors (three day retention time) for nine days. The communities were harvested and examined by conventional plating and by molecular analysis of the whole-community DNA using AFLP and T-RFLP. Additional, CLPP analysis was also applied. The effects on richness predicted by the numerical simulations were confirmed by the analyses used. The diluted communities fell into three groups, a low dilution, intermediate dilution, and high dilution group, which corresponded well with the groupings obtained for community richness in simulation. The grouping demonstrated the non-linear nature of dilution of whole communities. Furthermore, the results implied that the undiluted community consisted of a few dominant types accompanied by a number of rare (low abundance) types as is typical in unevenly distributed communities.

  3. Genetic and environmental determinants of insect herbivore community structure in a Betula pendula population

    PubMed Central

    Silfver, Tarja

    2014-01-01

    A number of recent studies have shown that intraspecific genetic variation of plants may have a profound effect on the herbivorous communities which depend on them. However less is known about the relative importance of intraspecific variation compared to other ecological factors, for example environmental variation or the effects of herbivore damage. We randomly selected 22 Betula pendula genotypes from a local population (< 0.9 ha), cloned them and planted cloned seedlings on two study sites separated at a regional scale (distance between sites about 30 km) to examine an insect community of 23-27 species on these genotypes. B. pendula genotypes did not differ in their species richness, but the total mean abundance and the structure of the insect herbivore community was significantly affected by the genotype, which could account for up to 27% of the total variation in community structure. B. pendula genotype accounted for two to four times more variation in the arthropod community structure than did environmental (block) variation on a local scale, while on a regional scale, genotypic and environmental (site) variation accounted for 4-14% of the arthropod community structure. The genetic effects were modified by environmental variation on both a local and regional scale over one study year, and locally, the largest part of the variation (38%) could be explained by the genotype × environment (block) interactions. Suppression of insect herbivores during one growing season led to changed arthropod community structure in the following growing season, but this effect was minimal and could explain only 4% of the total variation in insect community structure. Our results suggest that both genetic and environmental factors are important determinants of the community structure of herbivorous insects. Together these mechanisms appear to maintain the high diversity of insects in B. pendula forest ecosystems. PMID:24715977

  4. Genetic and environmental determinants of insect herbivore community structure in a Betula pendula population.

    PubMed

    Silfver, Tarja; Rousi, Matti; Oksanen, Elina; Roininen, Heikki

    2014-01-01

    A number of recent studies have shown that intraspecific genetic variation of plants may have a profound effect on the herbivorous communities which depend on them. However less is known about the relative importance of intraspecific variation compared to other ecological factors, for example environmental variation or the effects of herbivore damage. We randomly selected 22 Betula pendula genotypes from a local population (< 0.9 ha), cloned them and planted cloned seedlings on two study sites separated at a regional scale (distance between sites about 30 km) to examine an insect community of 23-27 species on these genotypes. B. pendula genotypes did not differ in their species richness, but the total mean abundance and the structure of the insect herbivore community was significantly affected by the genotype, which could account for up to 27% of the total variation in community structure. B. pendula genotype accounted for two to four times more variation in the arthropod community structure than did environmental (block) variation on a local scale, while on a regional scale, genotypic and environmental (site) variation accounted for 4-14% of the arthropod community structure. The genetic effects were modified by environmental variation on both a local and regional scale over one study year, and locally, the largest part of the variation (38%) could be explained by the genotype × environment (block) interactions. Suppression of insect herbivores during one growing season led to changed arthropod community structure in the following growing season, but this effect was minimal and could explain only 4% of the total variation in insect community structure. Our results suggest that both genetic and environmental factors are important determinants of the community structure of herbivorous insects. Together these mechanisms appear to maintain the high diversity of insects in B. pendula forest ecosystems. PMID:24715977

  5. Helium abundance and ionization structure in the Orion nebula: radio recombination lines observations

    NASA Astrophysics Data System (ADS)

    Poppi, S.; Tsivilev, A. P.; Cortiglioni, S.; Palumbo, G. G. C.; Sorochenko, R. L.

    2007-03-01

    Results of the Ori A HII region mapping based on hydrogen (H), helium (He) and carbon (C) Radio Recombination lines (RRL) are presented. Observations were made with the same angular resolution (2') using the 32 m VLBI dish of Medicina (Italy, 22.4 GHz) and the Pushchino RT-22 dish (Russia, 36.5 GHz). The behaviour of the ionized helium abundance, y^+, with distance from the center shows that the He+ zone size is smaller than that of H^+. Such a behaviour is different for the core and for the envelope, as well as for different directions from the center. The helium abundance, N(He)/N(H)=10.0(± 0.8)%, is measured. Derived line radial velocities, their widths and y+ data support the well-known "blister-type" structure of this HII region. LTE electron temperatures (7800-9600 K) are also measured. Appendices (Figs. 15, 16 and Sect. 4.1 "Carbon RRLs") are only available in electronic form at http://www.aanda.org

  6. Diversity, Community Composition and Abundance of Anammox Bacteria in Sediments of the North Marginal Seas of China.

    PubMed

    Shehzad, Ahmed; Liu, Jiwen; Yu, Min; Qismat, Shakeela; Liu, Jingli; Zhang, Xiao-Hua

    2016-06-25

    Over the past few decades, anammox bacteria have been recognized as key players that contribute significantly to the release of large amounts of nitrogen in the global marine nitrogen cycle. In the present study, the diversity, community composition, and abundance of anammox bacteria from the sediments of four diverse regions in the north marginal seas in China were determined via clone library construction and a quantitative PCR analysis. The clone libraries retrieved by the 16S rRNA gene and Hzo gene markers indicated that "Candidatus Scalindua" was the predominant group throughout the sites examined. The 16S rRNA gene clone libraries revealed exceptional diversity by identifying two potential novel anammox clades, as evidenced by the high sequence similarities between these two clades and known anammox genera, and their unique phylogenetic positions with high bootstrap values. However, their potential roles in the anammox reaction need to be validated. Six novel members of Planctomycetes, divergent from the known genera of anammox bacteria, were also detected. A phylogenetic analysis by Hzo protein sequences revealed the existence of two known genera, i.e., "Candidatus Jettenia" and "Candidatus Anammoxoglobus", which are rarely captured from marine sediments. Among all ecological parameters investigated, the distribution patterns and composition of anammox bacteria were found to be influenced by salinity, total organic matter, and temperature. The abundance of the anammox bacterial 16S rRNA gene from the sites examined ranged between 3.95×10(5) and 9.21×10(5) copies g(-1) wet sediment and positively correlated with the median size of the sediment sample. PMID:27180640

  7. Diversity, Community Composition and Abundance of Anammox Bacteria in Sediments of the North Marginal Seas of China

    PubMed Central

    Shehzad, Ahmed; Liu, Jiwen; Yu, Min; Qismat, Shakeela; Liu, Jingli; Zhang, Xiao-Hua

    2016-01-01

    Over the past few decades, anammox bacteria have been recognized as key players that contribute significantly to the release of large amounts of nitrogen in the global marine nitrogen cycle. In the present study, the diversity, community composition, and abundance of anammox bacteria from the sediments of four diverse regions in the north marginal seas in China were determined via clone library construction and a quantitative PCR analysis. The clone libraries retrieved by the 16S rRNA gene and Hzo gene markers indicated that “Candidatus Scalindua” was the predominant group throughout the sites examined. The 16S rRNA gene clone libraries revealed exceptional diversity by identifying two potential novel anammox clades, as evidenced by the high sequence similarities between these two clades and known anammox genera, and their unique phylogenetic positions with high bootstrap values. However, their potential roles in the anammox reaction need to be validated. Six novel members of Planctomycetes, divergent from the known genera of anammox bacteria, were also detected. A phylogenetic analysis by Hzo protein sequences revealed the existence of two known genera, i.e., “Candidatus Jettenia” and “Candidatus Anammoxoglobus”, which are rarely captured from marine sediments. Among all ecological parameters investigated, the distribution patterns and composition of anammox bacteria were found to be influenced by salinity, total organic matter, and temperature. The abundance of the anammox bacterial 16S rRNA gene from the sites examined ranged between 3.95×105 and 9.21×105 copies g−1 wet sediment and positively correlated with the median size of the sediment sample. PMID:27180640

  8. Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

    PubMed Central

    Feris, Kevin; Ramsey, Philip; Frazar, Chris; Moore, Johnnie N.; Gannon, James E.; Holben, William E.

    2003-01-01

    The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities. PMID:12957946

  9. Effects of Crayfish and Fish on Sediment Accumulation and Macroinvertebrate Community Structure in a Temperate Stream

    NASA Astrophysics Data System (ADS)

    Ewing, T. D.; Creed, R. P.

    2005-05-01

    A variety of large taxa can act as ecosystem engineers in stream communities. These taxa are often found in the same stream. We used an enclosure/exclosure experiment to evaluate the individual and combined effects of a crayfish and a benthic-feeding fish on sediment accumulation and macroinvertebrate abundance in a temperate stream. There were 5 treatments in the experiment: 1) central stoneroller enclosure, 2) crayfish enclosure, 3) crayfish plus central stoneroller enclosure, 4) manually brushing the substrate, and 5) a control. The brushed treatment allowed us to separate the consumptive effects of the crayfish and central stonerollers from the indirect effects resulting from their bioturbation. The control contained significantly more sediment than the other 4 treatments indicating that both crayfish and central stonerollers acted as ecosystem engineers. Reduction in sediment abundance had negative effects on the abundance of 2 genera while three taxa were more abundant in sediment-free substrata. Macroinvertebrate abundance in the brushed treatment was not different from the 3 treatments with crayfish or central stonerollers suggesting that the main effects of consumers in this experiment were indirect. Our results demonstrate that both crayfish and central stonerollers can influence lotic community structure by acting as ecosystem engineers.

  10. Nematode community structure and diversity pattern in sandy beaches of Qingdao, China

    NASA Astrophysics Data System (ADS)

    Hua, Er; Mu, Fanghong; Zhang, Zhinan; Yang, Shichao; Zhang, Ting; Li, Jia

    2016-02-01

    We investigated the diversity and structure of free-living marine nematode communities at three sandy beaches representing typical intertidal environments of a temperate zone in Qingdao, Shandong Province, China. Average nematode abundance ranged from 1006 to 2170 ind. 10 cm-2, and a total of 34 nematode genera were recorded, of which only 8 were common in all the studied beaches. Pielou's evenness and Shannon-Wiener diversity index were the lowest at the second beach where nematode abundance was the highest. The highest species diversity index coincided with the lowest nematode abundance at Shilaoren beach. Sediment median grain size, sorting coefficient, and chlorophyll-a content were essential for differentiation in nematode abundance and species diversity, whereas taxonomic diversity of nematode was homogeneous across the three beaches. In 0-20 cm sediment profile, nematode abundance declined abruptly with depth, whereas nematode diversity changed gently with obvious difference in 16-20 cm layer. Sediment granulometry and chlorophyll- a content were the two foremost factors which influenced the vertical distribution pattern of nematode generic diversity. Non-selective deposit feeders constituted the most dominant trophic group, followed by epistratum feeders. Bathylaimus (family: Tripyloididae) dominated at the second and Yangkou beach, while Theristus (family: Xyalidae) prevailed at Shilaoren beach. Omnivores and predators became important at Shilaoren beach because of the high proportion of Enoplolaimus. Even though, nematode community of the studied beaches did not differ significantly from each other.

  11. 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.

  12. Surprise maximization reveals the community structure of complex networks

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

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

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

    PubMed

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

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

  14. PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

    PubMed Central

    Pinto, Ameet J.; Raskin, Lutgarde

    2012-01-01

    As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on α- and β-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3–V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in β-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based α- and β-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of

  15. Fermentable non-starch polysaccharides increases the abundance of Bacteroides-Prevotella-Porphyromonas in ileal microbial community of growing pigs.

    PubMed

    Ivarsson, E; Roos, S; Liu, H Y; Lindberg, J E

    2014-11-01

    Most plant-origin fiber sources used in pig production contains a mixture of soluble and insoluble non-starch polysaccharides (NSP). The knowledge about effects of these sources of NSP on the gut microbiota and its fermentation products is still scarce. The aim of this study was to investigate effects of feeding diets with native sources of NSP on the ileal and fecal microbial composition and the dietary impact on the concentration of short-chain fatty acids (SCFA) and lactic acid. The experiment comprised four diets and four periods in a change-over design with seven post valve t-cecum cannulated growing pigs. The four diets were balanced to be similar in NSP content and included one of four fiber sources, two diets were rich in pectins, through inclusion of chicory forage (CFO) and sugar beet pulp, and two were rich in arabinoxylan, through inclusion of wheat bran (WB) and grass meal. The gut microbial composition was assessed with terminal restriction fragment (TRF) length polymorphism and the abundance of Lactobacillus spp., Enterobacteriaceae, Bacteroides-Prevotella-Porphyromonas and the β-xylosidase gene, xynB, were assessed with quantitative PCR. The gut microbiota did not cluster based on NSP structure (arabinoxylan or pectin) rather, the effect was to a high degree ingredient specific. In pigs fed diet CFO, three TRFs related to Prevotellaceae together consisted of more than 25% of the fecal microbiota, which is about 3 to 23 times higher (P<0.05) than in pigs fed the other diets. Whereas pigs fed diet WB had about 2 to 22 times higher abundance (P<0.05) of Megasphaera elsdenii in feces and about six times higher abundance (P<0.05) of Lactobacillus reuteri in ileal digesta than pigs fed the other diets. The total amount of digested NSP (r=0.57; P=0.002), xylose (r=0.53; P=0.004) and dietary fiber (r=0.60; P=0.001) in ileal digesta were positively correlated with an increased abundance of Bacteroides-Prevotella-Porphyromonas. The effect on SCFA was

  16. Seasonal Dynamics of Ant Community Structure in the Moroccan Argan Forest

    PubMed Central

    Keroumi, Abderrahim El; Naamani, Khalid; Soummane, Hassna; Dahbi, Abdallah

    2012-01-01

    In this study we describe the structure and composition of ant communities in the endemic Moroccan Argan forest, using pitfall traps sampling technique throughout the four seasons between May 2006 and February 2007. The study focused on two distinct climatic habitats within the Essaouira Argan forest, a semi-continental site at Lahssinate, and a coastal site at Boutazarte. Thirteen different ant species were identified, belonging to seven genera. Monomorium subopacum Smith and Tapinoma simrothi Krausse-Heldrungen (Hymenoptera: Formicidae) were the most abundant and behaviorally dominant ant species in the arganeraie. In addition, more specimens were captured in the semi-continental site than in the coastal area. However, no significant difference was observed in species richness, evenness, or diversity between both sites. Composition and community structure showed clear seasonal dynamics. The number of species, their abundance, their diversity, and their evenness per Argan tree were significantly dissimilar among seasons. The richness (except between summer and autumn), and the abundance and the evenness of ant species among communities, showed a significant difference between the dry period (summer and spring) and the rainy period (winter and autumn). Higher abundance and richness values occurred in the dry period of the year. Ant species dominance and seasonal climatic variations in the arganeraie might be among the main factors affecting the composition, structure, and foraging activity of ant communities. This study, together with recent findings on ant predation behavior below Argan trees, highlights the promising use of dominant ant species as potential agents of Mediterranean fruit fly bio-control in the Argan forest and surrounding ecosystems. PMID:23421815

  17. Spatial structure of the meroplankton community along a Patagonian fjord - The role of changing freshwater inputs

    NASA Astrophysics Data System (ADS)

    Meerhoff, Erika; Tapia, Fabián J.; Castro, Leonardo R.

