Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system.

PubMed

Revetta, R P; Gomez-Alvarez, V; Gerke, T L; Santo Domingo, J W; Ashbolt, N J

2016-07-01

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e. groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to 18 months. Differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity were associated with the classes Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Firmicutes. After 9 months the biofilm bacterial community from both GW and SW were dominated by Mycobacterium species. The distribution of the dominant operational taxonomic unit (OTU) (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature. In this study, the biofilm community structure observed between GW and SW were dissimilar, while communities from different locations receiving SW did not show significant differences. The results suggest that source water and/or the water quality shaped by their respective treatment processes may play an important role in shaping the bacterial communities in the distribution system. In addition, several bacterial groups were present in all samples, suggesting that they are an integral part of the core microbiota of this DWDS. These results provide an ecological insight into biofilm bacterial structure in chlorine-treated drinking water influenced by different water sources and their respective treatment processes. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Distribution of soft-bottom macrofauna in the deep open Baltic Sea in relation to environmental variability

NASA Astrophysics Data System (ADS)

Laine, Ari O.

2003-05-01

To analyse the large-scale distribution of soft-bottom macrofauna in the open Baltic Sea, samples for species abundance and biomass were collected in 1996-1997. Benthic community structure was used to classify and describe different assemblages and the observed distribution of communities was related to environmental factors. Distinct benthic assemblages were found that were dominated by only a few species ( Harmothoe sarsi, Saduria entomon, Monoporeia affinis, Pontoporeia femorata and Macoma balthica). These assemblages were related to different subareas and/or depth zones of the Baltic Sea. Salinity or the combined effects of salinity, dissolved oxygen and sediment organic matter content best explained the patterns in community distribution, indicating the importance of hydrography and sediment quality as structuring factors of the macrozoobenthos communities. When compared to long-term studies on Baltic macrozoobenthos it is evident that the results represent only a momentary state in the succession of the open-sea communities, which have been affected by past changes in hydrography, and will be subject to future changes in accordance with the variable environment, affected by climate.

Cascading failures in complex networks with community structure

NASA Astrophysics Data System (ADS)

Lin, Guoqiang; di, Zengru; Fan, Ying

2014-12-01

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

Potential Impacts of Climate Change on Insect Communities: A Transplant Experiment

PubMed Central

Nooten, Sabine S.; Andrew, Nigel R.; Hughes, Lesley

2014-01-01

Climate change will have profound impacts on the distribution, abundance and ecology of all species. We used a multi-species transplant experiment to investigate the potential effects of a warmer climate on insect community composition and structure. Eight native Australian plant species were transplanted into sites approximately 2.5°C (mean annual temperature) warmer than their native range. Subsequent insect colonisation was monitored for 12 months. We compared the insect communities on transplanted host plants at the warmer sites with control plants transplanted within the species' native range. Comparisons of the insect communities were also made among transplanted plants at warmer sites and congeneric plant species native to the warmer transplant area. We found that the morphospecies composition of the colonising Coleoptera and Hemiptera communities differed markedly between transplants at the control compared to the warmer sites. Community structure, as described by the distribution of feeding guilds, was also found to be different between the controls and transplants when the entire Coleoptera and Hemiptera community, including non-herbivore feeding guilds, was considered. However, the structure of the herbivorous insect community showed a higher level of consistency between plants at control and warm sites. There were marked differences in community composition and feeding guild structure, for both herbivores and non-herbivores, between transplants and congenerics at the warm sites. These results suggest that as the climate warms, considerable turnover in the composition of insect communities may occur, but insect herbivore communities may retain elements of their present-day structure. PMID:24465827

Distribution of periphytic algae in wetlands (Palm swamps, Cerrado), Brazil.

PubMed

Dunck, B; Nogueira, I S; Felisberto, S A

2013-05-01

The distribution of periphytic algae communities depends on various factors such as type of substrate, level of disturbance, nutrient availability and light. According to the prediction that impacts of anthropogenic activity provide changes in environmental characteristics, making impacted Palm swamps related to environmental changes such as deforestation and higher loads of nutrients via allochthonous, the hypothesis tested was: impacted Palm swamps have higher richness, density, biomass and biovolume of epiphytic algae. We evaluated the distribution and structure of epiphytic algae communities in 23 Palm swamps of Goiás State under different environmental impacts. The community structure attributes here analyzed were composition, richness, density, biomass and biovolume. This study revealed the importance of the environment on the distribution and structuration of algal communities, relating the higher values of richness, biomass and biovolume with impacted environments. Acidic waters and high concentration of silica were important factors in this study. Altogether 200 taxa were identified, and the zygnemaphycea was the group most representative in richness and biovolume, whereas the diatoms, in density of studied epiphyton. Impacted Palm swamps in agricultural area presented two indicator species, Gomphonema lagenula Kützing and Oedogonium sp, both related to mesotrophic to eutrophic conditions for total nitrogen concentrations of these environments.

Body size distributions signal a regime shift in a lake ecosystem

EPA Science Inventory

Communities of organisms, from mammals to microorganisms, have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at multiple spatial and temporal scales. In this st...

Community Detection Algorithm Combining Stochastic Block Model and Attribute Data Clustering

NASA Astrophysics Data System (ADS)

Kataoka, Shun; Kobayashi, Takuto; Yasuda, Muneki; Tanaka, Kazuyuki

2016-11-01

We propose a new algorithm to detect the community structure in a network that utilizes both the network structure and vertex attribute data. Suppose we have the network structure together with the vertex attribute data, that is, the information assigned to each vertex associated with the community to which it belongs. The problem addressed this paper is the detection of the community structure from the information of both the network structure and the vertex attribute data. Our approach is based on the Bayesian approach that models the posterior probability distribution of the community labels. The detection of the community structure in our method is achieved by using belief propagation and an EM algorithm. We numerically verified the performance of our method using computer-generated networks and real-world networks.

Habitat structure and body size distributions: Cross-ecosystem comparison for taxa with determinate and indeterminate growth

USGS Publications Warehouse

Nash, Kirsty L.; Allen, Craig R.; Barichievy, Chris; Nystrom, Magnus; Sundstrom, Shana M.; Graham, Nicholas A.J.

2014-01-01

Habitat structure across multiple spatial and temporal scales has been proposed as a key driver of body size distributions for associated communities. Thus, understanding the relationship between habitat and body size is fundamental to developing predictions regarding the influence of habitat change on animal communities. Much of the work assessing the relationship between habitat structure and body size distributions has focused on terrestrial taxa with determinate growth, and has primarily analysed discontinuities (gaps) in the distribution of species mean sizes (species size relationships or SSRs). The suitability of this approach for taxa with indeterminate growth has yet to be determined. We provide a cross-ecosystem comparison of bird (determinate growth) and fish (indeterminate growth) body mass distributions using four independent data sets. We evaluate three size distribution indices: SSRs, species size–density relationships (SSDRs) and individual size–density relationships (ISDRs), and two types of analysis: looking for either discontinuities or abundance patterns and multi-modality in the distributions. To assess the respective suitability of these three indices and two analytical approaches for understanding habitat–size relationships in different ecosystems, we compare their ability to differentiate bird or fish communities found within contrasting habitat conditions. All three indices of body size distribution are useful for examining the relationship between cross-scale patterns of habitat structure and size for species with determinate growth, such as birds. In contrast, for species with indeterminate growth such as fish, the relationship between habitat structure and body size may be masked when using mean summary metrics, and thus individual-level data (ISDRs) are more useful. Furthermore, ISDRs, which have traditionally been used to study aquatic systems, present a potentially useful common currency for comparing body size distributions across terrestrial and aquatic ecosystems.

Spatial P heterogeneity in forest soil: Influence on microbial P uptake and community structure

NASA Astrophysics Data System (ADS)

Zilla, Thomas; Angulo-Schipper, Bridith; Méndez, Juan Carlos; Dippold, Michaela A.; Kuzyakov, Yakov; Spielvogel, Sandra

2017-04-01

Other than nitrogen, phosphorus (P) is the most important growth limiting nutrient in soils. Yet, little information is available concerning the spatial heterogeneity of P content in forest soils. More so, the effects of a homogeneous vs. heterogeneous soil P distribution on microbial P acquisition and community structure have yet to be determined. Thus, a rhizotron experiment based on a P-deficient forest soil was conducted to investigate competitive P uptake strategies of microbes. F. sylvatica-bearing rhizotrons were labeled with Fe33PO4, a relatively immobile P source native to the study soil. Homogeneous and heterogeneous P patterns were created to study the effects of spatial P heterogeneity on plant and microbial P acquisition. P mobilization by microorganisms was tracked by an improved 33P-PLFA method, linking 33P incorporation in microbes with changes in microbial community structure in soils in situ. The microbial P uptake was enhanced in rhizotrons with high P availability and in those with a patchy P distribution. Characteristic PLFAs indicate a congregation of beech-associated ectomycorrhizal fungi in P-rich patches. These ectomycorrhizal fungi are likely to strongly increase P mobilization from the used Fe33PO4 in high P habitats. In contrast, habitats with low P availability require a more complex microbial community structure without a dominant group to mobilize this inaccessible P source. Therefore, hotspots of P are likely to promote the efforts of fungal hyphae for P mobilization - an effect which decreases with lower P content. Additionally, gram positive and negative bacteria exhibit a vastly higher P uptake under increasingly patchy P distributions. However, they form a smaller portion of the microbial community than in homogeneously P enriched rhizotrons, suggesting that filamentous organisms benefit from the patchy P distribution. Thus, only a heterogeneous P distribution promotes P acquisition of forest microbial communities from mineral P sources with low bioavailability. These novel insights into the effects of spatial P distributions on forest soil community dynamics will hopefully shed further light on microbial P cycling, thereby helping to tackle the impending global P crisis.|

Flowering and floral visitation predict changes in community structure provided that mycorrhizas remain intact.

PubMed

Bennett, Jonathan A; Cahill, James F

2018-06-01

Pollination is critical for plant fitness and population dynamics, yet little attention is paid to the role of flowering and plant-pollinator interactions in structuring plant communities, including community responses to environmental change. Changes in arbuscular mycorrhizal fungi (AMF), nutrient abundances, and plant litter all affect plant access to different resources, and are known regulators of community structure. Each factor can also affect flowering and plant-pollinator interactions, potentially contributing to changes in community structure. To test whether AMF, nutrients, and litter influenced the relationship between pollination and community structure, we conducted a 5-yr field experiment applying fungicide, adding fertilizer, and removing plant litter in native grassland. We measured the distribution of flowers and floral visits among species in year three and linked these measures to changes in plant composition and species richness between years three and five. We hypothesized that an uneven distribution of flowers and visits among species would lead to greater community change, but that the treatments would disrupt this relationship by altering sexual allocation and recruitment. Consistent with our hypothesis, communities with uneven flower distributions exhibited greater changes in community composition and richness under ambient conditions. However, AMF suppression neutralized this relationship and regulated the other treatment effects, highlighting the potential importance of AMF for stabilizing recruitment dynamics. Combined, AMF suppression and nutrient addition caused species losses when few species flowered, likely by compounding stresses for those species. The treatment effects on the relationship between flowering and community composition were more nuanced, but were likely driven by increased competition and altered flowering among species. By contrast, community composition was more stable when visitation rates were uneven among species, irrespective of any treatments. This suggests that some species require high visitation rates to maintain their populations due to greater dependence on sexual reproduction. Combined, these results highlight the importance of flowering and floral visitation to the dynamics of grassland communities. They also suggest that altered recruitment dynamics is a major, yet understudied, mechanism by which environmental change affects communities. Consequently, understanding the effects of environmental change on plant communities will require study of both plant growth and sexual reproduction. © 2018 by the Ecological Society of America.

Electronically Distributed Work Communities: Implications for Research on Telework.

ERIC Educational Resources Information Center

Hesse, Bradford W.; Grantham, Charles E.

1991-01-01

Describes the concept of telework, or telecommuting, and its influence on the electronic community and organizational structures. The electronically distributed organization is discussed, and implications for research on telework are suggested in the areas of privacy regulation, self-efficacy, temporal aspects of employee behavior, communication…

Molecular diversity of drinking water bacterial communities using 16S rRNA gene sequence analyses

EPA Science Inventory

Our understanding of the microbial community structure of drinking water distribution system has relied on culture-based methods. However, recent studies have suggested that the majority of bacteria inhabiting distribution systems are unable to grow on artificial media. The goal ...

Exploring Community Health through the Sustainable Livelihoods Framework

ERIC Educational Resources Information Center

Barnidge, Ellen K.; Baker, Elizabeth A.; Motton, Freda; Fitzgerald, Teresa; Rose, Frank

2011-01-01

Health disparities are a major concern in the United States. Research suggests that inequitable distribution of money, power, and resources shape the circumstances for daily life and create and exacerbate health disparities. In rural communities, inequitable distribution of these structural factors seems to limit employment opportunities. The…

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

PubMed

Schloss, Patrick D; Handelsman, Jo

2006-10-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

Epidemic spreading on complex networks with overlapping and non-overlapping community structure

NASA Astrophysics Data System (ADS)

Shang, Jiaxing; Liu, Lianchen; Li, Xin; Xie, Feng; Wu, Cheng

2015-02-01

Many real-world networks exhibit community structure where vertices belong to one or more communities. Recent studies show that community structure plays an import role in epidemic spreading. In this paper, we investigate how the extent of overlap among communities affects epidemics. In order to experiment on the characteristic of overlapping communities, we propose a rewiring algorithm that can change the community structure from overlapping to non-overlapping while maintaining the degree distribution of the network. We simulate the Susceptible-Infected-Susceptible (SIS) epidemic process on synthetic scale-free networks and real-world networks by applying our rewiring algorithm. Experiments show that epidemics spread faster on networks with higher level of overlapping communities. Furthermore, overlapping communities' effect interacts with the average degree's effect. Our work further illustrates the important role of overlapping communities in the process of epidemic spreading.

A mixing evolution model for bidirectional microblog user networks

NASA Astrophysics Data System (ADS)

Yuan, Wei-Guo; Liu, Yun

2015-08-01

Microblogs have been widely used as a new form of online social networking. Based on the user profile data collected from Sina Weibo, we find that the number of microblog user bidirectional friends approximately corresponds with the lognormal distribution. We then build two microblog user networks with real bidirectional relationships, both of which have not only small-world and scale-free but also some special properties, such as double power-law degree distribution, disassortative network, hierarchical and rich-club structure. Moreover, by detecting the community structures of the two real networks, we find both of their community scales follow an exponential distribution. Based on the empirical analysis, we present a novel evolution network model with mixed connection rules, including lognormal fitness preferential and random attachment, nearest neighbor interconnected in the same community, and global random associations in different communities. The simulation results show that our model is consistent with real network in many topology features.

Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States

PubMed Central

Shiro, Sokichi; Matsuura, Syota; Saiki, Rina; Sigua, Gilbert C.; Yamamoto, Akihiro; Umehara, Yosuke; Hayashi, Masaki

2013-01-01

We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean Rj genotypes (non-Rj, Rj2Rj3, and Rj4). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA Bradyrhizobium strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were Bradyrhizobium japonicum Bj123, in the northern United States, and Bradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to B. elkanii than for the cluster belonging to B. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically. PMID:23563944

Community Structure and Standing Stock of Epibenthic Zooplankton at Five Sites in Grays Harbor, Washington

DTIC Science & Technology

1981-09-01

4 GRAYS HARBOR AND CHEHALIS RIVER IMPROVEMENTS TO NAVIGATION ENVIRONMENTAL STUDIES COMMUNITY STRUCTURE AND STANDING © STOCK OF EPIBENTHIC... FISHERIES RESEARCH INSTITUTE %r UNIVERSITY OF WASHINGTON B of Engineers SEPTEMBER 1981 Seattle District(DISTRIBUTION STATEM EN T. -A-8-1 2 7 Approved...PERIOD COVERED Community Structure and Standing Stock of Final May 7. 1981 Epibenthic Zooplankton at Five Sites in 6. PERFORMING ORG. REPORT NUMBER

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor

PubMed Central

2015-01-01

Background Multiscale approaches for integrating submodels of various levels of biological organization into a single model became the major tool of systems biology. In this paper, we have constructed and simulated a set of multiscale models of spatially distributed microbial communities and study an influence of unevenly distributed environmental factors on the genetic diversity and evolution of the community members. Results Haploid Evolutionary Constructor software http://evol-constructor.bionet.nsc.ru/ was expanded by adding the tool for the spatial modeling of a microbial community (1D, 2D and 3D versions). A set of the models of spatially distributed communities was built to demonstrate that the spatial distribution of cells affects both intensity of selection and evolution rate. Conclusion In spatially heterogeneous communities, the change in the direction of the environmental flow might be reflected in local irregular population dynamics, while the genetic structure of populations (frequencies of the alleles) remains stable. Furthermore, in spatially heterogeneous communities, the chemotaxis might dramatically affect the evolution of community members. PMID:25708911

Dynamical origins of the community structure of an online multi-layer society

NASA Astrophysics Data System (ADS)

Klimek, Peter; Diakonova, Marina; Eguíluz, Víctor M.; San Miguel, Maxi; Thurner, Stefan

2016-08-01

Social structures emerge as a result of individuals managing a variety of different social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various layers in the multiplex network. Community sizes distributions are either fat-tailed or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex network. Depending on link and node fluctuation probabilities, the model exhibits an anomalous shattered fragmentation transition, where one layer fragments from one large component into many small components. The observed community size distributions are in good agreement with the predicted fragmentation in the model. This suggests that several detailed features of the fragmentation in societies can be traced back to the triadic closure processes.

Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline.

PubMed

Li, Guixiang; Xu, Guorui; Shen, Congcong; Tang, Yong; Zhang, Yuxin; Ma, Keming

2016-11-01

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.

Distributed learning automata-based algorithm for community detection in complex networks

NASA Astrophysics Data System (ADS)

Khomami, Mohammad Mehdi Daliri; Rezvanian, Alireza; Meybodi, Mohammad Reza

2016-03-01

Community structure is an important and universal topological property of many complex networks such as social and information networks. The detection of communities of a network is a significant technique for understanding the structure and function of networks. In this paper, we propose an algorithm based on distributed learning automata for community detection (DLACD) in complex networks. In the proposed algorithm, each vertex of network is equipped with a learning automation. According to the cooperation among network of learning automata and updating action probabilities of each automaton, the algorithm interactively tries to identify high-density local communities. The performance of the proposed algorithm is investigated through a number of simulations on popular synthetic and real networks. Experimental results in comparison with popular community detection algorithms such as walk trap, Danon greedy optimization, Fuzzy community detection, Multi-resolution community detection and label propagation demonstrated the superiority of DLACD in terms of modularity, NMI, performance, min-max-cut and coverage.

Delineating ecological regions in marine systems: Integrating physical structure and community composition to inform spatial management in the eastern Bering Sea

NASA Astrophysics Data System (ADS)

Baker, Matthew R.; Hollowed, Anne B.

2014-11-01

Characterizing spatial structure and delineating meaningful spatial boundaries have useful applications to understanding regional dynamics in marine systems, and are integral to ecosystem approaches to fisheries management. Physical structure and drivers combine with biological responses and interactions to organize marine systems in unique ways at multiple scales. We apply multivariate statistical methods to define spatially coherent ecological units or ecoregions in the eastern Bering Sea. We also illustrate a practical approach to integrate data on species distribution, habitat structure and physical forcing mechanisms to distinguish areas with distinct biogeography as one means to define management units in large marine ecosystems. We use random forests to quantify the relative importance of habitat and environmental variables to the distribution of individual species, and to quantify shifts in multispecies assemblages or community composition along environmental gradients. Threshold shifts in community composition are used to identify regions with distinct physical and biological attributes, and to evaluate the relative importance of predictor variables to determining regional boundaries. Depth, bottom temperature and frontal boundaries were dominant factors delineating distinct biological communities in this system, with a latitudinal divide at approximately 60°N. Our results indicate that distinct climatic periods will shift habitat gradients and that dynamic physical variables such as temperature and stratification are important to understanding temporal stability of ecoregion boundaries. We note distinct distribution patterns among functional guilds and also evidence for resource partitioning among individual species within each guild. By integrating physical and biological data to determine spatial patterns in community composition, we partition ecosystems along ecologically significant gradients. This may provide a basis for defining spatial management units or serve as a baseline index for analyses of structural shifts in the physical environment, species abundance and distribution, and community dynamics over time.

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 providing hubs/super nodes, etc.) involved in a service providing chain.

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

PubMed

Kim, Hye Min; Lee, Min Jin; Jung, Ji Young; Hwang, Chung Yeon; Kim, Mincheol; Ro, Hee-Myong; Chun, Jongsik; Lee, Yoo Kyung

2016-11-01

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Infaunal Benthic Communities from the Inner Shelf off Southwestern Africa Are Characterised by Generalist Species

PubMed Central

Steffani, Nina; Sedick, Safiyya; Rogers, John; Gibbons, Mark John

2015-01-01

Infaunal communities of benthic macro-organisms (≥ 1mm length) were studied from 81 samples collected across nine sites to the north and south of the Orange River in the Benguela upwelling ecosystem in 2003, with a view to describing communities and understanding the drivers of regional community structure, as well as to document diversity and to examine geographic affinities. Although the fauna was dominated by polychaetes and peracarid crustaceans, patterns in community structure could only weakly be explained by the measured environment (~35%). This is attributed to the generalist nature of the species recovered, which were widely distributed amongst different sediments, water-depths and latitudes. The fauna is dominated by species that enjoy a widespread regional and global distribution and is characterised by relatively low diversity, which is discussed. PMID:26618477

Species distribution modelling for plant communities: Stacked single species or multivariate modelling approaches?

Treesearch

Emilie B. Henderson; Janet L. Ohmann; Matthew J. Gregory; Heather M. Roberts; Harold S.J. Zald

2014-01-01

Landscape management and conservation planning require maps of vegetation composition and structure over large regions. Species distribution models (SDMs) are often used for individual species, but projects mapping multiple species are rarer. We compare maps of plant community composition assembled by stacking results from many SDMs with multivariate maps constructed...

Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

DTIC Science & Technology

2001-09-30

1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

Herbivore species richness, composition and community structure mediate predator richness effects and top-down control of herbivore biomass.

PubMed

Wilby, Andrew; Orwin, Kate H

2013-08-01

Changes in predator species richness can have important consequences for ecosystem functioning at multiple trophic levels, but these effects are variable and depend on the ecological context in addition to the properties of predators themselves. Here, we report an experimental study to test how species identity, community attributes, and community structure at the herbivore level moderate the effects of predator richness on ecosystem functioning. Using mesocosms containing predatory insects and aphid prey, we independently manipulated species richness at both predator and herbivore trophic levels. Community structure was also manipulated by changing the distribution of herbivore species across two plant species. Predator species richness and herbivore species richness were found to negatively interact to influence predator biomass accumulation, an effect which is hypothesised to be due to the breakdown of functional complementarity among predators in species-rich herbivore assemblages. The strength of predator suppression of herbivore biomass decreased as herbivore species richness and distribution across host plants increased, and positive predator richness effects on herbivore biomass suppression were only observed in herbivore assemblages of relatively low productivity. In summary, the study shows that the species richness, productivity and host plant distribution of prey communities can all moderate the general influence of predators and the emergence of predator species richness effects on ecosystem functioning.

Tidal Energy: The benthic effects of an operational tidal stream turbine.

PubMed

O'Carroll, J P J; Kennedy, R M; Creech, A; Savidge, G

2017-08-01

The effect of modified flow on epifaunal boulder reef communities adjacent to the SeaGen, the world's first grid-compliant tidal stream turbine, were assessed. The wake of the SeaGen was modelled and the outputs were used in conjunction with positional and substrate descriptor variables, to relate variation in epifaunal community structure to the modified physical environment. An Artificial Neural Network (ANN) and Generalised Linear Model (GLM) were used to make predictions on the distribution of Ecological Status (ES) of epifaunal communities in relation to the turbulent wake of the SeaGen. ES was assigned using the High Energy Hard Substrate (HEHS) index. ES was largely High throughout the survey area and it was not possible to make predictions on the spatial distribution of ES using an ANN or GLM. Spatial pattern in epifaunal community structure was detected when the study area was partitioned into three treatment areas: area D1; within one rotor diameter (16 m) of the centre of SeaGen, area D2; between one and three rotor diameters, and area D3; outside of three rotor diameters. Area D1 was found to be significantly more variable than D2 and D3 in terms of epifaunal community structure, bare rock distributions and ES. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community structure of copepods in the oceanic and neritic waters off Adélie and George V Land, East Antarctica, during the austral summer of 2008

NASA Astrophysics Data System (ADS)

Tachibana, Aiko; Watanabe, Yuko; Moteki, Masato; Hosie, Graham W.; Ishimaru, Takashi

2017-06-01

Copepods are one of the most important components of the Southern Ocean food web, and are widely distributed from surface to deeper waters. We conducted discrete depth sampling to clarify the community structure of copepods from the epi- to bathypelagic layers of the oceanic and neritic waters off Adélie and George V Land, East Antarctica, in the austral summer of 2008. Notably high diversity and species numbers were observed in the meso- and bathypelagic layers. Cluster analysis based on the similarity of copepod communities identified seven cluster groups, which corresponded well with water masses. In the epi- and upper- mesopelagic layers of the oceanic zone, the SB (Southern Boundary of the Antarctic Circumpolar Current) divided copepod communities. Conversely, in the lower meso- and bathypelagic layers (500-2000 m depth), communities were consistent across the SB. In these layers, the distributions of copepod species were separated by habitat depth ranges and feeding behaviour. The different food webs occur in the epipelagic layer with habitat segregation by zooplankton in their horizontal distribution ranges.

Trait-based assembly and phylogenetic structure in northeast Pacific rockfish assemblages.

PubMed

Ingram, Travis; Shurin, Jonathan B

2009-09-01

If natural communities are assembled according to deterministic rules, coexisting species will represent a nonrandom subset of the potential species pool. We tested for signatures of assembly rules in the distribution of species' traits in Pacific rockfish (Sebastes spp.) assemblages. We used morphology, dietary niche (estimated with stable nitrogen isotopes), and distribution data to identify traits that relate to local-scale resource use (the alpha-niche) and to environmental gradients (the beta-niche). We showed that gill raker morphology was related to trophic position (an alpha-niche axis), while relative eye size was associated with depth habitat (a beta-niche axis). We therefore hypothesized that, within assemblages of coexisting rockfish species, the gill raker trait would be overdispersed (evenly spaced) due to limiting similarity, while relative eye size would be clustered due to environmental filtering. We examined the evolutionary relatedness of coexisting species to ask whether phylogenetic community structure and trait distributions gave similar indications about the roles of assembly processes. We tested the trait distributions and phylogenetic structure of 30 published rockfish assemblages against a null model of random community assembly. As predicted, the gill raker trait tended to be more evenly spaced than expected by chance, as did overall body size, while relative eye size was more clustered than expected. Phylogenetic community structure appeared to reflect historical dispersal and speciation and did not provide consistent support for assembly rules. Our results indicate that rockfish community assembly is nonrandom with regard to species' traits and show how distinguishing traits related to the alpha- and beta-niches and incorporating functional morphology can provide for powerful tests of assembly rules.

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

PubMed

Richard, Ann M; Williams, ClarLynda R

2002-01-29

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.

Ectomycorrhizal fungi and interspecific competition: species interactions, community structure, coexistence mechanisms, and future research directions.

PubMed

Kennedy, Peter

2010-09-01

The field of ectomycorrhizal fungal (EMF) ecology has largely developed outside the ecological mainstream, owing in large part to the challenges in studying the structure and dynamics of EMF communities. With advances in molecular identification and other research techniques, however, there has been growing interest among mycologists and ecologists in understanding how different ecological factors affect EMF community structure and diversity. While factors such as soil chemistry and host specificity have long been considered important, an increasing number of laboratory and field studies have documented that interspecific competition also has a major impact on EMF species interactions and may significantly influence EMF community structure. In this review, I examine the progress that has been made in understanding the nature of EMF competition. Currently, there are four conclusions that can be drawn: negative competitive effects are rarely reciprocal; competitive outcomes are environmentally context-dependent; field distributions often reflect competitive interactions; and timing of colonization influences competitive success. In addition, I highlight recent studies documenting links between competitive coexistence and EMF community structure, including checkerboard distributions, lottery models, storage effects, and colonization-competition tradeoffs. Finally, I discuss several aspects of EMF competition needing further investigation and some newer methods with which to address them.

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared through 16S rRNA gene amplicon sequencing. Microbial community composition changed greatly along the salinity gradients. Using the salt-tolerance assessments to estimate bacterial trait-distributions we could determine substantial differences in tolerance to salt revealing a strong causal connection between environment and trait distributions. By constraining the community composition with salinity tolerance in ordinations, we could assign which community differences were directly due to a shift in community trait distributions. These analyses revealed that a substantial part (up to 30%) of the community composition differences were directly driven by environmental salt concentrations.. Even though communities in saline soils had trait-distributions aligned to their environment, their performance (respiration, growth rates) was lower than those in non-saline soils and remained low even after input of organic material. Using a trait-based approach we could connect filtered trait distributions along environmental gradients, to the composition of the microbial community. We show that soil salinity played an important role in shaping microbial community composition by selecting for communities with higher salt tolerance. The shift toward bacterial communities with trait distributions matched to salt environments probably compensated for much of the potential loss of function induced by salinity, resulting in a degree of apparent functional redundancy for decomposition. However, more tolerant communities still showed reduced functioning, suggesting a trade-off between salt tolerance and performance.

Benthic Algal Community Structures and Their Response to Geographic Distance and Environmental Variables in the Qinghai-Tibetan Lakes With Different Salinity

PubMed Central

Yang, Jian; Jiang, Hongchen; Liu, Wen; Wang, Beichen

2018-01-01

Uncovering the limiting factors for benthic algal distributions in lakes is of great importance to understanding of their role in global carbon cycling. However, limited is known about the benthic algal community distribution and how they are influenced by geographic distance and environmental variables in alpine lakes. Here, we investigated the benthic algal community compositions in the surface sediments of six lakes on the Qinghai-Tibetan Plateau (QTP), China (salinity ranging from 0.8 to 365.6 g/L; pairwise geographic distance among the studied lakes ranging 8–514 km) employing an integrated approach including Illumina-Miseq sequencing and environmental geochemistry. The results showed that the algal communities of the studied samples were mainly composed of orders of Bacillariales, Ceramiales, Naviculales, Oscillatoriales, Spirulinales, Synechococcales, and Vaucheriales. The benthic algal community compositions in these QTP lakes were significantly (p < 0.05) correlated with many environmental (e.g., dissolved inorganic and organic carbon, illumination intensity, total nitrogen and phosphorus, turbidity and water temperature) and spatial factors, and salinity did not show significant influence on the benthic algal community structures in the studied lakes. Furthermore, geographic distance showed strong, significant correlation (r = 0.578, p < 0.001) with the benthic algal community compositions among the studied lakes, suggesting that spatial factors may play important roles in influencing the benthic algal distribution. These results expand our current knowledge on the influencing factors for the distributions of benthic alga in alpine lakes. PMID:29636745

A hierarchical framework for investigating epiphyte assemblages: networks, meta-communities, and scale.

PubMed

Burns, K C; Zotz, G

2010-02-01

Epiphytes are an important component of many forested ecosystems, yet our understanding of epiphyte communities lags far behind that of terrestrial-based plant communities. This discrepancy is exacerbated by the lack of a theoretical context to assess patterns in epiphyte community structure. We attempt to fill this gap by developing an analytical framework to investigate epiphyte assemblages, which we then apply to a data set on epiphyte distributions in a Panamanian rain forest. On a coarse scale, interactions between epiphyte species and host tree species can be viewed as bipartite networks, similar to pollination and seed dispersal networks. On a finer scale, epiphyte communities on individual host trees can be viewed as meta-communities, or suites of local epiphyte communities connected by dispersal. Similar analytical tools are typically employed to investigate species interaction networks and meta-communities, thus providing a unified analytical framework to investigate coarse-scale (network) and fine-scale (meta-community) patterns in epiphyte distributions. Coarse-scale analysis of the Panamanian data set showed that most epiphyte species interacted with fewer host species than expected by chance. Fine-scale analyses showed that epiphyte species richness on individual trees was lower than null model expectations. Therefore, epiphyte distributions were clumped at both scales, perhaps as a result of dispersal limitations. Scale-dependent patterns in epiphyte species composition were observed. Epiphyte-host networks showed evidence of negative co-occurrence patterns, which could arise from adaptations among epiphyte species to avoid competition for host species, while most epiphyte meta-communities were distributed at random. Application of our "meta-network" analytical framework in other locales may help to identify general patterns in the structure of epiphyte assemblages and their variation in space and time.

Effect of short-term hypoxia on marine nematode community structure and vertical distribution pattern in three different sediment types of the North Sea.

PubMed

Taheri, Mehrshad; Braeckman, Ulrike; Vincx, Magda; Vanaverbeke, Jan

2014-08-01

The responses of nematode communities to short-term hypoxia (1 and 7 days) were investigated in three North Sea stations with different sediment types (coarse silt, fine sand and medium sand). In the field, nematode density, diversity, vertical distribution and community structure differ among the stations. In the laboratory, oxic and hypoxic treatments were established for 1 and 7 days for all sediment types. Comparison between field control and oxic day 1 treatments showed that experimental sediment handling did not affect nematode characteristics. Our results revealed that short-term hypoxia did not affect total density, diversity, community composition, vertical density profiles (except in the fine sand) and densities of five dominant species in all sediment types. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

PubMed

Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

2015-02-01

In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

Do priority effects outweigh environmental filtering in a guild of dominant freshwater macroinvertebrates?

PubMed

Little, Chelsea J; Altermatt, Florian

2018-04-11

Abiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we hypothesized that in 10 naturally replicated headwater streams in eastern Switzerland, locally dominant amphipod species would be associated with differences in environmental conditions. We conducted repeated surveys of amphipods and used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by the model, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect related to the specific linear configuration of streams determines which species colonizes and dominates a given stream catchment, thus suggesting a new solution a long-standing conundrum in freshwater ecology. © 2018 The Author(s).

Community financing of local ivermectin distribution in Nigeria: potential payment and cost-recovery outlook.

PubMed

Onwujekwe, O E; Shu, E N; Okonkwo, P O

2000-04-01

The preferred payment mechanism in a community financing scheme for local ivermectin distribution was elicited from randomly selected household heads from three communities in Nigeria using interviewer-administered structured questionnaires. The majority of the respondents in the three communities were prepared to pay for local ivermectin distribution. Additionally, the average amounts the respondents were prepared to pay per person treated ($0.28, $0.30 and $0.38 in Nike, Achi and Toro, respectively) were all more than the $0.20 ceiling recommended by the partners of the African Programme on Onchocerciasis Control (APOC). Thus, the cost-recovery outlook is bright in these communities. However, the preferred payment modality varied. Fee-for-service was the predominant payment modality in the Achi and Nike communities, while the Toro community preferred pre-payment. This study demonstrates that many communities have different payment preferences for endemic disease control efforts. This knowledge will help in developing acceptable and sustainable schemes. The imposition of unacceptable payment mechanisms will lead to an unwillingness to pay.

Network Skewness Measures Resilience in Lake Ecosystems

NASA Astrophysics Data System (ADS)

Langdon, P. G.; Wang, R.; Dearing, J.; Zhang, E.; Doncaster, P.; Yang, X.; Yang, H.; Dong, X.; Hu, Z.; Xu, M.; Yanjie, Z.; Shen, J.

2017-12-01

Changes in ecosystem resilience defy straightforward quantification from biodiversity metrics, which ignore influences of community structure. Naturally self-organized network structures show positive skewness in the distribution of node connections. Here we test for skewness reduction in lake diatom communities facing anthropogenic stressors, across a network of 273 lakes in China containing 452 diatom species. Species connections show positively skewed distributions in little-impacted lakes, switching to negative skewness in lakes associated with human settlement, surrounding land-use change, and higher phosphorus concentration. Dated sediment cores reveal a down-shifting of network skewness as human impacts intensify, and reversal with recovery from disturbance. The appearance and degree of negative skew presents a new diagnostic for quantifying system resilience and impacts from exogenous forcing on ecosystem communities.

Multilevel Drivers of HIV/AIDS among Black Philadelphians: Exploration Using Community Ethnography and Geographic Information Systems

PubMed Central

Brawner, Bridgette M.; Reason, Janaiya L.; Goodman, Bridget A.; Schensul, Jean J.; Guthrie, Barbara

2014-01-01

Background Unequal HIV/AIDS distribution is influenced by certain social and structural contexts that facilitate HIV transmission and concentrate HIV in disease epicenters. Thus, one of the first steps in designing effective community-level HIV/AIDS initiatives is to disentangle the influence of individual, social, and structural factors on HIV risk. Combining ethnographic methodology with geographic information systems (GIS) mapping can allow for a complex exploration of multilevel factors within communities that facilitate HIV transmission in highly affected areas. Objectives We present the formative comparative community-based case study findings of an investigation of individual-, social- , and structural-level factors that contribute to the HIV/AIDS epidemic among Black Philadelphians. Methods Communities were defined using census tracts. The methodology included ethnographic and GIS mapping, observation, informal conversations with residents and business owners, and secondary analyses of census tract-level data in four Philadelphia neighborhoods. Results Factors such as overcrowding, disadvantage, permeability in community boundaries, and availability and accessibility of health-related resources varied significantly. Further, HIV/AIDS trended with social and structural inequities above and beyond the community’s racial composition. Discussion This study was a first step to disentangle relationships between community-level factors and potential risk for HIV in an HIV epicenter. The findings also highlight stark sociodemographic differences within and across racial groups, and further substantiate the need for comprehensive, community-level HIV prevention interventions. These findings from targeted United States urban communities have potential applicability for examining the distribution of HIV/AIDS in broader national and international geosocial contexts. PMID:25738621

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

PubMed

Anderson, Rika E; Sogin, Mitchell L; Baross, John A

2015-01-01

Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

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

Mobberley, Jennifer M.; Lindemann, Stephen R.; Bernstein, Hans C.