    2014-12-01

    Freshwater inputs are major drivers of circulation, hydrographic structure, and productivity patterns along estuarine systems. We assessed the degree to which meroplankton community structure in the Baker/Martinez fjord complex (Chilean Patagonia, 47.5°S) responds to spatial and temporal changes in hydrographic conditions driven by seasonal changes in Baker river outflow. Zooplankton and hydrographic measurements were conducted along the fjord in early spring (October) and late summer (February), when river outflow was minimal and maximal, respectively. Major meroplankton groups found on these surveys were larval barnacles, crabs, bivalves and gastropods. There was a clear change in community structure between October and February, explained by a switch in the numerically dominant group from barnacle to bivalve larvae. This change in community structure was related to changes in hydrographic structure along the fjord, which are mainly associated with seasonal changes in the Baker river outflow. A variance partition analysis showed no significant spatial trend that could account for the variation in meroplankton along the Martinez channel, whereas temporal variability and environmental variables accounted for 36.6% and 27.6% of the variance, respectively. When comparing meroplankton among the Baker and Martinez channels in October, changes in environmental variables explained 44.9% of total variance, whereas spatial variability accounted for 23.5%. Early and late-stage barnacle larvae (i.e. nauplii and cyprids) were more abundant in water with lower temperature, and higher dissolved oxygen and chlorophyll-a concentration, whereas bivalve larvae were more strongly associated to warmer waters. The seasonal shift in numerical dominance, from barnacle larvae in early spring to bivalve larvae in late summer, suggests that reproduction of these groups is triggered by substantially different sets of conditions, both in terms of hydrography and food availability. The

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

    SciTech Connect

    Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.; Wilkins, Michael J.; Kantor, Rose S.; Thomas, Brian C.; Williams, Kenneth H.; Gilbert, Jack A.; Long, Philip E.; Banfield, Jillian F.

    2015-03-01

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

  19. Cross-habitat interactions among bivalve species control community structure on intertidal flats.

    PubMed

    Donadi, Serena; van der Heide, Tjisse; van der Zee, Els M; Eklöf, Johan S; van de Koppel, Johan; Weerman, Ellen J; Piersma, Theunis; Olff, Han; Eriksson, Britas Klemens

    2013-02-01

    Increasing evidence shows that spatial interactions between sedentary organisms can structure communities and promote landscape complexity in many ecosystems. Here we tested the hypothesis that reef-forming mussels (Mytilus edulis L.), a dominant intertidal ecosystem engineer in the Wadden Sea, promote abundances of the burrowing bivalve Cerastoderma edule L. (cockle) in neighboring habitats at relatively long distances coastward from mussel beds. Field surveys within and around three mussel beds showed a peak in cockle densities at 50-100 m toward the coast from the mussel bed, while cockle abundances elsewhere in the study area were very low. Field transplantation of cockles showed higher survival of young cockles (2-3 years old) and increased spat fall coastward of the mussel bed compared to within the bed and to areas without mussels, whereas growth decreased within and coastward of the mussel bed. Our measurements suggest that the observed spatial patterns in cockle numbers resulted from (1) inhibition effects by the mussels close to the beds due to preemptive algal depletion and deteriorated sediment conditions and (2) facilitation effects by the mussels farther away from the beds due to reduction of wave energy. Our results imply that these spatial, scale-dependent interactions between reef-forming ecosystem engineers and surrounding communities of sedentary benthic organisms can be an important determinant of the large-scale community structure in intertidal ecosystems. Understanding this interplay between neighboring communities of sedentary species is therefore essential for effective conservation and restoration of soft-bottom intertidal communities. PMID:23691667

  20. Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing.

    PubMed

    Köchling, Thorsten; Sanz, José Luis; Gavazza, Sávia; Florencio, Lourdinha

    2015-07-01

    Microorganisms are responsible for degrading the raw leachate generated in sanitary landfills, extracting the soluble fraction of the landfill waste and biotransforming organic matter and toxic residues. To increase our understanding of these highly contaminated ecosystems, we analyzed the microbial communities in the leachate produced by three landfill cells of different ages. Using high-throughput 454 pyrosequencing of the 16S rRNA gene, we describe the structure of the leachate communities and present their compositional characteristics. All three communities exhibited a high level of abundance but were undersampled, as indicated by the results of the rarefaction analysis. The distribution of the taxonomic operational units (OTUs) was highly skewed, suggesting a community structure with a few dominant members that are key for the degradation process and numerous rare microorganisms, which could act as a resilient microorganism seeder pool. Members of the phylum Firmicutes were dominant in all of the samples, accounting for up to 62% of the bacterial sequences, and their proportion increased with increasing landfill age. Other abundant phyla included Bacteroidetes, Proteobacteria, and Spirochaetes, which together with Firmicutes comprised 90% of the sequences. The data illustrate a microbial community that degrades organic matter in raw leachate in the early stages, before the methanogenic phase takes place. The genera found fit well into the classical pathways of anaerobic digestion processes. PMID:25652654

  1. The Community Structure of the Global Corporate Network

    PubMed Central

    Vitali, Stefania; Battiston, Stefano

    2014-01-01

    We investigate the community structure of the global ownership network of transnational corporations. We find a pronounced organization in communities that cannot be explained by randomness. Despite the global character of this network, communities reflect first of all the geographical location of firms, while the industrial sector plays only a marginal role. We also analyze the meta-network in which the nodes are the communities and the links are obtained by aggregating the links among firms belonging to pairs of communities. We analyze the network centrality of the top 50 communities and we provide a quantitative assessment of the financial sector role in connecting the global economy. PMID:25126722

  2. The community structure of the global corporate network.

    PubMed

    Vitali, Stefania; Battiston, Stefano

    2014-01-01

    We investigate the community structure of the global ownership network of transnational corporations. We find a pronounced organization in communities that cannot be explained by randomness. Despite the global character of this network, communities reflect first of all the geographical location of firms, while the industrial sector plays only a marginal role. We also analyze the meta-network in which the nodes are the communities and the links are obtained by aggregating the links among firms belonging to pairs of communities. We analyze the network centrality of the top 50 communities and we provide a quantitative assessment of the financial sector role in connecting the global economy. PMID:25126722

  3. Predicting Changes in Macrophyte Community Structure from Functional Traits in a Freshwater Lake: A Test of Maximum Entropy Model

    PubMed Central

    Fu, Hui; Zhong, Jiayou; Yuan, Guixiang; Guo, Chunjing; Lou, Qian; Zhang, Wei; Xu, Jun; Ni, Leyi; Xie, Ping; Cao, Te

    2015-01-01

    Trait-based approaches have been widely applied to investigate how community dynamics respond to environmental gradients. In this study, we applied a series of maximum entropy (maxent) models incorporating functional traits to unravel the processes governing macrophyte community structure along water depth gradient in a freshwater lake. We sampled 42 plots and 1513 individual plants, and measured 16 functional traits and abundance of 17 macrophyte species. Study results showed that maxent model can be highly robust (99.8%) in predicting the species relative abundance of macrophytes with observed community-weighted mean (CWM) traits as the constraints, while relative low (about 30%) with CWM traits fitted from water depth gradient as the constraints. The measured traits showed notably distinct importance in predicting species abundances, with lowest for perennial growth form and highest for leaf dry mass content. For tuber and leaf nitrogen content, there were significant shifts in their effects on species relative abundance from positive in shallow water to negative in deep water. This result suggests that macrophyte species with tuber organ and greater leaf nitrogen content would become more abundant in shallow water, but would become less abundant in deep water. Our study highlights how functional traits distributed across gradients provide a robust path towards predictive community ecology. PMID:26167856

  4. Genetic and Ontogenetic Variation in an Endangered Tree Structures Dependent Arthropod and Fungal Communities

    PubMed Central

    Gosney, Benjamin J.; O′Reilly-Wapstra, Julianne M.; Forster, Lynne G.; Barbour, Robert C.; Iason, Glenn R.; Potts, Brad M.

    2014-01-01

    Plant genetic and ontogenetic variation can significantly impact dependent fungal and arthropod communities. However, little is known of the relative importance of these extended genetic and ontogenetic effects within a species. Using a common garden trial, we compared the dependent arthropod and fungal community on 222 progeny from two highly differentiated populations of the endangered heteroblastic tree species, Eucalyptus morrisbyi. We assessed arthropod and fungal communities on both juvenile and adult foliage. The community variation was related to previous levels of marsupial browsing, as well as the variation in the physicochemical properties of leaves using near-infrared spectroscopy. We found highly significant differences in community composition, abundance and diversity parameters between eucalypt source populations in the common garden, and these were comparable to differences between the distinctive juvenile and adult foliage. The physicochemical properties assessed accounted for a significant percentage of the community variation but did not explain fully the community differences between populations and foliage types. Similarly, while differences in population susceptibility to a major marsupial herbivore may result in diffuse genetic effects on the dependent community, this still did not account for the large genetic-based differences in dependent communities between populations. Our results emphasize the importance of maintaining the populations of this rare species as separate management units, as not only are the populations highly genetically structured, this variation may alter the trajectory of biotic colonization of conservation plantings. PMID:25469641

  5. Genetic and ontogenetic variation in an endangered tree structures dependent arthropod and fungal communities.

    PubMed

    Gosney, Benjamin J; O Reilly-Wapstra, Julianne M; Forster, Lynne G; Barbour, Robert C; Iason, Glenn R; Potts, Brad M

    2014-01-01

    Plant genetic and ontogenetic variation can significantly impact dependent fungal and arthropod communities. However, little is known of the relative importance of these extended genetic and ontogenetic effects within a species. Using a common garden trial, we compared the dependent arthropod and fungal community on 222 progeny from two highly differentiated populations of the endangered heteroblastic tree species, Eucalyptus morrisbyi. We assessed arthropod and fungal communities on both juvenile and adult foliage. The community variation was related to previous levels of marsupial browsing, as well as the variation in the physicochemical properties of leaves using near-infrared spectroscopy. We found highly significant differences in community composition, abundance and diversity parameters between eucalypt source populations in the common garden, and these were comparable to differences between the distinctive juvenile and adult foliage. The physicochemical properties assessed accounted for a significant percentage of the community variation but did not explain fully the community differences between populations and foliage types. Similarly, while differences in population susceptibility to a major marsupial herbivore may result in diffuse genetic effects on the dependent community, this still did not account for the large genetic-based differences in dependent communities between populations. Our results emphasize the importance of maintaining the populations of this rare species as separate management units, as not only are the populations highly genetically structured, this variation may alter the trajectory of biotic colonization of conservation plantings. PMID:25469641

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

    NASA Astrophysics Data System (ADS)

    Fan, W.; Yeung, K. H.

    2015-03-01

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

  7. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

    Gordon-Bradley, N.; Li, N.

    2015-01-01

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

  9. Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach.

    PubMed

    Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

    2014-11-01

    Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems. PMID:25196726

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

    PubMed

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

    2016-01-01

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

  11. Relations between water physico-chemistry and benthic algal communities in a northern Canadian watershed: defining reference conditions using multiple descriptors of community structure.

    PubMed

    Thomas, Kathryn E; Hall, Roland I; Scrimgeour, Garry J

    2015-09-01

    Defining reference conditions is central to identifying environmental effects of anthropogenic activities. Using a watershed approach, we quantified reference conditions for benthic algal communities and their relations to physico-chemical conditions in rivers in the South Nahanni River watershed, NWT, Canada, in 2008 and 2009. We also compared the ability of three descriptors that vary in terms of analytical costs to define algal community structure based on relative abundances of (i) all algal taxa, (ii) only diatom taxa, and (iii) photosynthetic pigments. Ordination analyses showed that variance in algal community structure was strongly related to gradients in environmental variables describing water physico-chemistry, stream habitats, and sub-watershed structure. Water physico-chemistry and local watershed-scale descriptors differed significantly between algal communities from sites in the Selwyn Mountain ecoregion compared to sites in the Nahanni-Hyland ecoregions. Distinct differences in algal community types between ecoregions were apparent irrespective of whether algal community structure was defined using all algal taxa, diatom taxa, or photosynthetic pigments. Two algal community types were highly predictable using environmental variables, a core consideration in the development of Reference Condition Approach (RCA) models. These results suggest that assessments of environmental impacts could be completed using RCA models for each ecoregion. We suggest that use of algal pigments, a high through-put analysis, is a promising alternative compared to more labor-intensive and costly taxonomic approaches for defining algal community structure. PMID:26255271

  12. Relationships between an invasive crab, habitat availability and intertidal community structure at biogeographic scales.

    PubMed

    Gribben, Paul E; Simpson, Michael; Wright, Jeffrey T

    2015-09-01

    At local scales, habitat availability influences interactions between native and invasive species. Habitat availability may also predict patterns in native communities and invasive species at biogeographic scales when both native and invasive species have specific habitat requirements. The New Zealand porcelain crab, Petrolisthes elongatus, has invaded intertidal rocky shores around Tasmania, Australia, where it is found in high densities (>1800 m(2)) under rocks. A hierarchical sampling approach was used to investigate 1) the relationship between habitat availability (rock cover) and the biomass and abundance of P. elongatus, and 2) the relationship between P. elongatus biomass and native communities at local and regional scales. Invertebrate communities and habitat availability were sampled at multiple sites in the north and south regions of Tasmania. P. elongatus biomass and abundance were positively correlated with rock cover and patterns were consistent at the biogeographic scale (between regions). P. elongatus biomass was positively correlated with native species richness, biomass and abundance highlighting their co-dependence on rock cover. However, multivariate analyses indicated a different native community structure with increasing P. elongatus biomass. Flat, strongly adhering gastropods (chitons and limpets) were positively correlated with P. elongatus biomass, whereas mobile gastropods and crabs were negatively correlated with P. elongatus biomass. Despite local scale variation, there were clear consistent relationships between habitat-availability and the biomass of P. elongatus, and between native communities and the biomass of P. elongatus suggesting that the relationships between native and invasive species may be predictable at large spatial scales. Moreover, the strong relationships between P. elongatus biomass and changes in native community structure suggest a greater understanding of its impact is needed so that appropriate

  13. Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges

    PubMed Central

    Easson, Cole G.; Thacker, Robert W.

    2014-01-01

    Sponges (Porifera) can host diverse and abundant communities of microbial symbionts that make crucial contributions to host metabolism. Although these communities are often host-specific and hypothesized to co-evolve with their hosts, correlations between host phylogeny and microbiome community structure are rarely tested. As part of the Earth Microbiome Project (EMP), we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range. We tested whether (1) univariate metrics of microbiome diversity displayed significant phylogenetic signal across the host phylogeny; (2) host identity and host phylogeny were significant factors in multivariate analyses of taxonomic and phylogenetic dissimilarity; and (3) different minimum read thresholds impacted these results. We observed significant differences in univariate metrics of diversity among host species for all read thresholds, with strong phylogenetic signal in the inverse Simpson's index of diversity (D). We observed a surprisingly wide range of variability in community dissimilarity within host species (4–73%); this variability was not related to microbial abundance within a host species. Taxonomic and phylogenetic dissimilarity were significantly impacted by host identity and host phylogeny when these factors were considered individually; when tested together, the effect of host phylogeny was reduced, but remained significant. In our dataset, this outcome is largely due to closely related host sponges harboring distinct microbial taxa. Host identity maintained a strong statistical signal at all minimum read thresholds. Although the identity of specific microbial taxa varied substantially among host sponges, closely related hosts tended to harbor microbial communities with similar patterns of relative abundance. We hypothesize that microbiomes with low D might be structured by regulation of the microbial community by the host or by the presence of

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. In situ effects of titanium dioxide nanoparticles on community structure of freshwater benthic macroinvertebrates.

    PubMed

    Jovanović, Boris; Milošević, Djuradj; Piperac, Milica Stojković; Savić, Ana

    2016-06-01

    For the first time in the current literature, the effect of titanium dioxide (TiO2) nanoparticles on the community structure of macroinvertebrates has been investigated in situ. Macroinvertebrates were exposed for 100 days to an environmentally relevant concentration of TiO2 nanoparticles, 25 mg kg(-1) in sediment. Czekanowski's index was 0.61, meaning 39% of the macroinvertebrate community structure was affected by the TiO2 treatment. Non-metric multidimensional scaling (NMDS) visualized the qualitative and quantitative variability of macroinvertebrates at the community level among all samples. A distance-based permutational multivariate analysis of variance (PERMANOVA) revealed the significant effect of TiO2 on the macroinvertebrate community structure. The indicator value analysis showed that the relative frequency and abundance of Planorbarius corneus and Radix labiata were significantly lower in the TiO2 treatment than in the control. Meanwhile, Ceratopogonidae, showed a significantly higher relative frequency and abundance in the TiO2 treatment than in the control. PMID:26924756

  17. [Community structure characteristics of phytoplankton and related affecting factors in Hengshan Reservoir, Zhejiang, China].

    PubMed

    Yang, Liang-Jie; Yu, Peng-Fei; Zhu, Jun-Quan; Xu, Zhen; Lü, Guang-Han; Jin, Chun-Hua

    2014-02-01

    In order to reveal the community structure characteristics of phytoplankton and the relationships with environmental factors in Hengshan Reservoir, the phytoplankton species composition, abundance, biomass and 12 environmental factors at 4 sampling sites were analyzed from March 2011 to February 2012. A total of 246 phytoplankton species were identified, which belong to 78 genera and 7 phyla. The dominant species were Melosira varians, M. granulate, Cyclotella meneghiniana, Asterianella formosa, Synedra acus, Achnanthes exigua, Ankistrodesmus falcatus, Oscillatoria lacustris, Cryptomonas erosa, Chroomonas acuta, Phormidium tenue and Microcystis aeruginosa, etc. Seasonal variations of species were obvious. The annual abundance and biomass of the phytoplankton were 0.51 x 10(5)-14.22 x 10(5) ind x L(-1) and 0.07-1.27 mg x L(-1), respectively. The values of the Margelef index, Pielou index and Shannon index of the phytoplankton community were 1.10-3.33, 0.26-0.81 and 0.51-2.38, respectively. The phytoplankton community structure was of Bacillariophyta-Cryptophyta type in spring and winter, of Chlorophyta-Cyanophyta type in summer, and of Bacillariophyta type in autumn. Canonical correlation analysis (CCA) showed that temperature, transparency, chemical oxygen demand and pH had the closest relationships with the phytoplankton community structure in the reservoir. Water quality evaluation showed that Hengshan Reservoir was in a secondary pollution with a meso-trophic level. PMID:24830259

  18. Structure of the Tortricid-Parasitoid Community in a Recently Introduced Crop.

    PubMed

    Rocca, M; Greco, N M

    2015-12-01

    The introduction of exotic commercial plants represents a change in the food resources for the communities of herbivores. The blueberry is native to the northern hemisphere and was recently introduced in Argentina, so we expect to find polyphagous tortricids and a low complexity in the tortricid-parasitoid community. Tortricids are exophytic leaf-rollers and flower and fruit feeders, they can feed on different plant structures, and they may be present in every blueberry phenological stage. The aims of this study were (a) to estimate the relative abundance of tortricids in different plant structures and phenological stages of blueberry, (b) to evaluate the relative importance of the different parasitoid guilds, and (c) to describe the tortricid-parasitoid community in blueberry fields of Argentina. The abundance of tortricids in blueberries was low and mainly localized to flowers and fruits. Five parasitoid guilds were identified: early larval endoparasitoids (Apanteles sp. and Dolichogenidea m1 and m2), larval-prepupal endoparasitoids (Austroearinus sp.), larval-pupal endoparasitoids (Ichneumonidae), larval ectoparasitoids (Eulophidae), and pupal endoparasitoids (Brachymeria sp. and Conura sp.). Most parasitoids were koinobiont larval endoparasitoids. The tortricid-parasitoid food web was very simple in comparison to those of other systems, with high values of vulnerability and connectance. The results of this study suggest that the abundance of tortricids in blueberry crop in Argentina is low. From the point of view of production, the risk of economic losses and the likelihood of direct damage to the fruit would be very low. PMID:26385238

  19. Higher plant Ca(2+)-ATPase: primary structure and regulation of mRNA abundance by salt.

    PubMed Central

    Wimmers, L E; Ewing, N N; Bennett, A B

    1992-01-01

    Calcium-dependent regulatory mechanisms participate in diverse developmentally, hormonally, and environmentally regulated processes, with the precise control of cytosolic Ca2+ concentration being critical to such mechanisms. In plant cells, P-type Ca(2+)-ATPases localized in the plasma membrane and the endoplasmic reticulum are thought to play a central role in regulating cytoplasmic Ca2+ concentrations. Ca(2+)-ATPase activity has been identified in isolated plant cell membranes, but the protein has not been characterized at the molecular level. We have isolated a partial-length cDNA (LCA1) and a complete genomic clone (gLCA13) encoding a putative endoplasmic reticulum-localized Ca(2+)-ATPase in tomato. The deduced amino acid sequence specifies a protein (Lycopersicon Ca(2+)-ATPase) of 1048 amino acids with a molecular mass of 116 kDa, eight probable transmembrane domains, and all of the highly conserved functional domains common to P-type cation-translocating ATPases. In addition, the protein shares approximately 50% amino acid sequence identify with animal sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPases but less than 30% identity with other P-type ATPases. Genomic DNA blot hybridization analysis indicates that the Lycopersicon Ca(2+)-ATPase is encoded by a single gene. RNA blot hybridization analysis indicates the presence of three transcript sizes in root tissue and a single, much less abundant, transcript in leaves. Lycopersicon Ca(2+)-ATPase mRNA levels increase dramatically upon a 1-day exposure to 50 mM NaCl. Thus this report describes the primary structure of a higher-plant Ca(2+)-ATPase and the regulation of its mRNA abundance by salt stress. Images PMID:1384045

  20. Fish passage and abundance around grade control structures on incised streams

    USGS Publications Warehouse

    Thomas, J.T.; Papanicolaou, A.N.; Pierce, C.L.; Dermisis, D.C.; Litvan, M.E.; Larson, C.J.

    2009-01-01

    This paper summarizes research from separate studies of fish passage over weirs (Larson et al., 2004; Litvan, 2006; Litvan, et al., 2008a-c) and weir hydraulics (Papanicolaou and Dermisis, 2006; Papanicolaou and Dermisis, in press). Channel incision in the deep loess region of western Iowa has caused decreased biodiversity because streams have high sediment loads, altered flow regimes, lost habitat, and lost lateral connectivity with their former floodplains. In-stream grade control structures (GCS) are built to prevent further erosion, protect infrastructure, and reduce sediment loads. However, GCS can have a detrimental impact on fisheries abundance and migration, biodiversity, and longitudinal connectivity. Fish mark-recapture studies were performed on stretches of streams with and without GCS. GCS with vertical or 1:4 (rise/run) downstream slopes did not allow fish migration, but GCS with slopes ??? 1:15 did. GCS sites were characterized by greater proportions of pool habitat, maximum depths, fish biomass, slightly higher index of biotic integrity (IBI) scores, and greater macroinvertebrate abundance and diversity than non-GCS sites. After modification of three GCS, IBI scores increased and fish species exhibiting truncated distributions before were found throughout the study area. Another study examined the hydraulic performance of GCS to facilitate unimpeded fish passage by determining the mean and turbulent flow characteristics in the vicinity of the GCS via detailed, non-intrusive field tests. Mean flow depth (Y) and velocity (V) atop the GCS were critical for evaluating GCS performance. Turbulent flow measurements illustrated that certain GCS designs cause sudden constrictions which form eddies large enough to disorient fish. GCS with slopes ??? 1:15 best met the minimum requirements to allow catfish passage of a flow depth of ??? 0.31 m and a mean flow velocity of ??? 1.22 m/s. ?? 2009 ASCE.

  1. Plant hybrid zones affect biodiversity: Tools for a genetic-based understanding of community structure

    SciTech Connect

    Whitham, T.G.; Martinsen, G.D.; Keim, P.; Floate, K.D.; Dungey, H.S. |; Potts, B.M.

    1999-03-01

    Plant hybrid zones are dynamic centers of ecological and evolutionary processes for plants and their associated communities. Studies in the wild and in gardens with synthetic crosses showed that hybrid eucalypts supports the greatest species richness and abundances of insect and fungal taxa. In an updated review of 152 case studies of taxa associated with diverse hybridizing systems, there were 43 (28%) cases of hybrids being more susceptible than their parent species, 7 (5%) resistant, 35 (23%) additive, 35 (23%) dominant, and 32 (21%) showed no response to hybridization. Thus, most taxa respond to hybrids in ways that result in equal or greater abundance, and hybrids tend to accumulate the taxa of their parent species. These studies suggest that genetic-based plant traits affect the distribution of many species and that the variation in hybrids can be used as tools to examine the genetic components of community structure and biodiversity.

  2. Application of targeted metagenomics to explore abundance and diversity of CO₂-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea.

    PubMed

    Yousuf, Basit; Keshri, Jitendra; Mishra, Avinash; Jha, Bhavanath

    2012-09-10

    Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management. PMID:22766402

  3. Defined spatial structure stabilizes a synthetic multispecies bacterial community

    PubMed Central

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

    2008-01-01

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

  4. Environmental factors shaping the abundance and distribution of laccase-encoding bacterial community with potential phenolic oxidase capacity during composting.

    PubMed

    Lu, Lunhui; Zeng, Guangming; Fan, Changzheng; Guo, Jinsong; Zhang, Jiachao; Chen, Ming; Wu, Haipeng; Yuan, Yujie; He, Xiaoxiao; He, Yan

    2015-11-01

    Increasing molecular evidence points to a wide occurrence of laccase-like multicopper oxidase (LMCO)-encoding genes in bacteria. Most researches mainly focused on the bacterial LMCO diversity, whereas the processes and the environmental factors responsible for structuring bacterial LMCO communities remain relatively unknown in a composting system. Six gene libraries were constructed from samples in representative stages during composting. A total of 185 sequences obtained from sample DNA extracts were classified to 59 operational taxonomic units (OTUs) based on 10 % cutoff. The distribution profile of bacterial LMCO genes showed that proteobacterial- and actinobacterial-associated species were the dominant communities during composting. Pearson correlation analysis indicated that the pile temperature and water-soluble carbon (WSC) content were significantly positively correlated with bacterial LMCO gene OTU numbers, Chao1 and Shannon index, whereas the humic acid (HA)-like carbon content had the most significant effect on the distribution of the bacterial LMCO genes during composting by redundancy analysis. These findings will improve the understanding of the mutual relationship between environmental factors and bacterial LMCO community compositions in composting. PMID:26104868

  5. Algal exudates and stream organic matter influence the structure and function of denitrifying bacterial communities.

    PubMed

    Kalscheur, Kathryn N; Rojas, Miguel; Peterson, Christopher G; Kelly, John J; Gray, Kimberly A

    2012-11-01

    Within aquatic ecosystems, periphytic biofilms can be hot spots of denitrification, and previous work has suggested that algal taxa within periphyton can influence the species composition and activity of resident denitrifying bacteria. This study tested the hypothesis that algal species composition within biofilms influences the structure and function of associated denitrifying bacterial communities through the composition of organic exudates. A mixed population of bacteria was incubated with organic carbon isolated from one of seven algal species or from one of two streams that differed in anthropogenic inputs. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) revealed differences in the organic composition of algal exudates and stream waters, which, in turn, selected for distinct bacterial communities. Organic carbon source had a significant effect on potential denitrification rates (DNP) of the communities, with organics isolated from a stream with high anthropogenic inputs resulting in a bacterial community with the highest DNP. There was no correlation between DNP and numbers of denitrifiers (based on nirS copy numbers), but there was a strong relationship between the species composition of denitrifier communities (as indicated by tag pyrosequencing of nosZ genes) and DNP. Specifically, the relative abundance of Pseudomonas stutzeri-like nosZ sequences across treatments correlated significantly with DNP, and bacterial communities incubated with organic carbon from the stream with high anthropogenic inputs had the highest relative abundance of P. stutzeri-like nosZ sequences. These results demonstrate a significant relationship between bacterial community composition and function and provide evidence of the potential impacts of anthropogenic inputs on the structure and function of stream microbial communities. PMID:22828897

  6. Microzooplankton herbivory and community structure in the Amundsen Sea, Antarctica

    NASA Astrophysics Data System (ADS)

    Yang, Eun Jin; Jiang, Yong; Lee, SangHoon

    2016-01-01

    We examined microzooplankton abundance, community structure, and grazing impact on phytoplankton in the Amundsen Sea, Western Antarctica, during the early austral summer from December 2010 to January 2011. Our study area was divided into three regions based on topography, hydrographic properties, and trophic conditions: (1) the Oceanic Zone (OZ), with free sea ice and low phytoplankton biomass dominated by diatoms; (2) the Sea Ice Zone (SIZ), covered by heavy sea ice with colder water, lower salinity, and dominated by diatoms; and (3) the Amundsen Sea Polynya (ASP), with high phytoplankton biomass dominated by Phaeocystis antarctica. Microzooplankton biomass and communities associated with phytoplankton biomass and composition varied among regions. Heterotrophic dinoflagellates (HDF) were the most significant grazers in the ASP and OZ, whereas ciliates co-dominated with HDF in the SIZ. Microzooplankton grazing impact is significant in our study area, particularly in the ASP, and consumed 55.4-107.6% of phytoplankton production (average 77.3%), with grazing impact increasing with prey and grazer biomass. This result implies that a significant proportion of the phytoplankton production is not removed by sinking or other grazers but grazed by microzooplankton. Compared with diatom-based systems, Phaeocystis-based production would be largely remineralized and/or channeled through the microbial food web through microzooplankton grazing. In these waters the major herbivorous fate of phytoplankton is likely mediated by the microzooplankton population. Our study confirms the importance of herbivorous protists in the planktonic ecosystems of high latitudes. In conclusion, microzooplankton herbivory may be a driving force controlling phytoplankton growth in early summer in the Amundsen Sea, particularly in the ASP.

  7. Structure and function of a mitochondrial late embryogenesis abundant protein are revealed by desiccation.

    PubMed

    Tolleter, Dimitri; Jaquinod, Michel; Mangavel, Cécile; Passirani, Catherine; Saulnier, Patrick; Manon, Stephen; Teyssier, Emeline; Payet, Nicole; Avelange-Macherel, Marie-Hélène; Macherel, David

    2007-05-01

    Few organisms are able to withstand desiccation stress; however, desiccation tolerance is widespread among plant seeds. Survival without water relies on an array of mechanisms, including the accumulation of stress proteins such as the late embryogenesis abundant (LEA) proteins. These hydrophilic proteins are prominent in plant seeds but also found in desiccation-tolerant organisms. In spite of many theories and observations, LEA protein function remains unclear. Here, we show that LEAM, a mitochondrial LEA protein expressed in seeds, is a natively unfolded protein, which reversibly folds into alpha-helices upon desiccation. Structural modeling revealed an analogy with class A amphipathic helices of apolipoproteins that coat low-density lipoprotein particles in mammals. LEAM appears spontaneously modified by deamidation and oxidation of several residues that contribute to its structural features. LEAM interacts with membranes in the dry state and protects liposomes subjected to drying. The overall results provide strong evidence that LEAM protects the inner mitochondrial membrane during desiccation. According to sequence analyses of several homologous proteins from various desiccation-tolerant organisms, a similar protection mechanism likely acts with other types of cellular membranes. PMID:17526751

  8. Community Structural Instability, Anomie, Imitation and Adolescent Suicidal Behavior

    ERIC Educational Resources Information Center

    Thorlindsson, Thorolfur; Bernburg, Jon Gunnar

    2009-01-01

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

  9. Investigating Effects of Invasive Species on Plant Community Structure

    ERIC Educational Resources Information Center

    Franklin, Wilfred

    2008-01-01

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

  10. Is benthic food web structure related to diversity of marine macrobenthic communities?

    NASA Astrophysics Data System (ADS)

    Sokołowski, A.; Wołowicz, M.; Asmus, H.; Asmus, R.; Carlier, A.; Gasiunaité, Z.; Grémare, A.; Hummel, H.; Lesutiené, J.; Razinkovas, A.; Renaud, P. E.; Richard, P.; Kędra, M.