2017-03-21

Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements. Draft reconstructed genomes of abundantmore » organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence upon metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.« less

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.

[Fleas on small mammals in the surrounding area of Erhai Lake].

PubMed

Dong, Wen-Ge; Guo, Xian-Guo; Men, Xing-Yuan; Gong, Zheng-Da; Wu, Dian; Zhang, Zheng-Kun; Zhang, Li-Yun

2009-12-01

To investigate the distribution pattern, species diversity and community structure of fleas on small mammals in the surrounding area of Erhai Lake, and the relationship between fleas and their hosts. Different geographical areas surrounding the Erhai Lake in Yunnan were selected as investigated spots. Small mammals were captured with baited cages. The cage-traps were examined and re-baited each morning. All fleas on the hosts were collected and identified. The richness (S), evenness (J'), diversity index (H'), dominance index (C'), total ectoparasite infestation rate (Rpt), total ectoparasite infestation index (Ipt), and constituent ratio (Cr) were used to measure the community structure. Altogether, 3,303 small mammals and 3,243 fleas were collected. From the 21 species of small mammal hosts, 13 species of fleas were identified. In southern area of the Lake, the species richness (21 species of small mammals & 12 species of fleas) was highest among the three selected areas. Seventeen species of small mammals and 8 species of fleas were found in eastern area, and only 13 species of small mammals and 7 species of fleas found in the west. This implied the probable influences of ecological environments on the fleas and their corresponding hosts. The community structure of fleas on small mammals was complex. The species diversity, species composition, community structure and distribution pattern of fleas were simultaneously influenced by the hosts' body surface microenvironment and the macroenvironment (habitat). The fleas are commonly distributed in small mammals in the areas and their communities are related to host species and the habitats.

Combining a popularity-productivity stochastic block model with a discriminative-content model for general structure detection.

PubMed

Chai, Bian-fang; Yu, Jian; Jia, Cai-Yan; Yang, Tian-bao; Jiang, Ya-wen

2013-07-01

Latent community discovery that combines links and contents of a text-associated network has drawn more attention with the advance of social media. Most of the previous studies aim at detecting densely connected communities and are not able to identify general structures, e.g., bipartite structure. Several variants based on the stochastic block model are more flexible for exploring general structures by introducing link probabilities between communities. However, these variants cannot identify the degree distributions of real networks due to a lack of modeling of the differences among nodes, and they are not suitable for discovering communities in text-associated networks because they ignore the contents of nodes. In this paper, we propose a popularity-productivity stochastic block (PPSB) model by introducing two random variables, popularity and productivity, to model the differences among nodes in receiving links and producing links, respectively. This model has the flexibility of existing stochastic block models in discovering general community structures and inherits the richness of previous models that also exploit popularity and productivity in modeling the real scale-free networks with power law degree distributions. To incorporate the contents in text-associated networks, we propose a combined model which combines the PPSB model with a discriminative model that models the community memberships of nodes by their contents. We then develop expectation-maximization (EM) algorithms to infer the parameters in the two models. Experiments on synthetic and real networks have demonstrated that the proposed models can yield better performances than previous models, especially on networks with general structures.

Combining a popularity-productivity stochastic block model with a discriminative-content model for general structure detection

NASA Astrophysics Data System (ADS)

Chai, Bian-fang; Yu, Jian; Jia, Cai-yan; Yang, Tian-bao; Jiang, Ya-wen

2013-07-01

Latent community discovery that combines links and contents of a text-associated network has drawn more attention with the advance of social media. Most of the previous studies aim at detecting densely connected communities and are not able to identify general structures, e.g., bipartite structure. Several variants based on the stochastic block model are more flexible for exploring general structures by introducing link probabilities between communities. However, these variants cannot identify the degree distributions of real networks due to a lack of modeling of the differences among nodes, and they are not suitable for discovering communities in text-associated networks because they ignore the contents of nodes. In this paper, we propose a popularity-productivity stochastic block (PPSB) model by introducing two random variables, popularity and productivity, to model the differences among nodes in receiving links and producing links, respectively. This model has the flexibility of existing stochastic block models in discovering general community structures and inherits the richness of previous models that also exploit popularity and productivity in modeling the real scale-free networks with power law degree distributions. To incorporate the contents in text-associated networks, we propose a combined model which combines the PPSB model with a discriminative model that models the community memberships of nodes by their contents. We then develop expectation-maximization (EM) algorithms to infer the parameters in the two models. Experiments on synthetic and real networks have demonstrated that the proposed models can yield better performances than previous models, especially on networks with general structures.

Recent warming leads to a rapid borealization of fish communities in the Arctic

NASA Astrophysics Data System (ADS)

Fossheim, Maria; Primicerio, Raul; Johannesen, Edda; Ingvaldsen, Randi B.; Aschan, Michaela M.; Dolgov, Andrey V.

2015-07-01

Arctic marine ecosystems are warming twice as fast as the global average. As a consequence of warming, many incoming species experience increasing abundances and expanding distribution ranges in the Arctic. The Arctic is expected to have the largest species turnover with regard to invading and locally extinct species, with a modelled invasion intensity of five times the global average. Studies in this region might therefore give valuable insights into community-wide shifts of species driven by climate warming. We found that the recent warming in the Barents Sea has led to a change in spatial distribution of fish communities, with boreal communities expanding northwards at a pace reflecting the local climate velocities. Increased abundance and distribution areas of large, migratory fish predators explain the observed community-wide distributional shifts. These shifts change the ecological interactions experienced by Arctic fish species. The Arctic shelf fish community retracted northwards to deeper areas bordering the deep polar basin. Depth might limit further retraction of some of the fish species in the Arctic shelf community. We conclude that climate warming is inducing structural change over large spatial scales at high latitudes, leading to a borealization of fish communities in the Arctic.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Community structure and scale-free collections of Erdős-Rényi graphs.

PubMed

Seshadhri, C; Kolda, Tamara G; Pinar, Ali

2012-05-01

Community structure plays a significant role in the analysis of social networks and similar graphs, yet this structure is little understood and not well captured by most models. We formally define a community to be a subgraph that is internally highly connected and has no deeper substructure. We use tools of combinatorics to show that any such community must contain a dense Erdős-Rényi (ER) subgraph. Based on mathematical arguments, we hypothesize that any graph with a heavy-tailed degree distribution and community structure must contain a scale-free collection of dense ER subgraphs. These theoretical observations corroborate well with empirical evidence. From this, we propose the Block Two-Level Erdős-Rényi (BTER) model, and demonstrate that it accurately captures the observable properties of many real-world social networks.

A test of the cross-scale resilience model: Functional richness in Mediterranean-climate ecosystems

USGS Publications Warehouse

Wardwell, D.A.; Allen, Craig R.; Peterson, G.D.; Tyre, A.J.

2008-01-01

Ecological resilience has been proposed to be generated, in part, in the discontinuous structure of complex systems. Environmental discontinuities are reflected in discontinuous, aggregated animal body mass distributions. Diversity of functional groups within body mass aggregations (scales) and redundancy of functional groups across body mass aggregations (scales) has been proposed to increase resilience. We evaluate that proposition by analyzing mammalian and avian communities of Mediterranean-climate ecosystems. We first determined that body mass distributions for each animal community were discontinuous. We then calculated the variance in richness of function across aggregations in each community, and compared observed values with distributions created by 1000 simulations using a null of random distribution of function, with the same n, number of discontinuities and number of functional groups as the observed data. Variance in the richness of functional groups across scales was significantly lower in real communities than in simulations in eight of nine sites. The distribution of function across body mass aggregations in the animal communities we analyzed was non-random, and supports the contentions of the cross-scale resilience model. ?? 2007 Elsevier B.V. All rights reserved.

Rapid change with depth in megabenthic structure-forming communities of the Makapu'u deep-sea coral bed

NASA Astrophysics Data System (ADS)

Long, Dustin J.; Baco, Amy R.

2014-01-01

Seamounts are largely unexplored undersea mountains rising abruptly from the ocean floor, which can support an increased abundance and diversity of organisms. Deep-sea corals are important benthic structure-formers on current-swept hard substrates in these habitats. While depth is emerging as a factor structuring the fauna of seamounts on a large spatial scale, most work addressing deep-sea coral and seamount community structure has not considered the role of small-scale variation in species distributions. Video from six ROV dives over a depth range of ~320-530 m were analyzed to assess the diversity and density of benthic megafaunal invertebrates across the Makapu'u deep-sea coral bed, offshore of Oahu, Hawaii. At the same time, the physical environment along the dive track was surveyed to relate biotic patterns with abiotic variables including depth, aspect, rugosity, substrate, slope and relief to test the factors structuring community assemblages. Despite the narrow range examined, depth was found to be the strongest structuring gradient, and six unique macrobenthic communities were found, with a 93% faunal dissimilarity over the depth surveyed. Relief, rugosity and slope were also factors in the final model. Alcyonacean octocorals were the dominant macrofaunal invertebrates at all but the deepest depth zone. The commercially harvested precious coral C. secundum was the dominant species at depths 370-470 m, with a distribution that is on average deeper than similar areas. This may be artificial due to the past harvesting of this species on the shallower portion of its range. Primnoid octocorals were the most abundant octocoral family overall. This work yields new insight on the spatial ecology of seamounts, pointing out that community changes can occur over narrow depth ranges and that communities can be structured by small-scale physiography.

CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A ...

EPA Pesticide Factsheets

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e., groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to eighteen months. Significant differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity between service areas were associated with Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria, and Firmicutes. After nine months the biofilm bacterial community from both areas were dominated by Mycobacterium species. The distribution of the dominant OTU (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature, but no clear relationship was seen with free chlorine residual, pH, turbidity or total organic carbon (TOC). The results suggest that biofilm microbial communities harbor distinct and diverse bacterial communities, and that source water, treatment processes and environmental conditions may play an important role in shaping the bacterial community in the distribution system. On the other hand, several bacterial groups were present i

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 modal octave and a similar proportion of common species. We suggested that what follows the LN distribution should follow (or better follow) the LC and LS, and that the LC, LS and LN distributions represent a "sequential distribution set" in which one can find a best fit to the observed SAD. ?? 2004 Elsevier B.V. All rights reserved.

Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary.

PubMed

Homonnay, Zalán G; Török, György; Makk, Judit; Brumbauer, Anikó; Major, Eva; Márialigeti, Károly; Tóth, Erika

2014-07-01

Bacterial communities of a bank-filtered drinking water system were investigated by aerobic cultivation and clone library analysis. Moreover, bacterial communities were compared using sequence-aided terminal restriction fragment length polymorphism (T-RFLP) fingerprinting at ten characteristic points located at both the collecting and the distributing part of the water supply system. Chemical characteristics of the samples were similar, except for the presence of chlorine residuals in the distribution system and increased total iron concentration in two of the samples. Assimilable organic carbon (AOC) concentration increased within the collection system, it was reduced by chlorination and it increased again in the distribution system. Neither fecal indicators nor pathogens were detected by standard cultivation techniques. Chlorination reduced bacterial diversity and heterotrophic plate counts. Community structures were found to be significantly different before and after chlorination: the diverse communities in wells and the collection system were dominated by chemolithotrophic (e.g., Gallionella and Nitrospira) and oligocarbophilic-heterotrophic bacteria (e.g., Sphingomonas, Sphingopyxis, and Bradyrhizobium). After chlorination in the distribution system, the most characteristic bacterium was related to the facultative methylotrophic Methylocella spp. Communities changed within the distribution system too, Mycobacterium spp. or Sphingopyxis spp. became predominant in certain samples. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Body size distributions signal a regime shift in a lake ecosystem

USGS Publications Warehouse

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

2016-01-01

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

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2012 CFR

2012-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2014 CFR

2014-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2013 CFR

2013-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2011 CFR

2011-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

Spatial distribution patterns of soil mite communities and their relationships with edaphic factors in a 30-year tillage cornfield in northeast China.

PubMed

Liu, Jie; Gao, Meixiang; Liu, Jinwen; Guo, Yuxi; Liu, Dong; Zhu, Xinyu; Wu, Donghui

2018-01-01

Spatial distribution is an important topic in community ecology and a key to understanding the structure and dynamics of populations and communities. However, the available information related to the spatial patterns of soil mite communities in long-term tillage agroecosystems remains insufficient. In this study, we examined the spatial patterns of soil mite communities to explain the spatial relationships between soil mite communities and soil parameters. Soil fauna were sampled three times (August, September and October 2015) at 121 locations arranged regularly within a 400 m × 400 m monitoring plot. Additionally, we estimated the physical and chemical parameters of the same sampling locations. The distribution patterns of the soil mite community and the edaphic parameters were analyzed using a range of geostatistical tools. Moran's I coefficient showed that, during each sampling period, the total abundance of the soil mite communities and the abundance of the dominant mite populations were spatially autocorrelated. The soil mite communities demonstrated clear patchy distribution patterns within the study plot. These patterns were sampling period-specific. Cross-semivariograms showed both negative and positive cross-correlations between soil mite communities and environmental factors. Mantel tests showed a significant and positive relationship between soil mite community and soil organic matter and soil pH only in August. This study demonstrated that in the cornfield, the soil mite distribution exhibited strong or moderate spatial dependence, and the mites formed patches with sizes less than one hundred meters. In addition, in this long-term tillage agroecosystem, soil factors had less influence on the observed pattern of soil mite communities. Further experiments that take into account human activity and spatial factors should be performed to study the factors that drive the spatial distribution of soil microarthropods.

Advancing system and policy changes for social and racial justice: comparing a Rural and Urban Community-Based Participatory Research Partnership in the U.S.

PubMed

Devia, Carlos; Baker, Elizabeth A; Sanchez-Youngman, Shannon; Barnidge, Ellen; Golub, Maxine; Motton, Freda; Muhammad, Michael; Ruddock, Charmaine; Vicuña, Belinda; Wallerstein, Nina

2017-02-21

The paper examines the role of community-based participatory research (CBPR) within the context of social justice literature and practice. Two CBPR case studies addressing health inequities related to Type 2 Diabetes and Cardiovascular disease were selected from a national cross-site study assessing effective academic-community research partnerships. One CBPR partnership works with African Americans in rural Pemiscot County, Missouri and the other CBPR partnership works with African American and Latinos in urban South Bronx, New York City. Data collection included semi-structured key informant interviews and focus groups. Analysis focused on partnerships' context/history and their use of multiple justice-oriented strategies to achieve systemic and policy changes in order to address social determinants of health in their communities. Community context and history shaped each partnership's strategies to address social determinants. Four social justice approaches (identity/recognition, procedural, distributive, and structural justice) used by both partnerships were identified. These social justice approaches were employed to address underlying causes of inequitable distribution of resources and power structures, while remaining within a scientific research framework. CBPR can bridge the role of science with civic engagement and political participation, empowering community members to become political agents who integrate evidence into their social justice organizing strategies.

Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats.

PubMed

Pessi, Igor S; Lara, Yannick; Durieu, Benoit; Maalouf, Pedro de C; Verleyen, Elie; Wilmotte, Annick

2018-05-01

The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their prominent role in the primary production and nutrient cycling in Antarctic lakes, cyanobacteria were only poorly represented in the biological dataset used to delineate these ACBRs. Here, we provide a first high-throughput sequencing insight into the spatial distribution of benthic cyanobacterial communities in Antarctic lakes located in four distinct, geographically distant ACBRs and covering a range of limnological conditions. Cyanobacterial community structure differed between saline and freshwater lakes. No clear bioregionalization was observed, as clusters of community similarity encompassed lakes from distinct ACBRs. Most phylotypes (77.0%) were related to cyanobacterial lineages (defined at ≥99.0% 16S rRNA gene sequence similarity) restricted to the cold biosphere, including lineages potentially endemic to Antarctica (55.4%). The latter were generally rare and restricted to a small number of lakes, while more ubiquitous phylotypes were generally abundant and present in different ACBRs. These results point to a widespread distribution of some cosmopolitan cyanobacterial phylotypes across the different Antarctic ice-free regions, but also suggest the existence of dispersal barriers both within and between Antarctica and the other continents.

A review of epiphyte community development: surface interactions and settlement on seagrass.

PubMed

Michael, Teena S; Shin, Hyun Woung; Hanna, Richard; Spafford, David C

2008-07-01

A focus of community ecology is the spatial distribution of species assemblages and the interactions among species and abiotic features of the environment. While the ubiquity of species associations is apparent, it is less clear if interactions within a community impart an organizational structure to the community. Do settlement processes in early stages of community development contribute to later community structure? What are the interfacial forces that lead to recruitment and colonization of diverse substrata? This review examines seagrasses as living substrates for epiphyte colonization and the surface interactions which may determine settlement success. These epiphytes include primary producers which contribute to biodiversity and are bioindicators of pollution/nutrient enrichment.

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 bacterial diversity in surface sediments and resulting in distinct bacterial communities even at depth within the burrow. In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface.

The species diversity and roots distribution of forest in course of succession in the lower sub-tropical Dinghushan, Guangdong, China

NASA Astrophysics Data System (ADS)

Hao, Y.

2017-12-01

The study of root biomass distribution provides a good insight into the role of the root system, their structure and function at the ecosystem level. Therefore, many studies of root distribution and root dynamics e have been carried out. In the sub-tropical area of South China, monsoon evergreen broad-leaved forest is one of the most characteristic and most valuable zonal vegetation with stand age of 400 years in Dinghushan, where we choose the 4 typical communities (Com.1 Pinus massoniana community; Com.2 Pinus massoniana + Castanopsis chinensis + Schima superba community; Com.3 Castanopsis fissa community; Com.4 Cryptocarya concinna + Castanopsis chinensis + Cryptocarya chinensis + Schima superba community) to study the species diversity and roots distribution. Root systems of representative communities were examined systemically with regard to their structure, underground stratification and biomass distribution, by the method of root biological measure and ecological technique, Excavation of skeleton roots and observation of fine roots were carried out. The conclusions mainly including: The root biomass was increased with the species diversity and evenness of the communities improved in lower sub-tropical evergreen broad-leaved forest in course of succession. The main reason is that the diversity increase resulted in the great increase of total individuals. The individual number is 93 in Com.1 and increase to 7024 in Com.4, and the number of species and total population of individual were fast increased 32 and 2680 after 25 years when man-made needle forest was founded. In a set of successional stages, the amount of tree roots linearly increased in communities series. In monsoon evergreen broad-leaved forest, the total tree root biomass amounted to 115.70 ton/ha, Needle and broad-leaved mixed forest dominated by coniferous 50.61ton/ ha, Broad-and needle-leaved mixed forest dominated by broad-leaved heliophytes 64.20 ton/ha. Root biomass of community in later successional stage tended to distribute in the upper soil layers with the succession process, and this trend became slower in the later successional stage of the forest. 35% of total root biomass distributed in 0-10 cm layer in Com.2 but it increase to 61% in Com.4. Furthermore, more diversity of the vegetation has more clearly layers roots.

Hydrological drivers of wetland vegetational biodiversity patterns within Everglades National Park, Florida

NASA Astrophysics Data System (ADS)

Todd, J.; Pumo, D.; Azaele, S.; Muneepeerakul, R.; Miralles-Wilhelm, F. R.; Rinaldo, A.; Rodriguez-Iturbe, I.

2009-12-01

The influence of hydrological dynamics on vegetational biodiversity and structuring of wetland environments is of growing interest as wetlands are modified by human alteration and the increasing threat from climate change. Hydrology has long been considered a driving force in shaping wetland communities as the frequency of inundation along with the duration and depth of flooding are key determinants of wetland structure. We attempt to link hydrological dynamics with vegetational distribution and species richness across Everglades National Park (ENP) using two publicly available datasets. The first, the Everglades Depth Estimation Network (EDEN),is a water-surface model which determines the median daily measure of water level across a 400mX400m grid over seven years of measurement. The second is a vegetation map and classification system at the 1:15,000 scale which categorizes vegetation within the Everglades into 79 community types. From these data, we have studied the probabilistic structure of the frequency, duration, and depth of hydroperiods. Preliminary results indicate that the percentage of time a location is inundated is a principal structuring variable with individual communities responding differently. For example, sawgrass appears to be more of a generalist community as it is found across a wide range of time inundated percentages while spike rush has a more restricted distribution and favors wetter environments disproportionately more than predicted at random. Further, the diversity of vegetation communities (e.g. a measure of biodiversity) found across a hydrologic variable does not necessarily match the distribution function for that variable on the landscape. For instance, the number of communities does not differ across the percentage of time inundated. Different measures of vegetation biodiversity such as the local number of community types are also studied at different spatial scales with some characteristics, like the slope of the semi-logarithmic relation between rank and occupancy, found to be robust to scale changes. The ENP offers an expansive natural environment in which to study how vegetational dynamics and community composition are affected by hydrologic variables from the small scale (at the individual community level) to the large (biodiversity measures at differing spatial scales).

Emergence of bursts and communities in evolving weighted networks.

PubMed

Jo, Hang-Hyun; Pan, Raj Kumar; Kaski, Kimmo

2011-01-01

Understanding the patterns of human dynamics and social interaction and the way they lead to the formation of an organized and functional society are important issues especially for techno-social development. Addressing these issues of social networks has recently become possible through large scale data analysis of mobile phone call records, which has revealed the existence of modular or community structure with many links between nodes of the same community and relatively few links between nodes of different communities. The weights of links, e.g., the number of calls between two users, and the network topology are found correlated such that intra-community links are stronger compared to the weak inter-community links. This feature is known as Granovetter's "The strength of weak ties" hypothesis. In addition to this inhomogeneous community structure, the temporal patterns of human dynamics turn out to be inhomogeneous or bursty, characterized by the heavy tailed distribution of time interval between two consecutive events, i.e., inter-event time. In this paper, we study how the community structure and the bursty dynamics emerge together in a simple evolving weighted network model. The principal mechanisms behind these patterns are social interaction by cyclic closure, i.e., links to friends of friends and the focal closure, links to individuals sharing similar attributes or interests, and human dynamics by task handling process. These three mechanisms have been implemented as a network model with local attachment, global attachment, and priority-based queuing processes. By comprehensive numerical simulations we show that the interplay of these mechanisms leads to the emergence of heavy tailed inter-event time distribution and the evolution of Granovetter-type community structure. Moreover, the numerical results are found to be in qualitative agreement with empirical analysis results from mobile phone call dataset.

A multistate dynamic site occupancy model for spatially aggregated sessile communities

USGS Publications Warehouse

Fukaya, Keiichi; Royle, J. Andrew; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2017-01-01

Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e. a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations.We developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error.By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real data set of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account.Results suggest the importance of accounting for resampling error and local community structure for developing management plans that are based on Markovian models. Our approach provides a solution to this problem that is applicable to broad sessile communities. It can even accommodate an anisotropic spatial correlation of species composition, and may also serve as a basis for inferring complex nonlinear ecological dynamics.

Estimating the effectiveness of further sampling in species inventories

USGS Publications Warehouse

Keating, K.A.; Quinn, J.F.; Ivie, M.A.; Ivie, L.L.

1998-01-01

Estimators of the number of additional species expected in the next ??n samples offer a potentially important tool for improving cost-effectiveness of species inventories but are largely untested. We used Monte Carlo methods to compare 11 such estimators, across a range of community structures and sampling regimes, and validated our results, where possible, using empirical data from vascular plant and beetle inventories from Glacier National Park, Montana, USA. We found that B. Efron and R. Thisted's 1976 negative binomial estimator was most robust to differences in community structure and that it was among the most accurate estimators when sampling was from model communities with structures resembling the large, heterogeneous communities that are the likely targets of major inventory efforts. Other estimators may be preferred under specific conditions, however. For example, when sampling was from model communities with highly even species-abundance distributions, estimates based on the Michaelis-Menten model were most accurate; when sampling was from moderately even model communities with S=10 species or communities with highly uneven species-abundance distributions, estimates based on Gleason's (1922) species-area model were most accurate. We suggest that use of such methods in species inventories can help improve cost-effectiveness by providing an objective basis for redirecting sampling to more-productive sites, methods, or time periods as the expectation of detecting additional species becomes unacceptably low.

Parallel structure among environmental gradients and three trophic levels in a subarctic estuary

USGS Publications Warehouse

Speckman, Suzann G.; Piatt, John F.; Minte-Vera, C. V.; Parrish, Julia K.

2005-01-01

We assessed spatial and temporal variability in the physical environment of a subarctic estuary, and examined concurrent patterns of chlorophyll α abundance (fluorescence), and zooplankton and forage fish community structure. Surveys were conducted in lower Cook Inlet, Alaska, during late July and early August from 1997 through 1999. Principle components analysis (PCA) revealed that spatial heterogeneity in the physical oceanographic environment of lower Cook Inlet could be modeled as three marine-estuarine gradients characterized by temperature, salinity, bottom depth, and turbidity. The gradients persisted from 1997 through 1999, and PCA explained 68% to 92% of the variance in physical oceanography for each gradient-year combination. Correlations between chlorophyll α abundance and distribution and the PCA axes were weak. Chlorophyll was reduced by turbidity, and low levels occurred in areas with high levels of suspended sediments. Detrended correspondence analysis (DCA) was used to order the sample sites based on species composition and to order the zooplankton and forage fish taxa based on similarities among sample sites for each gradient-year. Correlations between the structure of the physical environment (PCA axis 1) and zooplankton community structure (DCA axis 1) were strong (r = 0.43-0.86) in all years for the three marine-estuarine gradients, suggesting that zooplankton community composition was structured by the physical environment. The physical environment (PCA) and forage fish community structure (DCA) were weakly correlated in all years along Gradient 2, defined by halocline intensity and surface temperature and salinity, even though these physical variables were more important for defining zooplankton habitats. However, the physical environment (PCA) and forage fish community structure (DCA) were strongly correlated along the primary marine-estuarine gradient (#1) in 1997 (r = 0.87) and 1998 (r = 0.82). The correlation was poor (r = 0.32) in 1999, when fish community structure changed markedly in lower Cook Inlet. Capelin (Mallotus villosus), walleye pollock (Theragra chalcogramma), and arrowtooth flounder (Atheresthes stomias) were caught farther north than in previous years. Waters were significantly colder and more saline in 1999, a La Nina year, than in other years of the study. Interannual fluctuations in environmental conditions in lower Cook Inlet did not have substantial effects on zooplankton community structure, although abundance of individual taxa varied significantly. The abundance and distribution of chlorophyll α, zooplankton and forage fish were affected much more by spatial variability in physical oceanography than by interannual variability. Our examination of physical-biological linkages in lower Cook Inlet supports the concept of "bottom-up control," i.e., that variability in the physical environment structures higher trophic-level communities by influencing their distribution and abundance across space.

Parallel structure among environmental gradients and three trophic levels in a subarctic estuary

NASA Astrophysics Data System (ADS)

Speckman, Suzann G.; Piatt, John F.; Minte-Vera, Carolina V.; Parrish, Julia K.

2005-07-01

We assessed spatial and temporal variability in the physical environment of a subarctic estuary, and examined concurrent patterns of chlorophyll α abundance (fluorescence), and zooplankton and forage fish community structure. Surveys were conducted in lower Cook Inlet, Alaska, during late July and early August from 1997 through 1999. Principle components analysis (PCA) revealed that spatial heterogeneity in the physical oceanographic environment of lower Cook Inlet could be modeled as three marine-estuarine gradients characterized by temperature, salinity, bottom depth, and turbidity. The gradients persisted from 1997 through 1999, and PCA explained 68% to 92% of the variance in physical oceanography for each gradient-year combination. Correlations between chlorophyll α abundance and distribution and the PCA axes were weak. Chlorophyll was reduced by turbidity, and low levels occurred in areas with high levels of suspended sediments. Detrended correspondence analysis (DCA) was used to order the sample sites based on species composition and to order the zooplankton and forage fish taxa based on similarities among sample sites for each gradient-year. Correlations between the structure of the physical environment (PCA axis 1) and zooplankton community structure (DCA axis 1) were strong ( r = 0.43-0.86) in all years for the three marine-estuarine gradients, suggesting that zooplankton community composition was structured by the physical environment. The physical environment (PCA) and forage fish community structure (DCA) were weakly correlated in all years along Gradient 2, defined by halocline intensity and surface temperature and salinity, even though these physical variables were more important for defining zooplankton habitats. However, the physical environment (PCA) and forage fish community structure (DCA) were strongly correlated along the primary marine-estuarine gradient (#1) in 1997 ( r = 0.87) and 1998 ( r = 0.82). The correlation was poor ( r = 0.32) in 1999, when fish community structure changed markedly in lower Cook Inlet. Capelin ( Mallotus villosus), walleye pollock ( Theragra chalcogramma), and arrowtooth flounder ( Atheresthes stomias) were caught farther north than in previous years. Waters were significantly colder and more saline in 1999, a La Niña year, than in other years of the study. Interannual fluctuations in environmental conditions in lower Cook Inlet did not have substantial effects on zooplankton community structure, although abundance of individual taxa varied significantly. The abundance and distribution of chlorophyll α, zooplankton and forage fish were affected much more by spatial variability in physical oceanography than by interannual variability. Our examination of physical-biological linkages in lower Cook Inlet supports the concept of “bottom-up control,” i.e., that variability in the physical environment structures higher trophic-level communities by influencing their distribution and abundance across space.

Separating the effects of environment and space on tree species distribution: from population to community.

PubMed

Lin, Guojun; Stralberg, Diana; Gong, Guiquan; Huang, Zhongliang; Ye, Wanhui; Wu, Linfang

2013-01-01

Quantifying the relative contributions of environmental conditions and spatial factors to species distribution can help improve our understanding of the processes that drive diversity patterns. In this study, based on tree inventory, topography and soil data from a 20-ha stem-mapped permanent forest plot in Guangdong Province, China, we evaluated the influence of different ecological processes at different spatial scales using canonical redundancy analysis (RDA) at the community level and multiple linear regression at the species level. At the community level, the proportion of explained variation in species distribution increased with grid-cell sizes, primarily due to a monotonic increase in the explanatory power of environmental variables. At the species level, neither environmental nor spatial factors were important determinants of overstory species' distributions at small cell sizes. However, purely spatial variables explained most of the variation in the distributions of understory species at fine and intermediate cell sizes. Midstory species showed patterns that were intermediate between those of overstory and understory species. At the 20-m cell size, the influence of spatial factors was stronger for more dispersal-limited species, suggesting that much of the spatial structuring in this community can be explained by dispersal limitation. Comparing environmental factors, soil variables had higher explanatory power than did topography for species distribution. However, both topographic and edaphic variables were highly spatial structured. Our results suggested that dispersal limitation has an important influence on fine-intermediate scale (from several to tens of meters) species distribution, while environmental variability facilitates species distribution at intermediate (from ten to tens of meters) and broad (from tens to hundreds of meters) scales.

Evolutionary method for finding communities in bipartite networks.

PubMed

Zhan, Weihua; Zhang, Zhongzhi; Guan, Jihong; Zhou, Shuigeng

2011-06-01

An important step in unveiling the relation between network structure and dynamics defined on networks is to detect communities, and numerous methods have been developed separately to identify community structure in different classes of networks, such as unipartite networks, bipartite networks, and directed networks. Here, we show that the finding of communities in such networks can be unified in a general framework-detection of community structure in bipartite networks. Moreover, we propose an evolutionary method for efficiently identifying communities in bipartite networks. To this end, we show that both unipartite and directed networks can be represented as bipartite networks, and their modularity is completely consistent with that for bipartite networks, the detection of modular structure on which can be reformulated as modularity maximization. To optimize the bipartite modularity, we develop a modified adaptive genetic algorithm (MAGA), which is shown to be especially efficient for community structure detection. The high efficiency of the MAGA is based on the following three improvements we make. First, we introduce a different measure for the informativeness of a locus instead of the standard deviation, which can exactly determine which loci mutate. This measure is the bias between the distribution of a locus over the current population and the uniform distribution of the locus, i.e., the Kullback-Leibler divergence between them. Second, we develop a reassignment technique for differentiating the informative state a locus has attained from the random state in the initial phase. Third, we present a modified mutation rule which by incorporating related operations can guarantee the convergence of the MAGA to the global optimum and can speed up the convergence process. Experimental results show that the MAGA outperforms existing methods in terms of modularity for both bipartite and unipartite networks.

Size structure of marine soft-bottom macrobenthic communities across natural habitat gradients: implications for productivity and ecosystem function.

PubMed

Macdonald, Tara A; Burd, Brenda J; van Roodselaar, Albert

2012-01-01

Size distributions of biotic assemblages are important modifiers of productivity and function in marine sediments. We investigated the distribution of proportional organic biomass among logarithmic size classes (2(-6)J to 2(16)J) in the soft-bottom macrofaunal communities of the Strait of Georgia, Salish Sea on the west coast of Canada. The study examines how size structure is influenced by 3 fundamental habitat descriptors: depth, sediment percent fines, and organic flux (modified by quality). These habitat variables are uncorrelated in this hydrographically diverse area, thus we examine their effects in combination and separately. Cluster analyses and cumulative biomass size spectra reveal clear and significant responses to each separate habitat variable. When combined, habitat factors result in three distinct assemblages: (1) communities with a high proportion of biomass in small organisms, typical of shallow areas (<10 m) with coarse sediments (<10% fines) and low accumulation of organic material (<3.0 gC/m(2)/yr/δ(15)N); (2) communities with high proportion of biomass in the largest organisms found in the Strait, typical of deep, fine sediments with high modified organic flux (>3 g C/m(2)/yr/δ(15)N) from the Fraser River; and (3) communities with biomass dominated by moderately large organisms, but lacking the smallest and largest size classes, typical of deep, fine sediments experiencing low modified organic flux (<3.0 gC/m(2)/yr/δ(15)N). The remaining assemblages had intermediate habitat types and size structures. Sediment percent fines and flux appear to elicit threshold responses in size structure, whereas depth has the most linear influence on community size structure. The ecological implications of size structure in the Strait of Georgia relative to environmental conditions, secondary production and sediment bioturbation are discussed.

Size Structure of Marine Soft-Bottom Macrobenthic Communities across Natural Habitat Gradients: Implications for Productivity and Ecosystem Function

PubMed Central

Macdonald, Tara A.; Burd, Brenda J.; van Roodselaar, Albert

2012-01-01

Size distributions of biotic assemblages are important modifiers of productivity and function in marine sediments. We investigated the distribution of proportional organic biomass among logarithmic size classes (2−6J to 216J) in the soft-bottom macrofaunal communities of the Strait of Georgia, Salish Sea on the west coast of Canada. The study examines how size structure is influenced by 3 fundamental habitat descriptors: depth, sediment percent fines, and organic flux (modified by quality). These habitat variables are uncorrelated in this hydrographically diverse area, thus we examine their effects in combination and separately. Cluster analyses and cumulative biomass size spectra reveal clear and significant responses to each separate habitat variable. When combined, habitat factors result in three distinct assemblages: (1) communities with a high proportion of biomass in small organisms, typical of shallow areas (<10 m) with coarse sediments (<10% fines) and low accumulation of organic material (<3.0 gC/m2/yr/δ15N); (2) communities with high proportion of biomass in the largest organisms found in the Strait, typical of deep, fine sediments with high modified organic flux (>3 g C/m2/yr/δ15N) from the Fraser River; and (3) communities with biomass dominated by moderately large organisms, but lacking the smallest and largest size classes, typical of deep, fine sediments experiencing low modified organic flux (<3.0 gC/m2/yr/δ15N). The remaining assemblages had intermediate habitat types and size structures. Sediment percent fines and flux appear to elicit threshold responses in size structure, whereas depth has the most linear influence on community size structure. The ecological implications of size structure in the Strait of Georgia relative to environmental conditions, secondary production and sediment bioturbation are discussed. PMID:22911694

Variation in the magnitude of black-white differences in stroke mortality by community occupational structure.

PubMed Central

Casper, M; Wing, S; Strogatz, D

1991-01-01

STUDY OBJECTIVE--The aim was to examine the patterns of black-white differences in stroke mortality across communities with varying levels of occupational structure in the southern region of the United States DESIGN--Annual age adjusted race-sex specific rates for stroke mortality were calculated for the years 1979-1981 and related to socioeconomic conditions. SETTING--The study involved 211 state economic areas comprising the southern region of the USA. STUDY POPULATION--Data on stroke mortality for black and white men and women between the ages of 35 and 74 years living in the study area were acquired from the National Center for Health Statistics. MEASUREMENTS AND MAIN RESULTS--Occupational structure was measured as the proportion of white collar workers in each state economic area, and is an indicator of the employment opportunities and related social and economic resources of a community. Stratified analyses and linear regression modelling indicate that communities of lower occupational structure have (a) higher levels of stroke mortality for all four race-sex groups (p less than 0.05) and (b) larger racial inequalities in stroke mortality (p less than 0.01). For men and women, the excess stroke mortality among blacks compared to whites is larger in communities of lower occupational structure. CONCLUSIONS--Consideration of occupational structure and related patterns of economic development is crucial for understanding the distribution of stroke mortality within and between racial groups, as well as for planning effective public health interventions. The larger racial inequalities in communities of lower occupational structure in the south suggest that aspects of the black experience which are conducive to high rates of stroke mortality are exacerbated in those communities. Public health interventions to reduce the racial and social inequalities in stroke mortality should recognise the social context within which nutritional, occupational, medical care, and environmental determinants of stroke are distributed. PMID:1795152

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

PubMed

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

2017-04-01

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

Linking phytoplankton community metabolism to the individual size distribution.