    2012-08-01

    Numerical structure and the organisation of food webs within macrozoobenthic communities has been assessed in the European waters (Svalbard, Barents Sea, Baltic Sea, North Sea, Atlantic Ocean and the Mediterranean Sea) to address the interactions between biodiversity and ecosystem functioning. Abundance and classical species diversity indices (S, H', J) of macrofaunal communities were related to principal attributes of food webs (relative trophic level and food chain length, FCL) that were determined from carbon and nitrogen stable isotope values. Structure of marine macrobenthos varies substantially at a geographical scale; total abundance ranges from 63 ind. m-2 to 34,517 ind. m-2, species richness varies from 3 to 166 and the Shannon-Weaver diversity index from 0.26 to 3.26 while Pielou's evenness index is below 0.73. The major source of energy for macrobenthic communities is suspended particulate organic matter, consisting of phytoplankton and detrital particles, sediment particulate organic matter, and microphytobenthos in varying proportions. These food sources support the presence of suspension- and deposit-feeding communities, which dominate numerically on the sea floor. Benthic food webs include usually four to five trophic levels (FCL varies from 3.08 to 4.86). Most species are assigned to the second trophic level (primary consumers), fewer species are grouped in the third trophic level (secondary consumers), and benthic top predators are the least numerous. Most species cluster primarily at the lowest trophic level that is consistent with the typical organization of pyramidal food webs. Food chain length increases with biodiversity, highlighting a positive effect of more complex community structure on food web organisation. In more diverse benthic communities, energy is transferred through more trophic levels while species-poor communities sustain a shorter food chain.

  11. Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting.

    PubMed

    Chen, Yuxiang; Zhang, Yufen; Zhang, Quanguo; Xu, Lixin; Li, Ran; Luo, Xiaopei; Zhang, Xin; Tong, Jin

    2015-11-01

    In the present study, maize stover was vermicomposted with the epigeic earthworm Eisenia fetida. The results showed that, during vermicomposting process, the earthworms promoted decomposition of maize stover. Analysis of microbial communities of the vermicompost by high-throughput pyrosequencing showed more complex bacterial community structure in the substrate treated by the earthworms than that in the control group. The dominant microbial genera in the treatment with the earthworms were Pseudoxanthomonas, Pseudomonas, Arthrobacter, Streptomyces, Cryptococcus, Guehomyces, and Mucor. Compared to the control group, the relative abundance of lignocellulose degradation microorganisms increased. The results indicated that the earthworms modified the structure of microbial communities during vermicomposting process, activated the growth of lignocellulose degradation microorganisms, and triggered the lignocellulose decomposition. PMID:26139410

  12. [Macrobenthic community structure and bioassessment for water quality of Banqiao Reservoir in Huaihe River basin].

    PubMed

    Sun, Wei-sheng; Gu, Qian-hong; Dong, Jing; Cheng, Qing-qing; Li, Xue-jun; Zhang, Man

    2015-09-01

    In order to demonstrate macrobenthic community structure dynamics and conduct a biological evaluation of water quality in Banqiao Reservoir, we collected seasonal samples from January to November 2014 across 15 sampling sites. A total of 17 species belonging to five families, four classes, and 3 phyla were identified, including 8 chironomidae, 4 oligochaeta and 5 mollusc. Bellamya aeruginosa, Corbicula fluminea, Branchiura sowerbyi, Pelopia sp. and Glyptotendipes sp. were the important species in Banqiao Reservoir. The total density, biomass and biodiversity of marobenthos showed significant spatial and temporal differences. ANOSIM analysis indicated that the macrobenthic community structure also differed significantly among regions and seasons, and the main contributing species were Glyptotendipes sp., Pelopia sp. and B. sowerbyi. The abundance-biomass comparison curves (ABC curves) indicated that the current macrobenthic community in Banqiao Reservoir was stable. Combined with the biodiversity index, biological pollution index (BPI) and Hilsenhoff biotic index (BI), it was suggested that Banqiao Reservoir suffered slight pollution. PMID:26785570

  13. Human gut microbiota community structures in urban and rural populations in Russia

    PubMed Central

    Tyakht, Alexander V.; Kostryukova, Elena S.; Popenko, Anna S.; Belenikin, Maxim S.; Pavlenko, Alexander V.; Larin, Andrey K.; Karpova, Irina Y.; Selezneva, Oksana V.; Semashko, Tatyana A.; Ospanova, Elena A.; Babenko, Vladislav V.; Maev, Igor V.; Cheremushkin, Sergey V.; Kucheryavyy, Yuriy A.; Shcherbakov, Petr L.; Grinevich, Vladimir B.; Efimov, Oleg I.; Sas, Evgenii I.; Abdulkhakov, Rustam A.; Abdulkhakov, Sayar R.; Lyalyukova, Elena A.; Livzan, Maria A.; Vlassov, Valentin V.; Sagdeev, Renad Z.; Tsukanov, Vladislav V.; Osipenko, Marina F.; Kozlova, Irina V.; Tkachev, Alexander V.; Sergienko, Valery I.; Alexeev, Dmitry G.; Govorun, Vadim M.

    2013-01-01

    The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. PMID:24036685

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

    PubMed

    Haytova, D; Bileva, T

    2011-01-01

    Increasing efficiency of production of vegetable crops is directly related to search for appropriate solution to increase their productivity. Organic amendments have been used for centuries to improve soil fertility and crop yield. Our study suggests that organic amendments can also be used as nematicidal agents. The survey was conducted on Experimental field of Department Horticulture at Agricultural University of Plovdiv, Bulgaria in 2009 on nematode infested sites. Combination with two types of fertilizers was used to investigate their effects on the community of soil nematodes. Characterization and comparative analysis among treatments of soil nematode community structure based on different ecological measures such as total nematode abundance, number of genera, trophic diversity and etc., was made. Changes in the composition and structure of nematode community as result of different fertilizer types were assessed. PMID:22696945

  15. Community structure variability of Uropodina mites (Acari: Mesostigmata) in nests of the common mole, Talpa europaea, in Central Europe.

    PubMed

    Napierała, Agnieszka; Mądra, Anna; Leszczyńska-Deja, Kornelia; Gwiazdowicz, Dariusz J; Gołdyn, Bartłomiej; Błoszyk, Jerzy

    2016-04-01

    Underground nests of Talpa europaea, known as the common mole, are very specific microhabitats, which are also quite often inhabited by various groups of arthropods. Mites from the suborder Uropodina (Acari: Mesostigmata) are only one of them. One could expect that mole nests that are closely located are inhabited by communities of arthropods with similar species composition and structure. However, results of empirical studies clearly show that even nests which are close to each other can be different both in terms of the species composition and abundance of Uropodina communities. So far, little is known about the factors that can cause these differences. The major aim of this study was to identify factors determining species composition, abundance, and community structure of Uropodina communities in mole nests. The study is based on material collected during a long-term investigation conducted in western parts of Poland. The results indicate that the two most important factors influencing species composition and abundance of Uropodina communities in mole nests are nest-building material and depth at which nests are located. Composition of Uropodina communities in nests of moles was also compared with that of other microhabitats (e.g. rotten wood, forest litter, soil) based on data from 4421 samples collected in Poland. Communities of this habitat prove most similar to these of open areas, especially meadows, as well as some forest types. PMID:26861069

  16. ORGANIC VS CONVENTIONAL: SOIL NEMATODE COMMUNITY STRUCTURE AND FUNCTION.

    PubMed

    Kapp, C; Storey, S G; Malan, A P

    2014-01-01

    Global increases in human population are creating an ever-greater need for food production. Poor soil management practices have degraded soil to such an extent that rapidly improved management practices is the only way to ensure future food demands. In South Africa, deciduous fruit producers are realising the need for soil health, and for an increased understanding of the benefits of soil ecology, to ensure sustainable fruit production. This depends heavily on improved orchard management. Conventional farming relies on the addition of artificial fertilizers, and the application of chemicals, to prevent or minimise, the effects of the soil stages of pest insects, and of plant-parasitic nematodes. Currently, there is resistance toward conventional farming practices, which, it is believed, diminishes biodiversity within the soil. The study aimed to establish the soil nematode community structure and function in organically, and conventionally, managed deciduous fruit orchards. This was done by determining the abundance, the diversity, and the functionality of the naturally occurring free-living, and plant-parasitic, nematodes in deciduous fruit orchards in the Western Cape province of South Africa. The objective of the study was to form the basis for the use of nematodes as future indicators of soil health in deciduous fruit orchards. Orchards from neighbouring organic, and conventional, apricot farms, and from an organic apple orchard, were studied. All the nematodes were quantified, and identified, to family level. The five nematode-classified trophic groups were found at each site, while 14 families were identified in each orchard, respectively. Herbivores were dominant in all the orchards surveyed. Organic apples had the fewest herbivores and fungivores, with the highest number of carnivores. When comparing organic with conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic apricot orchards. The Maturity Index (MI

  17. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  18. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data. PMID:26881747

  19. Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia.

    PubMed

    Rabosky, Daniel L; Cowan, Mark A; Talaba, Amanda L; Lovette, Irby J

    2011-11-01

    Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, and diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking pattern of phylogenetic evenness within local communities for all groups: pairwise correlations in species abundance across sites are negatively related to phylogenetic similarity. By modeling site suitability on the basis of species' habitat preferences, we demonstrate that phylogenetic evenness generally persists even after controlling for habitat filtering among species. This phylogenetic evenness is coupled with evolutionary lability of habitat-associated traits, to the extent that closely related species are more divergent in habitat use than distantly related species. In contrast, lizard diets are phylogenetically conserved, and pairwise dietary overlap between species is negatively related to phylogenetic distance in two of the three clades. Our results suggest that contemporary and historical species interactions have led to similar patterns of community structure across multiple clades in one of the world's most diverse lizard communities. PMID:22030728

  20. Melting glacier impacts the community structure of Bacteria, Fungi and Archaea in Chilean Patagonia fjord system

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Marcelo, ,, Dr.; Galand, Pierre; Moffat, Carlos; Pantoja, Silvio

    2014-05-01

    Seasonal and spatial variability in microbial community composition was studied by analyzing sequences of Bacteria, Archaea and Fungi in the fjord adjacent to the glacier Jorge Montt (48º20'S; 73º30' W), which has evidenced one of the most significant retreats during the past century in Patagonian Icefields. A detailed description of prokaryotic (Bacteria and Archaea) and fungal communities was carried out by pyrosequencing of 16S rRNA gene and the ITS region, respectively. Our results showed high diversity of operational taxonomic units (OTUs) in bacteria followed by the fungal community. In contrast, Archaea was characterized by low OTU abundance in most of the sampling sites and depths. Similarity in OTU composition evidenced a microbial community structure associated with hydrographic features of the fjord basin, where strong stratification maintained by the continuous input of meltwaters produces differences in the microbial composition between surface and bottom waters. Our results also showed seasonal changes in microbial components, evidencing the presence of OTUs related to cold and glacier environments in surface waters during autumn, when a wider layer of meltwater was observed. We identified at least three different microbial communities inhabiting the downstream fjord ecosystem: i) a surface waters community in autumn, with a predominance of OTUs matching with Cyanobacteria, ii) a bottom water community in autumn, where fungal OTUs predominated, and iii) a microbial community during winter with a significant presence of OTUs of Archaea. The composition of these microbial communities agrees with patterns of bacterial communities in glacial environments, marine sediments and waters and with fungal composition in coastal, marine and continental airborne. Our results indicate that hydrodynamic and water column characteristics play a main role in structuring microbial community and suggest that the progressive input of meltwater can strongly impacts the

  1. Assessing mariculture water quality with the structural and functional characteristics of a ciliate community

    NASA Astrophysics Data System (ADS)

    Li, Jiqiu; Xu, Henglong; Lin, Xiaofeng; Al-Rasheid, Khaled A. S.

    2011-01-01

    Ciliated protozoa play important roles in micro-ecosystems, especially in marine biotopes. However, few studies have been carried out on the periphytic, or aufwuch, forms in mariculture waters so far. In this study, we sampled periphytic ciliate communities in two closed mariculture ponds (ponds CP1 and CP2) and a natural seawater reservoir (pond RP) using a glass slide method to evaluate their colonizing processes and general ecological features, as well as their application as water quality indicators. We analyzed species compositions, structural parameters (species number, richness, diversity, evenness, abundance and d BP) and functional parameters ( G, S eq and T 90%). Pond RP was characterized by higher levels of structural parameters (except for abundance and d BP) and more equal proportion of the major taxonomic groups. The values of S eq were significantly higher in pond RP and similar in both pond CP1 and CP2. It was also demonstrated that environmental factors, including NO2-H, NO3-H, NH3-H, soluble reactive phosphate, temperature and pH, were the first principal factors affecting the communities. Among them, temperature and chemical factors were all significantly and negatively correlated with species number ( P<0.01), richness ( P<0.01), diversity ( P<0.01), and positive correlated with abundance ( P<0.01). Opposite correlations between pH and structural parameters were observed. This study showed that there were significant differences in species composition, structural parameters and functional parameters of the periphytic ciliate communities among the ponds, which were in agreement with the water quality. Results of this study confirmed the periphytic ciliate communities to be useful bioindicators of water quality in intensive mariculture waters.

  2. The structure and evolution of plankton communities

    NASA Astrophysics Data System (ADS)

    Longhurst, Alan R.

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

  3. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    PubMed

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  4. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    PubMed

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-06-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production. PMID:26585859

  5. Linking N2O emission from biochar-amended composting process to the abundance of denitrify (nirK and nosZ) bacteria community.

    PubMed

    Li, Shuqing; Song, Lina; Jin, Yaguo; Liu, Shuwei; Shen, Qirong; Zou, Jianwen

    2016-12-01

    Manure composting has been recognized as an important anthropogenic source of nitrous oxide (N2O) contributing to global warming. However, biochar effect on N2O emissions from manure composting is rarely evaluated, especially by linking it to abundance of denitrifying bacteria community. Results of this study indicated that biochar amendment significantly reduced N2O emissions from manure composting, primarily due to suppression of the nirK gene abundance of denitrifying bacteria. Pearson's correlation analysis showed a significant positive correlation between nirK abundance and N2O fluxes, while a negative correlation between nosZ density and N2O fluxes. Simultaneously, a linear correlation between nirK gene abundance minus nosZ gene abundance with N2O fluxes was also observed. In addition, a statistical model for estimating N2O emissions based on the bacterial denitrifying functional genes was developed and verified to adequately fit the observed emissions. Our results highlighted that biochar amendment would be an alternative strategy for mitigating N2O emissions during manure composting, and the information of related functional bacterial communities could be helpful for understanding the mechanism of N2O emissions. PMID:27207069

  6. Short term changes in zooplankton community during the summer-autumn transition in the open NW Mediterranean Sea: species composition, abundance and diversity

    NASA Astrophysics Data System (ADS)

    Raybaud, V.; Nival, P.; Mousseau, L.; Gubanova, A.; Altukhov, D.; Khvorov, S.; Ibañez, F.; Andersen, V.

    2008-05-01

    Short term changes in zooplankton community were investigated at a fixed station in offshore waters of the Ligurian Sea (Dynaproc 2 cruise, September-October 2004). Mesozooplankton was sampled with vertical WP2 hauls (200 µm mesh-size) and large mesozooplankton, macrozooplankton and micronekton with a BIONESS multinet sampler (500 µm mesh-size). Temporal variations of total biomass, species composition and abundance of major taxa were studied. Intrusions of low salinity water masses were observed two times during the cruise. The first one, which was the most important, was associated with changes in zooplankton community composition. Among copepods, the abundance of Calocalanus, Euchaeta, Heterorhabdus, Mesocalanus, Nannocalanus, Neocalanus, Pleuromamma and also calanoid copepodites increased markedly. Among non-copepod taxa, only small ostracods abundance increased. After this low salinity event, abundance of all taxa nearly returned to their initial values. The influence of salinity on each zooplankton taxon was confirmed by a statistical analysis (Perry's method). Shannon diversity index, Pielou evenness and species richness were used to describe temporal variations of large copepod (>500 µm) diversity. Shannon index and Pielou evenness decreased at the beginning of the low salinity water intrusions, but not species richness. We suggest that low salinity water masses contained its own zooplankton community and passed through the sampling area, thus causing the replacement of zooplankton population.

  7. Short term changes in zooplankton community during the summer-autumn transition in the open NW Mediterranean Sea: species composition, abundance and diversity

    NASA Astrophysics Data System (ADS)

    Raybaud, V.; Nival, P.; Mousseau, L.; Gubanova, A.; Altukhov, D.; Khvorov, S.; Ibañez, F.; Andersen, V.