PubMed

Padfield, Daniel; Buckling, Angus; Warfield, Ruth; Lowe, Chris; Yvon-Durocher, Gabriel

2018-05-25

Quantifying variation in ecosystem metabolism is critical to predicting the impacts of environmental change on the carbon cycle. We used a metabolic scaling framework to investigate how body size and temperature influence phytoplankton community metabolism. We tested this framework using phytoplankton sampled from an outdoor mesocosm experiment, where communities had been either experimentally warmed (+ 4 °C) for 10 years or left at ambient temperature. Warmed and ambient phytoplankton communities differed substantially in their taxonomic composition and size structure. Despite this, the response of primary production and community respiration to long- and short-term warming could be estimated using a model that accounted for the size- and temperature dependence of individual metabolism, and the community abundance-body size distribution. This work demonstrates that the key metabolic fluxes that determine the carbon balance of planktonic ecosystems can be approximated using metabolic scaling theory, with knowledge of the individual size distribution and environmental temperature. © 2018 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan

PubMed Central

Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

2016-01-01

Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments. PMID:26849440

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Distribution drivers and physiological responses in geothermal bryophyte communities.

PubMed

García, Estefanía Llaneza; Rosenstiel, Todd N; Graves, Camille; Shortlidge, Erin E; Eppley, Sarah M

2016-04-01

Our ability to explain community structure rests on our ability to define the importance of ecological niches, including realized ecological niches, in shaping communities, but few studies of plant distributions have combined predictive models with physiological measures. Using field surveys and statistical modeling, we predicted distribution drivers in geothermal bryophyte (moss) communities of Lassen Volcanic National Park (California, USA). In the laboratory, we used drying and rewetting experiments to test whether the strong species-specific effects of relative humidity on distributions predicted by the models were correlated with physiological characters. We found that the three most common bryophytes in geothermal communities were significantly affected by three distinct distribution drivers: temperature, light, and relative humidity. Aulacomnium palustre, whose distribution is significantly affected by relative humidity according to our model, and which occurs in high-humidity sites, showed extreme signs of stress after drying and never recovered optimal values of PSII efficiency after rewetting. Campylopus introflexus, whose distribution is not affected by humidity according to our model, was able to maintain optimal values of PSII efficiency for 48 hr at 50% water loss and recovered optimal values of PSII efficiency after rewetting. Our results suggest that species-specific environmental stressors tightly constrain the ecological niches of geothermal bryophytes. Tests of tolerance to drying in two bryophyte species corresponded with model predictions of the comparative importance of relative humidity as distribution drivers for these species. © 2016 Botanical Society of America.

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

PubMed Central

da Silva, Pedro Giovâni; Hernández, Malva Isabel Medina

2015-01-01

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

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY ...

EPA Pesticide Factsheets

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, SAR model development, or building of chemical relational databases (CRD). The Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: 1) to adopt and encourage the use of a common standard file format (SDF) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; 2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data s

Willingness to pay for community-based ivermectin distribution: a study of three onchocerciasis-endemic communities in Nigeria.

PubMed

Onwujekwe, O E; Shu, E N; Nwagbo, D; Akpala, C O; Okonkwo, P O

1998-10-01

To determine the willingness to pay (WTP) for local ivermectin distribution in a community financing framework. Contingent valuation in three communities in Nigeria, using randomly selected household heads. WTP was elicited using a bidding game, and for collecting information on the households' socio-economic status, level of knowledge, priority ranking and perception of risk of contracting the disease, structured questionnaires were used. Ordinary least squares (OLS) multiple regression analysis was used to analyse factors associated with WTP. Between 92.1% and 93.3 % of respondents were willing to pay amounts ranging from 5 Naira (US$ 0.06) to 100 Naira (US$ 1.25) (median: 20 Naira, US$ 0.25) in the three communities, more than three times the modelled unit direct cost of distributing ivermectin by the communities themselves. Occupation of the respondent, marital status, average monthly expenditure on health care, manifestations of onchocerciasis, the type of savings scheme embarked on by the respondent, age-group, level of education and type of property were statistically significant (P < 0.05) variables affecting WTP. This study shows that there is WTP for local ivermectin distribution in the three study communities, and that it should be assessed before instituting community-directed treatment with ivermectin.

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

PubMed

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

2007-08-01

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

Two centuries of fire in a southwestern Virginia Pinus pungens community

Treesearch

E. K. Sutherland; H. Grissino-Mayer; C. A. Woodhouse; W. W. Covington; S. Horn; L. Huckaby; R. Kerr; J. Kush; M. Moore; T. Plumb

1995-01-01

Fire exclusion in fire-dependent forest communities can alter stand structure and composition. The objective was to construct a fire history of two Pinus pungens Lamb. communities growing in southwestern Virgina. Treering analysis of fire-scarred P. pungens specimens and a tree survey were used to determine species composition and age distributions. From 1798-1944,...

Emergence of Soft Communities from Geometric Preferential Attachment

PubMed Central

Zuev, Konstantin; Boguñá, Marián; Bianconi, Ginestra; Krioukov, Dmitri

2015-01-01

All real networks are different, but many have some structural properties in common. There seems to be no consensus on what the most common properties are, but scale-free degree distributions, strong clustering, and community structure are frequently mentioned without question. Surprisingly, there exists no simple generative mechanism explaining all the three properties at once in growing networks. Here we show how latent network geometry coupled with preferential attachment of nodes to this geometry fills this gap. We call this mechanism geometric preferential attachment (GPA), and validate it against the Internet. GPA gives rise to soft communities that provide a different perspective on the community structure in networks. The connections between GPA and cosmological models, including inflation, are also discussed. PMID:25923110

Towards a Dialogical Pedagogy: Some Characteristics of a Community of Mathematical Inquiry

ERIC Educational Resources Information Center

Kennedy, Nadia Stoyanova

2009-01-01

This paper discusses a teaching model called community of mathematical inquiry (CMI), characterized by dialogical and inquiry-driven communication and a dynamic structure of intertwined cognitive processes including distributed thinking, mathematical argumentation, integrated reasoning, conceptual transformation, internalization of critical…

Vegetation, soil, and flooding relationships in a blackwater floodplain forest

USGS Publications Warehouse

Burke, M.K.; King, S.L.; Gartner, D.; Eisenbies, M.H.

2003-01-01

Hydroperiod is considered the primary determinant of plant species distribution in temperate floodplain forests, but most studies have focused on alluvial (sediment-laden) river systems. Few studies have evaluated plant community relationships in blackwater river systems of the South Atlantic Coastal Plain of North America. In this study, we characterized the soils, hydroperiod, and vegetation communities and evaluated relationships between the physical and chemical environment and plant community structure on the floodplain of the Coosawhatchie River, a blackwater river in South Carolina, USA. The soils were similar to previous descriptions of blackwater floodplain soils but had greater soil N and P availability, substantially greater clay content, and lower soil silt content than was previously reported for other blackwater river floodplains. Results of a cluster analysis showed there were five forest communities on the site, and both short-term (4 years) and long-term (50 years) flooding records documented a flooding gradient: water tupelo community > swamp tupelo > laurel oak = overcup oak > mixed oak. The long-term hydrologic record showed that the floodplain has flooded less frequently from 1994 to present than in previous decades. Detrended correspondence analysis of environmental and relative basal area values showed that 27% of the variation in overstory community structure could be explained by the first two axes; however, fitting the species distributions to the DCA axes using Gaussian regression explained 67% of the variation. Axes were correlated with elevation (flooding intensity) and soil characteristics related to rooting volume and cation nutrient availability. Our study suggests that flooding is the major factor affecting community structure, but soil characteristics also may be factors in community structure in blackwater systems. ?? 2003, The Society of Wetland Scientists.

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.

"Providing a Roof" and More to Communities Affected by Typhoon Haiyan in the Philippines: the Médecins Sans Frontières Experience.

PubMed

Ali, Engy; Ferir, Marie-Christine; Reid, Tony; Gray, Henry; Van Den Boogaard, Wilma; Gonzales, Christopher; Zachariah, Rony

2017-06-01

Typhoon Haiyan hit the Philippines in November 2013 and left a trail of destruction. As part of its emergency response, Médecins Sans Frontières distributed materials for reconstructing houses and boats as standardized kits to be shared between households. Community engagement was sought and communities were empowered in deciding how to make the distributions. We aimed to answer, Was this effective and what lessons were learned? A cross-sectional survey using a semi-structured questionnaire was conducted in May 2014 and included all community leaders and 269 households in 22 barangays (community administrative areas). All houses were affected by the typhoon, of which 182 (68%) were totally damaged. All households reported having received and used the housing material. However, in 238 (88%) house repair was incomplete because the materials provided were insufficient or inappropriate for the required repairs. This experience of emergency mass distribution of reconstruction or repair materials of houses and boats led by the local community was encouraging. The use of "standardized kits" resulted in equity issues, because households were subjected to variable degrees of damage. A possible way out is to follow up the emergency distribution with a needs assessment and a tailored distribution. (Disaster Med Public Health Preparedness. 2017;11:285-289).

Light Structures Phototroph, Bacterial and Fungal Communities at the Soil Surface

PubMed Central

Davies, Lawrence O.; Schäfer, Hendrik; Marshall, Samantha; Bramke, Irene; Oliver, Robin G.; Bending, Gary D.

2013-01-01

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere. PMID:23894406

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

NASA Technical Reports Server (NTRS)

Franklin, R. B.; Garland, J. L.; Bolster, C. H.; Mills, A. L.

2001-01-01

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Structuring factors and recent changes in subtidal macrozoobenthic communities of a coastal lagoon, Arcachon Bay (France)

NASA Astrophysics Data System (ADS)

Blanchet, Hugues; de Montaudouin, Xavier; Chardy, Pierre; Bachelet, Guy

2005-09-01

Fourteen years after a previous investigation in Arcachon Bay (SW France), the quantitative distribution of subtidal macrozoobenthic communities was assessed in 2002 through a stratified sampling strategy involving a larger number of stations (89 vs. 18) than in 1988. A total of 226 taxa were recorded. Cluster Analysis and Correspondence Analysis identified nine station groups corresponding to benthic faunal assemblages and their characteristic species. Multiple Discriminant Analysis showed that the main environmental factors influencing the distribution of faunal assemblages were sediment parameters and distance from the ocean. Depth was a minor structuring factor. At the scale of the lagoon, biogenic structures such as Zostera marina beds, Crepidula fornicata-dominated bottoms or dead oyster shell bottoms did not display any particular assemblage of infauna. Comparison with previous quantitative data from the 1988 survey provided more precision on the distribution of benthic assemblages and revealed community changes at a 14-year scale. These modifications reflected a general increase of silt and clay content in the sediment in the internal parts of channels, inducing community change. These changes can be correlated to the recent first signs of a moderate eutrophication process which have appeared, since 1988, through the development of green macroalgae in some parts of the lagoon. This trend was enhanced in transverse channels with reduced hydrodynamics and led to muddy areas where green macroalgae tended to accumulate. Locally, the dredging of sandbanks induced stronger currents and allowed the marine influence to occur, and also induced community change. These observations confirm that surveys of macrobenthic communities are useful tools to assess coastal ecosystem change even in moderately disturbed environments.

Characterisation of the physical composition and microbial community structure of biofilms within a model full-scale drinking water distribution system.

PubMed

Fish, Katherine E; Collins, Richard; Green, Nicola H; Sharpe, Rebecca L; Douterelo, Isabel; Osborn, A Mark; Boxall, Joby B

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS.

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

PubMed Central

Fish, Katherine E.; Collins, Richard; Green, Nicola H.; Sharpe, Rebecca L.; Douterelo, Isabel; Osborn, A. Mark; Boxall, Joby B.

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS. PMID:25706303

Multispecies lottery competition: a diffusion analysis

USGS Publications Warehouse

Hatfield, J.S.; Chesson, P.L.; Tuljapurkar, S.; Caswell, H.

1997-01-01

The lottery model is a stochastic competition model designed for space-limited communities of sedentary organisms. Examples of such communities include coral reef fishes, aquatic sessile organisms, and many plant communities. Explicit conditions for the coexistence of two species and the stationary distribution of the two-species model were determined previously using an approximation with a diffusion process. In this chapter, a diffusion approximation is presented for the multispecies model for communities of two or more species, and a stage-structured model is investigated. The stage-structured model would be more reasonable for communities of long-lived species such as trees in a forest in which recruitment and death rates depend on the age or stage of the individuals.

Functional response of an adapted subtidal macrobenthic community to an oil spill: macrobenthic structure and bioturbation activity over time throughout an 18-month field experiment.

PubMed

Gilbert, Franck; Stora, Georges; Cuny, Philippe

2015-10-01

An experimental oil spill was carried out in order to assess in situ responses of a macrobenthic community of shallow subtidal sediments historically exposed to petroleum contamination. Both structural and functional (bioturbation activity) parameters of the community, subjected or not to a pulse acute contamination (25,000 ppm), were studied for 18 months. No difference in the community structure was detected between contaminated and control sediments, from 6 to 18 months of experimentation. Vertical distributions of organisms, however, were affected by the presence of oil contamination leading to a deeper burial of some polychaete species. In the same time, changes in sediment-reworking activity and more especially a deeper particle burying in sediments subjected to acute oil contamination were shown. These results highlight the need to complete the analysis of community structure by assessing functional aspects, such as bioturbation activity, a process integrating various aspects of benthic behaviour (e.g. feeding, locomotion, burrow building) in order to estimate real (structural and functional) and long-term effects of oil contamination on benthic communities.

Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau

PubMed Central

Zhong, Zhi-Ping; Liu, Ying; Miao, Li-Li; Wang, Fang; Chu, Li-Min; Wang, Jia-Li

2016-01-01

The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg2+, K+, Cl−, Na+, SO42−, and Ca2+) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO43− concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations. PMID:26746713

nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

PubMed

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

2016-10-01

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

Structure of Benthic Communities along the Taiwan Latitudinal Gradient

PubMed Central

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

2016-01-01

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

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension.

PubMed

Plante, Craig J; Fleer, Virginia; Jones, Martin L

2016-10-01

Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa-abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α-diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β-diversity) will increase. Co-occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa-abundances fit those predicted from NCMs reasonably well (R 2 of 0.68-0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co-occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α-diversity as compared to periods of immersion at both mudflat and sand bar sites. β-diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between-site metacommunity comparisons, low- and high-resuspension sites exhibited distinct community compositions while the low-energy mudflats contained higher microalgal biomass and greater α-diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats. © 2016 Phycological Society of America.

Macromolecular Structure Database. Final Progress Report

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

Gilliland, Gary L.

2003-09-23

The central activity of the PDB continues to be the collection, archiving and distribution of high quality structural data to the scientific community on a timely basis. In support of these activities NIST has continued its roles in developing the physical archive, in developing data uniformity, in dealing with NMR issues and in the distribution of PDB data through CD-ROMs. The physical archive holdings have been organized, inventoried, and a database has been created to facilitate their use. Data from individual PDB entries have been annotated to produce uniform values improving tremendously the accuracy of results of queries. Working withmore » the NMR community we have established data items specific for NMR that will be included in new entries and facilitate data deposition. The PDB CD-ROM production has continued on a quarterly basis, and new products are being distributed.« less

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.

PubMed

Douterelo, I; Sharpe, R L; Boxall, J B

2013-02-01

Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this might have on drinking water quality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of Pleistocene environmental changes on the distribution and community structure of the mammalian fauna of Mexico

NASA Astrophysics Data System (ADS)

Ceballos, Gerardo; Arroyo-Cabrales, Joaquín; Ponce, Eduardo

2010-05-01

Biological communities in Mexico experienced profound changes in species composition and structure as a consequence of the environmental fluctuations during the Pleistocene. Based on the recent and fossil Mexican mammal checklists, we determine the distribution, composition, diversity, and community structure of late Pleistocene mammalian faunas, and analyze extinction patterns and response of individual species to environmental changes. We conclude that (1) differential extinctions occurred at family, genus, and species level, with a major impact on species heavier than 100 kg, including the extinction all proboscideans and several ruminants; (2) Pleistocene mammal communities in Mexico were more diverse than recent ones; and (3) the current assemblages of species are relatively young. Furthermore, Pleistocene relicts support the presence of biogeographic corridors; important refugia existed as well as centers of speciation in isolated regions. We identified seven corridors: eastern USA-Sierra Madre Oriental corridor, Rocky Mountains-Sierra Madre Occidental corridor, Central United States-Northern Mexico corridor, Transvolcanic Belt-Sierra Madre del Sur corridor, western USA-Baja California corridor, Tamaulipas-Central America gulf lowlands corridor, and Sonora-Central America Pacific lowlands corridor. Our study suggests that present mammalian assemblages are very different than the ones in the late Pleistocene.

Microbiome variation in corals with distinct depth distribution ranges across a shallow-mesophotic gradient (15-85 m)

NASA Astrophysics Data System (ADS)

Glasl, Bettina; Bongaerts, Pim; Elisabeth, Nathalie H.; Hoegh-Guldberg, Ove; Herndl, Gerhard J.; Frade, Pedro R.

2017-06-01

Mesophotic coral ecosystems (MCEs) are generally poorly studied, and our knowledge of lower MCEs (below 60 m depth) is largely limited to visual surveys. Here, we provide a first detailed assessment of the prokaryotic community associated with scleractinian corals over a depth gradient to the lower mesophotic realm (15-85 m). Specimens of three Caribbean coral species exhibiting differences in their depth distribution ranges ( Agaricia grahamae, Madracis pharensis and Stephanocoenia intersepta) were collected with a manned submersible on the island of Curaçao, and their prokaryotic communities assessed using 16S rRNA gene sequencing analysis. Corals with narrower depth distribution ranges (depth-specialists) were associated with a stable prokaryotic community, whereas corals with a broader niche range (depth-generalists) revealed a higher variability in their prokaryotic community. The observed depth effects match previously described patterns in Symbiodinium depth zonation. This highlights the contribution of structured microbial communities over depth to the coral's ability to colonize a broader depth range.

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

PubMed

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

Nematode community structure in a vineyard soil.

PubMed

Ferris, H; McKenry, M V

1976-04-01

Distribution of the nematode community in a California vineyard was studied over a 13-month period. Omnivorous and microbivorous nematodes were similarly distributed in the root zone, with greatest densities occurring between vine rows and near the soil surface. Greatest densities of plant-parasitic nematodes were found in the vine row, with the individual species differing in their vertical distribution. Total nematode biomass was greatest between rows near the surface. Biomass of plant parasites was greatest in the upper 30 cm of soil in the row, whereas biomass of microbivores was greatest in this region between rows. Of the plant-parasitic nematodes, the variability in distribution among vines was greatest for Paratylenchus hamatus and least for Meloidogyne spp.

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus

PubMed Central

Libberton, Ben; Coates, Rosanna E.

2014-01-01

Nasal carriage of Staphylococcus aureus is a risk factor for infection, yet the bacterial determinants required for carriage are poorly defined. Interactions between S. aureus and other members of the bacterial flora may determine colonization and have been inferred in previous studies by using correlated species distributions. However, traits mediating species interactions are often polymorphic, suggesting that understanding how interactions structure communities requires a trait-based approach. We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. Across microbiomes, the cumulative community-level growth inhibition was negatively associated with S. aureus incidence. To fully understand the ecological processes structuring microbiomes, it will be crucial to account for intraspecific variation in the traits that mediate species interactions. PMID:24980973

Improvement of the SEP protocol based on community structure of node degree

NASA Astrophysics Data System (ADS)

Li, Donglin; Wei, Suyuan

2017-05-01

Analyzing the Stable election protocol (SEP) in wireless sensor networks and aiming at the problem of inhomogeneous cluster-heads distribution and unreasonable cluster-heads selectivity and single hop transmission in the SEP, a SEP Protocol based on community structure of node degree (SEP-CSND) is proposed. In this algorithm, network node deployed by using grid deployment model, and the connection between nodes established by setting up the communication threshold. The community structure constructed by node degree, then cluster head is elected in the community structure. On the basis of SEP, the node's residual energy and node degree is added in cluster-heads election. The information is transmitted with mode of multiple hops between network nodes. The simulation experiments showed that compared to the classical LEACH and SEP, this algorithm balances the energy consumption of the entire network and significantly prolongs network lifetime.

Surveying traffic congestion based on the concept of community structure of complex networks

NASA Astrophysics Data System (ADS)

Ma, Lili; Zhang, Zhanli; Li, Meng

2016-07-01

In this paper, taking the traffic of Beijing city as an instance, we study city traffic states, especially traffic congestion, based on the concept of network community structure. Concretely, using the floating car data (FCD) information of vehicles gained from the intelligent transport system (ITS) of the city, we construct a new traffic network model which is with floating cars as network nodes and time-varying. It shows that this traffic network has Gaussian degree distributions at different time points. Furthermore, compared with free traffic situations, our simulations show that the traffic network generally has more obvious community structures with larger values of network fitness for congested traffic situations, and through the GPSspg web page, we show that all of our results are consistent with the reality. Then, it indicates that network community structure should be an available way for investigating city traffic congestion problems.

Current state of macrobenthic communities in Baydaratskaya Bay (Kara Sea)

NASA Astrophysics Data System (ADS)

Kokarev, V. N.; Kozlovsky, V. V.; Azovsky, A. I.

2015-09-01

Macrobenthic communities in Baydaratskaya Bay were studied before and after the seafloor pipeline was begun to be laid out in the year 2011. Materials were collected during three surveys in 2007, 2012, and 2013. Ordination of the data based on community structure and composition revealed a clear depthrelated zonality of the communities. Stations deeper than 10 meters were dominated by bivalves, while shallower stations were dominated by nephtyid polychaetes. This structure persisted though the whole period studied, without any pronounced temporal trends. However, several deep-water stations near the pipeline path in the year 2013 revealed a distinct shift in the structure of macrofauna, with large bivalves disappearing, an increased abundance of small polychaetes, and a decrease in total biodiversity. Moreover, macrofauna were absent at one of these stations. We conclude that the structure and distribution of communities are relatively stable and mainly driven by depth. However, there are some local but evident disturbance effects, probably caused by recent human activity (dumping of dredged sediments).

Uncovering the drivers of host-associated microbiota with joint species distribution modelling.

PubMed

Björk, Johannes R; Hui, Francis K C; O'Hara, Robert B; Montoya, Jose M

2018-06-01

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations. © 2018 John Wiley & Sons Ltd.

Community core detection in transportation networks

NASA Astrophysics Data System (ADS)

De Leo, Vincenzo; Santoboni, Giovanni; Cerina, Federica; Mureddu, Mario; Secchi, Luca; Chessa, Alessandro

2013-10-01

This work analyzes methods for the identification and the stability under perturbation of a territorial community structure with specific reference to transportation networks. We considered networks of commuters for a city and an insular region. In both cases, we have studied the distribution of commuters’ trips (i.e., home-to-work trips and vice versa). The identification and stability of the communities’ cores are linked to the land-use distribution within the zone system, and therefore their proper definition may be useful to transport planners.

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Community-level consequences of cannibalism.

PubMed

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

2012-12-01

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

Habitat heterogeneity and intraguild interactions modify distribution and injury rates in two coexisting genera of damselflies

EPA Science Inventory

1. Sublethal effects of predation can affect both population and community structure. Despite this, little is known about how the frequency of injury varies in relation to habitat, aquatic community characteristics or between trophically similar, coexisting taxa. 2. In a tidal ...

Soil nutrients influence spatial distributions of tropical trees species

USGS Publications Warehouse

John, R.; Dalling, J.W.; Harms, K.E.; Yavitt, J.B.; Stallard, R.F.; Mirabello, M.; Hubbell, S.P.; Valencia, R.; Navarrete, H.; Vallejo, M.; Foster, R.B.

2007-01-01

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. ?? 2007 by The National Academy of Sciences of the USA.

Bacterial communities associated with an occurrence of colored water in an urban drinking water distribution system.

PubMed

Wu, Hui Ting; Mi, Zi Long; Zhang, Jing Xu; Chen, Chao; Xie, Shu Guang

2014-08-01

This study aimed to investigate bacterial community in an urban drinking water distribution system (DWDS) during an occurrence of colored water. Variation in the bacterial community diversity and structure was observed among the different waters, with the predominance of Proteobacteria. While Verrucomicrobia was also a major phylum group in colored water. Limnobacter was the major genus group in colored water, but Undibacterium predominated in normal tap water. The coexistence of Limnobacter as well as Sediminibacterium and Aquabacterium might contribute to the formation of colored water. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Species selection under long-term experimental warming and drought explained by climatic distributions.

PubMed

Liu, Daijun; Peñuelas, Josep; Ogaya, Romà; Estiarte, Marc; Tielbörger, Katja; Slowik, Fabian; Yang, Xiaohong; Bilton, Mark C

2018-03-01

Global warming and reduced precipitation may trigger large-scale species losses and vegetation shifts in ecosystems around the world. However, currently lacking are practical ways to quantify the sensitivity of species and community composition to these often-confounded climatic forces. Here we conducted long-term (16 yr) nocturnal-warming (+0.6°C) and reduced precipitation (-20% soil moisture) experiments in a Mediterranean shrubland. Climatic niche groups (CNGs) - species ranked or classified by similar temperature or precipitation distributions - informatively described community responses under experimental manipulations. Under warming, CNGs revealed that only those species distributed in cooler regions decreased. Correspondingly, under reduced precipitation, a U-shaped treatment effect observed in the total community was the result of an abrupt decrease in wet-distributed species, followed by a delayed increase in dry-distributed species. Notably, while partially correlated, CNG explanations of community response were stronger for their respective climate parameter, suggesting some species possess specific adaptations to either warming or drought that may lead to independent selection to the two climatic variables. Our findings indicate that when climatic distributions are combined with experiments, the resulting incorporation of local plant evolutionary strategies and their changing dynamics over time leads to predictable and informative shifts in community structure under independent climate change scenarios. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Quantifying forest vertical structure to determine bird habitat quality in the Greenbelt Corridor, Denton, TX

NASA Astrophysics Data System (ADS)

Matsubayashi, Shiho

This study presents the integration of light detection and range (LiDAR) and hyperspectral remote sensing to create a three-dimensional bird habitat map in the Greenbelt Corridor of the Elm Fork of the Trinity River. This map permits to examine the relationship between forest stand structure, landscape heterogeneity, and bird community composition. A biannual bird census was conducted at this site during the breeding seasons of 2009 and 2010. Census data combined with the three-dimensional map suggest that local breeding bird abundance, community structure, and spatial distribution patterns are highly influenced by vertical heterogeneity of vegetation surface. For local breeding birds, vertical heterogeneity of canopy surface within stands, connectivity to adjacent forest patches, largest forest patch index, and habitat (vegetation) types proved to be the most influential factors to determine bird community assemblages. Results also highlight the critical role of secondary forests to increase functional connectivity of forest patches. Overall, three-dimensional habitat descriptions derived from integrated LiDAR and hyperspectral data serve as a powerful bird conservation tool that shows how the distribution of bird species relates to forest composition and structure at various scales.

Clustering analysis of water distribution systems: identifying critical components and community impacts.

PubMed

Diao, K; Farmani, R; Fu, G; Astaraie-Imani, M; Ward, S; Butler, D

2014-01-01

Large water distribution systems (WDSs) are networks with both topological and behavioural complexity. Thereby, it is usually difficult to identify the key features of the properties of the system, and subsequently all the critical components within the system for a given purpose of design or control. One way is, however, to more explicitly visualize the network structure and interactions between components by dividing a WDS into a number of clusters (subsystems). Accordingly, this paper introduces a clustering strategy that decomposes WDSs into clusters with stronger internal connections than external connections. The detected cluster layout is very similar to the community structure of the served urban area. As WDSs may expand along with urban development in a community-by-community manner, the correspondingly formed distribution clusters may reveal some crucial configurations of WDSs. For verification, the method is applied to identify all the critical links during firefighting for the vulnerability analysis of a real-world WDS. Moreover, both the most critical pipes and clusters are addressed, given the consequences of pipe failure. Compared with the enumeration method, the method used in this study identifies the same group of the most critical components, and provides similar criticality prioritizations of them in a more computationally efficient time.

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

PubMed

Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

2016-10-01

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Leadership for Community Engagement--A Distributed Leadership Perspective

ERIC Educational Resources Information Center

Liang, Jia G.; Sandmann, Lorilee R.

2015-01-01

This article presents distributed leadership as a framework for analysis, showing how the phenomenon complements formal higher education structures by mobilizing leadership from various sources, formal and informal. This perspective more accurately portrays the reality of leading engaged institutions. Using the application data from 224…

Spatial Description of Drinking Water Bacterial Community Structures in Bulk Water Samples Collected in a Metropolitan Distribution System

EPA Science Inventory

The description of microorganisms inhabiting drinking water distribution systems has commonly been performed using techniques that are biased towards easy to culture bacterial populations. As most environmental microorganisms cannot be grown on artificial media, our understanding...

Bacterial Composition in a Metropolitan Drinking Water Distribution System Utilizing Different Source Waters

EPA Science Inventory

The microbial community structure was investigated from bulk phase water samples of multiple collection sites from two service areas within the Cincinnati drinking water distribution system (DWDS). Each area is associated with a different primary source of water (i.e., groundwat...

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe.

PubMed

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe

PubMed Central

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes. PMID:27074044

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

PubMed Central

Zhang, Shaocun; Cao, Xiaocang; Huang, He

2017-01-01

Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research. PMID:28286741

Diversity and community structure of pelagic cnidarians in the Celebes and Sulu Seas, southeast Asian tropical marginal seas

NASA Astrophysics Data System (ADS)

Grossmann, Mary M.; Nishikawa, Jun; Lindsay, Dhugal J.

2015-06-01

The Sulu Sea is a semi-isolated, marginal basin surrounded by high sills that greatly reduce water inflow at mesopelagic depths. For this reason, the entire water column below 400 m is stable and homogeneous with respect to salinity (ca. 34.00) and temperature (ca. 10 °C). The neighbouring Celebes Sea is more open, and highly influenced by Pacific waters at comparable depths. The abundance, diversity, and community structure of pelagic cnidarians was investigated in both seas in February 2000. Cnidarian abundance was similar in both sampling locations, but species diversity was lower in the Sulu Sea, especially at mesopelagic depths. At the surface, the cnidarian community was similar in both marginal seas, but, at depth, community structure was dependent first on sampling location and then on depth within each Sea. Cnidarians showed different patterns of dominance at the two sampling locations, with Sulu Sea communities often dominated by species that are rare elsewhere in the Indo-Pacific. Mesopelagic and bathypelagic species recorded in the Sulu Sea did not have significantly different vertical distributions in the Celebes Sea. However, some deep mesopelagic genera were absent from the Sulu Sea in the sampled depth range. These results suggest that a combination of environmental and physiological parameters determine the distribution and dominance of pelagic cnidarians.

A road map for integrating eco-evolutionary processes into biodiversity models.

PubMed

Thuiller, Wilfried; Münkemüller, Tamara; Lavergne, Sébastien; Mouillot, David; Mouquet, Nicolas; Schiffers, Katja; Gravel, Dominique

2013-05-01

The demand for projections of the future distribution of biodiversity has triggered an upsurge in modelling at the crossroads between ecology and evolution. Despite the enthusiasm around these so-called biodiversity models, most approaches are still criticised for not integrating key processes known to shape species ranges and community structure. Developing an integrative modelling framework for biodiversity distribution promises to improve the reliability of predictions and to give a better understanding of the eco-evolutionary dynamics of species and communities under changing environments. In this article, we briefly review some eco-evolutionary processes and interplays among them, which are essential to provide reliable projections of species distributions and community structure. We identify gaps in theory, quantitative knowledge and data availability hampering the development of an integrated modelling framework. We argue that model development relying on a strong theoretical foundation is essential to inspire new models, manage complexity and maintain tractability. We support our argument with an example of a novel integrated model for species distribution modelling, derived from metapopulation theory, which accounts for abiotic constraints, dispersal, biotic interactions and evolution under changing environmental conditions. We hope such a perspective will motivate exciting and novel research, and challenge others to improve on our proposed approach. © 2013 John Wiley & Sons Ltd/CNRS.

PCR-DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau.

PubMed

Han, Rui; Yuan, Yongze; Cao, Qianwen; Li, Quanhui; Chen, Laisheng; Zhu, Derui; Liu, Deli

2018-05-01

To investigate contribution of environmental factor(s) to microbial community structure(s) involved in rural household biogas fermentation at Qinghai Plateau, we collected slurry samples from 15 digesters, with low-temperature working conditions (11.1-15.7 °C) and evenly distributed at three counties (Datong, Huangyuan, and Ledu) with cold plateau climate, to perform polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and further sequencing. The bacterial communities in the total 15 digesters were classified into 38 genera with Mangroviflexus (12.1%) as the first dominant, and the archaeal communities into ten genera with Methanogenium (38.5%) as the most dominant. For each county, the digesters with higher biogas production, designated as HP digesters, exclusively had 1.6-3.1 °C higher fermentation temperature and the unique bacterial structure composition related, i.e., unclassified Clostridiales for all the HP digesters and unclassified Marinilabiliaceae and Proteiniclasticum for Ledu HP digesters. Regarding archaeal structure composition, Methanogenium exhibited significantly higher abundances at all the HP digesters and Thermogymnomonas was the unique species only identified at Ledu HP digesters with higher-temperature conditions. Redundancy analysis also confirmed the most important contribution of temperature to the microbial community structures investigated. This report emphasized the correlation between temperature and specific microbial community structure(s) that would benefit biogas production of rural household digesters at Qinghai Plateau.

On the proportional abundance of species: Integrating population genetics and community ecology.

PubMed

Marquet, Pablo A; Espinoza, Guillermo; Abades, Sebastian R; Ganz, Angela; Rebolledo, Rolando

2017-12-01

The frequency of genes in interconnected populations and of species in interconnected communities are affected by similar processes, such as birth, death and immigration. The equilibrium distribution of gene frequencies in structured populations is known since the 1930s, under Wright's metapopulation model known as the island model. The equivalent distribution for the species frequency (i.e. the species proportional abundance distribution (SPAD)), at the metacommunity level, however, is unknown. In this contribution, we develop a stochastic model to analytically account for this distribution (SPAD). We show that the same as for genes SPAD follows a beta distribution, which provides a good description of empirical data and applies across a continuum of scales. This stochastic model, based upon a diffusion approximation, provides an alternative to neutral models for the species abundance distribution (SAD), which focus on number of individuals instead of proportions, and demonstrate that the relative frequency of genes in local populations and of species within communities follow the same probability law. We hope our contribution will help stimulate the mathematical and conceptual integration of theories in genetics and ecology.

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

PubMed

Hu, Hang-Wei; Wang, Jun-Tao; Singh, Brajesh K; Liu, Yu-Rong; Chen, Yong-Liang; Zhang, Yu-Jing; He, Ji-Zheng

2018-04-24

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Dynamics of bacterial communities before and after distribution in a full-scale drinking water network.

PubMed

El-Chakhtoura, Joline; Prest, Emmanuelle; Saikaly, Pascal; van Loosdrecht, Mark; Hammes, Frederik; Vrouwenvelder, Hans

2015-05-01

Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic. Copyright © 2015 Elsevier Ltd. All rights reserved.

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Taïb, Najwa; Mangot, Jean-François; Bronner, Gisèle; Boucher, Delphine; Debroas, Didier

2013-07-01

Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A Long-Term Study of the Microbial Community Structure in a Simulated Chloraminated Drinking Water Distribution System

EPA Science Inventory

Free chlorine is used as the primary disinfectant in most drinking water distribution systems(DWDS). However, chlorine disinfection promotes the formation of disinfectant by-products (DBPs)and as a result, many US water treatment facilities use chloramination to ensure regulatory...

Evaluating distributed medical education: what are the community's expectations?

PubMed

Lovato, Chris; Bates, Joanna; Hanlon, Neil; Snadden, David

2009-05-01

This study aimed to explore community members' perceptions of present and future impacts of the implementation of an undergraduate medical education programme in an underserved community. We conducted semi-structured interviews with eight key informants representing the health, education, business, economy, media and political sectors. A two-stage approach was used. In the first stage, the interviews were analysed to identify sector-specific impacts informants perceived as already occurring or which they hoped to see in the future. The transcripts were then re-analysed to determine any underlying themes that crossed sectors. Community leaders described impacts that were already occurring in all sectors and also described changes in the community itself. Four underlying themes emerged: an increase in pride and status; partnership development; community self-efficacy, and community development. These underlying themes appear to characterise the development of social capital in the community. The implementation of distributed undergraduate medical education programmes in rural and underserved communities may impact their host communities in ways other than the production of a rural doctor workforce. Further studies to quantify impacts in diverse sectors and to explore possible links with social capital are needed.

Multi-frequency complex network from time series for uncovering oil-water flow structure.

PubMed

Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

2015-02-04

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

Differential habitat use or intraguild interactions: What structures a carnivore community?

Treesearch

Matthew E. Gompper; Damon B. Lesmeister; Justina C. Ray; Jay R. Malcolm; Roland Kays; Aaron W. Reed

2016-01-01

Differential habitat use and intraguild competition are both thought to be important drivers of animal population sizes and distributions. Habitat associations for individual species are well-established, and interactions between particular pairs of species have been highlighted in many focal studies. However, community-wide assessments of the relative strengths of...

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

PubMed

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

2017-09-01

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

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats

USGS Publications Warehouse

Price, James T.; Paladino, Frank V.; Lamont, Margaret M.; Witherington, Blair E.; Bates, Scott T.; Soule, Tanya

2017-01-01

The gut microbiome of herbivorous animals consists of organisms that efficiently digest the structural carbohydrates of ingested plant material. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities because they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a neritic distribution and herbivorous diet. As an alternative to direct sampling of the gut, we investigated the cloacal microbiomes of juvenile green turtles before and after recruitment to neritic waters to observe any changes in their microbial community structure. Cloacal swabs were taken from individual turtles for analysis of the 16S rRNA gene sequences using Illumina sequencing. One fecal sample was also obtained, allowing for a preliminary comparison with the bacterial community of the cloaca. We found significant variation in the juvenile green turtle bacterial communities between pelagic and neritic habitats, suggesting that environmental and dietary factors support different bacterial communities in green turtles from these habitats. This is the first study to characterize the cloacal microbiome of green turtles in the context of their ontogenetic shifts, which could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.