    2008-12-01

    Short term changes in zooplankton community were investigated at a fixed station in offshore waters of the Ligurian Sea (DYNAPROC 2 cruise, September-October 2004). Mesozooplankton were sampled with vertical WP-II hauls (200 μm mesh-size) and large mesozooplankton, macrozooplankton and micronekton with a BIONESS multinet sampler (500 μm mesh-size). Temporal variations of total biomass, species composition and abundance of major taxa were studied. Intrusions of low salinity water masses were observed two times during the cruise. The first one, which was the most intense, was associated with changes in zooplankton community composition. Among copepods, the abundance of Calocalanus, Euchaeta, Heterorhabdus, Mesocalanus, Nannocalanus, Neocalanus, Pleuromammaand also calanoid copepodites increased markedly. Among non-copepod taxa, only small ostracods abundance increased. After this low salinity event, abundance of all taxa nearly returned to their initial values. The influence of salinity on each zooplankton taxon was confirmed by a statistical analysis (Perry's method). The Shannon diversity index, Pielou evenness and species richness were used to describe temporal variations of large copepod (>500 μm) diversity. The Shannon index and Pielou evenness decreased at the beginning of the low salinity water intrusions, but not species richness. We suggest that low salinity water masses contained its own zooplankton community and passed through the sampling area, thus causing a replacement of the zooplankton population.

  8. Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China.

    PubMed

    Zhao, Jun; Zhang, Ruifu; Xue, Chao; Xun, Weibing; Sun, Li; Xu, Yangchun; Shen, Qirong

    2014-02-01

    Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems. PMID:24276539

  9. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

    PubMed Central

    Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

    2015-01-01

    The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

  10. Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134.

    PubMed

    Ning, Chao; Yan, Shi; Hu, Kang; Cui, Yin-Qiu; Jin, Li

    2016-02-01

    The human Y-chromosome haplogroup O-M134 is one of the most abundant paternal lineages in East Asian populations, comprising ~13% of Han Chinese males, and also common in Kazakh, Korean, Japanese, Thai and so on. Despite its considerable prevalence, its current substructure is poorly resolved with only one downstream marker (M117) previously investigated. Here we address this deficiency by investigating some single-nucleotide polymorphisms (SNPs) previously reported being potentially associated with O-M134 based on high-throughput DNA-sequencing data. Using a panel of 1301 Chinese males we first identified 154 haplogroup O-M134 subjects. We then investigated the phylogenetic structure within this haplogroup using 10 SNPs (F444, F629, F3451, F46, F48, F209, F2887, F3386, F1739 and F152). Two major branches were identified, O-M117 and O-F444 and the latter was further divided into two main subclades, O-F629 and O-F3451, accounting for 10.84 and 0.92% of the Han Chinese, respectively. This update of O-M134 diversification permits better resolution of male lineages in population studies of East Asia. PMID:26306641

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

    PubMed

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

    2015-01-01

    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

  12. 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

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

    PubMed Central

    Ratnavelu, Kuru

    2016-01-01

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

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

    PubMed

    Chin, Jia Hou; Ratnavelu, Kuru

    2016-01-01

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

  15. Microbial community structures in a closed raw water distribution system biofilm as revealed by 454-pyrosequencing analysis and the effect of microbial biofilm communities on raw water quality.

    PubMed

    Luo, Jianghan; Liang, Heng; Yan, Lijun; Ma, Jun; Yang, Yanling; Li, Guibai

    2013-11-01

    This is the first report on the characterization of the microbial biofilm community structure and water quality change along a closed and stable raw water distribution system. 454-pyrosequencing was employed to investigate the microbial communities in four biofilm samples. 25,426 optimized sequences were obtained. Results showed Proteobacteria was the dominant phylum in each biofilm sample. The abundance of Nitrospiraes in M6 biofilm, Firmicutes in M8 biofilm, Actinobacteria in M9 biofilm were higher by comparing with other three biofilm samples. The M6 microbial biofilm community structure was similar to that of M7, dissimilar to that of M9. Dissolved oxygen and nitrogen was probably major factors to influence the microbial biofilm communities. Nitrospiraes in M6 biofilm and Firmicutes in M8 biofilm were crucial to remove ammonia nitrogen and nitrate in raw water. How to enrich functional microbes in biofilm to pretreat raw water is an important area of future research. PMID:24055963

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

    ERIC Educational Resources Information Center

    Akin, Renea; Park, Toby J.

    2016-01-01

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

  17. The abundant symmetry structure of hierarchies of nonlinear equations obtained by reciprocal links

    NASA Astrophysics Data System (ADS)

    Carillo, Sandra; Fuchssteiner, Benno

    1989-07-01

    Explicit computation for a Kawamoto-type equation shows that there is a rich associated symmetry structure for four separate hierarchies of nonlinear integrodifferential equations. Contrary to the general belief that symmetry groups for nonlinear evolution equations in 1+1 dimensions have to be Abelian, it is shown that, in this case, the symmetry group is noncommutative. Its semisimple part is isomorphic to the affine Lie algebra A(1)1 associated to sl(2,C). In two of the additional hierarchies that were found, an explicit dependence of the independent variable occurs. Surprisingly, the generic invariance for the Kawamoto-type equation obtained in Rogers and Carillo [Phys. Scr. 36, 865 (1987)] via a reciprocal link to the Möbius invariance of the singularity equation of the Kaup-Kupershmidt (KK) equation only holds for one of the additional hierarchies of symmetry groups. Thus the generic invariance is not a universal property for the complete symmetry group of equations obtained by reciprocal links. In addition to these results, the bi-Hamiltonian formulation of the hierarchy is given. A direct Bäcklund transformation between the (KK) hierarchy and the hierarchy of singularity equation for the Caudrey-Dodd-Gibbon-Sawada-Kotera equation is exhibited: This shows that the abundant symmetry structure found for the Kawamoto equation must exist for all fifth-order equations, which are known to be completely integrable since these equations are connected either by Bäcklund transformations or reciprocal links. It is shown that similar results must hold for all hierarchies emerging out of singularity hierarchies via reciprocal links. Furthermore, general aspects of the results are discussed.

  18. The Role of Temporal Abundance Structure and Habitat Preferences in the Survival of Conodonts during the Mid-Early Silurian Ireviken Mass Extinction Event

    PubMed Central

    Spiridonov, Andrej; Brazauskas, Antanas; Radzevičius, Sigitas

    2015-01-01

    The Ireviken event was one of the most intense extinction episodes that occurred during the mid-Paleozoic era. It had a strong global effect on a range of clades, with conodonts, graptolites and chitinozoans affected most. Using geophysical proxies and conodont species parameters of their temporal abundance structure we investigate how they affected the selectivity of conodont species survival during this calamity. After performing bivariate logistic analyses on 34 species of conodonts, we find three variables that were statistically significantly associated with their odds of survival. These namely include spectral exponents that describe degrees of autocorrelation in a time series, the skewness of species abundance distribution, and average environmental preferences, which are mostly determined by ancient water depths at sampling sites. Model selection of multivariate logistic models found the best model includes species local abundance skewness and substrate preference. A similar pattern is revealed through the regression tree analysis. The apparent extinction selectivity points to a possible causes of environmental deterioration during the Ireviken event. The significant positive relationship between extinction risk and preferential existence in deeper environments suggests the open ocean causal mechanisms of biotic stress that occurred during the Ireviken event. Marine regressions, which were previously suggested as a causal factor in this extinction episode, on theoretical grounds should have had higher impact on species living in near-shore environments, through the processes of habitat loss which are associated with decreases of shelfal areas. In addition, the significant positive correlations found between skewness of abundance distributions and spectral exponent values and the probability of species survival suggest that community and ecosystem processes (which controlled species abundance fluctuation patterns) were significantly related to selectivity

  19. The role of temporal abundance structure and habitat preferences in the survival of conodonts during the mid-early Silurian Ireviken mass extinction event.

    PubMed

    Spiridonov, Andrej; Brazauskas, Antanas; Radzevičius, Sigitas

    2015-01-01

    The Ireviken event was one of the most intense extinction episodes that occurred during the mid-Paleozoic era. It had a strong global effect on a range of clades, with conodonts, graptolites and chitinozoans affected most. Using geophysical proxies and conodont species parameters of their temporal abundance structure we investigate how they affected the selectivity of conodont species survival during this calamity. After performing bivariate logistic analyses on 34 species of conodonts, we find three variables that were statistically significantly associated with their odds of survival. These namely include spectral exponents that describe degrees of autocorrelation in a time series, the skewness of species abundance distribution, and average environmental preferences, which are mostly determined by ancient water depths at sampling sites. Model selection of multivariate logistic models found the best model includes species local abundance skewness and substrate preference. A similar pattern is revealed through the regression tree analysis. The apparent extinction selectivity points to a possible causes of environmental deterioration during the Ireviken event. The significant positive relationship between extinction risk and preferential existence in deeper environments suggests the open ocean causal mechanisms of biotic stress that occurred during the Ireviken event. Marine regressions, which were previously suggested as a causal factor in this extinction episode, on theoretical grounds should have had higher impact on species living in near-shore environments, through the processes of habitat loss which are associated with decreases of shelfal areas. In addition, the significant positive correlations found between skewness of abundance distributions and spectral exponent values and the probability of species survival suggest that community and ecosystem processes (which controlled species abundance fluctuation patterns) were significantly related to selectivity

  20. Constraining the Thermal Structure, Abundances, and Dynamics of the Exoplanet HD 209458b

    NASA Astrophysics Data System (ADS)

    Zellem, Robert; Griffith, Caitlin A.; Lewis, Nikole K.; Swain, Mark R.; Knutson, Heather A.

    2014-11-01

    HD 209458b has been extensively studied from the UV to IR as it is one of the brightest of the transiting exoplanets and has a large planet-to-star contrast. However its thermal profile and abundances remain constrained to at best 3 orders of magnitude (Line et al. 2014), largely due to a lack of spectral coverage. We expand HD 209458b’s wavelength coverage with ground and space observations. Our ground H, K, and L-band secondary eclipse spectroscopy, which explores HD 209458b’s emission mechanisms, is motivated by multiple detections of bright 3.3 μm emission on HD 189733b, resembling the CH4 ν3 band and potentially non-LTE fluorescence (Swain et al. 2010; Waldmann et al. 2012). CH4 fluorescence has previously been observed on Titan (Kim et al. 2000), Saturn, and Jupiter (Drossart et al. 1999; Brown et al. 2003), thereby likening exoplanets to their Solar System counterparts. We find that the hotter HD 209458b lacks to ~3σ a bright 3.3 μm feature as seen on HD 189733b, which is consistent with thermochemical equilibrium predictions (Moses et al. 2011). We measure HD 209458b’s longitudinally-varying thermal structure with Spitzer/IRAC full-orbit phase curve observations, and revise a previous 4.5 μm emission measurement downward by ˜35%. This change is significant because the high 4.5 and 5.8 μm brightness temperatures were interpreted as a thermal inversion (e.g., Line et al. 2014). While our 4.5 μm photometric emission point does not require an inversion, the shape of the phase curve, particularly the location and brightness temperature of the hot spot, suggests that HD 209458b has a dayside inversion. However the nightside is much cooler than predicted by a GCM. This discrepancy is potentially due to the GCM lacking quenching where vertical mixing outpaces reaction rates, causing increased CO and CH4 abundances at higher altitudes. We explore evidence for CH4 quenching with IRAC 3.6 micron data, which overlap the wings of the CH4 ν3 band, allowing

  1. Constraining the Thermal Structure, Abundances, and Dynamics of the Exoplanet HD 209458b

    NASA Astrophysics Data System (ADS)

    Zellem, Robert; Griffith, Caitlin Ann; Lewis, Nikole; Swain, Mark R.; Knutson, Heather

    2015-01-01

    HD 209458b has been extensively studied from the UV to IR as it is one of the brightest of the transiting exoplanets and has a large planet-to-star contrast. However its thermal profile and abundances remain constrained to at best 3 orders of magnitude (Line et al. 2014), largely due to a lack of spectral coverage. We expand HD 209458b's wavelength coverage with ground and space observations. Our ground H, K, and L-band secondary eclipse spectroscopy, which explores HD 209458b's emission mechanisms, is motivated by multiple detections of bright 3.3 μm emission on HD 189733b, resembling the CH4 ν3 band and potentially non-LTE fluorescence (Swain et al. 2010; Waldmann et al. 2012). CH4 fluorescence has previously been observed on Titan (Kim et al. 2000), Saturn, and Jupiter (Drossart et al. 1999; Brown et al. 2003), thereby likening exoplanets to their Solar System counterparts. We find that the hotter HD 209458b lacks to ~3σ a bright 3.3 μm feature as seen on HD 189733b, which is consistent with thermochemical equilibrium predictions (Moses et al. 2011). We measure HD 209458b's longitudinally-varying thermal structure with Spitzer/IRAC full-orbit phase curve observations, and revise a previous 4.5 μm emission measurement downward by ˜35%. This change is significant because the high 4.5 and 5.8 μm brightness temperatures were interpreted as a thermal inversion (e.g., Line et al. 2014). While our 4.5 μm photometric emission point does not require an inversion, the shape of the phase curve, particularly the location and brightness temperature of the hot spot, suggests that HD 209458b has a dayside inversion. However the nightside is much cooler than predicted by a GCM. This discrepancy is potentially due to the GCM lacking quenching where vertical mixing outpaces reaction rates, causing increased CO and CH4 abundances at higher altitudes. We explore evidence for CH4 quenching with IRAC 3.6 micron data, which overlap the wings of the CH4 ν3 band, allowing us to

  2. A Stochastic Model for Detecting Overlapping and Hierarchical Community Structure

    PubMed Central

    Cao, Xiaochun; Wang, Xiao; Jin, Di; Guo, Xiaojie; Tang, Xianchao

    2015-01-01

    Community detection is a fundamental problem in the analysis of complex networks. Recently, many researchers have concentrated on the detection of overlapping communities, where a vertex may belong to more than one community. However, most current methods require the number (or the size) of the communities as a priori information, which is usually unavailable in real-world networks. Thus, a practical algorithm should not only find the overlapping community structure, but also automatically determine the number of communities. Furthermore, it is preferable if this method is able to reveal the hierarchical structure of networks as well. In this work, we firstly propose a generative model that employs a nonnegative matrix factorization (NMF) formulization with a l2,1 norm regularization term, balanced by a resolution parameter. The NMF has the nature that provides overlapping community structure by assigning soft membership variables to each vertex; the l2,1 regularization term is a technique of group sparsity which can automatically determine the number of communities by penalizing too many nonempty communities; and hence the resolution parameter enables us to explore the hierarchical structure of networks. Thereafter, we derive the multiplicative update rule to learn the model parameters, and offer the proof of its correctness. Finally, we test our approach on a variety of synthetic and real-world networks, and compare it with some state-of-the-art algorithms. The results validate the superior performance of our new method. PMID:25822148

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

    PubMed

    Cao, Xiaochun; Wang, Xiao; Jin, Di; Guo, Xiaojie; Tang, Xianchao

    2015-01-01

    Community detection is a fundamental problem in the analysis of complex networks. Recently, many researchers have concentrated on the detection of overlapping communities, where a vertex may belong to more than one community. However, most current methods require the number (or the size) of the communities as a priori information, which is usually unavailable in real-world networks. Thus, a practical algorithm should not only find the overlapping community structure, but also automatically determine the number of communities. Furthermore, it is preferable if this method is able to reveal the hierarchical structure of networks as well. In this work, we firstly propose a generative model that employs a nonnegative matrix factorization (NMF) formulization with a l(2,1) norm regularization term, balanced by a resolution parameter. The NMF has the nature that provides overlapping community structure by assigning soft membership variables to each vertex; the l(2,1) regularization term is a technique of group sparsity which can automatically determine the number of communities by penalizing too many nonempty communities; and hence the resolution parameter enables us to explore the hierarchical structure of networks. Thereafter, we derive the multiplicative update rule to learn the model parameters, and offer the proof of its correctness. Finally, we test our approach on a variety of synthetic and real-world networks, and compare it with some state-of-the-art algorithms. The results validate the superior performance of our new method. PMID:25822148

  4. Generic criticality of community structure in random graphs

    NASA Astrophysics Data System (ADS)

    Lipowski, Adam; Lipowska, Dorota

    2014-09-01

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

  5. Disturbance frequency and community structure in a twenty-five year intervention study

    USGS Publications Warehouse

    Trexler, J.C.; Loftus, W.F.; Perry, S.