A generalised significance test for individual communities in networks.

PubMed

Kojaku, Sadamori; Masuda, Naoki

2018-05-09

Many empirical networks have community structure, in which nodes are densely interconnected within each community (i.e., a group of nodes) and sparsely across different communities. Like other local and meso-scale structure of networks, communities are generally heterogeneous in various aspects such as the size, density of edges, connectivity to other communities and significance. In the present study, we propose a method to statistically test the significance of individual communities in a given network. Compared to the previous methods, the present algorithm is unique in that it accepts different community-detection algorithms and the corresponding quality function for single communities. The present method requires that a quality of each community can be quantified and that community detection is performed as optimisation of such a quality function summed over the communities. Various community detection algorithms including modularity maximisation and graph partitioning meet this criterion. Our method estimates a distribution of the quality function for randomised networks to calculate a likelihood of each community in the given network. We illustrate our algorithm by synthetic and empirical networks.

River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico.

PubMed

Ortmann, Alice C; Brannock, Pamela M; Wang, Lei; Halanych, Kenneth M

2018-04-17

Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms.

PubMed

Nagymáté, Zsuzsanna; Homonnay, Zalán G; Márialigeti, Károly

2016-01-01

Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution. Copyright © 2016 Elsevier GmbH. All rights reserved.

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.

Bacterial dynamics in steady-state biofilters: beyond functional stability.

PubMed

Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

2012-01-01

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

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.

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Community Structure of Tintinnid Ciliates of the Microzooplankton in the South West Pacific Ocean: Comparison of a High Primary Productivity with a Typical Oligotrophic Site.

PubMed

Dolan, John R; Gimenez, Audrey; Cornet-Barthaux, Veronique; de Verneil, Alain

2016-11-01

Transient 'hot spots' of phytoplankton productivity occur in the generally oligotrophic Southern Pacific Ocean and we hypothesized that the population structure of tintinnid ciliates, planktonic grazers, would differ from that of a typical oligotrophic sites. Samples were collected over a 1-wk period at each of two sites between Fiji and Tahiti: one of elevated chlorophyll a concentrations and primary productivity with an abundance of N-fixing cyanobacteria Trichodesmium, and a distant oligotrophic site. Tintinnid abundance differed between the sites by a factor of 2. A single species (Favella sp.), absent from the oligotrophic site, highly dominated the 'hot spot' site. However, total species richness was identical (71 spp.) as well as short-term temporal variability (2-4 d). At both sites, species abundance distributions most closely fit a log-series or log-normal distribution and the abundance distributions of ecological types, forms of distinct lorica oral diameter, were the typical geometric. Morphological diversity was only slightly lower at the high productivity site. We found that communities of these plankton grazers in 'hot spots' of phytoplankton productivity in oligotrophic systems, although harboring different species, differ little from surrounding oligotrophic areas in community structure. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Spatial distribution of bacterial communities and related biochemical properties in Luzhou-flavor liquor-fermented grains.

PubMed

Zheng, Jia; Wu, Chongde; Huang, Jun; Zhou, Rongqing; Liao, Xuepin

2014-12-01

Grain fermenting with separate layers in a fermentation pit is the typical and experiential brewing technology for Chinese Luzhou-flavor liquor. However, it is still unclear to what extent the bacterial communities in the different layers of fermented grains (FG) effects the liquor's quality. In this study, the spatial distributions of bacterial communities in Luzhou-flavor liquor FG (top, middle, and bottom layers) from 2 distinctive factories (Jiannanchun and Fenggu) were investigated using culture-independent approaches (phospholipid fatty acid [PLFA] and polymerase chain reaction-denaturing gel electrophoresis [DGGE]). The relationship between bacterial community and biochemical properties was also assessed by Canonical correspondence analysis (CCA). No significant variation in moisture was observed in spatial samples, and the highest content of acidity and total ester was detected in the bottom layer (P < 0.05). A high level of ethanol was observed in the top and middle layers of Fenggu and Jiannanchun, respectively. Significant spatial distribution of the total PLFA was only shown in the 50-y-old pits (P < 0.05), and Gram negative bacteria was the prominent community. Bacterial 16S rDNA DGGE analysis revealed that the most abundant bacterial community was in the top layers of the FG both from Fenggu and Jiannanchun, with Lactobacillaceae accounting for 30% of the total DGGE bands and Lactobacillus acetotolerans was the dominant species. FG samples from the same pit had a highly similar bacterial community structure according to the hierarchal cluster tree. CCA suggested that the moisture, acidity, ethanol, and reducing sugar were the main factors affecting the distribution of L. acetotolerans. Our results will facilitate the knowledge about the spatial distribution of bacterial communities and the relationship with their living environment. © 2014 Institute of Food Technologists®

Ordination of breeding birds in relation to environmental gradients in three southeastern United States floodplain forests

USGS Publications Warehouse

Wakeley, J.S.; Guilfoyle, M.P.; Antrobus, T.J.; Fischer, R.A.; Barrow, W.C.; Hamel, P.B.

2007-01-01

We used an ordination approach to identify factors important to the organization of breeding bird communities in three floodplains: Cache River, Arkansas (AR), Iatt Creek, Louisiana (LA), and the Coosawhatchie River, South Carolina (SC), USA. We used 5-min point counts to sample birds in each study area each spring from 1995 to 1998, and measured ground-surface elevations and a suite of other habitat variables to investigate bird distributions and community characteristics in relation to important environmental gradients. In both AR and SC, the average number of Neotropical migrant species detected was lowest in semipermanently flooded Nyssa aquatica Linnaeus habitats and greatest in the highest elevation floodplain zone. Melanerpes carolinus Linnaeus, Protonotaria citrea Boddaert, Quiscalus quiscula Linnaeus, and other species were more abundant in N. aquatica habitats, whereas Wilsonia citrina Boddaert, Oporornis formosus Wilson, Vireo griseus Boddaert, and others were more abundant in drier floodplain zones. In LA, there were no significant differences in community metrics or bird species abundances among forest types. Canonical correspondence analyses revealed that structural development of understory vegetation was the most important factor affecting bird distributions in all three study areas; however, potential causes of these structural gradients differed. In AR and SC, differences in habitat structure were related to the hydrologic gradient, as indexed by ground-surface elevation. In LA, structural variations were related mainly to the frequency of canopy gaps. Thus, bird communities in all three areas appeared to be organized primarily in response to repeated localized disturbance. Our results suggest that regular disturbance due to flooding plays an important role in structuring breeding bird communities in floodplains subject to prolonged inundation, whereas other agents of disturbance (e.g., canopy gaps) may be more important in headwater systems subject to only short-duration flooding. Management for avian community integrity in these systems should strive to maintain forest zonation and natural disturbance regimes. ?? 2007 Springer Science+Business Media B.V.

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

PubMed Central

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-01-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a ‘core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems. PMID:26251872

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system.

PubMed

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-03-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.

Soccer science and the Bayes community: exploring the cognitive implications of modern scientific communication.

PubMed

Shrager, Jeff; Billman, Dorrit; Convertino, Gregorio; Massar, J P; Pirolli, Peter

2010-01-01

Science is a form of distributed analysis involving both individual work that produces new knowledge and collaborative work to exchange information with the larger community. There are many particular ways in which individual and community can interact in science, and it is difficult to assess how efficient these are, and what the best way might be to support them. This paper reports on a series of experiments in this area and a prototype implementation using a research platform called CACHE. CACHE both supports experimentation with different structures of interaction between individual and community cognition and serves as a prototype for computational support for those structures. We particularly focus on CACHE-BC, the Bayes community version of CACHE, within which the community can break up analytical tasks into "mind-sized" units and use provenance tracking to keep track of the relationship between these units. Copyright © 2009 Cognitive Science Society, Inc.

Spatial and temporal repeatability in parasite community structure of tropical fish hosts.

PubMed

Vidal-Martínez, V M; Poulin, R

2003-10-01

An assessment is made of the repeatability of parasite community structure in space for a marine fish, and in space and time for a freshwater fish from south-eastern Mexico. The marine fish species was the red grouper, Epinephelus morio (collected from 9 localities), and the freshwater species was the cichlid, Cichlasoma urophthalmus (collected from 6 localities: including monthly at 2 localities for 1 year, and bimonthly at 1 locality in 1990 and 1999). Pairwise interspecific associations and analyses of nested patterns in the distributions of parasite species among hosts were used in both fish species, with comparisons over time made only with the cichlid. Positive interspecific associations, and nested patterns were noted in some localities for both fish species, and/or at some sampling times for the cichlid fish. However, non-random patterns in the structure of parasite communities in these 2 host species only were observed sporadically. When present, nestedness in both fish species was apparently linked with a positive association between total infection intensities and fish size. Additionally, adjacent localities were more likely to display similar parasite community structure than distant ones. This preliminary result suggests that distance between localities is an important determinant of predictability in parasite community structure.

A unified model explains commonness and rarity on coral reefs.

PubMed

Connolly, Sean R; Hughes, Terry P; Bellwood, David R

2017-04-01

Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species-abundance distributions, and species associations, and we test this model against the metacommunity structure of reef-building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the unified model simultaneously captures extremely well local species-abundance distributions, interspecific variation in the strength of spatial aggregation, patterns of community similarity, species accumulation, and regional species richness, performing far better than alternative models also examined here and in previous work on coral reefs. Our approach contributes to the development of synthetic theory for large-scale patterns of community structure in nature, and to addressing ongoing challenges in biodiversity conservation at macroecological scales. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

The effect of range changes on the functional turnover, structure and diversity of bird assemblages under future climate scenarios.

PubMed

Barbet-Massin, Morgane; Jetz, Walter

2015-08-01

Animal assemblages fulfill a critical set of ecological functions for ecosystems that may be altered substantially as climate change-induced distribution changes lead to community disaggregation and reassembly. We combine species and community perspectives to assess the consequences of projected geographic range changes for the diverse functional attributes of avian assemblages worldwide. Assemblage functional structure is projected to change highly unevenly across space. These differences arise from both changes in the number of species and changes in species' relative local functional redundancy or distinctness. They sometimes result in substantial losses of functional diversity that could have severe consequences for ecosystem health. Range expansions may counter functional losses in high-latitude regions, but offer little compensation in many tropical and subtropical biomes. Future management of local community function and ecosystem services thus relies on understanding the global dynamics of species distributions and multiscale approaches that include the biogeographic context of species traits. © 2015 John Wiley & Sons Ltd.

Spatiotemporal model of barley and cereal yellow dwarf virus transmission dynamics with seasonality and plant competition

Treesearch

S.M. Moore; C.A. Manore; V.A. Bokil; E.T. Borer; P.R. Hosseini

2011-01-01

Many generalist pathogens are influenced by the spatial distributions and relative abundances of susceptible host species. The spatial structure of host populations can influence patterns of infection incidence (or disease outbreaks), and the effects of a generalist pathogen on host community dynamics in a spatially heterogeneous community may differ from predictions...

RELATIVE INFLUENCE OF HYPOXIA, ANOXIA, AND ASSOCIATED ENVIRONMENTAL FACTORS AS DETERMINANTS OF MACROBENTHIC COMMUNITY STRUCTURE IN A NORTHERN GULF OF MEXICO ESTUARY

EPA Science Inventory

Seasonal patterns (i.e., December 1986, and April and October 1987) in benthic macroinfaunal abundance, distribution, and taxa composition at 19 sites in Perdido Bay, AL/FL, are evaluated to assess the relative importance of environmental factors as determinants of community stru...

Arthropod vertical stratification in temperate deciduous forests: Implications for conservation oriented management

Treesearch

Ulyshen Michael

2011-01-01

Studies on the vertical distribution patterns of arthropods in temperate deciduous forests reveal highly stratified (i.e., unevenly vertically distributed) communities. These patterns are determined by multiple factors acting simultaneously, including: (1) time (forest age, season, time of day); (2) forest structure (height, vertical foliage complexity, plant surface...

Distributed user services for supercomputers

NASA Technical Reports Server (NTRS)

Sowizral, Henry A.

1989-01-01

User-service operations at supercomputer facilities are examined. The question is whether a single, possibly distributed, user-services organization could be shared by NASA's supercomputer sites in support of a diverse, geographically dispersed, user community. A possible structure for such an organization is identified as well as some of the technologies needed in operating such an organization.

Mathematical Ecology Analysis of Geographical Distribution of Soybean-Nodulating Bradyrhizobia in Japan

PubMed Central

Saeki, Yuichi; Shiro, Sokichi; Tajima, Toshiyuki; Yamamoto, Akihiro; Sameshima-Saito, Reiko; Sato, Takashi; Yamakawa, Takeo

2013-01-01

We characterized the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in Japan and their geographical distribution in an ecological study of indigenous soybean rhizobia. We isolated bradyrhizobia from three kinds of Rj-genotype soybeans. Their genetic diversity and community structure were analyzed by PCR-RFLP analysis of the 16S–23S rRNA gene internal transcribed spacer (ITS) region with 11 Bradyrhizobium USDA strains as references. We used data from the present study and previous studies to carry out mathematical ecological analyses, multidimensional scaling analysis with the Bray-Curtis index, polar ordination analysis, and multiple regression analyses to characterize the relationship between soybean-nodulating bradyrhizobial community structures and their geographical distribution. The mathematical ecological approaches used in this study demonstrated the presence of ecological niches and suggested the geographical distribution of soybean-nodulating bradyrhizobia to be a function of latitude and the related climate, with clusters in the order Bj123, Bj110, Bj6, and Be76 from north to south in Japan. PMID:24240318

Anthropogenic impact on biogenic substance distribution and bacterial community in sediment along the Yarlung Tsangpo River on Tibet Plateau, China

NASA Astrophysics Data System (ADS)

Wang, C.; Peifang, W.; Wang, X.; Hou, J.; Miao, L.

2017-12-01

Lotic river system plays an important part in water-vapor transfer and biogenic substances migration and transformation. Anthropogenic activities, including wastewater discharging and river damming, have altered river ecosystem and continuum. However, as the longest alpine river in China and suffered from increasing anthropogenic activities, the Yarlung Tsangpo River has been rarely studied. Recently, more attention has also been paid to the bacteria in river sediment as they make vital contributions to the biogeochemical nutrient cycling. Here, the distribution of biogenic substances, including nitrogen, phosphorus, silicon and carbon, was explored in both water and sediment of the Yarlung Tsangpo River. By using the next generation 16S rRNA sequencing, the bacterial diversity and structure in river sediment were presented. The results indicated that the nutrient concentrations increased in densely populated sites, revealing that biogenic substance distribution corresponded with the intensity of anthropogenic activity along the river. Nitrogen, phosphorus, silicon and carbon in water and sediment were all retained by the Zangmu Dam which is the only dam in the mainstream of the river. Moreover, the river damming decreased the biomass and diversity of bacteria in sediment, but no significant alteration of community structure was observed upstream and downstream of the dam. The most dominant bacteria all along the river was Proteobacteria. Meanwhile, Verrucomicrobia and Firmicutes also dominated the community composition in upstream and downstream of the river, respectively. In addition, total organic carbon (TOC) was proved to be the most important environmental factor shaping the bacterial community in river sediment. Our study offered the preliminary insights into the biogenic substance distribution and bacterial community in sediment along an alpine river which was affected by anthropogenic activities. In the future, more studies are needed to reveal the relationship between anthropogenic activity, biogenic substance cycling and bacterial community, especially along the alpine rivers.

Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity.

PubMed

Findlay, S; Sinsabaugh, R L

2006-10-01

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Interrelations between plant communities and environmental factors of wetlands and surrounding lands in mid- and lower reaches of Tarim River].

PubMed

Zhao, Ruifeng; Zhou, Huarong; Qian, Yibing; Zhang, Jianjun

2006-06-01

A total of 16 quadrants of wetlands and surrounding lands in the mid- and lower reaches of Tarim River were surveyed, and the data about the characteristics of plant communities and environmental factors were collected and counted. By using PCA (principal component analysis) ordination and regression procedure, the distribution patterns of plant communities and the relationships between the characteristics of plant community structure and environmental factors were analyzed. The results showed that the distribution of the plant communities was closely related to soil moisture, salt, and nutrient contents. The accumulative contribution rate of soil moisture and salt contents in the first principal component accounted for 35.70%, and that of soil nutrient content in the second principal component reached 25.97%. There were 4 types of habitats for the plant community distribution, i. e., fenny--light salt--medium nutrient, moist--medium salt--medium nutrient, mesophytic--medium salt--low nutrient, and medium xerophytic-heavy salt--low nutrient. Along these habitats, swamp vegetation, meadow vegetation, riparian sparse forest, halophytic desert, and salinized shrub were distributed. In the wetlands and surrounding lands of mid- and lower reaches of Tarim River, the ecological dominance of the plant communities was markedly and unitary-linearly correlated with the compound gradient of soil moisture and salt contents. The relationships between species diversity, ecological dominance, and compound gradient of soil moisture and salt contents were significantly accorded to binary-linear regression model.

Diet is the primary determinant of bacterial community structure in the guts of higher termites.

PubMed

Mikaelyan, Aram; Dietrich, Carsten; Köhler, Tim; Poulsen, Michael; Sillam-Dussès, David; Brune, Andreas

2015-10-01

The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches. © 2015 John Wiley & Sons Ltd.

The effect of local environmental variables on the helminth parasite communities of the pointedbelly frog Leptodactylus podicipinus from ponds in the Pantanal wetlands.

PubMed

Campião, Karla Magalhães; Delatorre, Milena; Rodrigues, Rozangela Batista; da Silva, Reinaldo José; Ferreira, Vanda Lúcia

2012-04-01

Understanding the patterns of species distribution and abundance has been at the core of ecology. In general, these patterns are determined by species dispersion as well as by abiotic and biotic environmental conditions. Similarly, host-parasite relations and the structure of parasite assemblages are also shaped by environmental conditions and landscape composition. Herein, we assessed the influence of environmental variables and parasite species dispersion on the structure of helminth parasites communities in the frog Leptodactylus podicipinus. We sampled 10 ponds and recorded area, depth, altitude, pH, dissolved oxygen, salinity, temperature, and extent of soil, water, and vegetation cover as well as the distances between the ponds. We collected 121 frogs and found 9 helminth taxa; 2 of them were core species (prevalence higher than 50%), which contributed to the relatively high similarity observed among the ponds. Most of the helminths showed some variation in the frequencies of occurrence among communities from different ponds. The change in species composition among ponds was explained by the environmental variables but not by the distance between the ponds. Moreover, the results indicated that local processes (variation in environmental conditions) were more important than the regional processes (species distribution) in determining the structure of parasite communities. The variation in helminth communities among ponds in response to moderate differences in pond environmental characteristics points to the potential of helminth species as indicators of environmental conditions.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

[Effect of environmental factors on bacterial community structure in petroleum contaminated soil of Karamay oil field].

PubMed

Liang, Jianfang; Yang, Jiangke; Yang, Yang; Chao, Qunfang; Yin, Yalan; Zhao, Yaguan

2016-08-04

This study aimed to study the phylogenetic diversity and community structure of bacteria in petroleum contaminated soils from Karamay oil field, and to analyze the relationship between the community variation and the environment parameters, to provide a reference for bioremediation of petroleum contaminated soils. We collected samples from petroleum contaminated soils in 5 cm, 20 cm and 50 cm depth layers, and measured the environment parameters subsequently. We constructed three 16S rRNA gene clone libraries of these soil samples, and then determined the operation taxonomy units (OTUs) restriction fragment length polymorphism method, and finally sequenced the representative clones of every OUT. The diversity, richness and evenness index of the bacteria communities were calculated by using Biodap software. Neighbor-Joining phylogenetic tree was constructed based on 16S rRNA gene sequences of bacteria from Karamay oil field and the references from related environments. Canonial correspondence analysis (CCA) was used to analyze the relationship between environment parameters and species by using CANOCO 4.5 software. Environment parameters showed that 50 cm deep soil contained the highest amount of total nitrogen (TN) and total phosphorus (TP), whereas the 20 cm depth soil contained the lowest amount. The 5 cm depth soil contained the highest amount of total organic carbon (TOC), whereas the 50 cm depth soil contained the lowest amount. Among the 3 layers, 20 cm depth had the highest diversity and richness of bacteria, whereas the bacteria in 50 cm depth was the lowest. Phylogenic analyses suggested that the bacteria in Karamay oil field could be distributed into five groups at the level of phylum, Cluster I to V, respectively belong to Proteobacteria, Actinobacteria, Firmicute, Bacteroidetes, Planctomycetes. Cluster I accounts for 78.57% of all tested communities. CCA results showed that TN, TP, TOC significantly affected the bacteria community structure. Especially, TOC content is significantly related to the distribution of Pseudomonas. The petroleum-contaminated soil inhabited abundant of bacteria. The diversity index and spatial distribution of these communities were affected by the environment parameters in the soil.

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

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities.

PubMed

Lilleskov, Erik A; Bruns, Thomas D; Horton, Thomas R; Taylor, D; Grogan, Paul

2004-08-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied various measures of spatial pattern to characterize distributions at EMF community and species levels: Mantel tests, Mantel correlograms, variance/mean and standardized variograms. Mantel tests indicated that in four of eight sites community similarity decreased with distance, whereas Mantel correlograms also found spatial autocorrelation in those four plus two additional sites. In all but one of these sites elevated similarity was evident only at relatively small spatial scales (< 2.6 m), whereas one exhibited a larger scale pattern ( approximately 25 m). Evenness of biomass distribution among cores varied widely among taxa. Standardized variograms indicated that most of the dominant taxa showed patchiness at a scale of less than 3 m, with a range from 0 to < or =17 m. These results have implications for both sampling scale and intensity to achieve maximum efficiency of community sampling. In the systems we examined, cores should be at least 3 m apart to achieve the greatest sampling efficiency for stand-level community analysis. In some cases even this spacing may result in reduced sampling efficiency arising from patterns of spatial autocorrelation. Interpretation of the causes and significance of these patterns requires information on the genetic identity of individuals in the communities.

Structure and Spatial Distribution of the Chironomidae Community in Mesohabitats in a First Order Stream at the Poço D'Anta Municipal Biological Reserve in Brazil

PubMed Central

Vescovi Rosa, Beatriz Figueiraujo Jabour; de Oliveira, Vívian Campos; Alves, Roberto da Gama

2011-01-01

The Chironomidae occupy different habitats along the lotic system with their distribution determined by different factors such as the substrate characteristics and water speed. The input of vegetable material from the riparian forest allows a higher habitat diversity and food to the benthic fauna. The main aim of this paper is to verify the structure and spatial distribution of the Chironomidae fauna in different mesohabitats in a first order stream located at a Biological Reserve in the southeast of Brazil. In the months of July, August, and September 2007, and in January, February, and March 2008, samples were collected with a hand net (250 µm) in the following mesohabitats: litter from riffles, litter from pools, and sediment from pools. The community structure of each mesohabitat was analyzed through the abundance of organisms, taxa richness, Pielou's evenness, Shannon's diversity, and taxa dominance. Similarity among the mesohabitats was obtained by Cluster analysis, and Chironomidae larvae distribution through the Correspondence analysis. Indicator species analysis was used to identify possible taxa preference for a determined mesohabitat. The analyzed mesohabitats showed high species richness and diversity favored by the large environmental heterogeneity. Some taxa were indicators of the type of mesohabitat. The substrate was the main factor that determined taxa distribution in relation to water flow differences (riffle and pool). Stream characteristics such as low water speed and the presence of natural mechanisms of retention may have provided a higher faunistic similarity between the areas with different flows. The results showed that the physical characteristics of each environment presented a close relationship with the structure and spatial distribution of the Chironomidae fauna in lotic systems. PMID:21529258

The local environment determines the assembly of root endophytic fungi at a continental scale.

PubMed

Glynou, Kyriaki; Ali, Tahir; Buch, Ann-Katrin; Haghi Kia, Sevda; Ploch, Sebastian; Xia, Xiaojuan; Çelik, Ali; Thines, Marco; Maciá-Vicente, Jose G

2016-09-01

Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the occurrence of root endophytes in the non-mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring their communities at a continental scale. We sampled 52 plant populations across the northern Mediterranean and central Europe and used a cultivation approach to study their endophytic communities. Cultivation of roots yielded 2601 isolates, which were grouped into 296 operational taxonomic units (OTUs) by internal transcribed spacer sequencing of 1998 representative colonies. Climatic and spatial factors were the best descriptors of the structure of endophytic communities, outweighing soil characteristics, host genotype and geographical distance. OTU richness was negatively affected by precipitation, and the composition of communities followed latitudinal gradients of precipitation and temperature. Only six widespread OTUs belonging to the orders Pleosporales, Hypocreales and Helotiales represented about 50% of all isolates. Assessments of their individual distribution revealed particular ecological preferences or a cosmopolitan occurrence. Our findings support a strong influence of the local environment in determining root endophytic communities, and show a different niche occupancy by individual endophytes. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

PubMed

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

2014-02-01

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

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

Colonization and community structure of root-associated microorganisms of Sabina vulgaris with soil depth in a semiarid desert ecosystem with shallow groundwater.

PubMed

Taniguchi, Takeshi; Usuki, Hiroyuki; Kikuchi, Junichi; Hirobe, Muneto; Miki, Naoko; Fukuda, Kenji; Zhang, Guosheng; Wang, Linhe; Yoshikawa, Ken; Yamanaka, Norikazu

2012-08-01

Arbuscular mycorrhizal fungi (AMF) have been observed in deep soil layers in arid lands. However, change in AMF community structure with soil depth and vertical distributions of the other root-associated microorganisms are unclear. Here, we examined colonization by AMF and dark septate fungi (DSF), as well as the community structure of AMF and endophytic fungi (EF) and endophytic bacteria (EB) in association with soil depth in a semiarid desert with shallow groundwater. Roots of Sabina vulgaris and soils were collected from surface to groundwater level at 20-cm intervals. Soil chemistry (water content, total N, and available P) and colonization of AMF and DSF were measured. Community structures of AMF, EF, and EB were examined by terminal restriction fragment length polymorphism analysis. AMF colonization decreased with soil depth, although it was mostly higher than 50%. Number of AMF phylotypes decreased with soil depth, but more than five phylotypes were observed at depths up to 100 cm. Number of AMF phylotypes had a significant and positive relationship with soil moisture level within 0-15% of soil water content. DSF colonization was high but limited to soil surface. Number of phylotypes of EF and EB were diverse even in deep soil layers, and the community composition was associated with the colonization and community composition of AMF. This study indicates that AMF species richness in roots decreases but is maintained in deep soil layers in semiarid regions, and change in AMF colonization and community structure associates with community structure of the other root-associated microorganisms.

The Ground-Dwelling Arthropod Community of Península Valdés in Patagonia, Argentina

PubMed Central

Cheli, Germán H.; Corley, J. C.; Bruzzone, O.; del Brío, M.; Martínez, F.; Román, N. Martínez; Ríos, I.

2010-01-01

This is the first study based on a planned and intensive sampling effort that describes the community composition and structure of the ground-dwelling arthropod assemblage of Península Valdés (Patagonia). It was carried out using pitfall traps, opened for two weeks during the summers of 2005, 2006 and 2007. A total of 28, 111 individuals were caught. Ants (Hymenoptera: Formicidae) dominated this community, followed by beetles (Coleoptera) and spiders (Araneae). The most abundant species were Pheidole bergi Mayr (Hymenoptera: Formicidae) and Blapstinus punctulatus Solier (Coleoptera: Tenebrionidae). Two new species were very recently described as new based on specimens collected during this study: Valdesiana curiosa Carpintero, Dellapé & Cheli (Hemiptera, Miridae) and Anomaloptera patagonica Dellapé & Cheli (Hemiptera, Oxycarenidae). The order Coleoptera was the most diverse taxa. The distribution of abundance data was best described by the logarithmic series model both at the family and species levels, suggesting that ecological relationships in this community could be controlled by a few factors. The community was dominated by predators from a trophic perspective. This suggests that predation acts as an important factor driving the distribution and abundances of surface-dwelling arthropods in this habitat and as such serves as a key element in understanding desert, above-ground community structure. These findings may also be useful for management and conservation purposes in arid Patagonia. PMID:20572783

The ground-dwelling arthropod community of Península Valdés in Patagonia, Argentina.

PubMed

Cheli, Germán H; Corley, J C; Bruzzone, O; Brío, M Del; Martínez, F; Román, N Martínez; Ríos, I

2010-01-01

This is the first study based on a planned and intensive sampling effort that describes the community composition and structure of the ground-dwelling arthropod assemblage of Península Valdés (Patagonia). It was carried out using pitfall traps, opened for two weeks during the summers of 2005, 2006 and 2007. A total of 28,111 individuals were caught. Ants(Hymenoptera: Formicidae) dominated this community, followed by beetles (Coleoptera) and spiders (Araneae). The most abundant species were Pheidole bergi Mayr (Hymenoptera:Formicidae) and Blapstinus punctulatus Solier (Coleoptera: Tenebrionidae). Two new species were very recently described as new based on specimens collected during this study: Valdesianacuriosa Carpintero, Dellapé & Cheli (Hemiptera, Miridae) and Anomaloptera patagonica Dellapé& Cheli (Hemiptera, Oxycarenidae). The order Coleoptera was the most diverse taxa. The distribution of abundance data was best described by the logarithmic series model both at the family and species levels, suggesting that ecological relationships in this community could be controlled by a few factors. The community was dominated by predators from a trophic perspective. This suggests that predation acts as an important factor driving the distribution and abundances of surface-dwelling arthropods in this habitat and as such serves as a key element in understanding desert, above-ground community structure. These findings may also be useful for management and conservation purposes in arid Patagonia.

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) result in more extensive faunal turnover, thereby reducing the utility of ordinations that require at least some faunal similarity. Rank-abundance curves can be applied even in intervals of complete taxonomic turnover; curve shape is quantified by kurtosis, a statistical measure of whether a distribution is more (>3) or less (<3) peaked than a Gaussian distribution (kurtosis = 3). Rank-abundance curve kurtosis values are always greater than 3 for disturbed communities (n=20), and pre-disturbance and recovered communities generally range from 0 to 4. The average kurtosis for a pre-disturbance or recovered community is unique for each type of community (taxonomically or environmentally defined), requiring the establishment of a baseline for rank-abundance curve analysis. In each dataset, both rank-abundance curves and ordinations show a similar pattern of change in community structure during a disturbance. The rate and pattern of recovery varies relative to the spatial and temporal extent of the disturbance. The results of this study reveal that community structure is a useful measure of the impact of a disturbance, both in terms of the severity of the disturbance and in measuring the subsequent recovery. The methods and results of this research are applicable to multiple fields, from conservation biology to ecosystem health to paleoceanography and paleobiology.

a New Dynamic Community Model for Social Networks

NASA Astrophysics Data System (ADS)

Lu, Zhe-Ming; Wu, Zhen; Guo, Shi-Ze; Chen, Zhe; Song, Guang-Hua

2014-09-01

In this paper, based on the phenomenon that individuals join into and jump from the organizations in the society, we propose a dynamic community model to construct social networks. Two parameters are adopted in our model, one is the communication rate Pa that denotes the connection strength in the organization and the other is the turnover rate Pb, that stands for the frequency of jumping among the organizations. Based on simulations, we analyze not only the degree distribution, the clustering coefficient, the average distance and the network diameter but also the group distribution which is closely related to their community structure. Moreover, we discover that the networks generated by the proposed model possess the small-world property and can well reproduce the networks of social contacts.

Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary.

PubMed

Tremblay, Louis A; Clark, Dana; Sinner, Jim; Ellis, Joanne I

2017-09-20

The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

Modular and hierarchical structure of social contact networks

NASA Astrophysics Data System (ADS)

Ge, Yuanzheng; Song, Zhichao; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2013-10-01

Social contact networks exhibit overlapping qualities of communities, hierarchical structure and spatial-correlated nature. We propose a mixing pattern of modular and growing hierarchical structures to reconstruct social contact networks by using an individual’s geospatial distribution information in the real world. The hierarchical structure of social contact networks is defined based on the spatial distance between individuals, and edges among individuals are added in turn from the modular layer to the highest layer. It is a gradual process to construct the hierarchical structure: from the basic modular model up to the global network. The proposed model not only shows hierarchically increasing degree distribution and large clustering coefficients in communities, but also exhibits spatial clustering features of individual distributions. As an evaluation of the method, we reconstruct a hierarchical contact network based on the investigation data of a university. Transmission experiments of influenza H1N1 are carried out on the generated social contact networks, and results show that the constructed network is efficient to reproduce the dynamic process of an outbreak and evaluate interventions. The reproduced spread process exhibits that the spatial clustering of infection is accordant with the clustering of network topology. Moreover, the effect of individual topological character on the spread of influenza is analyzed, and the experiment results indicate that the spread is limited by individual daily contact patterns and local clustering topology rather than individual degree.

Latitudinal distribution of zooplankton communities in the Western Pacific along 160°E during summer 2014

NASA Astrophysics Data System (ADS)

Sun, Dong; Wang, Chunsheng

2017-05-01

A total of 51 mesozooplankton samples collected with a WP2 net from 0 to 200 m depth along 160°E (4°S-46°N) in the Western Pacific from June to July 2014 were analyzed. The latitudinal distribution of mesozooplankton community structure was analyzed. The average biomass and abundance in different provinces generally increased with latitude: the biomass of zooplankton ranged from 1.18 mg DW m- 3 (11°N) to 97.81 mg DW m- 3 (45°N), and the abundance of zooplankton ranged from 45.11 ind. m- 3 (3°S) to 439.84 ind. m- 3 (41°N). The community structure of zooplankton also showed a significant latitudinal variation. At lower latitudes, calanoid copepods were the most abundant group, while cyclopoid copepods were the most abundant group at higher latitudes. Multidimensional scaling analysis of community structure and other physical/chemical/biological characteristics supported five ecological provinces in the northwestern Pacific: the Western Pacific Warm Pool Province (WARM), the North Pacific Tropical Gyre (NPTG), the North Pacific Subtropical Gyre (NPST), the Kuroshio Current Province (KURO) and the Pacific Subarctic Gyres Province (PSAG). The Kuroshio Current Province can be regarded as a transitional zone between the subarctic and northern subtropical area, and this transitional zone corresponds much more closely to the ecocline concept, rather than the ecotone concept.

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Keystone taxa as drivers of microbiome structure and functioning.

PubMed

Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G A

2018-05-22

Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

PubMed

Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

2014-12-01

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L.

PubMed

Zhou, Xue; Tian, Lei; Zhang, Jianfeng; Ma, Lina; Li, Xiujun; Tian, Chunjie

2017-12-01

Sea buckthorn (Hippophae rhamnoides L.) is a pioneer plant used for land reclamation and an appropriate material for studying the interactions of symbiotic microorganisms because of its nitrogen-fixing root nodules and mycorrhiza. We used high-throughput sequencing to reveal the diversities and community structures of rhizospheric fungi and their link with nitrogen-fixing Frankia harbored in sea buckthorn collected along an altitude gradient from the Qinghai Tibet Plateau to interior areas. We found that the fungal diversities and compositions varied between different sites. Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla. The distribution of sea buckthorn rhizospheric fungi was driven by both environmental factors and the geographic distance. Among all examined soil characteristics, altitude, AP, and pH were found to have significant (p < 0.05) effect on the rhizospheric fungal community. The rhizospheric fungal communities became more distinct as the distance increased. Moreover, co-inertia analysis identified significant co-structures between Frankia and AMF communities in the rhizosphere of sea buckthorn. We conclude that at the large scale, there are certain linkages between nitrogen-fixing bacteria and the AMF expressed in the distributional pattern. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities.

PubMed

Ramírez, Santiago R; Hernández, Carlos; Link, Andres; López-Uribe, Margarita M

2015-05-01

Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia - a region where Central and South American biotas converge - to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet-to-dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly and provide a glimpse to the potential effects that climatic alterations may have on both pollinator communities and the ecosystem services they provide.

Distribution and abundance of phytobenthic communities: Implications for connectivity and ecosystem functioning in a Black Sea Marine Protected Area

NASA Astrophysics Data System (ADS)

Berov, Dimitar; Todorova, Valentina; Dimitrov, Lubomir; Rinde, Eli; Karamfilov, Ventzislav

2018-01-01

The distribution and abundance of macroalgal communities in a Marine Protected Area (MPA) along the Bulgarian Black Sea coast were mapped and quantified, with particular focus on the previously unstudied P. crispa lower-infralittoral communities on Ostrea edulis biogenic reefs. Data from high resolution geophysical substrate mapping were combined with benthic community observations from georeferenced benthic photographic surveys and sampling. Multivariate analysis identified four distinct assemblages of lower-infralittoral macroalgal communities at depths between 10 and 17 m, dominated by Phyllophora crispa, Apoglossum ruscifoluim, Zanardinia typus and Gelidium spp. Maxent software analysis showed distinct preferences of the identified communities to areas with specific ranges of depth, inclination and curvature, with P. crispa more frequently occurring on vertical oyster biogenic reef structures. By combining production rates from literature, biomass measurements and the produced habitat maps, the highest proportion of primary production and DOC release was shown for the upper infralittoral Cystoseira barbata and Cystoseira bosphorica, followed by the production of the lower-infralittoral macroalgae. The observed distribution of P. crispa within the studied MPA was related to the network of Natura 2000 maritime MPAs along the Bulgarian Black Sea coast, which indicated that the connectivity of the populations of the species within the established network is insufficient within this cell of ecosystem functioning.

Environment-Dependent Distribution of the Sediment nifH-Harboring Microbiota in the Northern South China Sea

PubMed Central

Yang, Jinying; Li, Jing; Luan, Xiwu; Zhang, Yunbo; Gu, Guizhou; Xue, Rongrong; Zong, Mingyue; Klotz, Martin G.

2013-01-01

The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N2 fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH4+ concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N2 fixation and NH4+ production. Several other environmental factors, including sediment pore water PO43− concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery. PMID:23064334

Electric power scheduling - A distributed problem-solving approach

NASA Technical Reports Server (NTRS)

Mellor, Pamela A.; Dolce, James L.; Krupp, Joseph C.

1990-01-01

Space Station Freedom's power system, along with the spacecraft's other subsystems, needs to carefully conserve its resources and yet strive to maximize overall Station productivity. Due to Freedom's distributed design, each subsystem must work cooperatively within the Station community. There is a need for a scheduling tool which will preserve this distributed structure, allow each subsystem the latitude to satisfy its own constraints, and preserve individual value systems while maintaining Station-wide integrity.

To cut or not to cut? Assessing the modular structure of brain networks.

PubMed

Chang, Yu-Teng; Pantazis, Dimitrios; Leahy, Richard M

2014-05-01

A wealth of methods has been developed to identify natural divisions of brain networks into groups or modules, with one of the most prominent being modularity. Compared with the popularity of methods to detect community structure, only a few methods exist to statistically control for spurious modules, relying almost exclusively on resampling techniques. It is well known that even random networks can exhibit high modularity because of incidental concentration of edges, even though they have no underlying organizational structure. Consequently, interpretation of community structure is confounded by the lack of principled and computationally tractable approaches to statistically control for spurious modules. In this paper we show that the modularity of random networks follows a transformed version of the Tracy-Widom distribution, providing for the first time a link between module detection and random matrix theory. We compute parametric formulas for the distribution of modularity for random networks as a function of network size and edge variance, and show that we can efficiently control for false positives in brain and other real-world networks. Copyright © 2014 Elsevier Inc. All rights reserved.

Longitudinal distribution of Chironomidae (Diptera) downstream from a dam in a neotropical river.

PubMed

Pinha, G D; Aviz, D; Lopes Filho, D R; Petsch, D K; Marchese, M R; Takeda, A M

2013-08-01

The damming of a river causes dangerous consequences on structure of the environment downstream of the dam, modifying the sediment composition, which impose major adjustments in longitudinal distribution of benthic community. The construction of Engenheiro Sérgio Motta Dam in the Upper Paraná River has caused impacts on the aquatic communities, which are not yet fully known. This work aimed to provide more information about the effects of this impoundment on the structure of Chironomidae larvae assemblage. The analysis of data of physical and chemical variables in relation to biological data of 8 longitudinal sections in the Upper Paraná River showed that composition of Chironomidae larvae of stations near Engenheiro Sérgio Motta Dam differed of the other stations (farther of the Dam). The predominance of coarse sediments at stations upstream and finer sediments further downstream affected the choice of habitat by different morphotypes of Chironomidae and it caused a change in the structure of this assemblage in the longitudinal stretch.

Seasonal sediment dynamics shape temperate bedrock reef communities

USGS Publications Warehouse

Figurski, Jared D.; Freiwald, Jan; Lonhart, Steve I.; Storlazzi, Curt

2016-01-01

Mobilized seafloor sediment can impact benthic reef communities through burial, scour, and turbidity. These processes are ubiquitous in coastal oceans and, through their influence on the survival, fitness, and interactions of species, can alter the structure and function of benthic communities. In northern Monterey Bay, California, USA, as much as 30% of the seafloor is buried or exposed seasonally, making this an ideal location to test how subtidal temperate rocky reef communities vary in the presence and absence of chronic sediment-based disturbances. Designated dynamic plots were naturally inundated by sediment in summer (50 to 100% cover) and swept clean in winter, whereas designated stable plots remained free of sediment during our study. Multivariate analyses indicated significant differences in the structure of sessile and mobile communities between dynamic and stable reef habitats. For sessile species, community structure in disturbed plots was less variable in space and time than in stable plots due to the maintenance of an early successional state. In contrast, community structure of mobile species varied more in disturbed plots than in stable plots, reflecting how mobile species distribute in response to sediment dynamics. Some species were found only in these disturbed areas, suggesting that the spatial mosaic of disturbance could increase regional diversity. We discuss how the relative ability of species to tolerate disturbance at different life history stages and their ability to colonize habitat translate into community-level differences among habitats, and how this response varies between mobile and sessile communities.

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. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

European seaweeds under pressure: Consequences for communities and ecosystem functioning

NASA Astrophysics Data System (ADS)

Mineur, Frédéric; Arenas, Francisco; Assis, Jorge; Davies, Andrew J.; Engelen, Aschwin H.; Fernandes, Francisco; Malta, Erik-jan; Thibaut, Thierry; Van Nguyen, Tu; Vaz-Pinto, Fátima; Vranken, Sofie; Serrão, Ester A.; De Clerck, Olivier

2015-04-01

Seaweed assemblages represent the dominant autotrophic biomass in many coastal environments, playing a central structural and functional role in several ecosystems. In Europe, seaweed assemblages are highly diverse systems. The combined seaweed flora of different European regions hold around 1550 species (belonging to nearly 500 genera), with new species continuously uncovered, thanks to the emergence of molecular tools. In this manuscript we review the effects of global and local stressors on European seaweeds, their communities, and ecosystem functioning. Following a brief review on the present knowledge on European seaweed diversity and distribution, and the role of seaweed communities in biodiversity and ecosystem functioning, we discuss the effects of biotic homogenization (invasive species) and global climate change (shifts in bioclimatic zones and ocean acidification) on the distribution of individual species and their effect on the structure and functioning of seaweed communities. The arrival of new introduced species (that already account for 5-10% of the European seaweeds) and the regional extirpation of native species resulting from oceans' climate change are creating new diversity scenarios with undetermined functional consequences. Anthropogenic local stressors create additional disruption often altering dramatically assemblage's structure. Hence, we discuss ecosystem level effects of such stressors like harvesting, trampling, habitat modification, overgrazing and eutrophication that impact coastal communities at local scales. Last, we conclude by highlighting significant knowledge gaps that need to be addressed to anticipate the combined effects of global and local stressors on seaweed communities. With physical and biological changes occurring at unexpected pace, marine phycologists should now integrate and join their research efforts to be able to contribute efficiently for the conservation and management of coastal systems.

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

PubMed Central

Thiem, Dominika; Gołębiewski, Marcin; Hulisz, Piotr; Piernik, Agnieszka; Hrynkiewicz, Katarzyna

2018-01-01

Black alder (Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall). The dominant type of root microsymbionts of alder were ectomycorrhizal fungi, whose distribution depended on site (salinity): Tomentella, Lactarius, and Phialocephala were more abundant at the saline site. Mortierella and Naucoria (representatives of saprotrophs or endophytes) displayed the opposite tendency. Arbuscular mycorrhizal fungi belonged to Glomeromycota (orders Paraglomales and Glomales), however, they represented less than 1% of all identified fungi. Bacterial community structure depended on test site but not on season. Sequences affiliated with Rhodanobacter, Granulicella, and Sphingomonas dominated at the saline site, while Bradyrhizobium and Rhizobium were more abundant at the non-saline site. Moreover, genus Frankia was observed only at the saline site. In conclusion, bacterial and fungal community structure of alder root microsymbionts and endophytes depends on five soil chemical parameters: salinity, phosphorus, pH, saturation percentage (SP) as well as total organic carbon (TOC), and seasonality does not appear to be an important factor shaping microbial communities. Ectomycorrhizal fungi are the most abundant symbionts of mature alders growing in saline soils. However, specific distribution of nitrogen-fixing Frankia (forming root nodules) and association of arbuscular fungi at early stages of plant development should be taken into account in further studies. PMID:29720967

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

PubMed

Thiem, Dominika; Gołębiewski, Marcin; Hulisz, Piotr; Piernik, Agnieszka; Hrynkiewicz, Katarzyna

2018-01-01

Black alder ( Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall). The dominant type of root microsymbionts of alder were ectomycorrhizal fungi, whose distribution depended on site (salinity): Tomentella , Lactarius , and Phialocephala were more abundant at the saline site. Mortierella and Naucoria (representatives of saprotrophs or endophytes) displayed the opposite tendency. Arbuscular mycorrhizal fungi belonged to Glomeromycota (orders Paraglomales and Glomales), however, they represented less than 1% of all identified fungi. Bacterial community structure depended on test site but not on season. Sequences affiliated with Rhodanobacter , Granulicella , and Sphingomonas dominated at the saline site, while Bradyrhizobium and Rhizobium were more abundant at the non-saline site. Moreover, genus Frankia was observed only at the saline site. In conclusion, bacterial and fungal community structure of alder root microsymbionts and endophytes depends on five soil chemical parameters: salinity, phosphorus, pH, saturation percentage (SP) as well as total organic carbon (TOC), and seasonality does not appear to be an important factor shaping microbial communities. Ectomycorrhizal fungi are the most abundant symbionts of mature alders growing in saline soils. However, specific distribution of nitrogen-fixing Frankia (forming root nodules) and association of arbuscular fungi at early stages of plant development should be taken into account in further studies.

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

PubMed

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

2014-01-01

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

The Co-Distribution of Nitrifying Archaea and Diazotrophic Bacteria in Geothermal Springs

NASA Astrophysics Data System (ADS)

Hamilton, T. L.; Jewell, T. N. M.; de la Torre, J. R.; Boyd, E. S.

2014-12-01

Microbial processes that regulate availability of nutrients play key roles in shaping community composition. All life requires fixed nitrogen (N), and its bioavailability is what often limits ecosystem productivity. Biological nitrogen fixation, or the reduction of dinitrogen (N2) to ammonia (NH3), is a keystone process in N limited ecosystems, providing nitrogen for members of the community. N2 fixing organisms likely represent a 'bottom up control' on the structure of communities that develop in N limited environments. N2 fixation is catalyzed by a limited number of metabolically diverse bacteria and some methanogenic archaea and occurs in a variety of physically and geochemically diverse environments. Nitrification, or the sequential oxidation of NH4+ to nitrite (NO2-) and ultimately nitrate (NO3-), is catalyzed by several lineages of Proteobacteria at temperatures of < 62°C and by members of the Thaumarcheota at temperatures up to 90°C. Nitrification can thus be considered a 'top down control' on the structure of communities that develop in N limited environments. Our research in Yellowstone National Park (YNP) reveals a strong correspondence between the distribution of ammonia oxidizing archaea (AOA) and nitrogen fixing aquificae (NFA) in nitrogen-limited geothermal hot springs over large environmental gradients. Based on the physiology of AOA and NFA, we propose that the strong co-distributional pattern results from interspecies interactions, namely competition for bioavailable ammonia. Our recent work has shown that in springs where the niche dimension of AOA and NFA overlap (e.g., Perpetual Spouter; pH 7.1, 86.4°C), the dissimilar affinities for NH4 result in AOA metabolism maintaining a low NH4(T) pool and selecting for inclusion of NFA during the assembly of these communities. Here, we examine in situ physiological interactions of AOA and NFA, tracking changes in transcript levels of key genes involved in nitrogen metabolism and carbon fixation of these organisms in springs where the niche dimension of AOA and NFA overlap (e.g., Perpetual Spouter). These data suggest affinity for substrate and electron donor use play key roles in structuring the biodiversity of this hydrothermal community, and likely influences the structure of other N limited hydrothermal and non-hydrothermal ecosystems.

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

PubMed

Lee, Seung-Hoon; Kang, Hojeong

2016-02-01

The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.

Soil nutrients influence spatial distributions of tropical tree species.

PubMed

John, Robert; Dalling, James W; Harms, Kyle E; Yavitt, Joseph B; Stallard, Robert F; Mirabello, Matthew; Hubbell, Stephen P; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B

2007-01-16

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

PubMed Central

Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

PubMed

Stanish, Lee F; Hull, Natalie M; Robertson, Charles E; Harris, J Kirk; Stevens, Mark J; Spear, John R; Pace, Norman R

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

Habitat fragmentation effects on the orchid bee communities in remnant forests of southeastern Brazil.

PubMed

Knoll, Fátima do Rosário Naschenveng; Penatti, N C

2012-10-01

The effect of habitat fragmentation on the structure of orchid bee communities was analyzed by the investigation of the existence of a spatial structure in the richness and abundance of Euglossini species and by determining the relationship between these data and environmental factors. The surveys were carried out in four different forest fragments and one university campus. Richness, abundance, and diversity of species were analyzed in relation to abiotic (size of the area, extent of the perimeter, perimeter/area ratio, and shape index) and biotic characteristics (vegetation index of the fragment and of the matrix of each of the locations studied). We observed a highly significant positive correlation between the diversity index and the vegetation index of the fragment, landscape and shape index. Our analysis demonstrated that the observed variation could be explained mainly by the vegetation index and the size of the fragment. Variations in relative abundance showed a tendency toward an aggregated spatial distribution between the fragments studied, as well as between the sampling stations within the same habitat, demonstrating the existence of a spatial structure on a small scale in the populations of Euglossini. This distribution will determine the composition of species that coexist in the area after fragmentation. These data help in understanding the differences and similarities in the structure of communities of Euglossini resulting from forest fragmentation.

Upland Hardwood Forests and Related Communities of the Arkansas Ozarks in the Early 19th Century

Treesearch

Thomas L. Foti

2004-01-01

Historic accounts of the 19 th Century Arkansas Ozarks mention such communities as oak forests, pine forests, barrens and prairies. I document the region-wide distribution of these types based on data from the first land survey conducted by the General Land Office (GLO). Structural classes used here include closed forest, open forest, woodland, savanna, open savanna...

Community structure, biodiversity, and ecosystem services in treeline whitebark pine communities: Potential impacts from a non-native pathogen

Treesearch

Diana F. Tomback; Lynn M. Resler; Robert E. Keane; Elizabeth R. Pansing; Andrew J. Andrade; Aaron C. Wagner

2016-01-01

Whitebark pine (Pinus albicaulis) has the largest and most northerly distribution of any white pine (Subgenus Strobus) in North America, encompassing 18° latitude and 21° longitude in western mountains. Within this broad range, however, whitebark pine occurs within a narrow elevational zone, including upper subalpine and treeline forests, and functions...

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

PubMed

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

2018-07-01

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

Distribution of functional traits in subtropical trees across environmental and forest use gradients

NASA Astrophysics Data System (ADS)

Blundo, Cecilia; Malizia, Lucio R.; González-Espinosa, Mario

2015-11-01

The relationship between functional traits and environmental factors contribute to understanding community structure and predicting which species will be able to elude environmental filters in different habitats. We selected 10 functional traits related to morphology, demography and regeneration niche in 54 subtropical premontane tree species to describe their main axes of functional differentiation. We derived species traits, environmental variables and species abundance data from 20 1-ha permanent plots established in a seasonal subtropical premontane forest in northwestern Argentina. We analyzed the relationship between species functional traits and environmental factors through RLQ and fourth-corner analyzes. We found an axis of structural differentiation that segregates understory from canopy species, and an axis of functional differentiation that segregates species that maximize resource acquisition from those that promote resource conservation. Environmental and forest use gradients operate hierarchically over subtropical premontane tree species influencing the distribution of demographic and morphological traits. The interaction between climatic and topographic factors influences the distribution of species functional traits at the regional scale. In addition, the history of forest use seems to operate at the landscape scale and explains the distribution of species traits reflecting a trade-off between resource acquisition and resource conservation strategies in secondary forests across different successional stages. Our results support the idea that functional traits may be used to analyze community structure and dynamics through niche differentiation and environmental filtering processes.

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

PubMed Central

Wessén, Ella; Söderström, Mats; Stenberg, Maria; Bru, David; Hellman, Maria; Welsh, Allana; Thomsen, Frida; Klemedtson, Leif; Philippot, Laurent; Hallin, Sara

2011-01-01

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers. PMID:21228891

Visibility graph analysis on quarterly macroeconomic series of China based on complex network theory

NASA Astrophysics Data System (ADS)

Wang, Na; Li, Dong; Wang, Qiwen

2012-12-01

The visibility graph approach and complex network theory provide a new insight into time series analysis. The inheritance of the visibility graph from the original time series was further explored in the paper. We found that degree distributions of visibility graphs extracted from Pseudo Brownian Motion series obtained by the Frequency Domain algorithm exhibit exponential behaviors, in which the exponential exponent is a binomial function of the Hurst index inherited in the time series. Our simulations presented that the quantitative relations between the Hurst indexes and the exponents of degree distribution function are different for different series and the visibility graph inherits some important features of the original time series. Further, we convert some quarterly macroeconomic series including the growth rates of value-added of three industry series and the growth rates of Gross Domestic Product series of China to graphs by the visibility algorithm and explore the topological properties of graphs associated from the four macroeconomic series, namely, the degree distribution and correlations, the clustering coefficient, the average path length, and community structure. Based on complex network analysis we find degree distributions of associated networks from the growth rates of value-added of three industry series are almost exponential and the degree distributions of associated networks from the growth rates of GDP series are scale free. We also discussed the assortativity and disassortativity of the four associated networks as they are related to the evolutionary process of the original macroeconomic series. All the constructed networks have “small-world” features. The community structures of associated networks suggest dynamic changes of the original macroeconomic series. We also detected the relationship among government policy changes, community structures of associated networks and macroeconomic dynamics. We find great influences of government policies in China on the changes of dynamics of GDP and the three industries adjustment. The work in our paper provides a new way to understand the dynamics of economic development.

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

PubMed

David, Aaron S; Seabloom, Eric W; May, Georgiana

2016-05-01

Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

The role of topographic structure and soil macrofauna presence at spoil heaps during spontaneous succession.

NASA Astrophysics Data System (ADS)

Walmsley, Alena; Vachová, Pavla; Vach, Marek

2016-04-01

This research was investigating whether topographic features, which determine soil nutrient and moisture distribution, in combination with soil fauna (wireworm and earthworm) presence, affect plant community composition at a spontaneously revegetated post mining area with an undulating surface. Two sites of different age with 3 types of topographic features were selected, soil moisture and nutrient content were measured, plant community composition and soil macrofauna community was sampled at each position. Wireworms were present at all positions and were most abundant at bottoms of waves at the younger site; their presence was correlated with several plant species, but the direction of the interaction isn't clear. Earthworms were only present at the older site and had highest abundance at flat sections. Earthworm presence affected the amount of nitrogen in soil - the most nitrogen content was at the site with highest earthworm density and was followed by higher diversity of plant community. The plant community composition was generally correlated with plant available nutrient content - especially P and N. We infer that topographic features affect nutrient and soil fauna distribution, which consequently influences plant community composition.

Response of Soil Fungi Community Structure to Salt Vegetation Succession in the Yellow River Delta.

PubMed

Wang, Yan-Yun; Guo, Du-Fa

2016-10-01

High-throughput sequencing technology was used to reveal the composition and distribution of fungal community structure in the Yellow River Delta under bare land and four kinds of halophyte vegetation (saline seepweed, Angiospermae, Imperata and Apocynum venetum [A. venetum]). The results showed that the soil quality continuously improved with the succession of salt vegetation types. The soil fungi richness of mild-salt communities (Imperata and A. venetum) was relatively higher, with Shannon index values of 5.21 and 5.84, respectively. The soil fungi richness of severe-salt-tolerant communities (saline seepweed, Angiospermae) was relatively lower, with Shannon index values of 4.64 and 4.66, respectively. The UniFrac metric values ranged from 0.48 to 0.67 when the vegetation was in different succession stages. A total of 60,174 valid sequences were obtained for the five vegetation types, and they were classified into Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycotina. Ascomycota had the greatest advantage among plant communities of Imperata and A. venetum, as indicated by relative abundances of 2.69 and 69.97 %, respectively. Basidiomycota had the greatest advantage among mild-salt communities of saline seepweed and Angiospermae, with relative abundances of 9.43 and 6.64 %, respectively. Soil physical and chemical properties were correlated with the distribution of the fungi, and Mucor was significantly correlated with soil moisture (r = 0.985; P < 0.01). Soil quality, salt vegetation and soil fungi were influenced by each other.

Interpretation of the Relationship between Benthic Fauna, Geologic Distributions, and Methane Seeps at Southern Hydrate Ridge, Oregon Continental Margin

NASA Astrophysics Data System (ADS)

Bigham, K.; Kelley, D. S.; Delaney, J. R.

2016-12-01

Deposits of methane sequestered along continental margins and their associated seeps are found worldwide. These seeps are of increasing interest and importance because of their potential as an energy source, their contribution to greenhouse gases, and the unique community of chemosynthetic microorganisms and fauna that they host. One of the best­studied methane seep sites is Southern Hydrate Ridge, which is at a water depth of 800 m. It is located 90 km west of Newport, Oregon. Despite extensive geophysical and biological research completed here, no studies have quantified the relationship of seep sites and seafloor geology to the spatial distribution and abundances of microbial and macrofaunal communities. High resolution, georeferenced photomosaics of the individual seeps and the associated biological communities at this site were collected in 2011, using the remotely operated vehicle ROPOS. Detailed analyses of these images has allowed for the quantification and characterization of the diversity and structure of the faunal community. Results show that both the distribution and abundances of seep organisms are highly variable. Further examination of these photomosaics may improve understanding of the relationships between faunal distributions and seep locations, with implications for the impacts that chemical gradients have on these ecosystems.

Distribution, vertical position and ecological implications of shallow gas in Bahía Blanca estuary (Argentina)

NASA Astrophysics Data System (ADS)

Bravo, M. E.; Aliotta, S.; Fiori, S.; Ginsberg, S.

2018-03-01

There has been a growing interest in the study of shallow gas due its importance in relation to the marine environment, climate change and human activities. In Bahía Blanca estuary, Argentina, shallow gas has a wide distribution. Acoustic turbidity and blanking are the main seismic evidence for the presence of shallow gas in the estuary. The former prevails in the inner sector of the estuary where gas is either near or in contact with the seabed. Gas deposits are generally associated with paleochannels corresponding to the Holocene paleodeltaic environment. Distribution studies of shallow gas in this estuary are necessary because its presence implies not only a geological risk for harbor activities but also because it may have noxious effects on the marine ecosystem, mainly on benthic communities. The comparison of benthic communities at a gas site (GS) with those at a control site (CS) indicated that gas could generate impoverishment in terms of individuals' abundance (GS: N = 357; CS: N = 724). Also, diversity indices showed great differences in the community structure at each site. This indicates that methane gas may act as a natural disturbance agent in estuarine ecosystems. The presence of gas in seabed sediments must therefore be taken into account when distribution studies are conducted of estuarine benthic communities.

A search for stability gradients in North American breeding bird communities

USGS Publications Warehouse

Noon, B.R.; Dawson, D.K.; Kelly, J.P.

1985-01-01

To search for the existence of stability gradients in North American breeding land bird communities we operationally defined stability (after Jarvinen 1979) as year-to-year persistence in species composition and distribution of species abundances. From the census data for 174 study plots we derived nine indices that estimate the annual variability of species composition, the species abundance distribution, diversity, and breeding density. The resulting matrix of study plot by stability indices was used to estimate the correlation structure of the stability indices. The correlation matrix was, in turn, subjected to a principal components analysis to derive synthetic gradients of variation. We then searched for patterns of variation in these stability gradients associated with either geographic location or habitat type. Three independent principal component axes reproduced most of the variation in the initial data and were interpreted as gradients of variation in species turnover, diversity, and breeding abundance. Thus, the annual stability of community structure apparently responds independently to species and abundance variation. Despite the clarity of the derived gradients, few patterns emerged when the plots were ordinated by either habitat or geographic location. In general, grasslands showed greater annual variation in diversity than forested habitats, and, for some habitats, northern communities were less stable than more southern communities. However, few of these patterns were very strong, and we interpret them cautiously.

Avian community responses to variability in river hydrology.

PubMed

Royan, Alexander; Hannah, David M; Reynolds, S James; Noble, David G; Sadler, Jonathan P

2013-01-01

River flow is a major driver of morphological structure and community dynamics in riverine-floodplain ecosystems. Flow influences in-stream communities through changes in water velocity, depth, temperature, turbidity and nutrient fluxes, and perturbations in the organisation of lower trophic levels are cascaded through the food web, resulting in shifts in food availability for consumer species. River birds are sensitive to spatial and phenological mismatches with aquatic prey following flow disturbances; however, the role of flow as a determinant of riparian ecological structure remains poorly known. This knowledge is crucial to help to predict if, and how, riparian communities will be influenced by climate-induced changes in river flow characterised by more extreme high (i.e. flood) and/or low (i.e. drought) flow events. Here, we combine national-scale datasets of river bird surveys and river flow archives to understand how hydrological disturbance has affected the distribution of riparian species at higher trophic levels. Data were analysed for 71 river locations using a Generalized Additive Model framework and a model averaging procedure. Species had complex but biologically interpretable associations with hydrological indices, with species' responses consistent with their ecology, indicating that hydrological-disturbance has implications for higher trophic levels in riparian food webs. Our quantitative analysis of river flow-bird relationships demonstrates the potential vulnerability of riparian species to the impacts of changing flow variability and represents an important contribution in helping to understand how bird communities might respond to a climate change-induced increase in the intensity of floods and droughts. Moreover, the success in relating parameters of river flow variability to species' distributions highlights the need to include river flow data in climate change impact models of species' distributions.

Composition, structure, and dynamics of the Illinois Ozark Hills Forest

Treesearch

Lisa M. Helmig; James S. Fralish

2011-01-01

In the mature oak-hickory ecosystem of the Illinois Ozark Hills, forest community composition, dynamics, and structure were studied to examine the extent of conversion to mesophytic species and eventually predict the broad threshold time of complete conversion. Tree, sapling, and seedling data were collected from 87 plots distributed throughout the region. Data for the...

Extracting knowledge from the World Wide Web

PubMed Central

Henzinger, Monika; Lawrence, Steve

2004-01-01

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

Is the ecological belt zonation of the Swiss Alps relevant for moth diversity and turnover?

NASA Astrophysics Data System (ADS)

Beck, Jan; Rüdlinger, Cecil M.; McCain, Christy M.

2017-04-01

Mountain ecosystems are traditionally envisioned as elevational belts of homogenous vegetation, separated by intervening ecotones. Recent research has cast doubt on such predictable layering at least in animal communities. We test the link of two a priori defined ecological belt zonations to noctuid moth distributions in the Swiss Alps. Predictions, in particular, were a coincidence of proposed ecotones with increased range endpoint frequencies and with increased species turnover or species richness between equidistant elevational bands. Using >320,000 distributional records for >500 noctuid species, we found no support for these three predictions despite several contrasting analytical approaches. Concurrent with recently published vertebrate data, we conclude that simple ecological belt zonations are unrelated to the moth communities found along mountain slopes. Rather, species are distributed idiosyncratically following their specific niche requirements. Additional rigorous evidence, particularly comparing insect clades spanning a spectrum of host-plant relationships, may be required to support the relevance of the ecological belt concept in structuring mountain ecosystems beyond tree and plant communities.

Spatial and geographical changes in the mesozooplankton community in the Bering and Chukchi Seas during the summers of 2007 and 2008

NASA Astrophysics Data System (ADS)

Matsuno, Kohei; Landeira Sanchez, Jose M.; Yamaguchi, Atsushi; Hirawake, Toru; Kikuchi, Takashi

2016-09-01

From July to August 2007 and June to July 2008, the horizontal/geographical changes in the zooplankton community in the Bering and Chukchi Seas were studied. The geographical patterns, which were common for these two years, were observed for salinity, chlorophyll a (Chl. a), zooplankton chaetognaths, hydrozoans and the whole zooplankton community. Among them, the patterns of salinity and Chl. a were related with the horizontal distribution of the water masses. The distributions of the two carnivorous taxa were correlated with their prey (copepods or barnacle larvae). The analysis of the structural equation model (SEM) revealed that the horizontal distribution of the zooplankton abundance and biomass were governed by the different taxa. Thus, the zooplankton abundance was governed by the numerically dominant but smaller-bodied taxa, such as the barnacle larvae and copepod Pseudocalanus spp., while the zooplankton biomass was determined by the large-bodied copepods, such as Calanus glacialis/marshallae and Eucalanus bungii.

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

PubMed Central

Green, Stefan J.; Prakash, Om; Jasrotia, Puja; Overholt, Will A.; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2012-01-01

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment. PMID:22179233

Risk assessment of salinity and turbidity in Victoria (Australia) to stream insects' community structure does not always protect functional traits.

PubMed

Kefford, Ben J; Schäfer, Ralf B; Metzeling, Leon

2012-01-15

Ecological risk assessments mostly consider measures of community composition (structure) across large spatial scales. These assessments, using species sensitivity distributions (SSDs) or the relative species retention (RSR), may not be protective of ecosystem functions and services at smaller spatial scales. Here we examine how changes in biological traits, as proxy for ecosystem functions/services, at a fine spatial scale relate to larger scale assessment of structure. We use functional traits of stream insect species in south-east Australia in two habitats (riffle and edge/pool). We find that the protection of community structure in terms of 95% of species over multiple sites against adverse effects of salinity (as electrical conductivity) and turbidity will mostly, but not always, protect traits at smaller scales. Considering different combinations of trait modalities, contaminants and habitat, a mean of 17.5% (range 0%-36.8) of cases would result in under-protection of trait modalities despite protecting species composition (in terms of Jaccard's Index). This under-protection of trait modalities is only because of the different spatial scales that community structure and the traits were considered. We recommend that where the protection of biological traits, ecosystem functions or ecosystem services from stressors is a management goal, protective targets should not be solely set using measures of community structure such as SSDs or RSR. To protect both structural and functional attributes separate risk assessments should be done. Copyright © 2011 Elsevier B.V. All rights reserved.

Impact of anthropogenic activities on water quality and plankton communities in the Day River (Red River Delta, Vietnam).

PubMed

Hoang, Hang Thi Thu; Duong, Thi Thuy; Nguyen, Kien Trung; Le, Quynh Thi Phuong; Luu, Minh Thi Nguyet; Trinh, Duc Anh; Le, Anh Hung; Ho, Cuong Tu; Dang, Kim Dinh; Némery, Julien; Orange, Didier; Klein, Judith

2018-01-08

Planktons are a major component of food web structure in aquatic ecosystems. Their distribution and community structure are driven by the combination and interactions between physical, chemical, and biological factors within the environment. In the present study, water quality and the community structure of phytoplankton and zooplankton were monthly investigated from January to December 2015 at 11 sampling sites along the gradient course of the Day River (Red River Delta, northern Vietnam). The study demonstrated that the Day River was eutrophic with the average values of total phosphorus concentration 0.17 mg/L, total nitrogen concentration 1.98 mg/L, and Chl a 54 μg/L. Microscopic plankton analysis showed that phytoplankton comprised 87 species belonging to seven groups in which Chlorophyceae, Bacillariophyceae, and Cyanobacteria accounted for the most important constituents of the river's phytoplankton assemblage. A total 53 zooplankton species belonging to three main groups including Copepoda, Cladocera, and Rotatoria were identified. Plankton biomass values were greatest in rainy season (3002.10-3 cell/L for phytoplankton and 12.573 individuals/m 3 for zooplankton). Using principal correspondence and Pearson correlation analyses, it was found that the Day River was divided into three main site groups based on water quality and characteristics of plankton community. Temperature and nutrients (total phosphorus and total nitrogen) are key factors regulating plankton abundance and distribution in the Day River.

Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China.

PubMed

Qian, Hong; Chen, Shengbin; Zhang, Jin-Long

2017-07-17

Niche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China

PubMed Central

Lin, Huirong; Zhang, Shuting; Gong, Song; Zhang, Shenghua; Yu, Xin

2015-01-01

The composition and microbial community structure of the drinking water system biofilms were investigated using microstructure analysis and 454 pyrosequencing technique in Xiamen city, southeast of China. SEM (scanning electron microscope) results showed different features of biofilm morphology in different fields of PVC pipe. Extracellular matrix material and sparse populations of bacteria (mainly rod-shaped and coccoid) were observed. CLSM (confocal laser scanning microscope) revealed different distributions of attached cells, extracellular proteins, α-polysaccharides, and β-polysaccharides. The biofilms had complex bacterial compositions. Differences in bacteria diversity and composition from different tap materials and ages were observed. Proteobacteria was the common and predominant group in all biofilms samples. Some potential pathogens (Legionellales, Enterobacteriales, Chromatiales, and Pseudomonadales) and corrosive microorganisms were also found in the biofilms. This study provides the information of characterization and visualization of the drinking water biofilms matrix, as well as the microbial community structure and opportunistic pathogens occurrence. PMID:26273617

[Species, Damage and Community Structure of Weeds in Scrophularia ningpoensis Fields in Nanchuan, Chongqing].

PubMed

Han, Feng; Xiao, Jie-yi; Cao, Hou-qiang; Luo, Chuan; Yang, Tian-jian; Lin, Mao-xiang

2015-10-01

To investigate the damage and community structure of weeds in Scrophularia ningpoensis fields in Nanchuan, Chongqing. From 2013 to 2014, an investigation was carried out by inverted W-9 point sampling method to study the weed species. 96 weed species belonged to 75 genera of 30 families were observed, including 18 species of Asteraceae weeds (accounted for 18.75%), 10 species of Poaceae weeds (accounted for 10.42%). Moreover, there were 57 species of annual weeds (accounted for 59.38%) and 39 species of perennial weeds (accounted for 40.63%). The overall abundance of Erigeron annuus, Digitaria adscendens, Torilis scabra, Polygonum nepalense, Ranunculus japonicas, Stellaria media and Commelina communis were relatively higher than that of the others. The difference of weed species and community structure might result from the physical and chemical characteristics of soil, moisture content, cropping system, tillage type, environmental and climatic conditions, crop distribution and weed control.

Phytoplankton community structure is influenced by seabird guano enrichment in the Southern Ocean

NASA Astrophysics Data System (ADS)

Shatova, O. A.; Wing, S. R.; Hoffmann, L. J.; Wing, L. C.; Gault-Ringold, M.

2017-05-01

Phytoplankton biomass, productivity and community structure are strongly influenced by differences in nutrient concentrations among oceanographic water masses. Changes in community composition, particularly in the distribution of cell sizes, can result in dramatic changes in the energetics of pelagic food webs and ecosystem function in terms of biogeochemical cycling and carbon sequestration. Here we examine responses of natural phytoplankton communities from four major water masses in the Southern Ocean to enrichment from seabird guano, a concentrated source of bioactive metals (Mn, Fe, Co, Ni, Cu, Zn) and macronutrients (N, P), in a series of incubation experiments. Phytoplankton communities from sub-tropical water, modified sub-tropical water from the Snares Island wake, sub-Antarctic water and Antarctic water from the Ross Sea, each showed dramatic changes in community structure following additions of seabird guano. We observed particularly high growth of prymnesiophytes in response to the guano-derived nutrients within sub-Antarctic and sub-tropical frontal zones, resulting in communities dominated by larger cell sizes than in control incubations. Community changes within treatments enriched with guano were distinct, and in most cases more extensive, than those observed for treatments with additions of macronutrients (N, P) or iron (Fe) alone. These results provide the first empirical evidence that seabird guano enrichment can drive significant changes in the structure and composition of natural phytoplankton communities. Our findings have important implications for understanding the consequences of accumulation of bioactive metals and macronutrients within food webs and the role of seabirds as nutrient vectors within the Southern Ocean ecosystem.

Contrasting clonal structure among Pocillopora (Scleractinia) communities at two environmentally distinct sites in the Gulf of California

NASA Astrophysics Data System (ADS)

Pinzón, J. H.; Reyes-Bonilla, H.; Baums, I. B.; LaJeunesse, T. C.

2012-09-01

The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10 km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9 m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples = 0.35; observed Genotypic diversity/expected Genotypic diversity = 0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity ( N g / N = 0.85; G o / G e = 0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will advance ecological research and aid in the conservation of these corals.

Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters.

PubMed

Gomez-Alvarez, Vicente; Humrighouse, Ben W; Revetta, Randy P; Santo Domingo, Jorge W

2015-03-01

We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.

Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China

PubMed Central

Huang, Liuqin; Deng, Ye; Wang, Shang; Zhou, Yu; Liu, Li

2014-01-01

The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients. PMID:25002421

Colonization of habitat islands in the deep sea: recruitment to glass sponge stalks

NASA Astrophysics Data System (ADS)

Beaulieu, Stace E.

2001-04-01

Biogenic structures in the deep sea often act as hard substratum 'islands' for the attachment of encrusting fauna. At an abyssal station in the NE Pacific, stalks of hexactinellid sponges in the genus Hyalonema are habitat islands for species-rich epifaunal communities. An experimental study was conducted to (1) determine the colonization rates of artificial Hyalonema stalks, (2) compare the species composition and diversity of recruits to newly available substrata to that of the natural communities, and (3) examine the vertical distribution of recruits. Four sets of six artificial sponge stalks, constructed of Hyalonema spicules, were deployed at 4100 m depth for 3- to 5-month periods. There was no difference in net colonization or immigration rate among the four deployments. Colonization rates were similar to those reported for other deep-sea, hard substratum recruitment experiments. The taxa that recruited to the artificial stalks were a subset of the taxa found in natural communities. However, several taxa important in structuring natural communities did not recruit to the artificial stalks. The two taxa with the highest invasion rates, a calcareous foraminiferan ( Cibicides lobatulus) and a serpulid polychaete ( Bathyvermilia sp.), also were the two taxa with greatest relative abundance in natural communities. Vertical distributions of Cibicides and an agglutinated foraminiferan ( Telammina sp.) were skewed towards the top of the artificial stalks, potentially because of active habitat selection. These results have several implications for natural Hyalonema stalk communities. Most importantly, species composition and abundance of individuals in the stalk communities appear to be maintained by frequent recruitment of a few common taxa and infrequent recruitment of many rare taxa. An argument is presented for temporal-mosaic maintenance of diversity in these deep-sea, hard substratum communities.

Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides.