    2005-01-01

    Models of community regulation commonly incorporate gradients of disturbance inversely related to the role of biotic interactions in regulating intermediate trophic levels. Higher trophic-level organisms are predicted to be more strongly limited by intermediate levels of disturbance than are the organisms they consume. We used a manipulation of the frequency of hydrological disturbance in an intervention analysis to examine its effects on small-fish communities in the Everglades, USA. From 1978 to 2002, we monitored fishes at one long-hydroperiod (average 350 days) and at one short-hydroperiod (average 259 days; monitoring started here in 1985) site. At a third site, managers intervened in 1985 to diminish the frequency and duration of marsh drying. By the late 1990s, the successional dynamics of density and relative abundance at the intervention site converged on those of the long-hydroperiod site. Community change was manifested over 3 to 5 years following a dry-down if a site remained inundated; the number of days since the most recent drying event and length of the preceding dry period were useful for predicting population dynamics. Community dissimilarity was positively correlated with the time since last dry. Community dynamics resulted from change in the relative abundance of three groups of species linked by life-history responses to drought. Drought frequency and intensity covaried in response to hydrological manipulation at the landscape scale; community-level successional dynamics converged on a relatively small range of species compositions when drought return-time extended beyond 4 years. The density of small fishes increased with diminution of drought frequency, consistent with disturbance-limited community structure; less-frequent drying than experienced in this study (i.e., longer return times) yields predator-dominated regulation of small-fish communities in some parts of the Everglades. ?? Springer-Verlag 2005.

  6. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    PubMed Central

    Bougouffa, S.; Yang, J. K.; Lee, O. O.; Wang, Y.; Batang, Z.; Al-Suwailem, A.

    2013-01-01

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools. PMID:23542623

  7. Phytoplankton community structure and environmental parameters in aquaculture areas of Daya Bay, South China Sea.

    PubMed

    Wang, Zhaohui; Zhao, Jiangang; Zhang, Yujuan; Cao, Yu

    2009-01-01

    Environmental characteristics and phytoplankton community structure were investigated in two aquaculture areas in Dapeng Cove of Daya Bay, South China Sea, between April 2005 and June 2006. Phytoplankton abundance ranged between 5.0 and 8877.5 cells/mL, with an average of 751.8 cells/mL. The seasonal cycle of phytoplankton were demonstrated by frequent oscillations, with recurrent high abundances from late spring to autumn and a peak stage in late winter. Diatoms were the predominant phytoplankton group, accounting for 93.21% of the total abundance. The next most abundant group was the dinoflagellates, which made up only 1.24% of total abundance. High concentrations of Alexandrium tamarense (Lebour) Balech with a maximum of 603.0 cells/mL were firstly recorded in this area known for high rates of paralytic shellfish poisoning (PSP) contamination. Temperatures and salinities were within the suitable values for the growth of phytoplankton, and were important in phytoplankton seasonal fluctuations. The operation of the Daya Bay Nuclear Power Station (DNPS) exerts influences on the phytoplankton community and resulted in the high abundances of toxic dinoflagellate species during the winter months. Dissolved inorganic nitrogen (DIN) and dissolved silicate (DSi) were sufficient, and rarely limited for the growth of phytoplankton. Dissolved inorganic phosphorus (DIP) was the most necessary element for phytoplankton growth. The enriched environments accelerated the growth of small diatoms, and made for the shift in predominant species from large diatom Rhizosolenia spp. to chain-forming diatoms such as Skeletonema costatum, Pseudo-nitzschia spp. and Thalassiosira subtilis. PMID:19999976

  8. Does bird community structure vary with landscape patchiness? A Chihuahuan Desert perspective

    USGS Publications Warehouse

    Gutzwiller, K.J.; Barrow, W.C., Jr.

    2002-01-01

    During the springs of 1995-1997, we studied birds and landscapes at 70 sites in the Chihuahuan Desert to assess relations between bird community structure and landscape patchiness. Within each of two spatial extents (1-kin and 2-km-radius areas centered on each site), we measured the number of patches of individual land-cover types and the total number of patches of all land-cover types. Mean bird richness, and the mean abundance and probability of occurrence of most bird species were significantly correlated with one or more of these variables. Contrary to evidence from other systems, positive association with landscape patchiness did not increase with the degree to which species were habitat generalists, was not negatively related to body size, and did not differ between neotropical migrants and nonmigrants. For the communities' primary constituent species as a group, the strength of positive and negative associations with patchiness did not differ between landscape extents. Within the 1-km but not the 2-km extent, habitat specialists were more positively and negatively associated with patchiness than were habitat generalists. In general, however, neither habitat breadth, body size, nor migratory status seemed to be responsible for associations with landscape patchiness. Mean richness, and the mean abundance and probability of occurrence of most species were significantly correlated with patchiness within one or both extents, and patchiness of all of the most extensive land-cover types was influential. The simplest explanation for most of the bird-patchiness relations we found is that the associations reflected species-specific habitat needs. Through effects on avian richness, abundance, and occurrence, landscape patchiness affected bird community structure. A more complete understanding of the effects of landscape patchiness on bird community structure is likely to emerge when ecologists study the patchiness of major land-cover types at various spatial extents.

  9. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  10. Field-based experimental acidification alters fouling community structure and reduces diversity.

    PubMed

    Brown, Norah E M; Therriault, Thomas W; Harley, Christopher D G

    2016-09-01

    Increasing levels of CO2 in the atmosphere are affecting ocean chemistry, leading to increased acidification (i.e. decreased pH) and reductions in calcium carbonate saturation state. Many species are likely to respond to acidification, but the direction and magnitude of these responses will be based on interspecific and ontogenetic variation in physiology and the relative importance of calcification. Differential responses to ocean acidification (OA) among species will likely result in important changes in community structure and diversity. To characterize the potential impacts of OA on community composition and structure, we examined the response of a marine fouling community to experimental CO2 enrichment in field-deployed flow-through mesocosm systems. Acidification significantly altered the community structure by altering the relative abundance of species and reduced community variability, resulting in more homogenous biofouling communities from one experimental tile to the next both among and within the acidified mesocosms. Mussel (Mytilus trossulus) recruitment was reduced by over 30% in the elevated CO2 treatment compared to the ambient treatment by the end of the experiment. Strong differences in mussel cover (up to 40% lower in acidified conditions) developed over the second half of the 10-week experiment. Acidification did not appear to affect the mussel growth, as average mussel sizes were similar between treatments at the end of the experiment. Hydroid (Obelia dichotoma) cover was significantly reduced in the elevated CO2 treatment after 8 weeks. Conversely, the percentage cover of bryozoan colonies (Mebranipora membranacea) was higher under acidified conditions with differences becoming apparent after 6 weeks. Neither recruitment nor final size of barnacles (Balanus crenatus) was affected by acidification. By the end of the experiment, diversity was 41% lower in the acidified treatment relative to ambient conditions. Overall, our findings support the

  11. Virality Prediction and Community Structure in Social Networks

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  12. Community structure in traffic zones based on travel demand

    NASA Astrophysics Data System (ADS)

    Sun, Li; Ling, Ximan; He, Kun; Tan, Qian

    2016-09-01

    Large structure in complex networks can be studied by dividing it into communities or modules. Urban traffic system is one of the most critical infrastructures. It can be abstracted into a complex network composed of tightly connected groups. Here, we analyze community structure in urban traffic zones based on the community detection method in network science. Spectral algorithm using the eigenvectors of matrices is employed. Our empirical results indicate that the traffic communities are variant with the travel demand distribution, since in the morning the majority of the passengers are traveling from home to work and in the evening they are traveling a contrary direction. Meanwhile, the origin-destination pairs with large number of trips play a significant role in urban traffic network's community division. The layout of traffic community in a city also depends on the residents' trajectories.

  13. Virality prediction and community structure in social networks.

    PubMed

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

    2013-01-01

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

  14. Changes in Soil Microbial Community Structure Influenced by Agricultural Management Practices in a Mediterranean Agro-Ecosystem

    PubMed Central

    García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Scow, Kate

    2013-01-01

    Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage. PMID:24260409

  15. The role of hypoxia in structuring macrobenthos community off the Louisiana shelf

    NASA Astrophysics Data System (ADS)

    Shivarudrappa, S. K.; Briggs, K.

    2013-12-01

    Core samples were collected from 24 box cores belonging to four different provinces with varying hypoxia frequency and history in the northern Gulf of Mexico. Macrobenthos from these four provinces were sampled in spring, summer and late-summer seasons. According to historical data of bottom water oxygen concentration since 1985, the control province was exposed to hypoxia <25% of the time, the province 1 was exposed to hypoxia between 50% and 75% of the time, the province 2 was exposed to hypoxia between 25% and 50% of the time, and the province 3 was exposed to hypoxia more than 75% of the time. Samples from the three cruises performed between April 2009 and August 2010 were vertically sectioned to 25 cm sediment depth and analyzed for abundance, biomass, species diversity, and feeding types. Seasonal variability within provinces and between provinces was analyzed in terms of abundance and biomass. The Bray-Curtis dissimilarity indices indicated the four provinces have similar community composition, yet showed the impact of hypoxia in assemblages making up the four communities. Diversity indices were highest for the control province and lowest for province 3 during all three seasons, whereas diversity indices for provinces 1 and 2 showed variable seasonal variations due to hypoxia. Separation of the control province from province 3 at all three samplings by principal component analysis indicated the communities of these two provinces did not change over the period of the study. This difference in assemblages was confirmed by rarefaction curves of expected species diversity. Impact of grain size and organic matter concentration on the community structure was assessed using non-metric multi-dimensional scaling. Different species dominated by their abundance or their biomass at all four provinces, but the effect was magnified in the provinces other than the control. Capitellid, cossurid and spionid polychaetes dominated by abundance, whereas maldanid and nephtyid

  16. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

    PubMed Central

    Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

    2014-01-01

    Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

  17. Seasonal variations in phytoplankton community structure in the Sanggou, Ailian, and Lidao Bays

    NASA Astrophysics Data System (ADS)

    Yuan, Mingli; Zhang, Cuixia; Jiang, Zengjie; Guo, Shujin; Sun, Jun

    2014-12-01

    The seasonal variations in phytoplankton community structure were investigated for the Sanggou Bay (SGB) and the adjacent Ailian Bay (ALB) and Lidao Bay (LDB) in Shandong Peninsula, eastern China. The species composition and cell abundance of phytoplankton in the bay waters in spring (April 2011), summer (August 2011), autumn (October 2011), and winter (January 2012) were examined using the Utermöhl method. A total of 80 taxa of phytoplankton that belong to 39 genera of 3 phyla were identified. These included 64 species of 30 genera in the Phylum Bacillariophyta, 13 species of 8 genera in the Phylum Dinophyta, and 3 species of 1 genus in the Phylum Chrysophyta. During the four seasons, the number of phytoplankton species (43) was the highest in spring, followed by summer and autumn (40), and the lowest number of phytoplankton species (35) was found in winter. Diatoms, especially Paralia sulcata (Ehrenberg) Cleve and Coscinodiscus oculus-iridis Ehrenberg, were predominant in the phytoplankton community throughout the study period, whereas the dominance of dinoflagellate appeared in summer only. The maximum cell abundance of phytoplankton was detected in summer (average 8.08 × 103 cells L-1) whereas their minimum abundance was found in autumn (average 2.60 × 103 cells L-1). The phytoplankton abundance was generally higher in the outer bay than in the inner bay in spring and autumn. In summer, the phytoplankton cells were mainly concentrated in the south of inner SGB, with peak abundance observed along the western coast. In winter, the distribution of phytoplankton cells showed 3 patches, with peak abundance along the western coast as well. On seasonal average, the Shannon-Wiener diversity indices of phytoplankton community ranged from 1.17 to 1.78 (autumn > summer > spring > winter), and the Pielou's evenness indices of phytoplankton ranged from 0.45 to 0.65 (autumn > spring > summer > winter). According to the results of canonical correspondence analysis

  18. Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Van Geel, Maarten; Dewil, Raf; Lievens, Bart; Appels, Lise

    2016-06-01

    Comparative analyses of bacterial and archaeal community structures and dynamics in three biogas digesters during start-up and subsequent operation using microwaved, ultrasonicated or untreated waste activated sludge were performed based on 454 pyrosequencing datasets of part of 16S ribosomal RNA sequences and quantitative PCR. The pre-treatment increased the solubility, and thus the availability of the substrate for microbial degradation and significantly affected the succession of the anaerobic community structure over the course of the digestion. Bacteroidetes, Proteobacteria and Firmicutes were the dominant phyla in all digesters throughout operation. Proteobacteria decreased in relative abundance from 23-26 % to 11-13 % in association with enhanced substrate availability. Negative correlations between relative abundance of Alpha-, Beta- and Gammaproteobacteria and the substrate availability and/or biogas production were disclosed in statistical analyses. Clostridiales was the dominant order in Firmicutes, and Clostridiales, Clostridia and Firmicutes relative abundance and richness were shown to positively correlate with substrate availability and biogas generation. Methanogenic communities had a fairly restricted structure, highly dominated by Methanosaeta and Methanobrevibacter phylotypes. A gradual decline in Methanobrevibacter and increased representation of Methanosaeta concilii over time were particularly apparent in the digester receiving untreated waste activated sludge, whereas more diversified archaeal communities were maintained in the pre-treatment digesters. The quantitative PCR analyses revealed a methanogenic community distribution that coincided with the 454 pyrosequencing data. PMID:26816092

  19. 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

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

    PubMed

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

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  2. Community, trophic structure and functioning in two contrasting Laminaria hyperborea forests

    NASA Astrophysics Data System (ADS)

    Leclerc, Jean-Charles; Riera, Pascal; Laurans, Martial; Leroux, Cédric; Lévêque, Laurent; Davoult, Dominique

    2015-01-01

    Worldwide kelp forests have been the focus of several studies concerning ecosystem dysfunction in the past decades. Multifactorial kelp threats have been described and include deforestation due to human impact, cascading effects and climate change. Here, we compared community and trophic structure in two contrasting kelp forests off the coasts of Brittany. One has been harvested five years before sampling and shelters abundant omnivorous predators, almost absent from the other, which has been treated as preserved from kelp harvest. δ15N analyses conducted on the overall communities were linked to the tropho-functional structure of different strata featuring these forests (stipe and holdfast of canopy kelp and rock). Our results yielded site-to-site differences of community and tropho-functional structures across kelp strata, particularly contrasting in terms of biomass on the understorey. Similarly, isotope analyses inferred the top trophic position of Marthasterias glacialis and Echinus esculentus which may be considered as strong interactors in the sub-canopy. We interrogate these patterns and propose a series of probable and testable alternative hypotheses to explain them. For instance, we propose that differences of trophic structure and functioning result from confounded effects of contrasting wave dissipation depending on kelp size-density structure and community cascading involving these omnivorous predators. Given the species diversity and complexity of food web highlighted in these habitats, we call for further comprehensive research about the overall strata and tropho-functional groups for conservation management in kelp forests.

  3. The influence of trophic status and large-scale climatic change on the structure of fish communities in Perialpine lakes.

    PubMed

    Massol, François; David, Patrice; Gerdeaux, Daniel; Jarne, Philippe

    2007-05-01

    1. A recurrent question in ecology is the influence of environmental factors, particularly nutrients and climatic variables, on community structure and functioning, and their interaction with internal community processes (e.g. competition). 2. Perialpine lakes have been subject to two main kinds of human-induced changes over the last 50 years: eutrophication-reoligotrophication, represented by lake-specific changes in total phosphorus concentration (TP), and long-term global climatic change, captured by average winter temperature (AWT). 3. Changes in fish communities (abundance of seven species from fishery data) in 11 Perialpine lakes during 31 years (1970-2000) were investigated in relation to variation in TP and AWT using models incorporating the effects of fish maturation age, and potentially discriminating effects on adult survival and recruitment. 4. We show that phosphorus concentration affects fish abundance in species-specific ways. These effects are mediated by recruitment rather than by adult survival. Phosphorus effects are probably modulated by interspecific interactions, as increasing TP enhances total community biomass, which in turn is either positively or negatively associated with species abundance depending on species position in trophic chains. 5. Climatic change has very little effect on fish abundances, which is not consistent with the prediction of larger changes in species near their southern distribution boundary. 6. We propose several hypotheses to account for those findings, and place our study in the wider framework of community ecology. PMID:17439470

  4. The influence of trophic status and large-scale climatic change on the structure of fish communities in Perialpine lakes

    PubMed Central

    Massol, François; David, Patrice; Gerdeaux, Daniel; Jarne, Philippe

    2007-01-01

    Summary A recurrent question in ecology is the influence of environmental factors, particularly nutrients and climatic variables, on community structure and functioning, and their interaction with internal community processes (e.g. competition). Perialpine lakes have been subject to two main kinds of human-induced changes over the last fifty years: eutrophication - reoligotrophication, represented by lake-specific changes in total phosphorus concentration (TP), and long-term global climatic change, captured by average winter temperature (AWT). Changes in fish communities (abundance of seven species from fishery data) in 11 Perialpine lakes during 31 years (1970–2000) were investigated in relation to variation in TP and AWT using models incorporating the effects of fish maturation age, and potentially discriminating effects on adult survival and recruitment. We show that phosphorus concentration affects fish abundance in species-specific ways. These effects are mediated by recruitment rather than by adult survival. Phosphorus effects are probably modulated by interspecific interactions, as increasing TP enhances total community biomass, which in turn is either positively or negatively associated with species abundance depending on species position in trophic chains. Climatic change has very little effect on fish abundances, which is not consistent with the prediction of larger changes in species near their southern distribution boundary. We propose several hypotheses to account for those findings, and place our study in the wider framework of community ecology. PMID:17439470

  5. Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments▿

    PubMed Central

    Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

    2009-01-01

    Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions. PMID:19304820

  6. The Influence of Intense Chemical Pollution on the Community Composition, Diversity and Abundance of Anammox Bacteria in the Jiaojiang Estuary (China)

    PubMed Central

    Hu, Baolan; Shen, Lidong; Du, Ping; Zheng, Ping; Xu, Xiangyang; Zeng, Jiangning

    2012-01-01

    Continuous chemical pollution is one of the most serious environmental problems in the Jiaojiang Estuary of the East Sea (China). This chemical pollution has significantly changed the estuarine environmental conditions and may have profoundly influenced the distribution of anammox bacterial communities in this estuary. Here, we investigated the influence of chemical pollution on the community composition, diversity and abundance of anammox bacteria in Jiaojiang estuarine sediments. Phylogenetic analysis of 16S rRNA genes showed that the majority of anammox bacterial sequences retrieved from the estuarine intertidal sediments were associated with Kuenenia. In contrast, different anammox communities composed of Brocadia, Kuenenia, Scalindua and Jettenia were found in the estuarine subtidal sediments. Redundancy analysis (RDA) indicated that the sediment nitrobenzene and organic content had significant impacts on the distribution of anammox communities in the intertidal sediments. Pearson correlation analysis showed that the diversity of anammox bacteria in the intertidal sediments was positively correlated with the organic content. In contrast, RDA results showed that the nitrobenzene content, NO3− concentration and salinity significantly influenced the distribution of anammox communities in the subtidal sediments. The diversity and relative abundance of anammox bacteria in the subtidal sediments were positively correlated with NO3− concentration. PMID:22470481

  7. Summertime community structure of intertidal macrobenthos in Changdao Archipelago, Shandong Province, China

    NASA Astrophysics Data System (ADS)

    Wang, Xiaochen; Li, Xinzheng; Li, Baoquan; Wang, Hongfa

    2009-09-01

    The community structure of intertidal macrobenthos in Changdao Archipelago (north of Shandong Peninsula, between Bohai Bay and the northern Yellow Sea) was examined based on samples collected from 14 stations in five transects in June 2007. Three stations corresponding to high, medium and low tidal areas were set up for each transect. A total of 68 macrobenthic species were found in the research region, most of which belonged to Mollusca and Crustacea. The average abundance and biomass of the macrobenthos was 1 383 ind./m2 and 372.41 g/m2, respectively. The use of an arbitrary similarity level of 20% resulted in identification of five groups among the 14 stations in the research region. There were remarkable differences in the biomass, abundance and Shannon-Wiener diversity index of the different sediments. Specifically, the order of biomass was rocky shores > gravel > mud-sand > coarse sand > stiff mud, while the order of abundance was rocky shores > coarse sand > mud-sand > gravel > stiff mud, and that of the diversity index was mud-sand > gravel > stiff mud > rocky shores > coarse sand. The above results revealed that the sediment type was the most important factor affecting the structure of the macrobenthic community of the intertidal zone.

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

    ERIC Educational Resources Information Center

    Morest, Vanessa Smith

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Vedlitz, Arnold; Johnson, Charles A.

    1982-01-01

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

  10. Exploratory Visualization of Graphs Based on Community Structure

    ERIC Educational Resources Information Center

    Liu, Yujie

    2013-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  12. [Analysis of Prokaryotic Community Structure in River Waters of the Ningbo Sanjiang Mouth].

    PubMed

    Hu, An-yi; Li, Jiang-wei; Yang, Xiao-yong; Wang, Hong-jie; Yu, Chang-ping

    2015-07-01

    The prokaryotic community structure in river waters of the Ningbo Sanjiang Mouth was analyzed for the first time using 16S rRNA gene based-Illumina Miseq high-throughput sequencing. A total of 215 504 high-quality sequences were obtained, and the results of alpha-diversity analysis revealed that Yongjiang River Watershed (YRW) harbored high diversity and richness of prokaryotic communities. Taxonomic assignment analysis indicated that β-Proteobacterium, Actinobacteria and Bacteroidetes dominated in the river water of YRW, and accounted for 78. 88% of the total prokaryotic communities. Hydrological condition may play an important role in influencing the composition and structure of YRW prokaryotic community. In addition, several kinds of sewer- and fecal-pollution indicator bacterial groups were observed in this area with the highest abundance of pollution indicator bacteria occurring in the water sample of Yuyao River, implying that the Yuyao River might have a high potential risk of sewer- and fecal-pollution. Moreover, a total of 76 species and 18 subspecies of potential pathogenic bacteria, which accounted for 2. 19% and 0. 40% of total sequences respectively, were identified using BLASTN analysis with a local pathogenic bacteria database. Overall, this study provided an important basic data for shedding light on the structure and ecological function of YRW prokaryotic community. PMID:26489316

  13. Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer

    USGS Publications Warehouse

    Haack, S.K.; Fogarty, L.R.; West, T.G.; Alm, E.W.; McGuire, J.T.; Long, D.T.; Hyndman, D.W.; Forney, L.J.

    2004-01-01

    In a contaminated water-table aquifer, we related microbial community structure on aquifer sediments to gradients in 24 geochemical and contaminant variables at five depths, under three recharge conditions. Community amplified ribsosomal DNA restriction analysis (ARDRA) using universal 16S rDNA primers and denaturing gradient gel electrophoresis (DGGE) using bacterial 16S rDNA primers indicated: (i) communities in the anoxic, contaminated central zone were similar regardless of recharge; (ii) after recharge, communities at greatest depth were similar to those in uncontaminated zones; and (iii) after extended lack of recharge, communities at upper and lower aquifer margins differed from communities at the same depths on other dates. General aquifer geochemistry was as important as contaminant or terminal electron accepting process (TEAP) chemistry in discriminant analysis of community groups. The Shannon index of diversity (H) and the evenness index (E), based on DGGE operational taxonomic units (OTUs), were statistically different across community groups and aquifer depths. Archaea or sulphate-reducing bacteria 16S rRNA abundance was not clearly correlated with TEAP chemistry indicative of methanogenesis or sulphate reduction. Eukarya rRNA abundance varied by depth and date from 0 to 13% of the microbial community. This contaminated aquifer is a dynamic ecosystem, with complex interactions between physical, chemical and biotic components, which should be considered in the interpretation of aquifer geochemistry and in the development of conceptual or predictive models for natural attenuation or remediation.

  14. [Effects of Corbicula fluminea bioturbation on the community composition and abundance of ammonia-oxidizing archaea and bacteria in surface sediments].

    PubMed

    Wang, Xue; Zhao, Da-Yong; Zeng, Jin; Yu, Duo-Wei; Wu, Qing-Long

    2014-06-01

    To better understand the effects of Corbicula fluminea bioturbation on the ammonia-oxidizing microorganisms in the surface sediment, sediment-water microcosms with different densities of Corbicula fluminea were constructed. Clone libraries and real-time qPCR were applied to analyze the community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. The results obtained indicated that the bioturbation of Corbicula fluminea accelerated the release of nitrogen from the surface sediment. In the amoA gene clone libraries, the identified AOA amoA gene sequences affiliated with the two known clusters (marine and soil clusters). The identified AOB amoA gene sequences mostly belonged to the Nitrosomonas of beta-Proteobacteria. The abundance of the bacterial amoA gene was higher than that of the archaeal amoA gene in all treatments. With increasing density of Corbicula fluminea, decreased abundances of the bacterial amoA gene were observed. At the same time, the diversity of AOA and AOB reduced in the Corbicula fluminea containing microcosms. In conclusion, the bioturbation of Corbicula fluminea could affected the community composition and abundance of ammonia-oxidizing microorganisms in surface sediments. PMID:25158512

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

    PubMed Central

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

    1999-01-01

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

  16. Structure of dung beetle communities in an altitudinal gradient of neotropical dry forest.

    PubMed

    Domínguez, D; Marín-Armijos, D; Ruiz, C

    2015-02-01

    To understand the effects of global warming in tropical insect communities, it is necessary to comprehend how such communities respond to different abiotic factors that covariate with altitude. In this study, we partially answer this question applied to dung beetle communities distributed along an altitudinal gradient. The sampling was conducted in seven stations 100 m apart each in altitude in a dry mountain scrub in southern Ecuador. A total of 7422 individuals belonging to six species were captured. Canthon balteatus Boheman was the most abundant with 6502 individuals, and Onoreidium ohausi (Arrow) was the least abundant with 20 individuals. We found significant changes in the structure of the dung beetle communities with altitude. Two abiotic factors showed a relationship with the abundance pattern for all species (altitude, Z = 0.011, p < 0.01, and temperature, Z = 0.859, p < 0.01). Canthon balteatus Boheman showed a positive relationship with altitude (Z = 1.422, p < 0.001) and temperature (Z = 1.121, p < 0.001), Dichotomius problematicus (Lüederwaldt) a positive relationship with precipitation (Z = 0.113, p < 0.001), and Malagoniella cupreicollis (Waterhouse) a positive relationship with temperature (Z = 0.668, p < 0.001) and negative with precipitation (Z = -0.189, p < 0.001). Phanaeus achilles Boheman, Onthophagus sp., and O. ohausi (Arrow) did not show any relationship with the studied variables, nor was the richness correlated with the studied variables. These results suggest that the effects of global warming over dung beetle communities will be difficult to predict because of species-specific responses to global warming. PMID:26013011

  17. Denitrification in Agriculturally Impacted Streams: Seasonal Changes in Structure and Function of the Bacterial Community

    PubMed Central

    Manis, Erin; Royer, Todd V.; Johnson, Laura T.; Leff, Laura G.

    2014-01-01

    Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage), whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ) and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3-) and that seasonal drying of stream channels has a negative impact on NO3- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change in abundance or

  18. Influence of Diadema antillarum populations (Echinodermata: Diadematidae) on algal community structure in Jardines de la Reina, Cuba.

    PubMed

    Martín Blanco, Félix; Clero Alonso, Lídice; González Sansón, Gaspar; Amargós Fabián, Pina

    2011-09-01

    The 1983-1984 mass mortality of Diadema antillarum produced severe damages on Caribbean reefs contributing to substantial changes in community structure that still persist. Despite the importance of Diadema grazing in structuring coral reefs, available information on current abundances and algal-urchin interactions in Cuba is scarce. We analyzed spatial variations in Diadema abundance and its influence on algal community structure in 22 reef sites in Jardines de la Reina, in June/2004 and April/2005. Urchins were counted in five 30 x 2m transects per site, and algal coverage was estimated in randomly located 0.25m side quadrats (15 per site). Abundances of Diadema were higher at reef crests (0.013-1.553 ind/m2), while reef slope populations showed values up to three orders of magnitude lower and were overgrown by macroalgae (up to 87%, local values). Algal community structure at reef slopes were dominated by macroalgae, especially Dictyota, Lobophora and Halimeda while the most abundant macroalgae at reef crests were Halimeda and Amphiroa. Urchin densities were negatively and positively correlated with mean coverage of macroalgae and crustose coralline algae, respectively, when analyzing data pooled across all sites, but not with data from separate habitats (specially reef crest), suggesting, along with historical fish biomass, that shallow reef community structure is being shaped by the synergistic action of other factors (e.g. fish grazing) rather than the influence of Diadema alone. However, we observed clear signs of Diadema grazing at reef crests and decreased macroalgal cover according to 2001 data, what suggest that grazing intensity at this habitat increased at the same time that Diadema recruitment began to be noticeable. Furthermore, the excessive abundance of macroalgae at reef slopes and the scarcity of crustose coralline algae seems to be due by the almost complete absence of D. antillarum at mid depth reefs, where local densities of this urchin were

  19. The effects of climate variability on the structure of the phytoplankton community in Tumaco Bay, Colombia

    NASA Astrophysics Data System (ADS)

    Honkala, Ingrid Garcia-Hansen

    2009-12-01

    Spatiotemporal variability in the diatom and dinoflagellate community structure and chlorophyll a (chl a) concentrations in Tumaco Bay during the 1993--2005 period was related clearly to seasonal and interannual variability in environmental conditions due to the migration of the Inter-tropical Convergence Zone (ITCZ) and the influence of El Nino Southern Oscillation (ENSO) events. A total of 134 species of diatoms that belong to 57 genera, and 78 species of dinoflagellates that belong to 25 genera were identified during the survey. The diatom community was the dominant group in the waters of the bay, being the most abundant with the greatest number of species observed. The most important species was the centric diatom Skeletonema costatum (Cleve 1878). It was found that the migration of the ITCZ on the region caused a strong annual cycle. With the migration of the ITCZ to the south, Northeasterly Trade Winds dominated the area from about December to April producing oceanic and coastal upwelling. Colder sea surface temperatures (SST), the rising of the thermocline and halocline to the surface, increased nutrients and abundant rainfall were detected. This time of the year was described as the rainy season (RS)/cold phase. Opposite conditions were observed the rest of the year, defined as the dry season (DS)/warm phase. Southeasterly Trade Winds dominated at this time of the year due to the migration of the ITCZ back to the north. This seasonal cycle was affected by interannual variability due to ENSO. Five El Nino and four La Nina events were identified. In general, La Nina episodes were characterized by a shallow thermocline, cold SST, higher salinities, and the highest concentrations of nutrients. Opposite characteristics were observed during El Nino events. However, during the highest precipitations observed in every El Nino event, nutrient concentrations increased significantly. Important environmental correlates of community structure were identified using

  20. Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion.