PubMed

Shiau, Yo-Jin; Cai, Yuanfeng; Lin, Yu-Te; Jia, Zhongjun; Chiu, Chih-Yu

2018-04-01

Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH 4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13 CH 4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

Structure and dynamics of stock market in times of crisis

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Cai, Xu

2016-02-01

Daily correlations among 322 S&P 500 constituent stocks are investigated by means of correlation-based (CB) network. By using the heterogeneous time scales, we identify global expansion and local clustering market behaviors during crises, which are mainly caused by community splits and inter-sector edge number decreases. The CB networks display distinctive community and sector structures. Graph edit distance is applied to capturing the dynamics of CB networks in which drastic structure reconfigurations can be observed during crisis periods. Edge statistics reveal the power-law nature of edges' duration time distribution. Despite the networks' strong structural changes during crises, we still find some long-duration edges that serve as the backbone of the stock market. Finally the dynamical change of network structure has shown its capability in predicting the implied volatility index (VIX).

Effect of disinfectant, water age, and pipe materials on bacterial and eukaryotic community structure in drinking water biofilm.

PubMed

Wang, Hong; Masters, Sheldon; Edwards, Marc A; Falkinham, Joseph O; Pruden, Amy

2014-01-01

Availability of safe, pathogen-free drinking water is vital to public health; however, it is impossible to deliver sterile drinking water to consumers. Recent microbiome research is bringing new understanding to the true extent and diversity of microbes that inhabit water distribution systems. The purpose of this study was to determine how water chemistry in main distribution lines shape the microbiome in drinking water biofilms and to explore potential associations between opportunistic pathogens and indigenous drinking water microbes. Effects of disinfectant (chloramines, chlorine), water age (2.3 days, 5.7 days), and pipe material (cement, iron, PVC) were compared in parallel triplicate simulated water distribution systems. Pyrosequencing was employed to characterize bacteria and terminal restriction fragment polymorphism was used to profile both bacteria and eukaryotes inhabiting pipe biofilms. Disinfectant and water age were both observed to be strong factors in shaping bacterial and eukaryotic community structures. Pipe material only influenced the bacterial community structure (ANOSIM test, P < 0.05). Interactive effects of disinfectant, pipe material, and water age on both bacteria and eukaryotes were noted. Disinfectant concentration had the strongest effect on bacteria, while dissolved oxygen appeared to be a major driver for eukaryotes (BEST test). Several correlations of similarity metrics among populations of bacteria, eukaryotes, and opportunistic pathogens, as well as one significant association between mycobacterial and proteobacterial operational taxonomic units, provides insight into means by which manipulating the microbiome may lead to new avenues for limiting the growth of opportunistic pathogens (e.g., Legionella) or other nuisance organisms (e.g., nitrifiers).

Hillslope characterization: Identifying key controls on local-scale plant communities' distribution using remote sensing and subsurface data fusion.

NASA Astrophysics Data System (ADS)

Falco, N.; Wainwright, H. M.; Dafflon, B.; Leger, E.; Peterson, J.; Steltzer, H.; Wilmer, C.; Williams, K. H.; Hubbard, S. S.

2017-12-01

Mountainous watershed systems are characterized by extreme heterogeneity in hydrological and pedological properties that influence biotic activities, plant communities and their dynamics. To gain predictive understanding of how ecosystem and watershed system evolve under climate change, it is critical to capture such heterogeneity and to quantify the effect of key environmental variables such as topography, and soil properties. In this study, we exploit advanced geophysical and remote sensing techniques - coupled with machine learning - to better characterize and quantify the interactions between plant communities' distribution and subsurface properties. First, we have developed a remote sensing data fusion framework based on the random forest (RF) classification algorithm to estimate the spatial distribution of plant communities. The framework allows the integration of both plant spectral and structural information, which are derived from multispectral satellite images and airborne LiDAR data. We then use the RF method to evaluate the estimated plant community map, exploiting the subsurface properties (such as bedrock depth, soil moisture and other properties) and geomorphological parameters (such as slope, curvature) as predictors. Datasets include high-resolution geophysical data (electrical resistivity tomography) and LiDAR digital elevation maps. We demonstrate our approach on a mountain hillslope and meadow within the East River watershed in Colorado, which is considered to be a representative headwater catchment in the Upper Colorado Basin. The obtained results show the existence of co-evolution between above and below-ground processes; in particular, dominant shrub communities in wet and flat areas. We show that successful integration of remote sensing data with geophysical measurements allows identifying and quantifying the key environmental controls on plant communities' distribution, and provides insights into their potential changes in the future climate conditions.

Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes.

PubMed

Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J

2007-10-01

To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

Addressing the Health of Formerly Imprisoned Persons in a Distressed Neighborhood Through a Community Collaborative Board

PubMed Central

Smith, Vivian C.; Jemal, Alexis

2016-01-01

This article provides a case study evaluating the structure and dynamic process of a Community Collaborative Board that had the goal of creating an evidence-based substance abuse/health intervention for previously incarcerated individuals. Meeting agendas, attendance, minutes, video recording of meetings, and in-depth interviews with 13 Community Collaborative Board members were used to conduct an independent process evaluation. Open coding identified quotes exemplifying specific themes and/or patterns across answers related to the desired domain. Several themes were identified regarding membership engagement, retention, and power distribution. Results showed member retention was due to strong personal commitment to the targeted problem. Analysis also revealed an unequal power distribution based on participants' background. Nevertheless, the development of an innovative, community-based health intervention manual was accomplished. Aspects of the process, such as incentives, subcommittees, and trainings, enhanced the Board's ability to integrate the community and scientific knowledge to accomplish its research agenda. Community-based participatory research was a useful framework in enhancing quality and efficiency in the development of an innovative, substance abuse/health intervention manual for distressed communities. Overall, this article sheds light on a process that illustrates the integration of community-based and scientific knowledge to address the health, economic, and societal marginalization of low-income, minority communities. PMID:26055460

IPR 1.0: an efficient method for calculating solar radiation absorbed by individual plants in sparse heterogeneous woody plant communities

NASA Astrophysics Data System (ADS)

Zhang, Y.; Chen, W.; Li, J.

2013-12-01

Climate change may alter the spatial distribution, composition, structure, and functions of plant communities. Transitional zones between biomes, or ecotones, are particularly sensitive to climate change. Ecotones are usually heterogeneous with sparse trees. The dynamics of ecotones are mainly determined by the growth and competition of individual plants in the communities. Therefore it is necessary to calculate solar radiation absorbed by individual plants for understanding and predicting their responses to climate change. In this study, we developed an individual plant radiation model, IPR (version 1.0), to calculate solar radiation absorbed by individual plants in sparse heterogeneous woody plant communities. The model is developed based on geometrical optical relationships assuming crowns of woody plants are rectangular boxes with uniform leaf area density. The model calculates the fractions of sunlit and shaded leaf classes and the solar radiation absorbed by each class, including direct radiation from the sun, diffuse radiation from the sky, and scattered radiation from the plant community. The solar radiation received on the ground is also calculated. We tested the model by comparing with the analytical solutions of random distributions of plants. The tests show that the model results are very close to the averages of the random distributions. This model is efficient in computation, and is suitable for ecological models to simulate long-term transient responses of plant communities to climate change.

Pyrosequencing reveals regional differences in fruit-associated fungal communities

PubMed Central

Taylor, Michael W; Tsai, Peter; Anfang, Nicole; Ross, Howard A; Goddard, Matthew R

2014-01-01

We know relatively little of the distribution of microbial communities generally. Significant work has examined a range of bacterial communities, but the distribution of microbial eukaryotes is less well characterized. Humans have an ancient association with grape vines (Vitis vinifera) and have been making wine since the dawn of civilization, and fungi drive this natural process. While the molecular biology of certain fungi naturally associated with vines and wines is well characterized, complementary investigations into the ecology of fungi associated with fruiting plants is largely lacking. DNA sequencing technologies allow the direct estimation of microbial diversity from a given sample, avoiding culture-based biases. Here, we use deep community pyrosequencing approaches, targeted at the 26S rRNA gene, to examine the richness and composition of fungal communities associated with grapevines and test for geographical community structure among four major regions in New Zealand (NZ). We find over 200 taxa using this approach, which is 10-fold more than previously recovered using culture-based methods. Our analyses allow us to reject the null hypothesis of homogeneity in fungal species richness and community composition across NZ and reveal significant differences between major areas. PMID:24650123

Electric power scheduling: A distributed problem-solving approach

NASA Technical Reports Server (NTRS)

Mellor, Pamela A.; Dolce, James L.; Krupp, Joseph C.

1990-01-01

Space Station Freedom's power system, along with the spacecraft's other subsystems, needs to carefully conserve its resources and yet strive to maximize overall Station productivity. Due to Freedom's distributed design, each subsystem must work cooperatively within the Station community. There is a need for a scheduling tool which will preserve this distributed structure, allow each subsystem the latitude to satisfy its own constraints, and preserve individual value systems while maintaining Station-wide integrity. The value-driven free-market economic model is such a tool.

Disturbance Frequency Determines Morphology and Community Development in Multi-Species Biofilm at the Landscape Scale

PubMed Central

Milferstedt, Kim; Santa-Catalina, Gaëlle; Godon, Jean-Jacques; Escudié, Renaud; Bernet, Nicolas

2013-01-01

Many natural and engineered biofilm systems periodically face disturbances. Here we present how the recovery time of a biofilm between disturbances (expressed as disturbance frequency) shapes the development of morphology and community structure in a multi-species biofilm at the landscape scale. It was hypothesized that a high disturbance frequency favors the development of a stable adapted biofilm system while a low disturbance frequency promotes a dynamic biofilm response. Biofilms were grown in laboratory-scale reactors over a period of 55-70 days and exposed to the biocide monochloramine at two frequencies: daily or weekly pulse injections. One untreated reactor served as control. Biofilm morphology and community structure were followed on comparably large biofilm areas at the landscape scale using automated image analysis (spatial gray level dependence matrices) and community fingerprinting (single-strand conformation polymorphisms). We demonstrated that a weekly disturbed biofilm developed a resilient morphology and community structure. Immediately after the disturbance, the biofilm simplified but recovered its initial complex morphology and community structure between two biocide pulses. In the daily treated reactor, one organism largely dominated a morphologically simple and stable biofilm. Disturbances primarily affected the abundance distribution of already present bacterial taxa but did not promote growth of previously undetected organisms. Our work indicates that disturbances can be used as lever to engineer biofilms by maintaining a biofilm between two developmental states. PMID:24303024

Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

USGS Publications Warehouse

Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

2007-01-01

The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

Shifting the balance of fermentation products between hydrogen and volatile fatty acids: microbial community structure and function.

PubMed

Miceli, Joseph F; Torres, César I; Krajmalnik-Brown, Rosa

2016-12-01

Fermentation is a key process in many anaerobic environments. Varying the concentration of electron donor fed to a fermenting community is known to shift the distribution of products between hydrogen, fatty acids and alcohols. Work to date has focused mainly on the fermentation of glucose, and how the microbial community structure is affected has not been explored. We fed ethanol, lactate, glucose, sucrose or molasses at 100 me- eq. L -1 , 200 me- eq. L -1 or 400 me- eq. L -1 to batch-fed cultures with fermenting, methanogenic communities. In communities fed high concentrations of electron donor, the fraction of electrons channeled to methane decreased, from 34% to 6%, while the fraction of electrons channeled to short chain fatty acids increased, from 52% to 82%, averaged across all electron donors. Ethanol-fed cultures did not produce propionate, but did show an increase in electrons directed to acetate as initial ethanol concentration increased. In glucose, sucrose, molasses and lactate-fed cultures, propionate accumulation co-occurred with known propionate producing organisms. Overall, microbial communities were determined by the substrate provided, rather than its initial concentration, indicating that a change in community function, rather than community structure, is responsible for shifts in the fermentation products produced. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Predictors of Arbuscular Mycorrhizal Fungal Communities in the Brazilian Tropical Dry Forest.

PubMed

Sousa, Natália M F; Veresoglou, Stavros D; Oehl, Fritz; Rillig, Matthias C; Maia, Leonor C

2018-02-01

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.

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

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Soil nutrients influence spatial distributions of tropical tree species

PubMed Central

John, Robert; Dalling, James W.; Harms, Kyle E.; Yavitt, Joseph B.; Stallard, Robert F.; Mirabello, Matthew; Hubbell, Stephen P.; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B.

2007-01-01

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757–1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<104 km2) and regional scales. At local scales (<1 km2), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant–soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36–51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant–soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. PMID:17215353

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities.

PubMed

Frelat, Romain; Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs.

[Distribution characteristics of soil nematodes in reclaimed land of copper-mine-tailings in different plant associations].

PubMed

Zhu, Yong-heng; Li, Ke-zhong; Zhang, Heng; Han, Fei; Zhou, Ju-hua; Gao, Ting-ting

2015-02-01

A survey was carried out to investigate soil nematode communities in the plant associations of gramineae (Arthraxon lanceolatus, AL; Imperata cylindrica, IC) and leguminosae (Glycine soja, GS) in reclaimed land of copper-mine-tailings and in the plant associations of gramineae (Digitaria chrysoblephara, DC-CK) of peripheral control in Fenghuang Mountain, Tongling City. A total of 1277 nematodes were extracted and sorted into 51 genera. The average individual density of the nematodes was 590 individuals · 100 g(-1) dry soil. In order to analyze the distribution character- istics of soil nematode communities in reclaimed land of copper-mine-tailings, Shannon community diversity index and soil food web structure indices were applied in the research. The results showed that the total number of nematode genus and the Shannon community diversity index of soil nematode in the three plant associations of AL, IC and GS were less than that in the plant associations of DC-CK. Compared with the ecological indices of soil nematode communities among the different plant associations in reclaimed land of copper-mine-tailings and peripheral natural habitat, we found that the structure of soil food web in the plant associations of GS was more mature, with bacterial decomposition being dominant in the soil organic matter decomposition, and that the soil ecosystem in the plant associations of GS was not stable with low interference. This indicated that the soil food web in the plant associations of leguminosae had a greater development potential to improve the ecological stability of the reclaimed land of copper-mine-tailings. On the other hand, the structure of soil food web in the plant associations of AL and IC were relatively stable in a structured state with fungal decomposition being dominant in the decomposition of soil organic matter. This indicated that the soil food web in the plant associations of gramineae was at a poor development level.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil.

PubMed

Mendes, Lucas William; Taketani, Rodrigo Gouvêa; Navarrete, Acácio Aparecido; Tsai, Siu Mui

2012-06-01

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

COMPARISONS OF ZOOPLANKTON COMMUNITY SIZE STRUCTURE IN THE GREAT LAKES

EPA Science Inventory

Zooplankton mean-size and size-spectra distribution potentially reflect the condition of trophic interactions and ecosystem health because they are affected by both resource availability and planktivore pressure. We assessed zooplankton mean-size and size-spectra using an optical...

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

The importance of scaling for detecting community patterns: success and failure in assemblages of introduced species

USGS Publications Warehouse

Allen, Craig R.; Angeler, David G.; Moulton, Michael P.; Holling, Crawford S.

2015-01-01

Community saturation can help to explain why biological invasions fail. However, previous research has documented inconsistent relationships between failed invasions (i.e., an invasive species colonizes but goes extinct) and the number of species present in the invaded community. We use data from bird communities of the Hawaiian island of Oahu, which supports a community of 38 successfully established introduced birds and where 37 species were introduced but went extinct (failed invasions). We develop a modified approach to evaluate the effects of community saturation on invasion failure. Our method accounts (1) for the number of species present (NSP) when the species goes extinct rather than during its introduction; and (2) scaling patterns in bird body mass distributions that accounts for the hierarchical organization of ecosystems and the fact that interaction strength amongst species varies with scale. We found that when using NSP at the time of extinction, NSP was higher for failed introductions as compared to successful introductions, supporting the idea that increasing species richness and putative community saturation mediate invasion resistance. Accounting for scale-specific patterns in body size distributions further improved the relationship between NSP and introduction failure. Results show that a better understanding of invasion outcomes can be obtained when scale-specific community structure is accounted for in the analysis.

Large Scale Data Analysis and Knowledge Extraction in Communication Data

DTIC Science & Technology

2017-03-31

this purpose, we developed a novel method the " Correlation Density Ran!C’ which finds probability density distribution of related frequent event on all...which is called " Correlation Density Rank", is developed to derive the community tree from the network. As in the real world, where a network is...Community Structure in Dynamic Social Networks using the Correlation Density Rank," 2014 ASE BigData/SocialCom/Cybersecurity Conference, Stanford

Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France.

PubMed

Lehours, Anne-C; Bardot, Corinne; Thenot, Aurelie; Debroas, Didier; Fonty, Gerard

2005-11-01

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

Landscape structure affects distribution of potential disease vectors (Diptera: Culicidae).

PubMed

Zittra, Carina; Vitecek, Simon; Obwaller, Adelheid G; Rossiter, Heidemarie; Eigner, Barbara; Zechmeister, Thomas; Waringer, Johann; Fuehrer, Hans-Peter

2017-04-26

Vector-pathogen dynamics are controlled by fluctuations of potential vector communities, such as the Culicidae. Assessment of mosquito community diversity and, in particular, identification of environmental parameters shaping these communities is therefore of key importance for the design of adequate surveillance approaches. In this study, we assess effects of climatic parameters and habitat structure on mosquito communities in eastern Austria to deliver these highly relevant baseline data. Female mosquitoes were sampled twice a month from April to October 2014 and 2015 at 35 permanent and 23 non-permanent trapping sites using carbon dioxide-baited traps. Differences in spatial and seasonal abundance patterns of Culicidae taxa were identified using likelihood ratio tests; possible effects of environmental parameters on seasonal and spatial mosquito distribution were analysed using multivariate statistical methods. We assessed community responses to environmental parameters based on 14-day-average values that affect ontogenesis. Altogether 29,734 female mosquitoes were collected, and 21 of 42 native as well as two of four non-native mosquito species were reconfirmed in eastern Austria. Statistical analyses revealed significant differences in mosquito abundance between sampling years and provinces. Incidence and abundance patterns were found to be linked to 14-day mean sunshine duration, humidity, water-level maxima and the amount of precipitation. However, land cover classes were found to be the most important factor, effectively assigning both indigenous and non-native mosquito species to various communities, which responded differentially to environmental variables. These findings thus underline the significance of non-climatic variables for future mosquito prediction models and the necessity to consider these in mosquito surveillance programmes.

Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.

PubMed

Collins, Courtney G; Stajich, Jason E; Weber, Sören E; Pombubpa, Nuttapon; Diez, Jeffrey M

2018-04-19

Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next-generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change. © 2018 John Wiley & Sons Ltd.

Primary and complex stressors in polluted mediterranean rivers: Pesticide effects on biological communities

NASA Astrophysics Data System (ADS)

Ricart, Marta; Guasch, Helena; Barceló, Damià; Brix, Rikke; Conceição, Maria H.; Geiszinger, Anita; José López de Alda, Maria; López-Doval, Julio C.; Muñoz, Isabel; Postigo, Cristina; Romaní, Anna M.; Villagrasa, Marta; Sabater, Sergi

2010-03-01

SummaryWe examined the presence of pesticides in the Llobregat river basin (Barcelona, Spain) and their effects on benthic biological communities (invertebrates and diatoms). The Llobregat river is one of Barcelona's major drinking water resources. It has been highly polluted by industrial, agricultural, and urban wastewaters, and—as a typical Mediterranean river—is regularly subjected to periodic floods and droughts. Water scarcity periods result in reduced water flow and dilution capacity, increasing the potential environmental risk of pollutants. Seven sites were selected, where we analysed the occurrence of 22 pesticides (belonging to the classes of triazines, organophosphates, phenylureas, anilides, chloroacetanilides, acidic herbicides and thiocarbamates) in the water and sediment, and the benthic community structure. Biofilm samples were taken to measure several metrics related to both the algal and bacterial components of fluvial biofilms. Multivariate analyses revealed a potential relationship between triazine-type herbicides and the distribution of the diatom community, although no evidence of disruption in the invertebrate community distribution was found. Biofilm metrics were used as response variables rather than abundances of individual species to identify possible cause-effect relationships between pesticide pollution and biotic responses. Certain effects of organophosphates and phenylureas in both structural and functional aspects of the biofilm community were suggested, but the sensitivity of each metric to particular stressors must be assessed before we can confidently assign causality. Complemented with laboratory experiments, which are needed to confirm causality, this approach could be successfully incorporated into environmental risk assessments to better summarise biotic integrity and improve the ecological management.

Context-Sensitive Detection of Local Community Structure

DTIC Science & Technology

2011-04-01

characters in the Victor Hugo novel Les Miserables (lesmis).[77 vertices, 254 edges] [Knu93]. • The neural network of the nematode C. Elegans (c.elegans...adjectives and nouns in the Novel David Cop- perfield by Charles Dickens.[112 vertices, 425 edges] [New06]. • Les Miserables . Co-appearance network of...exponential distribution. The degree distributions of the Network Science, Les Miserables , and Word Adjacencies networks display a similar heavy tail. By

The influence of natural and anthropic environmental variables on the structure and spatial distribution along longitudinal gradient of macroinvertebrate communities in southern Brazilian streams

PubMed Central

Batalla Salvarrey, Andrea Vanessa; Kotzian, Carla Bender; Spies, Márcia Regina; Braun, Bruna

2014-01-01

Abstract Southern Brazilian rivers and streams have been intensively affected by human activities, especially agriculture and the release of untreated domestic sewage. However, data about the aquatic macroinvertebrates in these streams are scarce and limited to only certain groups. In addition, studies focusing on the structure and spatial distribution of these communities are lacking. This study analyzed the effects of natural and anthropic variables on the community structure of macroinvertebrates along a longitudinal gradient in three microbasins located in a region of landscape transition in the state of Rio Grande do Sul, Brazil. Sampling was conducted in the Vacacaí-Mirim River (August 2008) and in the Ibicuí-Mirim and Tororaipí rivers (August 2009) following an environmental gradient including 1 st , 2 nd , 3 rd , and 4 th order segments. Local natural factors that were analyzed include water temperature, pH, electrical conductivity, dissolved oxygen, substrate granulometry, and the presence of aquatic vegetation. Anthropic variables that were analyzed include including bank erosion, land use, urbanization, riparian deforestation, and fine sediments input. A total of 42 families and 129 taxa were found, with predominance of environmentally tolerant taxa. Geological context (landscape transition and large hydrographic basins) tended to influence natural environmental factors along the rivers’ longitudinal gradients. However, changes in anthropic variables were not affected by these geological differences and therefore did not correlate with patterns of spatial distribution in macroinvertebrate communities. Only 1 st order stream segments showed a community composition with high richness of taxa intolerant to anthropic disturbance. Richness as a whole tended to be higher in 3 rd to 4 th order set of segments, but this trend was a result of local anthropic environmental disturbances. Future inventories conducted in similar landscape transition regions of Brazil, for conservation purposes, must consider stream segments of different orders, microbasins, and major basins in order to obtain data that faithfully reflect the regional diversity. Additionally, it is necessary to consider environmental gradients of land use and anthropic impacts in order to suggest appropriate strategies for conserving the environmental integrity of streams. PMID:25373160

Distribution and spatial variation of hydrothermal faunal assemblages at Lucky Strike (Mid-Atlantic Ridge) revealed by high-resolution video image analysis

NASA Astrophysics Data System (ADS)

Cuvelier, Daphne; Sarrazin, Jozée; Colaço, Ana; Copley, Jon; Desbruyères, Daniel; Glover, Adrian G.; Tyler, Paul; Serrão Santos, Ricardo

2009-11-01

Whilst the fauna inhabiting hydrothermal vent structures in the Atlantic Ocean is reasonably well known, less is understood about the spatial distributions of the fauna in relation to abiotic and biotic factors. In this study, a major active hydrothermal edifice (Eiffel Tower, at 1690 m depth) on the Lucky Strike vent field (Mid-Atlantic Ridge (MAR)) was investigated. Video transects were carried out by ROV Victor 6000 and complete image coverage was acquired. Four distinct assemblages, ranging from dense larger-sized Bathymodiolus mussel beds to smaller-sized mussel clumps and alvinocaridid shrimps, and two types of substrata were defined based on high definition photographs and video imagery. To evaluate spatial variation, faunal distribution was mapped in three dimensions. A high degree of patchiness characterizes this 11 m high sulfide structure. The differences observed in assemblage and substratum distribution were related to habitat characteristics (fluid exits, depth and structure orientation). Gradients in community structure were observed, which coincided with an increasing distance from the fluid exits. A biological zonation model for the Eiffel Tower edifice was created in which faunal composition and distribution can be visually explained by the presence/absence of fluid exits.

Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

PubMed

Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

2013-04-01

Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P < 0.01), while others showed a significant quantity correlation with soil microbe quantity (P < 0.05).

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.

PubMed

Yang, Yuyin; Dai, Yu; Li, Ningning; Li, Bingxin; Xie, Shuguang; Liu, Yong

2017-02-01

Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale.

PubMed

Niu, Lihua; Zhang, Xue; Li, Yi; Wang, Peifang; Zhang, Wenlong; Wang, Chao; Wang, Qing

2017-07-01

Due to the important roles of archaea in wastewater treatment processes, archaeal communities have been studied extensively in various anaerobic reactors, but the knowledge of archaeal communities in full-scale activated sludge wastewater treatment plants (WWTPs) remains quite poor. In this study, 454-pyrosequencing was for the first time employed to investigate archaeal communities from 20 full-scale activated sludge WWTPs distributed at a 3,660-meter elevational scale in China. Results showed that archaeal communities from WWTPs were dominated by Methanosarcinales (84.6%). A core archaeal population (94.5%) composed of Methanosaeta, Methanosarcina, Methanogenium and Methanobrevibacter was shared among WWTPs. The elevational pattern of archaeal communities was observed in WWTPs, with an elevational threshold associated with archaeal community richness and structures at approximately 1,500 meters above sea level (masl). A declining trend in community richness with increasing elevation was observed at higher elevations, whereas no trend was presented at lower elevations. Spearman correlation analysis indicated that the archaeal community richness at higher elevations was associated with more environmental variables than that at lower elevations. Redundancy analysis indicated that wastewater variables were the dominant contributors to the variation of community structures at higher elevations, followed by operational variables and elevation.

Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function.

PubMed

Ruiz-González, Clara; Archambault, Esther; Laforest-Lapointe, Isabelle; Del Giorgio, Paul A; Kembel, Steven W; Messier, Christian; Nock, Charles A; Beisner, Beatrix E

2018-06-14

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Species area relationships in mediterranean-climate plant communities

USGS Publications Warehouse

Keeley, Jon E.; Fotheringham, C.J.

2003-01-01

Aim To determine the best-fit model of species–area relationships for Mediterranean-type plant communities and evaluate how community structure affects these species–area models.Location Data were collected from California shrublands and woodlands and compared with literature reports for other Mediterranean-climate regions.Methods The number of species was recorded from 1, 100 and 1000 m2 nested plots. Best fit to the power model or exponential model was determined by comparing adjusted r2 values from the least squares regression, pattern of residuals, homoscedasticity across scales, and semi-log slopes at 1–100 m2 and 100–1000 m2. Dominance–diversity curves were tested for fit to the lognormal model, MacArthur's broken stick model, and the geometric and harmonic series.Results Early successional Western Australia and California shrublands represented the extremes and provide an interesting contrast as the exponential model was the best fit for the former, and the power model for the latter, despite similar total species richness. We hypothesize that structural differences in these communities account for the different species–area curves and are tied to patterns of dominance, equitability and life form distribution. Dominance–diversity relationships for Western Australian heathlands exhibited a close fit to MacArthur's broken stick model, indicating more equitable distribution of species. In contrast, Californian shrublands, both postfire and mature stands, were best fit by the geometric model indicating strong dominance and many minor subordinate species. These regions differ in life form distribution, with annuals being a major component of diversity in early successional Californian shrublands although they are largely lacking in mature stands. Both young and old Australian heathlands are dominated by perennials, and annuals are largely absent. Inherent in all of these ecosystems is cyclical disequilibrium caused by periodic fires. The potential for community reassembly is greater in Californian shrublands where only a quarter of the flora resprout, whereas three quarters resprout in Australian heathlands.Other Californian vegetation types sampled include coniferous forests, oak savannas and desert scrub, and demonstrate that different community structures may lead to a similar species–area relationship. Dominance–diversity relationships for coniferous forests closely follow a geometric model whereas associated oak savannas show a close fit to the lognormal model. However, for both communities, species–area curves fit a power model. The primary driver appears to be the presence of annuals. Desert scrub communities illustrate dramatic changes in both species diversity and dominance–diversity relationships in high and low rainfall years, because of the disappearance of annuals in drought years.Main conclusions Species–area curves for immature shrublands in California and the majority of Mediterranean plant communities fit a power function model. Exceptions that fit the exponential model are not because of sampling error or scaling effects, rather structural differences in these communities provide plausible explanations. The exponential species–area model may arise in more than one way. In the highly diverse Australian heathlands it results from a rapid increase in species richness at small scales. In mature California shrublands it results from very depauperate richness at the community scale. In both instances the exponential model is tied to a preponderance of perennials and paucity of annuals. For communities fit by a power model, coefficients z and log c exhibit a number of significant correlations with other diversity parameters, suggesting that they have some predictive value in ecological communities.

Vertical distribution of archaeal communities associated with anaerobic degradation of pentabromodiphenyl ether (BDE-99) in river-based groundwater recharge with reclaimed water.

PubMed

Yan, Yulin; Ma, Mengsi; Liu, Xiang; Ma, Weifang; Li, Yangyao

2018-02-01

When groundwater is recharged with reclaimed water, the presence of trace amounts of biorefractory pentabromodiphenyl ether (PBDE, specifically BDE-99) might cause potential groundwater pollution. A laboratory-scale column was designed to investigate the distribution of the community of archaea in this scenario and the associated anaerobic degradation of BDE-99. The concentration of BDE-99 decreased significantly as soil depth increased, and fluorescence in situ hybridization (FISH) analysis suggested that archaea exerted significant effects on the biodegradation of PBDE. Through 454 pyrosequencing of 16s rRNA genes, we found that the distribution and structure of the archaeal community associated with anaerobic degradation of BDE-99 in the river-based aquifer media changed significantly between different soil depths. The primary debrominated metabolites varied with changes in the vertically distributed archaeal community. The archaea in the surface layer were dominated by Methanomethylovorans, and the middle layer was mainly composed of Nitrososphaera. Nitrosopumilus and Nitrososphaera were equally abundant in the bottom layer. In addition, Methanomethylovorans abundance depended on the depth of soil, and the relative abundance of Nitrosopumilus increased with increasing depth, which was associated with the oxidation-reduction potential and the content of intermediate metabolites. We propose that Nitrososphaera and Nitrosopumilus might be the key archaeal taxa mediating the biodegradation of BDE-99.

Institutional and financial guide to geothermal district heating, serial no. 2

NASA Astrophysics Data System (ADS)

1982-03-01

General planning considerations which affect nearly every community are reviewed, and alternative operating structures which are available to communities are reviewed, including local governments, nonprofit cooperatives, private enterprises, and joint ventures. The financing options available to publicly-owned and privately-owned district heating systems are then summarized. The geothermal production and distribution activities most appropriate to each type of operating structure are reviewed, along with typical equity and debt funding sources. The tax advantages for private developers are described, as are the issues of customer contracts and service prices, and customer retrofit financing. The treatment is limited to an introductory overview.

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration.

PubMed

Douterelo, I; Sharpe, R; Boxall, J

2014-07-01

To characterize bacterial communities during the early stages of biofilm formation and their role in water discolouration in a fully representative, chlorinated, experimental drinking water distribution systems (DWDS). Biofilm development was monitored in an experimental DWDS over 28 days; subsequently the system was disturbed by raising hydraulic conditions to simulate pipe burst, cleaning or other system conditions. Biofilm cell cover was monitored by fluorescent microscopy and a fingerprinting technique used to assess changes in bacterial community. Selected samples were analysed by cloning and sequencing of the 16S rRNA gene. Fingerprinting analysis revealed significant changes in the bacterial community structure over time (P < 0·05). Cell coverage increased over time accompanied by an increase in bacterial richness and diversity. Shifts in the bacterial community structure were observed along with an increase in cell coverage, bacterial richness and diversity. Species related to Pseudomonas spp. and Janthinobacterium spp. dominated the process of initial attachment. Based on fingerprinting results, the hydraulic regimes did not affect the bacteriological composition of biofilms, but they did influence their mechanical stability. This study gives a better insight into the early stages of biofilm formation in DWDS and will contribute to the improvement of management strategies to control the formation of biofilms and the risk of discolouration. © 2014 The Authors. published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Temporal assessment of microbial communities in soils of two contrasting mangroves.

PubMed

Rigonato, Janaina; Kent, Angela D; Gumiere, Thiago; Branco, Luiz Henrique Zanini; Andreote, Fernando Dini; Fiore, Marli Fátima

Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove. A positive correlation of community structure between diazotrophs and cyanobacteria was observed, suggesting the functional importance of this phylum as nitrogen fixers in mangroves soils. Different ecological patterns explained the microbial behavior in the pristine and polluted mangroves. Stochastic models in the pristine mangrove indicate that there is not a specific environmental factor that determines the bacterial distribution, while cyanobacteria and diazotrophs better fitted in deterministic model in the same area. For the contaminated mangrove site, deterministic models better represented the variations in the communities, suggesting that the presence of oil might change the microbial ecological structures over time. Mangroves represent a unique environment threatened by global change, and this study contributed to the knowledge of the microbial distribution in such areas and its response on persistent contamination historic events. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration

PubMed Central

Douterelo, I; Sharpe, R; Boxall, J

2014-01-01

Aims To characterize bacterial communities during the early stages of biofilm formation and their role in water discolouration in a fully representative, chlorinated, experimental drinking water distribution systems (DWDS). Methods and Results Biofilm development was monitored in an experimental DWDS over 28 days; subsequently the system was disturbed by raising hydraulic conditions to simulate pipe burst, cleaning or other system conditions. Biofilm cell cover was monitored by fluorescent microscopy and a fingerprinting technique used to assess changes in bacterial community. Selected samples were analysed by cloning and sequencing of the 16S rRNA gene. Fingerprinting analysis revealed significant changes in the bacterial community structure over time (P < 0·05). Cell coverage increased over time accompanied by an increase in bacterial richness and diversity. Conclusions Shifts in the bacterial community structure were observed along with an increase in cell coverage, bacterial richness and diversity. Species related to Pseudomonas spp. and Janthinobacterium spp. dominated the process of initial attachment. Based on fingerprinting results, the hydraulic regimes did not affect the bacteriological composition of biofilms, but they did influence their mechanical stability. Significance and Importance of the Study This study gives a better insight into the early stages of biofilm formation in DWDS and will contribute to the improvement of management strategies to control the formation of biofilms and the risk of discolouration. PMID:24712449

Floristic Diversity and Distribution Pattern of Plant Communities along Altitudinal Gradient in Sangla Valley, Northwest Himalaya

PubMed Central

Rana, J. C.; Devi, Usha; Randhawa, S. S.; Kumar, Rajesh

2014-01-01

Himalayas are globally important biodiversity hotspots and are facing rapid loss in floristic diversity and changing pattern of vegetation due to various biotic and abiotic factors. This has necessitated the qualitative and quantitative assessment of vegetation here. The present study was conducted in Sangla Valley of northwest Himalaya aiming to assess the structure of vegetation and its trend in the valley along the altitudinal gradient. In the forest and alpine zones of the valley, 15 communities were recorded. Study revealed 320 species belonging to 199 genera and 75 families. Asteraceae, Rosaceae, Apiaceae, and Ranunculaceae were dominant. Among genera, Artemisia followed by Polygonum, Saussurea, Berberis, and Thalictrum were dominant. Tree and shrub's density ranged from 205 to 600 and from 105 to 1030 individual per hectare, respectively, whereas herbs ranged from 22.08 to 78.95 individual/m2. Nearly 182 species were native to the Himalaya. Maximum altitudinal distribution of few selected climate sensitive species was found to be highest in northeast and north aspects. This study gives an insight into the floristic diversity and community structure of the fragile Sangla Valley which was hitherto not available. PMID:25383363

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE PAGES

Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...

2017-08-04

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis.

PubMed

Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua

2015-10-01

Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

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

Justice, N. B.; Sczesnak, A.; Hazen, T. C.

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

[Phytoplankton's community structure and its relationships with environmental factors in the rivers of Tongling City, Anhui Province of East China in winter].

PubMed

Wang, Li; Wei, Wei; Zhou, Ping; Li, Yang; Sun, Qing-Ye

2013-01-01

Tongling is one of the main non-ferrous metal mining areas in China, and the biodiversity in the river ecosystem of this area is seriously affected by heavy metals as a result of mining activities. In the winter in 2010, an investigation was conducted on the community structure of phytoplankton and its relationships with environmental factors in the main sections of the rivers in Tongling. A total of 203 phytoplankton species were identified, belonging to 96 genera and 8 phyla. The community structure of the phytoplankton differed obviously in different river sections, but the communities were all dominated by Bacillariophyta, Chlorophyta and Cyanophyta. The phytoplankton abundance ranged from 9.1 x 10(3) to 6.5 x 10(7) cells x L(-1), and the quantity of the phytoplankton in the river sections directly carried with mining waste water was significantly low. The Shannon index of the phytoplankton community at different sampling sites ranged from 0 to 3.45, with a significant discrepancy in different river sections. There existed significant correlations between the density and group number of phytoplankton and the COD(Cr) and cadmium, copper and zinc concentrations in the rivers, and the concentrations of river total nitrogen, NH4(+)-N, NO3(-)-N, and copper, COD(Cr) and pH were the main environmental variables affecting the phytoplankton' s community structure and its spatial distribution. Although the nutritional status of the river waters had greater effects on the community structure of phytoplankton, the effects of the heavy metals there from mining enterprises could not be neglected.

Prey dispersal rate affects prey species composition and trait diversity in response to multiple predators in metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

1. Recent studies indicate that large-scale spatial processes can alter local community structuring mechanisms to determine local and regional assemblages of predators and their prey. In metacommunities, this may occur when the functional diversity represented in the regional predator species pool interacts with the rate of prey dispersal among local communities to affect prey species diversity and trait composition at multiple scales. 2. Here, we test for effects of prey dispersal rate and spatially and temporally heterogeneous predation from functionally dissimilar predators on prey structure in pond mesocosm metacommunities. An experimental metacommunity consisted of three pond mesocosm communities supporting two differentially size-selective invertebrate predators and their zooplankton prey. In each metacommunity, two communities maintained constant predation and supported either Gyrinus sp. (Coleoptera) or Notonecta ungulata (Hemiptera) predators generating a spatial prey refuge while the third community supported alternating predation from Gyrinus sp. and N. ungulata generating a temporal prey refuge. Mesocosm metacommunities were connected at either low (0.7% day(-1)) or high (10% day(-1)) planktonic prey dispersal. The diversity, composition and body size of zooplankton prey were measured at local and regional (metacommunity) scales. 3. Metacommunities experiencing the low prey dispersal rate supported the greatest regional prey species diversity (H') and evenness (J'). Neither dispersal rate nor predation regime affected local prey diversity or evenness. The spatial prey refuge at low dispersal maintained the largest difference in species composition and body size diversity between communities under Gyrinus and Notonecta predation, suggesting that species sorting was operating at the low dispersal rate. There was no effect of dispersal rate on species diversity or body size distribution in the temporal prey refuge. 4. The frequency distribution, but not the range, of prey body sizes within communities depended upon prey dispersal rate and predator identity. Taken together, these results demonstrate that prey dispersal rate can moderate the strength of predation to influence prey species diversity and the local frequency distribution of prey traits in metacommunities supporting ecologically different predators.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

PubMed Central

Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

2016-01-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). PMID:26888080

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

PubMed

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

[Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

PubMed

Espinoza Mendiola, Mario

2008-12-01

Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific habitats that serve as essential fish habitats can improve tropical fish conservation and management strategies, thus increasing local diversity, and thereby, the biological importance of the area.

Effects of simulated nitrogen deposition on ectomycorrhizae community structure in hybrid larch and its parents grown in volcanic ash soil: The role of phosphorous.

PubMed

Wang, Xiaona; Agathokleous, Evgenios; Qu, Laiye; Fujita, Saki; Watanabe, Makoto; Tamai, Yutaka; Mao, Qiaozhi; Koyama, Akihiro; Koike, Takayoshi

2018-03-15

With the rapid industrial development and modern agricultural practices, increasing nitrogen (N) deposition can cause nutrient imbalance in immature volcanic ash soil commonly found in Japan. Larch species, widely distributed in northeast Eurasia, are associated with ectomycorrhizal (ECM) fungi which play a critical role in nutrient acquisition for their hosts. In this study, we investigated species richness and diversity of ECM fungi associated with a hybrid larch (F 1 ) and its parents, Dahurian larch (Larix gmelinii var. japonica) and Japanese larch (L. kaempferi), under simulated N deposition (0 and 100kgha -1 yr -1 ) with/without phosphorous (P) (0 and 50kgha -1 yr -1 ). Seedlings planted in immature volcanic ash with low nutrient availability were subjected to the N and P treatments for fifteen months. We found that response of ECM community structure to the increased nutrient availability depended on host genotypes. Nutrient addition significantly affected ECM structure in Japanese larch, but no such significant effect was found for Dahurian larch. Effects of the nutrient addition to ECM fungal community in F 1 were intermediate. F 1 was tolerant to high N loading, which was due to consistent, relatively high association with Suillus sp. and Hebeloma sp. F 1 showed heterosis in relative biomass, which was most apparent under high N treatments. This co-variation of ECM fungal community structure and F 1 biomass in response to N loading suggest that ECM community structure might play an important role in host growth. The present findings indicate effects of N deposition on ECM fungal community structure can depend on larch species, thus it is challenging to predict general trends. Copyright © 2017 Elsevier B.V. All rights reserved.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

PubMed Central

Jochum, Lara M.; Chen, Xihan; Lever, Mark A.; Loy, Alexander; Jørgensen, Bo Barker; Schramm, Andreas

2017-01-01

ABSTRACT Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community. PMID:28939599

Impact of disinfection on drinking water biofilm bacterial community.

PubMed

Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

Sewage reflects the microbiomes of human populations.

PubMed

Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2015-02-24

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics. Copyright © 2015 Newton et al.

Relationships between species feeding traits and environmental conditions in fish communities: a three-matrix approach.

PubMed

Brind'Amour, Anik; Boisclair, Daniel; Dray, Stéphane; Legendre, Pierre

2011-03-01

Understanding the relationships between species biological traits and the environment is crucial to predicting the effect of habitat perturbations on fish communities. It is also an essential step in the assessment of the functional diversity. Using two complementary three-matrix approaches (fourth-corner and RLQ analyses), we tested the hypothesis that feeding-oriented traits determine the spatial distributions of littoral fish species by assessing the relationship between fish spatial distributions, fish species traits, and habitat characteristics in two Laurentian Shield lakes. Significant associations between the feeding-oriented traits and the environmental characteristics suggested that fish communities in small lakes (displaying low species richness) can be spatially structured. Three groups of traits, mainly categorized by the species spatial and temporal feeding activity, were identified. The water column may be divided in two sections, each of them corresponding to a group of traits related to the vertical distribution of the prey coupled with the position of the mouth. Lake areas of low structural complexity were inhabited by functional assemblages dominated by surface feeders while structurally more complex areas were occupied by mid-water and benthic feeders. A third group referring to the time of feeding activity was observed. Our work could serve as a guideline study to evaluate species traits x environment associations at multiple spatial scales. Our results indicate that three-matrix statistical approaches are powerful tools that can be used to study such relationships. These recent statistical approaches open up new research directions such as the study of spatially based biological functions in lakes. They also provide new analytical tools for determining, for example, the potential size of freshwater protected areas.

IPR 1.0: an efficient method for calculating solar radiation absorbed by individual plants in sparse heterogeneous woody plant communities

NASA Astrophysics Data System (ADS)

Zhang, Y.; Chen, W.; Li, J.

2014-07-01

Climate change may alter the spatial distribution, composition, structure and functions of plant communities. Transitional zones between biomes, or ecotones, are particularly sensitive to climate change. Ecotones are usually heterogeneous with sparse trees. The dynamics of ecotones are mainly determined by the growth and competition of individual plants in the communities. Therefore it is necessary to calculate the solar radiation absorbed by individual plants in order to understand and predict their responses to climate change. In this study, we developed an individual plant radiation model, IPR (version 1.0), to calculate solar radiation absorbed by individual plants in sparse heterogeneous woody plant communities. The model is developed based on geometrical optical relationships assuming that crowns of woody plants are rectangular boxes with uniform leaf area density. The model calculates the fractions of sunlit and shaded leaf classes and the solar radiation absorbed by each class, including direct radiation from the sun, diffuse radiation from the sky, and scattered radiation from the plant community. The solar radiation received on the ground is also calculated. We tested the model by comparing with the results of random distribution of plants. The tests show that the model results are very close to the averages of the random distributions. This model is efficient in computation, and can be included in vegetation models to simulate long-term transient responses of plant communities to climate change. The code and a user's manual are provided as Supplement of the paper.

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago.

PubMed

Salerno, Jennifer L; Bowen, Brian W; Rappé, Michael S

2016-08-01

Factors driving the distribution of marine microorganisms are widely debated and poorly understood. Recent studies show that free-living marine microbes exhibit geographical patterns indicative of limited dispersal. In contrast, host-associated microbes face a different set of dispersal challenges, and hosts may function as habitat 'islands' for resident microbial populations. Here, we examine the biogeographical distributions of planktonic and adjacent coral-associated bacterial communities across the Hawaiian Archipelago, Johnston Atoll (∼1400 km southwest of Hawaii) and American Samoa in the Pacific Ocean and investigate the potential underlying processes driving observed patterns. Statistical analyses of bacterial community structure, determined using a small-subunit ribosomal RNA gene-based approach, showed that bacterioplankton and coral-associated bacterial communities were distinct, and correlated with geographical distance between sites. In addition, biogeographical patterns of bacterial associates paralleled those of their host coral Porites lobata, highlighting the specificity of these associations and the impact that host dispersal may have on bacterial biogeography. Planktonic and coral-associated bacterial communities from distant Johnston Atoll were shown to be connected with communities from the center of the Hawaiian Archipelago, a pattern previously observed in fish and invertebrates. No significant correlations were detected with habitat type, temperature or depth. However, non-distance-based geographical groupings were detected, indicating that, in addition to dispersal, unidentified environmental factors also affected the distributions of bacterial communities investigated here. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: does metabolic restriction limit niche differentiation potential?

PubMed

Carbonero, Franck; Oakley, Brian B; Hawkins, Robert J; Purdy, Kevin J

2012-05-01

A reductionist ecological approach of using a model genus was adopted in order to understand how microbial community structure is driven by metabolic properties. The distribution along an estuarine gradient of the highly specialised genus Methanosaeta was investigated and compared to the previously determined distribution of the more metabolically flexible Desulfobulbus. Methanosaeta genotypic distribution along the Colne estuary (Essex, UK) was determined by DNA- and RNA-based denaturing gradient gel electrophoresis and 16S rRNA gene sequence analyses. Methanosaeta distribution was monotonic, with a consistently diverse community and no apparent niche partitioning either in DNA or RNA analyses. This distribution pattern contrasts markedly with the previously described niche partitioning and sympatric differentiation of the model generalist, Desulfobulbus. To explain this difference, it is hypothesised that Methanosaeta's strict metabolic needs limit its adaptation potential, thus populations do not partition into spatially distinct groups and so do not appear to be constrained by gross environmental factors such as salinity. Thus, at least for these two model genera, it appears that metabolic flexibility may be an important factor in spatial distribution and this may be applicable to other microbes.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas

PubMed Central

Zhou, Haixia; Dang, Hongyue; Klotz, Martin G.

2016-01-01

Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments. PMID:27489551

[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].

PubMed

Li, Hu; Huang, Fu-yi; Su, Jian-qiang; Hong, You-wei; Yu, Shen

2015-12-01

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE ) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.

An emotional contagion model for heterogeneous social media with multiple behaviors

NASA Astrophysics Data System (ADS)

Xiong, Xi; Li, Yuanyuan; Qiao, Shaojie; Han, Nan; Wu, Yue; Peng, Jing; Li, Binyong

2018-01-01

The emotion varies and propagates with the spatial and temporal information of individuals through social media, which uncovers several interaction mechanisms and features the community structure in order to facilitate individuals' communication and emotional contagion in social networks. Aiming to show the detailed process and characteristics of emotional contagion within social media, we propose an emotional independent cascade model in which individual emotion can affect the subsequent emotion of his/her friends. The transmissibility is introduced to measure the capability of propagating emotion with respect to an individual in social networks. By analyzing the patterns of emotional contagion on Twitter data, we find that the value of transmissibility differs on different layers and on different community structures. Extensive experiments were conducted and the results reveal that, the polar emotion of hub users can lead to the disappearance of opposite emotion, and the transmissibility makes no sense. The final emotional distribution depends on the initial emotional distribution and the transmissibilities. Individuals from a small community are more likely to change their mood by the influence of community leaders. In addition, we compared the proposed model with two other models, the emotion-based spreader-ignorant-stifler model and the standard independent cascade model. The results demonstrate that the proposed model can reflect the real-world situation of emotional contagion for heterogeneous social media while the computational complexities of all these three models are similar.

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea.

PubMed

Xu, Dapeng; Jiao, Nianzhi; Ren, Rui; Warren, Alan

2017-05-01

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75-m depth. The communities of microbial eukaryotes were clustered into shallow-, middle-, and deep-water groups according to the depth from which they were collected, indicating a depth-related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50-m deep, being most abundant near the sea floor where they contributed ca. 64-97% and 40-74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

The Effect of Phylogeny, Environment and Morphology on Communities of a Lianescent Clade (Bignonieae-Bignoniaceae) in Neotropical Biomes

PubMed Central

Alcantara, Suzana; Ree, Richard H.; Martins, Fernando R.; Lohmann, Lúcia G.

2014-01-01

The influence of ecological traits to the distribution and abundance of species is a prevalent issue in biodiversity science. Most studies of plant community assembly have focused on traits related to abiotic aspects or direct interactions among plants, with less attention paid to ignore indirect interactions, as those mediated by pollinators. Here, we assessed the influence of phylogeny, habitat, and floral morphology on ecological community structure in a clade of Neotropical lianas (tribe Bignonieae, Bignoniaceae). Our investigation was guided by the long-standing hypothesis that habitat specialization has promoted speciation in Bignonieae, while competition for shared pollinators influences species co-occurrence within communities. We analyzed a geo-referenced database for 94 local communities occurring across the Neotropics. The effect of floral morphological traits and abiotic variables on species co-occurrence was investigated, taking into account phylogenetic relationships. Habitat filtering seems to be the main process driving community assembly in Bignonieae, with environmental conditions limiting species distributions. Differing specialization to abiotic conditions might have evolved recently, in contrast to the general pattern of phylogenetic clustering found in communities of other diverse regions. We find no evidence that competition for pollinators affects species co-occurrence; instead, pollinator occurrence seems to have acted as an “environmental filter” in some habitats. PMID:24594706

Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean.

PubMed

Baltar, Federico; Arístegui, Javier; Gasol, Josep M; Lekunberri, Itziar; Herndl, Gerhard J

2010-08-01

To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic 'hotspots' of prokaryotic activity (in the epi- and mesopelagic realms).

Comparative study of rhizobacterial community structure of plant species in oil-contaminated soil.

PubMed

Lee, Eun-Hee; Cho, Kyong-Suk; Kim, Jaisoo

2010-09-01

In this study, the identity and distribution of plants and the structure of their associated rhizobacterial communities were examined in an oil-contaminated site. The number of plant species that formed a community or were scattered was 24. The species living in soil highly contaminated with total petroleum hydrocarbon (TPH) (9,000-4,5000 mg/g-soil) were Cynodon dactylon, Persicaria lapathifolia, and Calystegia soldanella (a halophytic species). Among the 24 plant species, the following have been known to be effective for oil removal: C. dactylon, Digitaria sanguinalis, and Cyperus orthostachyus. Denaturing gradient gel electrophoresis (DGGE) profile analysis showed that the following pairs of plant species had highly similar (above 70%) rhizobacterial community structures: Artemisia princeps and Hemistepta lyrata; C. dactylon and P. lapathifolia; Carex kobomugi and Cardamine flexuosa; and Equisetum arvense and D. sanguinalis. The major groups of rhizobacteria were Betaproteobacteria, Gamma-proteobacteria, Chloroflexi, Actinobacteria, and unknown. Based on DGGE analysis, P. lapathifolia, found for the first time in this study growing in the presence of high TPH, may be a good species for phytoremediation of oil-contaminated soils and in particular, C. soldanella may be useful for soils with high TPH and salt concentrations. Overall, this study suggests that the plant roots, regardless of plant species, may have a similar influence on the bacterial community structure in oil-contaminated soil.

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

PubMed

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

2017-04-01

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

Characterization of the ecological requirements for three plethodontid salamander species

Treesearch

Jessica A. Wooten; William B. Sutton; Thomas K. Pauley

2010-01-01

Increased availability of habitat and climate data has facilitated much research concerning the influence of these characteristics on the structure of salamander communities. We aimed to outline environmental requirements influencing the distribution of three sympatric plethodontid salamander species, including Plethodon cinereus, Desmognathus ochrophaeus...

Spatial variation of phytoplankton community structure in Daya Bay, China.

PubMed

Jiang, Zhao-Yu; Wang, You-Shao; Cheng, Hao; Zhang, Jian-Dong; Fei, Jiao

2015-10-01

Daya Bay is one of the largest and most important gulfs in the southern coast of China, in the northern part of the South China Sea. The phylogenetic diversity and spatial distribution of phytoplankton from the Daya Bay surface water and the relationship with the in situ water environment were investigated by the clone library of the large subunit of ribulose-1, 5-bisphosphate carboxylase (rbcL) gene. The dominant species of phytoplankton were diatoms and eustigmatophytes, which accounted for 81.9 % of all the clones of the rbcL genes. Prymnesiophytes were widely spread and wide varieties lived in Daya Bay, whereas the quantity was limited. The community structure of phytoplankton was shaped by pH and salinity and the concentration of silicate, phosphorus and nitrite. The phytoplankton biomass was significantly positively affected by phosphorus and nitrite but negatively by salinity and pH. Therefore, the phytoplankton distribution and biomass from Daya Bay were doubly affected by anthropic activities and natural factors.

Structural Factors Influencing Patterns of Drug Selling and Use and HIV Risk in the San Salvador Metropolitan Area

PubMed Central

Dickson-Gomez, Julia

2013-01-01

This article explores differences in the social context in which crack sales and use and HIV risk take place in seven low-income communities in San Salvador, and structural factors that may influence these differences. The organization of drug selling varied among the communities on a number of dimensions including: whether drug sales were open or closed systems; the type of drug-selling site; and the participation of drug users in drug-distribution roles. Drug-use sites also varied according to whether crack was used in private, semiprivate, or public spaces, and whether individuals used drugs alone or with other drug users. Three patterns of drug use and selling were identified based on the dimensions outlined above. Structural factors that influenced these patterns included the geographic location of the communities, their physical layout, gang involvement in drug sales, and police surveillance. Implications for HIV risk and prevention are explored for each pattern. PMID:20550091

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

PubMed Central

Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O.; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A.; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs. PMID:29136658

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

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

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE PAGES

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

2015-06-28

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Multi-objective optimal dispatch of distributed energy resources

NASA Astrophysics Data System (ADS)

Longe, Ayomide

This thesis is composed of two papers which investigate the optimal dispatch for distributed energy resources. In the first paper, an economic dispatch problem for a community microgrid is studied. In this microgrid, each agent pursues an economic dispatch for its personal resources. In addition, each agent is capable of trading electricity with other agents through a local energy market. In this paper, a simple market structure is introduced as a framework for energy trades in a small community microgrid such as the Solar Village. It was found that both sellers and buyers benefited by participating in this market. In the second paper, Semidefinite Programming (SDP) for convex relaxation of power flow equations is used for optimal active and reactive dispatch for Distributed Energy Resources (DER). Various objective functions including voltage regulation, reduced transmission line power losses, and minimized reactive power charges for a microgrid are introduced. Combinations of these goals are attained by solving a multiobjective optimization for the proposed ORPD problem. Also, both centralized and distributed versions of this optimal dispatch are investigated. It was found that SDP made the optimal dispatch faster and distributed solution allowed for scalability.

Noah’s Ark Conservation Will Not Preserve Threatened Ecological Communities under Climate Change

PubMed Central

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Background Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. Methods We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. Results All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. Conclusions As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term. PMID:25881302

Noah's Ark conservation will not preserve threatened ecological communities under climate change.

PubMed

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term.

ESTEST: A Framework for the Verification and Validation of Electronic Structure Codes

NASA Astrophysics Data System (ADS)

Yuan, Gary; Gygi, Francois

2011-03-01

ESTEST is a verification and validation (V& V) framework for electronic structure codes that supports Qbox, Quantum Espresso, ABINIT, the Exciting Code and plans support for many more. We discuss various approaches to the electronic structure V& V problem implemented in ESTEST, that are related to parsing, formats, data management, search, comparison and analyses. Additionally, an early experiment in the distribution of V& V ESTEST servers among the electronic structure community will be presented. Supported by NSF-OCI 0749217 and DOE FC02-06ER25777.

Influence of the tidal front on the three-dimensional distribution of spring phytoplankton community in the eastern Yellow Sea.

PubMed

Choi, Byoung-Ju; Lee, Jung A; Choi, Jae-Sung; Park, Jong-Gyu; Lee, Sang-Ho; Yih, Wonho

2017-04-01

Hydrographic observation and biological samplings were conducted to assess the distribution of phytoplankton community over the sloping shelf of the eastern Yellow Sea in May 2012. The concentration of chlorophyll a was determined and phytoplankton was microscopically examined to conduct quantitative and cluster analyses. A cluster analysis of the phytoplankton species and abundance along four observation lines revealed the three-dimensional structure of the phytoplankton community distribution: the coastal group in the mixed region, the offshore upper layer group preferring stable water column, and the offshore lower layer group. The subsurface maximum of phytoplankton abundance and chlorophyll a concentration appeared as far as 64 km away from the tidal front through the middle layer intrusion. The phytoplankton abundance was high in the shore side of tidal front during the spring tide. The phytoplankton abundance was relatively high at 10-m depth in the mixed region while the concentration of chlorophyll a was high below the depth. The disparity between the profiles of the phytoplankton abundance and the chlorophyll a concentration in the mixed region was related to the depth-dependent species change accompanied by size-fraction of the phytoplankton community. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai-Tibetan Plateau.

PubMed

Yan, Yujing; Yang, Xian; Tang, Zhiyao

2013-11-01

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages.

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai-Tibetan Plateau

PubMed Central

Yan, Yujing; Yang, Xian; Tang, Zhiyao

2013-01-01

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages. PMID:24340197

Ecology of mangroves in the Jewfish Chain, Exuma, Bahamas

USGS Publications Warehouse

Wilcox, L. V.; Yocom, Thomas G.; Forbes, A. M.

1976-01-01

The structure and function of mangrove communities in the Jewfish Chain, Exumas, Bahamas, were investigated for 3-1/2 years. Mangrove vegetation in the Jewfish Chain is similar to that in all the Caribbean-Florida area; Rhizophora mangle L. dominates and is interspersed with Avicennia germinans (L.) Lamk. and Laguncularia racemosa (L.) Gaertn. There is no apparent zonation of these three species. The mangrove communities in the Jewfish Chain occur only where they are protected from prevailing winds, storms, and tides, although all are periodically devastated by hurricanes. We found little or no evidence of coast building within these protected locations. The importance of the mangroves appears to be in providing protection and food for other flora and fauna within this unique ecosystem. Twenty-four species of algae were found in the mangroves, 9 of which had not previously been reported from the Bahamas. Distribution of these algae appears to be correlated to incident solar radiation, desiccation, and tide level. A total of 56 species of fish were found in the mangroves, 2 of which were not previously known from the Bahamas. Many fish taken were juveniles, suggesting that mangroves are a nursery ground for numerous species. Nine species of molluscs were found. Each species had a distinct distribution pattern relative to distance from the seaward edge of the mangroves, as well as a distinct vertical distribution pattern. Seventeen species of decapod crustaceans were recorded. Though several species of birds were noted in the mangroves, three species were most abundant: the white-crowned pigeon (Columba leucocephala) uses the mangrove for nesting but feeds in nearby shrub-thorn communities; the gray kingbird (Tyrannus dominicensis) and green heron (Butorides virescens) nest and feed in the mangroves. Our data do not completely describe a stereotyped mangrove community in the Bahamas, but they do give an indication of community structure and suggest several aspects of function.

Spatial organization and drivers of the virtual water trade: a community-structure analysis

NASA Astrophysics Data System (ADS)

D'Odorico, Paolo; Carr, Joel; Laio, Francesco; Ridolfi, Luca

2012-09-01

The trade of agricultural commodities can be associated with a virtual transfer of the local freshwater resources used for the production of these goods. Thus, trade of food products virtually transfers large amounts of water from areas of food production to far consumption regions, a process termed the ‘globalization of water’. We consider the (time-varying) community structure of the virtual water network for the years 1986-2008. The communities are groups of countries with dense internal connections, while the connections are sparser among different communities. Between 1986 and 2008, the ratio between virtual water flows within communities and the total global trade of virtual water has continuously increased, indicating the existence of well defined clusters of virtual water transfers. In some cases (e.g. Central and North America and Europe in recent years) the virtual water communities correspond to geographically coherent regions, suggesting the occurrence of an ongoing process of regionalization of water resources. However, most communities also include countries located on different ‘sides’ of the world. As such, geographic proximity only partly explains the community structure of virtual water trade. Similarly, the global distribution of people and wealth, whose effect on the virtual water trade is expressed through simple ‘gravity models’, is unable to explain the strength of virtual water communities observed in the past few decades. A gravity model based on the availability of and demand for virtual water in different countries has higher explanatory power, but the drivers of the virtual water fluxes are yet to be adequately identified.

Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

NASA Astrophysics Data System (ADS)

Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

2017-11-01

The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments

PubMed Central

Hödl, Iris; Mari, Lorenzo; Bertuzzo, Enrico; Suweis, Samir; Besemer, Katharina; Rinaldo, Andrea; Battin, Tom J

2014-01-01

Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in ‘ripple-like’ and ‘star-like’ architectures – as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms. PMID:23879839

The KnowRISK project - Know your city, Reduce seISmic risK through non-structural elements

NASA Astrophysics Data System (ADS)

Sousa Oliveria, Carlos; Amaral Ferreira, Mónica; Lopez, Mário; Sousa Silva, Delta; Musacchio, Gemma; Rupakhety, Rajesh; Falsaperla, Susanna; Meroni, Fabrizio; Langer, Horst

2016-04-01

Historically, there is a tendency to focus on seismic structural performance of buildings, neglecting the potential for damage of non-structural elements. In particular, non-structural elements of buildings are their architectural parts (i.e. partitions, ceilings, cladding), electrical and mechanical components (i.e., distribution panels, piping, plumbing), and contents (e.g., furniture, bookcases, computers and desktop equipment). Damage of these elements often contributes significantly to earthquake impacts. In the 1999 Izmit Earthquake, Turkey, 50% of the injuries and 3% of human losses were caused by non-structural failures. In the 2010-2011 Christchurch Earthquakes (New Zealand), 40% of building damage was induced by non-structural malfunctions. Around 70%-85% of construction cost goes into these elements, and their damage can strongly influence the ability of communities to cope with and recover from earthquakes. The project Know your city, Reduce seISmic risK through non-structural elements (KnowRISK) aims at facilitating local communities' access to expert knowledge on non-structural seismic protection solutions. The project will study seismic scenarios critical for non-structural damage, produce a portfolio of non-structural protection measures and investigate the level of awareness in specific communities. We will implement risk communication strategies that will take into account the social and cultural background and a participatory approach to raise awareness in local communities. The paradox between the progress of scientific knowledge and the ongoing increase of losses from natural disasters worldwide is a well-identified gap in the UN Hyogo Framework for Action 2005-2015, in which one of the main priorities is the investment on "knowledge use, innovation and education to build a culture of safety and resilience". The KnowRISK is well aligned with these priorities and will contribute to participatory action aimed at: i) transferring expert knowledge on seismic risk and non-structural protective solutions into practical knowledge and ii) communication tools designed to engage communities in disaster risk reduction

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

PubMed Central

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

PubMed Central

Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

2012-01-01

Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

Rice root-associated bacteria – insights in community structures across ten cultivars

PubMed Central

Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

2015-01-01

In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing.

PubMed

Izuno, Ayako; Kanzaki, Mamoru; Artchawakom, Taksin; Wachrinrat, Chongrak; Isagi, Yuji

2016-01-01

Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%-92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone.

PubMed

Solon, Adam J; Vimercati, Lara; Darcy, J L; Arán, Pablo; Porazinska, Dorota; Dorador, C; Farías, M E; Schmidt, S K

2018-01-05

The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.

Sandy beaches: state of the art of nematode ecology.

PubMed

Maria, Tatiana F; Vanaverbeke, Jan; Vanreusel, Ann; Esteves, André M

2016-01-01

In this review, we summarize existing knowledge of the ecology of sandy-beach nematodes, in relation to spatial distribution, food webs, pollution and climate change. We attempt to discuss spatial scale patterns (macro-, meso- and microscale) according to their degree of importance in structuring sandy-beach nematode assemblages. This review will provide a substantial background on current knowledge of sandy-beach nematodes, and can be used as a starting point to delineate further investigations in this field. Over decades, sandy beaches have been the scene of studies focusing on community and population ecology, both related to morphodynamic models. The combination of physical factors (e.g. grain size, tidal exposure) and biological interactions (e.g. trophic relationships) is responsible for the spatial distribution of nematodes. In other words, the physical factors are more important in structuring nematodes communities over large scale of distribution while biological interactions are largely important in finer-scale distributions. It has been accepted that biological interactions are assumed to be of minor importance because physical factors overshadow the biological interactions in sandy beach sediments; however, the most recent results from in-situ and ex-situ experimental investigations on behavior and biological factors on a microscale have shown promise for understanding the mechanisms underlying larger-scale patterns and processes. Besides nematodes are very promising organisms used to understand the effects of pollution and climate changes although these subjects are less studied in sandy beaches than distribution patterns.

A Long-Term Study of the Microbial Community Structure in a Simulated Chloraminated Drinking Water Distribution System - abstract

EPA Science Inventory

Many US water treatment facilities use chloramination to limit regulated disinfectant by-product formation. However, chloramination has been shown to promote nitrifying bacteria, and 30 to 63% of water utilities using secondary chloramine disinfection experience nitrification ep...

ACETOGENIC AND SULPHATE-REDUCING BACTERIA INHABITING THE RHIZOPLANE AND DEEP CORTEX CELLS OF THE SEAGRASS HALODULE WRIGHTII

EPA Science Inventory

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizosphere that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacter...

The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp.

PubMed

Dai, Wenfang; Yu, Weina; Zhang, Jinjie; Zhu, Jinyong; Tao, Zhen; Xiong, Jinbo

2017-08-01

Increasing evidence has revealed a close interplay between the gut bacterial communities and host growth performance. However, until recently, studies generally ignored the contribution of eukaryotes, endobiotic organisms. To fill this gap, we used Illumina sequencing technology on eukaryotic 18S rRNA gene to compare the structures of gut eukaryotic communities among cohabitating retarded, overgrown, and normal shrimp obtained from identically managed ponds. Results showed that a significant difference between gut eukaryotic communities differed significantly between water and intestine and among three shrimp categories. Structural equation modeling revealed that changes in the gut eukaryotic community were positively related to digestive enzyme activities, which in turn influenced shrimp growth performance (λ = 0.97, P < 0.001). Overgrown shrimp exhibited a more complex and cooperative gut eukaryotic interspecies interaction than retarded and normal shrimp, which may facilitate their nutrient acquisition efficiency. Notably, the distribution of dominant eukaryotic genera and shifts in keystone species were closely concordant with shrimp growth performance. In summary, this study provides an integrated overview on direct roles of gut eukaryotic communities in shrimp growth performance instead of well-studied bacterial assembly.

Phylogenetic overdispersion of plant species in southern Brazilian savannas.

PubMed

Silva, I A; Batalha, M A

2009-08-01

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.

Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence.

PubMed

Schimann, Heidy; Bach, Cyrille; Lengelle, Juliette; Louisanna, Eliane; Barantal, Sandra; Murat, Claude; Buée, Marc

2017-02-01

The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

PubMed Central

Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-François; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-Christophe

2016-01-01

Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales. PMID:27594854

An Adaptive Complex Network Model for Brain Functional Networks

PubMed Central

Gomez Portillo, Ignacio J.; Gleiser, Pablo M.

2009-01-01

Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution. PMID:19738902

Liking and hyperlinking: Community detection in online child sexual exploitation networks.

PubMed

Westlake, Bryce G; Bouchard, Martin

2016-09-01

The online sexual exploitation of children is facilitated by websites that form virtual communities, via hyperlinks, to distribute images, videos, and other material. However, how these communities form, are structured, and evolve over time is unknown. Collected using a custom-designed webcrawler, we begin from known child sexual exploitation (CE) seed websites and follow hyperlinks to connected, related, websites. Using a repeated measure design we analyze 10 networks of 300 + websites each - over 4.8 million unique webpages in total, over a period of 60 weeks. Community detection techniques reveal that CE-related networks were dominated by two large communities hosting varied material -not necessarily matching the seed website. Community stability, over 60 weeks, varied across networks. Reciprocity in hyperlinking between community members was substantially higher than within the full network, however, websites were not more likely to connect to homogeneous-content websites. Copyright © 2016 Elsevier Inc. All rights reserved.

Altitude acts as an environmental filter on phylogenetic composition, traits and diversity in bee communities.

PubMed

Hoiss, Bernhard; Krauss, Jochen; Potts, Simon G; Roberts, Stuart; Steffan-Dewenter, Ingolf

2012-11-07

Knowledge about the phylogeny and ecology of communities along environmental gradients helps to disentangle the role of competition-driven processes and environmental filtering for community assembly. In this study, we evaluated patterns in species richness, phylogenetic structure and life-history traits of bee communities along altitudinal gradients in the Alps, Germany. We found a linear decline in species richness and abundance but increasing phylogenetic clustering in communities with increasing altitude. The proportion of social- and ground-nesting species, as well as mean body size and altitudinal range of bee communities, increased with increasing altitude, whereas the mean geographical distribution decreased. Our results suggest that community assembly at high altitudes is dominated by environmental filtering effects, whereas the relative importance of competition increases at low altitudes. We conclude that inherent phylogenetic and ecological species attributes at high altitudes pose a threat for less competitive alpine specialists with ongoing climate change.

Altitude acts as an environmental filter on phylogenetic composition, traits and diversity in bee communities

PubMed Central

Hoiss, Bernhard; Krauss, Jochen; Potts, Simon G.; Roberts, Stuart; Steffan-Dewenter, Ingolf

2012-01-01

Knowledge about the phylogeny and ecology of communities along environmental gradients helps to disentangle the role of competition-driven processes and environmental filtering for community assembly. In this study, we evaluated patterns in species richness, phylogenetic structure and life-history traits of bee communities along altitudinal gradients in the Alps, Germany. We found a linear decline in species richness and abundance but increasing phylogenetic clustering in communities with increasing altitude. The proportion of social- and ground-nesting species, as well as mean body size and altitudinal range of bee communities, increased with increasing altitude, whereas the mean geographical distribution decreased. Our results suggest that community assembly at high altitudes is dominated by environmental filtering effects, whereas the relative importance of competition increases at low altitudes. We conclude that inherent phylogenetic and ecological species attributes at high altitudes pose a threat for less competitive alpine specialists with ongoing climate change. PMID:22933374

Household Structure and Suburbia Residence in U.S. Metropolitan Areas: Evidence from the American Housing Survey.

PubMed

Jung, Gowoon; Yang, Tse-Chuan

2016-01-01

Suburbs have demographically diversified in terms of race, yet little research has been done on household structures in suburbs. Using the 2011 American Housing Survey and 2009-2013 American Community Survey, this study investigates the distributions of household structures in suburbia and central cities, and the relationship between household structures and residential attainment. The findings of this research include: (1) The distribution of household structures differs between suburbia and central cities. Married-couple households are the most common household type in both central cities and suburbs, but they are more likely to reside in suburbia than in central cities; (2) Household structure is a determinant of residential attainment and the relationship varies by race/ethnicity groups. Among Hispanics and Asians, multigenerational household structure is indicative of central city residence, but this association does not hold for whites and blacks. For multigenerational households, the odds of living in suburbia decreases by almost 40 percent among Hispanics and by almost 50 percent for Asians.

Household Structure and Suburbia Residence in U.S. Metropolitan Areas: Evidence from the American Housing Survey

PubMed Central

Jung, Gowoon; Yang, Tse-Chuan

2016-01-01

Suburbs have demographically diversified in terms of race, yet little research has been done on household structures in suburbs. Using the 2011 American Housing Survey and 2009–2013 American Community Survey, this study investigates the distributions of household structures in suburbia and central cities, and the relationship between household structures and residential attainment. The findings of this research include: (1) The distribution of household structures differs between suburbia and central cities. Married-couple households are the most common household type in both central cities and suburbs, but they are more likely to reside in suburbia than in central cities; (2) Household structure is a determinant of residential attainment and the relationship varies by race/ethnicity groups. Among Hispanics and Asians, multigenerational household structure is indicative of central city residence, but this association does not hold for whites and blacks. For multigenerational households, the odds of living in suburbia decreases by almost 40 percent among Hispanics and by almost 50 percent for Asians. PMID:27917300

How much does the time lag between wildlife field-data collection and LiDAR-data acquisition matter for studies of animal distributions? A case study using bird communities

Treesearch

Kerri T. Vierling; Charles E. Swift; Andrew T. Hudak; Jody C. Vogeler; Lee A. Vierling

2014-01-01

Vegetation structure quantified by light detection and ranging (LiDAR) can improve understanding of wildlife occupancy and species-richness patterns. However, there is often a time lag between the collection of LiDAR data and wildlife data. We investigated whether a time lag between the LiDAR acquisition and field-data acquisition affected mapped wildlife distributions...

Limiting similarity and functional diversity along environmental gradients

USGS Publications Warehouse

Schwilk, D.W.; Ackerly, D.D.

2005-01-01

Recent developments in community models emphasize the importance of incorporating stochastic processes (e.g. ecological drift) in models of niche-structured community assembly. We constructed a finite, spatially explicit, lottery model to simulate the distribution of species in a one-dimensional landscape with an underlying gradient in environmental conditions. Our framework combines the potential for ecological drift with environmentally-mediated competition for space in a heterogeneous environment. We examined the influence of niche breadth, dispersal distances, community size (total number of individuals) and the breadth of the environmental gradient on levels of species and functional trait diversity (i.e. differences in niche optima). Three novel results emerge from this model: (1) niche differences between adjacent species (e.g. limiting similarity) increase in smaller communities, because of the interaction of competitive effects and finite population sizes; (2) immigration from a regional species pool, stochasticity and niche-assembly generate a bimodal distribution of species residence times ('transient' and 'resident') under a heterogeneous environment; and (3) the magnitude of environmental heterogeneity has a U-shaped effect on diversity, because of shifts in species richness of resident vs. transient species. These predictions illustrate the potential importance of stochastic (although not necessarily neutral) processes in community assembly. ??2005 Blackwell Publishing Ltd/CNRS.