    PubMed

    Stiborova, Hana; Wolfram, Jan; Demnerova, Katerina; Macek, Tomas; Uhlik, Ondrej

    2015-11-01

    Stabilized sewage sludge is applied to agricultural fields and farmland due to its high organic matter content. The aim of this study was to investigate the effects of two types of sludge stabilization, mesophilic anaerobic digestion (MAD) and thermophilic anaerobic digestion (TAD), on bacterial communities in sludge, including the presence of pathogenic microorganisms. Bacterial community structure and phylogenetic diversity were analyzed in four sewage sludge samples from the Czech Republic. Analysis of 16S ribosomal RNA (rRNA) genes showed that investigated sludge samples harbor diverse bacterial populations with only a few taxa present across all samples. Bacterial diversity was higher in sludge samples after MAD versus TAD treatment, and communities in MAD-treated sludge shared the highest genetic similarities. In all samples, the bacterial community was dominated by reads affiliated with Proteobacteria. The sludge after TAD treatment had considerably higher number of reads of thermotolerant/thermophilic taxa, such as the phyla Deinococcus-Thermus and Thermotogae or the genus Coprothermobacter. Only one operational taxonomic unit (OTU), which clustered with Rhodanobacter, was detected in all communities at a relative abundance >1 %. All of the communities were screened for the presence of 16S rRNA gene sequences of pathogenic bacteria using a database of 122 pathogenic species and ≥98 % identity threshold. The abundance of such sequences ranged between 0.23 and 1.57 % of the total community, with lower numbers present after the TAD treatment, indicating its higher hygienization efficiency. Sequences clustering with nontuberculous mycobacteria were present in all samples. Other detected sequences of pathogenic bacteria included Streptomyces somaliensis, Acinetobacter calcoaceticus, Alcaligenes faecalis, Gordonia spp., Legionella anisa, Bordetella bronchiseptica, Enterobacter aerogenes, Brucella melitensis, and Staphylococcus aureus. PMID:25921720

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

    USGS Publications Warehouse

    DeAngelis, Donald L.

    2005-01-01

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

  2. Assessing the structure and temporal dynamics of seabird communities: the challenge of capturing marine ecosystem complexity.

    PubMed

    Moreno, Rocío; Stowasser, Gabriele; McGill, Rona A R; Bearhop, Stuart; Phillips, Richard A

    2016-01-01

    Understanding interspecific interactions, and the influences of anthropogenic disturbance and environmental change on communities, are key challenges in ecology. Despite the pressing need to understand these fundamental drivers of community structure and dynamics, only 17% of ecological studies conducted over the past three decades have been at the community level. Here, we assess the trophic structure of the procellariiform community breeding at South Georgia, to identify the factors that determine foraging niches and possible temporal changes. We collected conventional diet data from 13 sympatric species between 1974 and 2002, and quantified intra- and inter-guild, and annual variation in diet between and within foraging habits. In addition, we tested the reliability of stable isotope analysis (SIA) of seabird feathers collected over a 13-year period, in relation to those of their potential prey, as a tool to assess community structure when diets are diverse and there is high spatial heterogeneity in environmental baselines. Our results using conventional diet data identified a four-guild community structure, distinguishing species that mainly feed on crustaceans; large fish and squid; a mixture of crustaceans, small fish and squid; or carrion. In total, Antarctic krill Euphausia superba represented 32%, and 14 other species a further 46% of the combined diet of all 13 predators, underlining the reliance of this community on relatively few types of prey. Annual variation in trophic segregation depended on relative prey availability; however, our data did not provide evidence of changes in guild structure associated with a suggested decline in Antarctic krill abundance over the past 40 years. Reflecting the differences in δ(15) N of potential prey (crustaceans vs. squid vs. fish and carrion), analysis of δ(15) N in chick feathers identified a three-guild community structure that was constant over a 13-year period, but lacked the trophic cluster representing

  3. Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

    PubMed

    McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

    2014-05-01

    Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior. PMID:24579829

  4. Effects of application of corn straw on soil microbial community structure during the maize growing season.

    PubMed

    Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

    2015-01-01

    This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. PMID:24652702

  5. Edge ratio and community structure in networks

    NASA Astrophysics Data System (ADS)

    Cafieri, Sonia; Hansen, Pierre; Liberti, Leo

    2010-02-01

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

  6. Community composition, abundance and biomass of tintinnids (Ciliata: Protozoa) in the Western Harbour, south-eastern Mediterranean Sea, Egypt.

    PubMed

    Heneash, Ahmed M M; Abdel-Rahman, Nasser S; Gharib, Samiha M

    2015-08-01

    Seasonal variations in species composition, abundance and biomass of tintinnids (Protozoa: Ciliata) were investigated in the Western Harbour, seasonally during 2012. There were remarkable seasonal variations in environmental parameters, phytoplankton concentrations and abundance and biomass of tintinnids: highest in spring and lowest in autumn. Annual average abundance and biomass of tintinnids were 8.435 ind. l(-1) and 3.725 μg C l(-1), respectively. A total of 29 species of tintinnids belonging to 11 genera was identified. Of which, Tintinnopsis was the most abundant genus in terms of number of species (9), but Favella was the best quantitatively (89% of the total tintinnids). The overall mean abundance and biomass were highest (mean 24.415 ind. l(-1) and 10.355 μg C l(-1), respectively) during spring than the remaining seasons. Due to significant positive relationship between the total biomass of tintinnids and phytoplankton concentrations, food supply is not a problem for tintinnids harbouring in the Western Harbour. Hence, predation loss by meso- and macrozooplankton might be the possible reasons for the estimated low biomass of tintinnids in the present study. Some of the seasonal environmental factors as water salinity, nitrite, dissolved oxygen and pH values exert an influence on the species composition, abundance and biomass of tintinnids. PMID:26202815

  7. Growing network model for community with group structure

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

  8. Growing network model for community with group structure.

    PubMed

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

    2005-03-01

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

  9. Method to find community structures based on information centrality

    NASA Astrophysics Data System (ADS)

    Fortunato, Santo; Latora, Vito; Marchiori, Massimo

    2004-11-01

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

  10. Exploring community structure in networks by consensus dynamics

    NASA Astrophysics Data System (ADS)

    He, He; Yang, Bo; Hu, Xiaoming

    2016-05-01

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

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

    PubMed

    Perkin, Joshuah S; Gido, Keith B

    2012-12-01

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

  12. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    PubMed

    Wieters, Evie A; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; Navarrete, Sergio A

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10's km) and local (10's m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3-4 main 'groups' of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or "insurance", against spatial variability

  13. Biogeographical Boundaries, Functional Group Structure and Diversity of Rocky Shore Communities along the Argentinean Coast

    PubMed Central

    Wieters, Evie A.; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; Navarrete, Sergio A.

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10′s km) and local (10′s m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3–4 main ‘groups’ of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or “insurance”, against spatial

  14. Distributed network management in the flat structured mobile communities

    NASA Astrophysics Data System (ADS)

    Balandina, Elena

    2005-10-01

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

  15. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany.

    PubMed

    Opitz, Sebastian; Küsel, Kirsten; Spott, Oliver; Totsche, Kai Uwe; Herrmann, Martina

    2014-10-01

    We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics. PMID:24953994

  16. Zooplankton community structure in a cyclonic and mode-water eddy in the Sargasso Sea

    NASA Astrophysics Data System (ADS)

    Eden, Bethany R.; Steinberg, Deborah K.; Goldthwait, Sarah A.; McGillicuddy, Dennis J., Jr.

    2009-10-01

    Mesoscale eddies are important suppliers of nutrients to the surface waters of oligotrophic gyres, but little is known about the biological response, particularly that of higher trophic levels, to these physical perturbations. During the summers of 2004 and 2005, we followed the development of a cyclonic eddy and an anti-cyclonic mode-water eddy in the Sargasso Sea. Zooplankton (>150 μm) were collected across both eddies in 9 discrete depth intervals between 0 and 700 m. Comparison of the abundance of major taxa of mesozooplankton in the upper 150 m at eddy center and outside the eddies (day and night) indicated that the cyclone and mode-water eddy supported similar mesozooplankton communities, with several taxa significantly higher in abundance inside than outside the eddies, when compared with the Bermuda Atlantic Time-series Study site as representative of mean conditions. In both eddies copepod peak abundance occurred in the 50-100 m depth interval, coincident with the chlorophyll a maximum, suggesting elevated food concentration in the eddies may have influenced zooplankton vertical distribution. The two eddies differed in the strength of diel vertical migration of zooplankton, as indicated by the ratio of night:day abundance in the epipelagic zone, which was higher at the center of the mode-water eddy for most taxa. Over the sampling interval of 1-2 months, abundance of the three most common taxa (copepods, chaetognaths, and ostracods) decreased in the cyclone and increased in the mode-water eddy. This further supports previous findings that over the sampling period the cyclone was in a decay phase, while the mode-water eddy was sustaining nutrient fluxes and high phytoplankton concentrations. A more detailed analysis of community structure in the mode-water eddy indicated the 0-700 m integrated abundance of doliolids was significantly higher inside the mode-water eddy than outside. The presence of a mesopelagic (200-700 m) layer of lepadid barnacle cyprids

  17. Mesozooplankton community structure in the Scotia Sea during the CCAMLR 2000 survey: January February 2000

    NASA Astrophysics Data System (ADS)

    Ward, Peter; Grant, Sharon; Brandon, Mark; Siegel, Volker; Sushin, Vyacheslav; Loeb, Valerie; Griffiths, Huw

    2004-06-01

    An analysis of mesozooplankton community structure in the Scotia Sea was carried out, based on 123 RMT1 double oblique hauls (0-200 m) taken during the CCAMLR 2000 Survey. Standardized sample data (log abundance per 1000 m 3) were grouped into taxonomic categories and subjected to cluster analysis and multi-dimensional scaling. Two ordinations were performed, the first based on a reduced taxonomic dataset (31 categories out of a full 120) obtained by pooling ontogenetic stages within species and by including only those taxa that contributed at least 4% to total abundance at any one station. This disclosed two major station groups, which separated north and south, forming 'warm' and 'cold' water communities respectively, whereas four minor groups were mainly associated with stations around the Antarctic Peninsula and within the Weddell Scotia Confluence. Mean zooplankton abundance (238 000 individuals per 1000 m 3) within the northerly group G1 was up to 12 times higher than in other groups. The second ordination using all taxonomic categories disclosed an additional intermediate group (G1a), which was geographically consistent with the southern part of the northern group 1 from the previous ordination. However, because of taxonomic similarities between all the major station groups it was concluded that they represented a single community, which differed only in its phenological development and the mass occurrence of patchily distributed organisms such as krill larvae. Testing the relationships of station groups with the position of water masses and frontal boundaries indicated that the Weddell Front was broadly coincident with the boundary of the northern and southern communities over much of its length. However, the presence of stations belonging to group G2, to the north of the Weddell Front, to the west of the Antarctic Peninsula, and around the South Sandwich Islands, was consistent with the distribution of ice-influenced surface water. Low zooplankton

  18. Wave stress and coral community structure in Hawaii

    NASA Astrophysics Data System (ADS)

    Dollar, S. J.

    1982-10-01

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

  19. Potential drivers of microbial community structure and function in Arctic spring snow

    PubMed Central

    Maccario, Lorrie; Vogel, Timothy M.; Larose, Catherine

    2014-01-01

    The Arctic seasonal snowpack can extend at times over a third of the Earth’s land surface. This chemically dynamic environment interacts constantly with different environmental compartments such as atmosphere, soil and meltwater, and thus, strongly influences the entire biosphere. However, the microbial community associated with this habitat remains poorly understood. Our objective was to investigate the functional capacities, diversity and dynamics of the microorganisms in snow and to test the hypothesis that their functional signature reflects the snow environment. We applied a metagenomic approach to nine snow samples taken over 2 months during the spring season. Fungi, Bacteroidetes, and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season. Functional data that strongly correlated with chemical parameters like mercury or nitrogen species supported that this variation could be explained by fluctuations in environmental conditions. Through inter-environmental comparisons we examined potential drivers of snowpack microbial community functioning. Known cold adaptations were detected in all compared environments without any apparent differences in their relative abundance, implying that adaptive mechanisms related to environmental factors other than temperature may play a role in defining the snow microbial community. Photochemical reactions and oxidative stress seem to be decisive parameters in structuring microbial communities inside Arctic snowpacks. PMID:25147550

  20. Environmental control on fish and macrocrustacean spring community-structure, on an intertidal sandy beach.

    PubMed

    Benazza, Achwak; Selleslagh, Jonathan; Breton, Elsa; Rabhi, Khalef; Cornille, Vincent; Bacha, Mahmoud; Lecuyer, Eric; Amara, Rachid

    2015-01-01

    The inter-annual variability of the fish and macrocrustacean spring community on an intertidal sandy beach near the Canche estuary (North of France) was studied from 2000 to 2013 based on weekly spring sampling over an 11-year period. Twenty-eight species representing 21 families were collected during the course of the study. The community was dominated by a few abundant species accounting for > 99% of the total species densities. Most individuals caught were young-of-the-year indicating the importance of this ecosystem for juvenile fishes and macrocrustaceans. Although standard qualitative community ecology metrics (species composition, richness, diversity, evenness and similarity) indicated notable stability over the study period, community structure showed a clear change since 2009. Densities of P. platessa, P. microps and A. tobianus decreased significantly since 2009, whereas over the period 2010-2013, the contribution of S. sprattus to total species density increased 4-fold. Co-inertia and generalised linear model analyses identified winter NAO index, water temperature, salinity and suspended particular matter as the major environmental factors explaining these changes. Although the recurrent and dense spring blooms of the Prymnesiophyte Phaeocystis globosa is one of the main potential threats in shallow waters of the eastern English Channel, no negative impact of its temporal change was detected on the fish and macrocrustacean spring community structure. PMID:25617852

  1. Environmental Control on Fish and Macrocrustacean Spring Community-Structure, on an Intertidal Sandy Beach

    PubMed Central

    Benazza, Achwak; Selleslagh, Jonathan; Breton, Elsa; Rabhi, Khalef; Cornille, Vincent; Bacha, Mahmoud; Lecuyer, Eric; Amara, Rachid

    2015-01-01

    The inter-annual variability of the fish and macrocrustacean spring community on an intertidal sandy beach near the Canche estuary (North of France) was studied from 2000 to 2013 based on weekly spring sampling over an 11-year period. Twenty-eight species representing 21 families were collected during the course of the study. The community was dominated by a few abundant species accounting for > 99% of the total species densities. Most individuals caught were young-of-the-year indicating the importance of this ecosystem for juvenile fishes and macrocrustaceans. Although standard qualitative community ecology metrics (species composition, richness, diversity, evenness and similarity) indicated notable stability over the study period, community structure showed a clear change since 2009. Densities of P. platessa, P. microps and A. tobianus decreased significantly since 2009, whereas over the period 2010-2013, the contribution of S. sprattus to total species density increased 4-fold. Co-inertia and generalised linear model analyses identified winter NAO index, water temperature, salinity and suspended particular matter as the major environmental factors explaining these changes. Although the recurrent and dense spring blooms of the Prymnesiophyte Phaeocystis globosa is one of the main potential threats in shallow waters of the eastern English Channel, no negative impact of its temporal change was detected on the fish and macrocrustacean spring community structure. PMID:25617852

  2. Polar front associated variation in prokaryotic community structure in Arctic shelf seafloor

    PubMed Central

    Nguyen, Tan T.; Landfald, Bjarne

    2015-01-01

    Spatial variations in composition of marine microbial communities and its causes have largely been disclosed in studies comprising rather large environmental and spatial differences. In the present study, we explored if a moderate but temporally permanent climatic division within a contiguous arctic shelf seafloor was traceable in the diversity patterns of its bacterial and archaeal communities. Soft bottom sediment samples were collected at 10 geographical locations, spanning spatial distances of up to 640 km, transecting the oceanic polar front in the Barents Sea. The northern sampling sites were generally colder, less saline, shallower, and showed higher concentrations of freshly sedimented phytopigments compared to the southern study locations. Sampling sites depicted low variation in relative abundances of taxa at class level, with persistent numerical dominance by lineages of Gamma- and Deltaproteobacteria (57–66% of bacterial sequence reads). The Archaea, which constituted 0.7–1.8% of 16S rRNA gene copy numbers in the sediment, were overwhelmingly (85.8%) affiliated with the Thaumarchaeota. Beta-diversity analyses showed the environmental variations throughout the sampling range to have a stronger impact on the structuring of both the bacterial and archaeal communities than spatial effects. While bacterial communities were significantly influenced by the combined effect of several weakly selective environmental differences, including temperature, archaeal communities appeared to be more uniquely structured by the level of freshly sedimented phytopigments. PMID:25667586