The effects of food web structure on ecosystem function exceeds those of precipitation.

PubMed

Trzcinski, M Kurtis; Srivastava, Diane S; Corbara, Bruno; Dézerald, Olivier; Leroy, Céline; Carrias, Jean-François; Dejean, Alain; Céréghino, Régis

2016-09-01

Ecosystems are being stressed by climate change, but few studies have tested food web responses to changes in precipitation patterns and the consequences to ecosystem function. Fewer still have considered whether results from one geographic region can be applied to other regions, given the degree of community change over large biogeographic gradients. We assembled, in one field site, three types of macroinvertebrate communities within water-filled bromeliads. Two represented food webs containing both a fast filter feeder-microbial and slow detritivore energy channels found in Costa Rica and Puerto Rico, and one represented the structurally simpler food webs in French Guiana, which only contained the fast filter feeder-microbial channel. We manipulated the amount and distribution of rain entering bromeliads and examined how food web structure mediated ecosystem responses to changes in the quantity and temporal distribution of precipitation. Food web structure affected the survival of functional groups in general and ecosystem functions such as decomposition and the production of fine particulate organic matter. Ecosystem processes were more affected by decreased precipitation than were the abundance of micro-organisms and metazoans. In our experiments, the sensitivity of the ecosystem to precipitation change was primarily revealed in the food web dominated by the single filter feeder-microbial channel because other top-down and bottom-up processes were weak or absent. Our results show stronger effects of food web structure than precipitation change per se on the functioning of bromeliad ecosystems. Consequently, we predict that ecosystem function in bromeliads throughout the Americas will be more sensitive to changes in the distribution of species, rather than to the direct effects caused by changes in precipitation. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Functional Process Zones Characterizing Aquatic Insect Communities in Streams of the Brazilian Cerrado.

PubMed

Godoy, B S; Simião-Ferreira, J; Lodi, S; Oliveira, L G

2016-04-01

Stream ecology studies see to understand ecological dynamics in lotic systems. The characterization of streams into Functional Process Zones (FPZ) has been currently debated in stream ecology because aquatic communities respond to functional processes of river segments. Therefore, we tested if different functional process zones have different number of genera and trophic structure using the aquatic insect community of Neotropical streams. We also assessed whether using physical and chemical variables may complement the approach of using FPZ to model communities of aquatic insects in Cerrado streams. This study was conducted in 101 streams or rivers from the central region of the state of Goiás, Brazil. We grouped the streams into six FPZ associated to size of the river system, presence of riparian forest, and riverbed heterogeneity. We used Bayesian models to compare number of genera and relative frequency of the feeding groups between FPZs. Streams classified in different FPZs had a different number of genera, and the largest and best preserved rivers had an average of four additional genera. Trophic structure exhibited low variability among FPZs, with little difference both in the number of genera and in abundance. Using functional process zones in Cerrado streams yielded good results for Ephemeroptera, Plecoptera, and Trichoptera communities. Thus, species distribution and community structure in the river basin account for functional processes and not necessarily for the position of the community along a longitudinal dimension of the lotic system.

Prey Distribution, Physical Habitat Features, and Guild Traits Interact to Produce Contrasting Shorebird Assemblages among Foraging Patches

PubMed Central

VanDusen, Beth M.; Fegley, Stephen R.; Peterson, Charles H.

2012-01-01

Worldwide declines in shorebird populations, driven largely by habitat loss and degradation, motivate environmental managers to preserve and restore the critical coastal habitats on which these birds depend. Effective habitat management requires an understanding of the factors that determine habitat use and value to shorebirds, extending from individuals to the entire community. While investigating the factors that influenced shorebird foraging distributions among neighboring intertidal sand flats, we built upon species-level understandings of individual-based, small-scale foraging decisions to develop more comprehensive guild- and community-level insights. We found that densities and community composition of foraging shorebirds varied substantially among elevations within some tidal flats and among five flats despite their proximity (all located within a 400-m stretch of natural, unmodified inlet shoreline). Non-dimensional multivariate analyses revealed that the changing composition of the shorebird community among flats and tidal elevations correlated significantly (ρs = 0.56) with the spatial structure of the benthic invertebrate prey community. Sediment grain-sizes affected shorebird community spatial patterns indirectly by influencing benthic macroinvertebrate community compositions. Furthermore, combining sediment and macroinvertebrate information produced a 27% increase in correlation (ρs = 0.71) with shorebird assemblage patterns over the correlation of the bird community with the macroinvertebrate community alone. Beyond its indirect effects acting through prey distributions, granulometry of the flats influenced shorebird foraging directly by modifying prey availability. Our study highlights the importance of habitat heterogeneity, showing that no single patch type was ideal for the entire shorebird community. Generally, shorebird density and diversity were greatest at lower elevations on flats when they became exposed; these areas are at risk from human intervention by inlet sand mining, construction of groins and jetties that divert sediments from flats, and installation of seawalls on inlet shorelines that induce erosion of flats. PMID:23285153

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities.

PubMed

Vitali, Francesco; Mastromei, Giorgio; Senatore, Giuliana; Caroppo, Cesarea; Casalone, Enrico

2016-01-01

In this study, we evaluate the long-lasting effects on soil microbial communities of a change within a single land-use category, specifically the conversion from natural forest to forest plantation. To minimize the effects of impacts other than land-use (i.e., climatic and anthropogenic), we chose three sites within a Natural Park, with homogeneous orographic and soil texture characteristics. We compared microbial diversity in a total of 156 soil samples from two natural mixed forests and a similar forest converted to poplar plantation about thirty years ago. The diversity and structure of bacterial and fungal communities were investigated by terminal restriction fragments length polymorphism (T-RFLP) analysis of the 16S-rRNA gene and the ITS-rDNA regions, respectively. Bacterial and fungal communities from the forest plantation, compared to those from natural forest soils, showed different community structure and lower α-diversity values, consistently with the significantly higher pH values and lower organic matter content of those soils. β-diversity values, the number of measured and estimated dominant OTUs, and their distribution among the three sites showed that microbial communities from the two natural forests were much more similar to each other than they were to communities from the poplar plantation, suggesting an effect of the forest conversion on the composition and diversity of soil microbial communities. α-diversity in cultivated forest soils had narrower temporal fluctuations than in natural forest soils, suggesting higher temporal stability of microbial communities. Overall, we demonstrated that the conversion from natural forest to forest plantation altered soil microbial communities, changing their structure, lowering their diversity, and causing a spatial and temporal homogenization. Copyright © 2015 Elsevier GmbH. All rights reserved.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments.

PubMed

Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren; Lu, Jingrang

2017-10-26

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L . pneumophila , Mycobacterium spp., P. aeruginosa , V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management within a distribution system.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments

PubMed Central

Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren

2017-01-01

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L. pneumophila, Mycobacterium spp., P. aeruginosa, V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management within a distribution system. PMID:29072631

A local immunization strategy for networks with overlapping community structure

NASA Astrophysics Data System (ADS)

Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

2017-02-01

Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

[Community structure of soil fauna in Eucalyptus grandis plantations at different slope locations].

PubMed

Zhao, Yu; Zhong, Yu; Zhang, Jian; Yang, Wan-qin

2010-09-01

To understand the effects of slope location on the community structure of soil fauna in Eucalyptus grandis plantation, an investigation was made on the soil fauna in 3 E. grandis plantations at different slope locations in the hilly area of Sichuan Province from January to October 2009. A total of 39,2762 individuals were observed, belonging to 146 groups, 7 phyla, 16 classes, and 31 orders. The community composition, trophic group, diversity, and seasonal dynamics of soil fauna in the plantations all varied with slope. The abundance of macro-fauna, xeric meso- and micro-fauna, saprophagous macro-fauna, and omnivorous xeric meso- and micro-fauna increased with the decrease of slope, indicating that soil fauna had sensitive responses to the soil environmental factors affected by slope. Significant differences in the diversity of soil saprophagous macro-fauna and hygrophilous meso- and micro-fauna were observed at different slope locations, suggesting that these two faunal groups could be used as the indicators of the habitat heterogeneity of E. grandis plantations at different slope. Overall, slope location had definite effects on the community structure and distribution of soil fauna in the E. grandis plantations, but the effects were not statistically significant.

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space▿

PubMed Central

Rudi, Knut; Zimonja, Monika; Kvenshagen, Bente; Rugtveit, Jarle; Midtvedt, Tore; Eggesbø, Merete

2007-01-01

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities. PMID:17337554

A secreted antibacterial neuropeptide shapes the microbiome of Hydra.

PubMed

Augustin, René; Schröder, Katja; Murillo Rincón, Andrea P; Fraune, Sebastian; Anton-Erxleben, Friederike; Herbst, Eva-Maria; Wittlieb, Jörg; Schwentner, Martin; Grötzinger, Joachim; Wassenaar, Trudy M; Bosch, Thomas C G

2017-09-26

Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood. Here, we show that sensory and ganglion neurons in the ectodermal epithelium of the model organism hydra (a member of the animal phylum Cnidaria) secrete neuropeptides with antibacterial activity that may shape the microbiome on the body surface. In particular, a specific neuropeptide, which we call NDA-1, contributes to the reduction of Gram-positive bacteria during early development and thus to a spatial distribution of the main colonizer, the Gram-negative Curvibacter sp., along the body axis. Our findings warrant further research to test whether neuropeptides secreted by nerve cells contribute to the spatial structure of microbial communities in other organisms.Certain neuropeptides, in addition to their neuromodulatory functions, display antibacterial activities of unclear significance. Here, the authors show that a secreted neuropeptide modulates the distribution of bacterial communities on the body surface during development of the model organism Hydra.

Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.

PubMed

Cheng, Weixiao; Chen, Hong; Yan, ShuHai; Su, Jianqiang

2014-09-01

Short-chain fatty acids (SCFAs) can be produced by primary and waste activated sludge anaerobic fermentation. The yield and product spectrum distribution of SCFAs can be significantly affected by different initial pH values. However, most studies have focused on the physical and chemical aspects of SCFA production by waste activated sludge fermentation at different pH values. Information on the bacterial community structures during acidogenic fermentation is limited. In this study, comparisons of the bacterial communities during the co-substrate fermentation of food wastes and sewage sludge at different pH values were performed using the barcoded Illumina paired-end sequencing method. The results showed that different pH environments harbored a characteristic bacterial community, including sequences related to Lactobacillus, Prevotella, Mitsuokella, Treponema, Clostridium, and Ureibacillus. The most abundant bacterial operational taxonomic units in the different pH environments were those related to carbohydrate-degrading bacteria, which are associated with constituents of co-substrate fermentation. Further analyses showed that during organic matter fermentation, a core microbiota composed of Firmicutes, Proteobacteria, and Bacteroidetes existed. Comparison analyses revealed that the bacterial community during fermentation was significantly affected by the pH, and that the diverse product distribution was related to the shift in bacterial communities.

Monitoring Change: SIPI Students Engage in Long-Term Ecological Research

ERIC Educational Resources Information Center

Porter, Margaret; Bennett, T. M. Bull

2013-01-01

American Indian tribes across the nation are facing pressing ecological challenges related to alterations in species distribution, access and availability of water, shifting community structures, and other phenomena correlated to climate change. At the Southwestern Indian Polytechnic Institute (SIPI, Albuquerque, NM), faculty and staff believe the…

RESEARCH OPPORTUNITIES AND CHALLENGES REGARDING IMPROVEMENT OF STRUCTURAL INTEGRITY MONITORING FOR DRINKING WATER MAINS

EPA Science Inventory

The United States’ water and wastewater infrastructure is large (i.e., 16,000 publicly owned treatment works, 59,000 community water supplies, 600,000 miles of sewer, 1,000,000 miles of drinking water distribution piping), complex and expensive. The reliable and efficient functio...

Distributions of ectomycorrhizal and foliar endophytic fungal communities associated with Pinus ponderosa along a spatially constrained elevation gradient.

PubMed

Bowman, Elizabeth A; Arnold, A Elizabeth

2018-04-01

Understanding distributions of plant-symbiotic fungi is important for projecting responses to environmental change. Many coniferous trees host ectomycorrhizal fungi (EM) in association with roots and foliar endophytic fungi (FE) in leaves. We examined how EM and FE associated with Pinus ponderosa each vary in abundance, diversity, and community structure over a spatially constrained elevation gradient that traverses four plant communities, 4°C in mean annual temperature, and 15 cm in mean annual precipitation. We sampled 63 individuals of Pinus ponderosa in 10 sites along a 635 m elevation gradient that encompassed a geographic distance of 9.8 km. We used standard methods to characterize each fungal group (amplified and sequenced EM from root tips; isolated and sequenced FE from leaves). Abundance and diversity of EM were similar across sites, but community composition and distributions of the most common EM differed with elevation (i.e., with climate, soil chemistry, and plant communities). Abundance and composition of FE did not differ with elevation, but diversity peaked in mid-to-high elevations. Our results suggest relatively tight linkages between EM and climate, soil chemistry, and plant communities. That FE appear less linked with these factors may speak to limitations of a culture-based approach, but more likely reflects the small spatial scale encompassed by our study. Future work should consider comparable methods for characterizing these functional groups, and additional transects to understand relationships of EM and FE to environmental factors that are likely to shift as a function of climate change. © 2018 Botanical Society of America.

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Biotic variation in coastal water bodies in Sussex, England: Implications for saline lagoons

NASA Astrophysics Data System (ADS)

Joyce, Chris B.; Vina-Herbon, Cristina; Metcalfe, Daniel J.

2005-12-01

Coastal water bodies are a heterogeneous resource typified by high spatial and temporal variability and threatened by anthropogenic impacts. This includes saline lagoons, which support a specialist biota and are a priority habitat for nature conservation. This paper describes the biotic variation in coastal water bodies in Sussex, England, in order to characterise the distinctiveness of the saline lagoon community and elucidate environmental factors that determine its distribution. Twenty-eight coastal water bodies were surveyed for their aquatic flora and invertebrate fauna and a suite of exploratory environmental variables compiled. Ordination and cluster analyses were used to examine patterns in community composition and relate these to environmental parameters. Biotic variation in the coastal water body resource was high. Salinity was the main environmental parameter explaining the regional distribution of taxa; freshwater and saline assemblages were evident and related to sea water ingress. Freshwater sites were indicated by the plant Myriophyllum spicatum and gastropod mollusc Lymnaea peregra, while more saline communities supported marine and brackish water taxa, notably a range of chlorophytic algae and the bivalve mollusc Cerastoderma glaucum. Site community differences were also related to bank slope and parameters describing habitat heterogeneity. A saline lagoon community was discerned within the matrix of biotic variation consisting of specialist lagoonal species with associated typically euryhaline taxa. For fauna, the latter were the molluscs Abra tenuis and Hydrobia ulvae, and the crustaceans Corophium volutator and Palaemonetes varians, and for flora they were the algae Ulva lactuca, Chaetomorpha mediterranea, Cladophora spp. and Enteromorpha intestinalis. One non-native polychaete species, Ficopomatus enigmaticus, also strongly influenced community structure within the lagoonal resource. The community was not well defined as specialist and associated taxa were distributed throughout the spectrum of sites surveyed. Implications for the identification and conservation of saline lagoons are discussed.

Persistence and stability of fish community structure in a southwest New York stream

USGS Publications Warehouse

Hansen, Michael J.; Ramm, Carl W.

1994-01-01

We used multivariate and nonparametric statistics to examine persistence and stability of fish species in the upper 43 km of French Creek, New York. Species occurred in upstream and downstream groups in 1937 that persisted in 1979. However, the downstream group expanded its range in the drainage from 1937 to 1979 at the expense of the upstream group. A dam prevented further upstream expansion of the downstream group. Ranks of species abundances were stable, as tests of group similarity were significant. The abundances and distributions of benthic species were stable across seven sampling dates in 1980 despite several floods and repeated removals by sampling that could have altered community structure. We conclude that the fish community in French Creek persisted and was stable over the 42-yr interval, 1937-1979, and that abundances of benthic species were stable in summer 1980.

[Community structure and seasonal change of soil micro-arthropodes in the Lower Reaches of Liaohe River Plain under different land utilization].

PubMed

Ke, Xin; Liang, Wenju; Yu, Wantai; Xie, Rongdong; Weng, Chaolian; Yang, Yiming; Yin, Wenying

2004-04-01

The data on the soil micro-arthropodes under four land utilization types (fallow, forest, upland field and paddy) in the Lower Reaches of Liaohe River Plain were collected in a period from October 2000 to October 2001. Using the community parameters of population density, group richness, diversity index and evenness, the community structure and its seasonal changes were described. There were 12 groups of soil micro-arthropodes in this region, and of the groups, Collembola and Acarina were dominant, and Diptera, Coleoptera and Hymenoptera were often seen in fallow, forest and upland field, while Collembola, Acarina and Diptera were dominant in paddy. Both land utilization and seasonal change influenced the population density, group richness and diversity index of soil micro-arthropodes. The vertical distribution in both density and group number of arthropods in soil was in the order of surface > middle > bottom.

A nonuniform popularity-similarity optimization (nPSO) model to efficiently generate realistic complex networks with communities

NASA Astrophysics Data System (ADS)

Muscoloni, Alessandro; Vittorio Cannistraci, Carlo

2018-05-01

The investigation of the hidden metric space behind complex network topologies is a fervid topic in current network science and the hyperbolic space is one of the most studied, because it seems associated to the structural organization of many real complex systems. The popularity-similarity-optimization (PSO) model simulates how random geometric graphs grow in the hyperbolic space, generating realistic networks with clustering, small-worldness, scale-freeness and rich-clubness. However, it misses to reproduce an important feature of real complex networks, which is the community organization. The geometrical-preferential-attachment (GPA) model was recently developed in order to confer to the PSO also a soft community structure, which is obtained by forcing different angular regions of the hyperbolic disk to have a variable level of attractiveness. However, the number and size of the communities cannot be explicitly controlled in the GPA, which is a clear limitation for real applications. Here, we introduce the nonuniform PSO (nPSO) model. Differently from GPA, the nPSO generates synthetic networks in the hyperbolic space where heterogeneous angular node attractiveness is forced by sampling the angular coordinates from a tailored nonuniform probability distribution (for instance a mixture of Gaussians). The nPSO differs from GPA in other three aspects: it allows one to explicitly fix the number and size of communities; it allows one to tune their mixing property by means of the network temperature; it is efficient to generate networks with high clustering. Several tests on the detectability of the community structure in nPSO synthetic networks and wide investigations on their structural properties confirm that the nPSO is a valid and efficient model to generate realistic complex networks with communities.

Fishing degrades size structure of coral reef fish communities.

PubMed

Robinson, James P W; Williams, Ivor D; Edwards, Andrew M; McPherson, Jana; Yeager, Lauren; Vigliola, Laurent; Brainard, Russell E; Baum, Julia K

2017-03-01

Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size-structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra and biomass of coral reef fish communities at 38 US-affiliated Pacific islands that ranged in human presence from near pristine to human population centers. Size spectra 'steepened' steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. Reef fish biomass was substantially lower on inhabited islands than uninhabited ones, even at inhabited islands with the lowest levels of human presence. We found that on populated islands size spectra exponents decreased (analogous to size spectra steepening) linearly with declining biomass, whereas on uninhabited islands there was no relationship. Size spectra were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to oceanographic conditions, being influenced by both oceanic productivity and sea surface temperature. Our results suggest that community size structure may be a more robust indicator than fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size-based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems. © 2016 John Wiley & Sons Ltd.

Is there a seamount effect on microbial community structure and biomass? The case study of Seine and Sedlo seamounts (northeast Atlantic).

PubMed

Mendonça, Ana; Arístegui, Javier; Vilas, Juan Carlos; Montero, Maria Fernanda; Ojeda, Alicia; Espino, Minerva; Martins, Ana

2012-01-01

Seamounts are considered to be "hotspots" of marine life but, their role in oceans primary productivity is still under discussion. We have studied the microbial community structure and biomass of the epipelagic zone (0-150 m) at two northeast Atlantic seamounts (Seine and Sedlo) and compared those with the surrounding ocean. Results from two cruises to Sedlo and three to Seine are presented. Main results show large temporal and spatial microbial community variability on both seamounts. Both Seine and Sedlo heterotrophic community (abundance and biomass) dominate during winter and summer months, representing 75% (Sedlo, July) to 86% (Seine, November) of the total plankton biomass. In Seine, during springtime the contribution to total plankton biomass is similar (47% autotrophic and 53% heterotrophic). Both seamounts present an autotrophic community structure dominated by small cells (nano and picophytoplankton). It is also during spring that a relatively important contribution (26%) of large cells to total autotrophic biomass is found. In some cases, a "seamount effect" is observed on Seine and Sedlo microbial community structure and biomass. In Seine this is only observed during spring through enhancement of large autotrophic cells at the summit and seamount stations. In Sedlo, and despite the observed low biomasses, some clear peaks of picoplankton at the summit or at stations within the seamount area are also observed during summer. Our results suggest that the dominance of heterotrophs is presumably related to the trapping effect of organic matter by seamounts. Nevertheless, the complex circulation around both seamounts with the presence of different sources of mesoscale variability (e.g. presence of meddies, intrusion of African upwelling water) may have contributed to the different patterns of distribution, abundances and also changes observed in the microbial community.

Drug-related offenses and the structure of communities in rural Australia.

PubMed

Donnermeyer, Joseph F; Barclay, Elaine M; Jobes, Patrick C

2002-01-01

This article examines the relationship of drug use with the social and economic characteristics of rural communities in New South Wales (NSW), Australia. Data is derived from the 1996 Australian Census of Population and Housing, and data on drug-related offenses from the NSW police between 1995 and 1999. Arrest rates for breaking and entering, assault, and vandalism showed statistically significant associations across types of rural communities, but drug-related arrests varied considerably less. The widespread, relatively-even distribution of drug arrests in rural NSW suggests that the underlying causes of drug-related violations are unique when compared to other types of crime.

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers.

PubMed

Li, Huan; Li, Shang; Tang, Wei; Yang, Yang; Zhao, Jianfu; Xia, Siqing; Zhang, Weixian; Wang, Hong

2018-06-01

Secondary water supply systems (SWSSs) refer to the in-building infrastructures (e.g., water storage tanks) used to supply water pressure beyond the main distribution systems. The purpose of this study was to investigate the influence of SWSSs on microbial community structure and the occurrence of opportunistic pathogens, the latter of which are an emerging public health concern. Higher numbers of bacterial 16S rRNA genes, Legionella and mycobacterial gene markers were found in public building taps served by SWSSs relative to the mains, regardless of the flushing practice (P < 0.05). In residential buildings, genes of L. pneumomhila, Acanthamoeba and Vermamoeba vermiformis were primarily detected in tanks and taps compared to the mains. Long water retention time, warm temperature and loss of disinfectant residuals promoted microbial growth and colonization of potential pathogens in SWSSs. Varied levels of microbial community shifts were found in different types of SWSSs during water transportation from the distribution main to taps, highlighting the critical role of SWSSs in shaping the drinking water microbiota. Overall, the results provided insight to factors that might aid in controlling pathogen proliferation in real-world water systems using SWSSs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physical-biological coupling in the Amundsen Sea, Antarctica: Influence of physical factors on phytoplankton community structure and biomass

NASA Astrophysics Data System (ADS)

Lee, Youngju; Yang, Eun Jin; Park, Jisoo; Jung, Jinyoung; Kim, Tae Wan; Lee, SangHoon

2016-11-01

To understand the spatial distribution of phytoplankton communities in various habitats in the Amundsen Sea, western Antarctica, a field survey was conducted at 15 stations during the austral summer, from December 2013 to January 2014. Water samples were analyzed by microscopy. We found high phytoplankton abundance and biomass in the Amundsen Sea polynya (ASP). Their strong positive correlation with water temperature suggests that phytoplankton biomass accumulated in the surface layer of the stratified polynya. In the ASP, the predominant phytoplankton species was Phaeocystis antarctica, while diatoms formed a major group in the sea ice zone, especially Fragilariopsis spp., Chaetoceros spp., and Proboscia spp. Although this large diatom abundance sharply decreased just off the marginal sea ice zone, weakly silicified diatoms, due to their high buoyancy, were distributed at almost all stations on the continental shelf. Dictyocha speculum appeared to favor the area between the marginal sea ice zone and the ASP in contrast to cryptophytes and picophytoplankton, whose abundance was higher in the area between the continental shelf and the open ocean of Amundsen Sea. Several environmental factors were found to affect the spatial variation of phytoplankton species, but the community structure appeared to be controlled mainly by the seawater density related to sea-ice melting and water circulation in the Amundsen Sea.

Differences in composition of shallow-water marine benthic communities associated with two ophiolitic rock substrata

NASA Astrophysics Data System (ADS)

Bavestrello, Giorgio; Bo, Marzia; Betti, Federico; Canessa, Martina; Gaggero, Laura; Rindi, Fabio; Cattaneo-Vietti, Riccardo

2018-01-01

On marine rocky shores, several physical, chemical and biological processes operate to maintain the benthic assemblages' heterogeneity, but among the abiotic factors, the composition and texture of the rocky substrata have been only sporadically considered. However, biomineralogical studies have demonstrated an unsuspected ability of the benthic organisms to interact at different levels with rocky substrata. Therefore, the mineralogy of the substratum can affect the structure of benthic communities. To evaluate this hypothesis, the macrobenthic assemblages developed on two different ophiolitic rocks (serpentinites and metagabbros) in contact at a restricted stretch of the western Ligurian Riviera (western Mediterranean Sea), with identical environmental and climatic conditions, were analysed. Samplings were carried out at four bathymetric levels (+1m, 0m, -1m, and -3m respect to the mean sea level) and the analysis of the data evidenced differences in terms of species distribution and percent coverage. Algal communities growing on metagabbros were poorer in species richness and showed a much simpler structure when compared to the assemblages occurring on the serpentinites. The most widely distributed animal organism, the barnacle Chthamalus stellatus, was dominant on serpentinites, and virtually absent on metagabbros. Our results suggest a complex pattern of interactions between lithology and benthic organisms operating through processes of inhibition/facilitation related to the mineral properties of the substratum.

A Long-Term Study of the Microbial Community Structure in a ...

EPA Pesticide Factsheets

Free chlorine is used as the primary disinfectant in most drinking water distribution systems(DWDS). However, chlorine disinfection promotes the formation of disinfectant by-products (DBPs)and as a result, many US water treatment facilities use chloramination to ensure regulatory compliance of targeted DBPs. However, 30 to 63% of water utilities using secondary chloramine disinfection experience nitrification episodes that detrimentally impact water quality in theirdistribution systems. While each disinfection strategy aims at mitigating the presence of pathogens, they do not completely eradicate growth of microorganisms in distribution systems. The latter has been documented using a variety of culture-based assays and culture independent approaches, such as 16S rRNA gene sequence analysis using Sanger chemistry. Most of the previous approaches are limited in scope. High-throughput sequencing approaches offer a more comprehensive view of the genetic complexity of natural and engineered environments, allowing usto better assess the microbial taxonomic diversity and metabolic potential within any given community. These approaches enhanced our understanding of processes unique to some microbiomes and provided the genetic information to track multiple populations carrying a variety of functions. In this study, we examined the microbiome of a simulated chloraminated DWDS. These results provide evidence of variations in the DWDS microbial community structure and their

Community-directed treatment with ivermectin in two Nigerian communities: an analysis of first year start-up processes, costs and consequences.

PubMed

Onwujekwe, Obinna; Chima, Reginald; Shu, Elvis; Okonkwo, Paul

2002-10-01

To determine the start-up processes, costs and consequences of community-directed treatment with ivermectin (CDTI) in two onchocerciasis endemic rural towns of Southeast Nigeria; namely Achi and Nike. The other objectives were to discover the community-financing mechanisms, local ivermectin distribution strategies and communities' organisational capacity to handle the programme. Structured questionnaires, informal interviews, observations, discussions with community members at general village assemblies and community outreach lectures were used at different stages of the study. The towns had the organisational capacity to implement the programme. Coverage with ivermectin was between 31-73% in Achi (mean = 58.6%), and 36.6-72% in Nike (mean = 61.95%). The unit financial costs were $0.17 in Nike and $0.13 in Achi, but the unit aggregate cost was $0.37 in Nike and $0.39 in Achi. When research costs were removed, the unit aggregate cost was $0.22 in Achi and $0.20 in Nike. Provider's financial costs and communities' non-financial costs were the biggest contributors to the aggregate cost. The cost would decrease in subsequent years since the research cost and parts of the mobilisation and training costs would not be incurred after the first year. Governments and sponsors of CDTI should find means of continuously strengthening the programme and providing technical support to the communities. As both CDTI and communities are dynamic entities, continuous health education campaigns are needed to keep reminding the people of the benefit of long-term ivermectin distribution, together with the need for community ownership of the programme.

[Spatio-temporal distribution of carabids and spiders between semi-natural field margin and the adjacent crop fields in agricultural landscape].

PubMed

Zhang, Xu Zhu; Han, Yin; Yu, Zhen Rong; Liu, Yun Hui

2017-06-18

This study was conducted before and after harvesting of wheat and maize in a typical agricultural landscape of the North China Plain. We investigated the diversity of two important natural enemy groups, carabids and spiders, using pitfall traps at crop field margin with different vegetation structures and their neighboring crop field. Throughout the comparison of the spatial and temporal distribution of the diversity of carabids and spiders in field margin and neighboring field, and the investigation of the relationship between arthropod communities and vegetation structure, this study aimed to understand the role of semi-natural field margin in biodiversity conservation of different natural enemy taxa. Results showed that the abundance of spiders was significantly higher in field margin than in neighboring fields over the entire period. No significant difference of the diversity of carabids in field margin and crop field was observed, but the community composition was different. Number of spider families increased in field margin but deceased in crop field after harvesting, indicating a migration activity between field and field margin. Vegetation structure in the field margin had different association with carabids than with spiders, with diversity of dominant carabid species positively associated with herb coverage and negatively with wood coverage, while the diversity of spider family Linyphiidae was positively associated with herb coverage only. Semi-natural habitat benefited the conservation of the diversity of arthropod natural enemies in crop field via promoting their dispersal to crop field, while such impacts differed from different vegetation structures and varied from target beneficial natural enemy communities. Future studies should focus on in-depth understanding of the food and habitat source requirement of different natural enemy taxa, and hence to design suitable semi-natural habitats to maintain a high diversity of natural enemy communities.

Continental-scale distributions of dust-associated bacteria and fungi

PubMed Central

Barberán, Albert; Ladau, Joshua; Pollard, Katherine S.; Menninger, Holly L.; Dunn, Robert R.; Fierer, Noah

2015-01-01

It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans. PMID:25902536

The Rhode Island Medical Emergency Distribution System (MEDS).

PubMed

Banner, Greg

2004-01-01

The State of Rhode Island conducted an exercise to obtain and dispense a large volume of emergency medical supplies in response to a mass casualty incident. The exercise was conducted in stages that included requesting supplies from the Strategic National Stockpile and distributing the supplies around the state. The lessons learned included how to better structure an exercise, what types of problems were encountered with requesting and distributing supplies, how to better work with members of the private medical community who are not involved in disaster planning, and how to become aware of the needs of special population groups.

Is the nestedness of metazoan parasite assemblages of marine fishes from the southeastern Pacific coast a pattern associated with the geographical distributional range of the host?

PubMed

González, M T; Oliva, M E

2009-04-01

Nested structure is a pattern originally described in island biogeography to characterize how a set of species is distributed among a set of islands. In parasite communities, nestedness has been intensively studied among individual fish from a locality. However, nested patterns among parasite assemblages from different host populations (localities) have scarcely been investigated. We recorded the occurrence of parasites in 9 fish species widely distributed along the southeastern Pacific coast to determine whether the ecto- and endoparasite assemblages of marine fishes show a nested structure associated with host distributional range. Nestedness was tested using Brualdi-Sanderson index of discrepancy (BR); and 5 null models incorporated in a 'Nestedness' programme (Ulrich, 2006). The ecto- and endoparasite richness do not show similar patterns of latitudinal gradients among fish hosts, with 33-66% of analysed ectoparasite assemblages, and 25-75% of endoparasite assemblages showing nested structures through the host distributional range. For ectoparasites, species richness gradients and nested structure (when present) might be associated with decreased host densities or could reflect negative environmental conditions in the distributional border of the host species, whereas for endoparasites might be caused by geographical breaks of prey or changes in prey availability (intermediate hosts). The sampled extension of the distributional range of the host species, as well as the lack of specificity of some parasites, could influence the detection of nestedness.

Placement, support, and retention of health professionals: national, cross-sectional findings from medical and dental community service officers in South Africa.

PubMed

Hatcher, Abigail M; Onah, Michael; Kornik, Saul; Peacocke, Julia; Reid, Stephen

2014-02-26

In South Africa, community service following medical training serves as a mechanism for equitable distribution of health professionals and their professional development. Community service officers are required to contribute a year towards serving in a public health facility while receiving supervision and remuneration. Although the South African community service programme has been in effect since 1998, little is known about how placement and practical support occur, or how community service may impact future retention of health professionals. National, cross-sectional data were collected from community service officers who served during 2009 using a structured self-report questionnaire. A Supervision Satisfaction Scale (SSS) was created by summing scores of five questions rated on a three-point Likert scale (orientation, clinical advising, ongoing mentorship, accessibility of clinic leadership, and handling of community service officers' concerns). Research endpoints were guided by community service programmatic goals and analysed as dichotomous outcomes. Bivariate and multivariate logistical regressions were conducted using Stata 12. The sample population comprised 685 doctors and dentists (response rate 44%). Rural placement was more likely among unmarried, male, and black practitioners. Rates of self-reported professional development were high (470 out of 539 responses; 87%). Participants with higher scores on the SSS were more likely to report professional development. Although few participants planned to continue work in rural, underserved communities (n = 171 out of 657 responses, 25%), those serving in a rural facility during the community service year had higher intentions of continuing rural work. Those reporting professional development during the community service year were twice as likely to report intentions to remain in rural, underserved communities. Despite challenges in equitable distribution of practitioners, participant satisfaction with the compulsory community service programme appears to be high among those who responded to a 2009 questionnaire. These data offer a starting point for designing programmes and policies that better meet the health needs of the South African population through more appropriate human resource management. An emphasis on professional development and supervision is crucial if South Africa is to build practitioner skills, equitably distribute health professionals, and retain the medical workforce in rural, underserved areas.

Joint effects of social class and community occupational structure on coronary mortality among black men and white men, upstate New York, 1988–92

PubMed Central

Armstrong, D; Strogatz, D; Barnett, E; Wang, R

2003-01-01

Study objective: Occupational structure represents the unequal geographical distribution of more desirable jobs among communities (for example, white collar jobs). This study examines joint effects of social class, race, and county occupational structure on coronary mortality rates for men, ages 35–64 years, 1988–92, in upstate New York. Design: Upstate New York's 57 counties were classified into three occupational structure categories; counties with the lowest percentages of the labour force in managerial, professional, and technical occupations were classified in category I, counties with the highest percentages were in category III. Age adjusted coronary heart disease (CHD) mortality rates, 35–64 years, (from vital statistics and census data) were calculated for each occupational structure category. Main results: An inverse association between CHD mortality and occupational structure was observed among blue collar and white collar workers, among black men and white men, with the lowest CHD mortality observed among white collar, white men in category III (135/100 000). About two times higher mortality was observed among blue collar than white collar workers. Among blue collar workers, mortality was 1.3–1.8 times higher among black compared with white workers, and the highest rates were observed among black, blue collar workers (689/100 000). Also, high residential race segregation was shown in all areas. Conclusions: Results suggest the importance of community conditions in coronary health of local populations; however, differential impact on subpopulations was shown. Blue collar and black workers may especially lack economic and other resources to use available community services and/or may experience worse working and living conditions compared with white collar and white workers in the same communities. PMID:12700223

A Tailored Approach to Launch Community Coalitions Focused on Achieving Structural Changes: Lessons Learned from a HIV Prevention Mobilization Study

PubMed Central

Chutuape, Kate S.; Willard, Nancy; Walker, Bendu C.; Boyer, Cherrie B.; Ellen, Jonathan

2014-01-01

Public health HIV prevention efforts have begun to focus on addressing social and structural factors contributing to HIV risk, such as unstable housing, unemployment and access to healthcare. With a limited body of evidence-based structural interventions for HIV, communities tasked with developing structural changes need a defined process to clarify their purpose and goals. This paper describes the adaptations made to a coalition development model with the purpose of improving the start-up phase for a second group of coalitions. Modifications focused on preparing coalitions to more efficiently apply structural change concepts to their strategic planning activities, create more objectives that met study goals, and enhance coalition procedures, such as building distributed coalition leadership, to better support the mobilization process. We report on primary modifications to the process, findings for the coalitions and recommendations for public health practitioners that are seeking to start a similar coalition. PMID:26785397

Reconfiguration of Cortical Networks in MDD Uncovered by Multiscale Community Detection with fMRI.

PubMed

He, Ye; Lim, Sol; Fortunato, Santo; Sporns, Olaf; Zhang, Lei; Qiu, Jiang; Xie, Peng; Zuo, Xi-Nian

2018-04-01

Major depressive disorder (MDD) is known to be associated with altered interactions between distributed brain regions. How these regional changes relate to the reorganization of cortical functional systems, and their modulation by antidepressant medication, is relatively unexplored. To identify changes in the community structure of cortical functional networks in MDD, we performed a multiscale community detection algorithm on resting-state functional connectivity networks of unmedicated MDD (uMDD) patients (n = 46), medicated MDD (mMDD) patients (n = 38), and healthy controls (n = 50), which yielded a spectrum of multiscale community partitions. we selected an optimal resolution level by identifying the most stable community partition for each group. uMDD and mMDD groups exhibited a similar reconfiguration of the community structure of the visual association and the default mode systems but showed different reconfiguration profiles in the frontoparietal control (FPC) subsystems. Furthermore, the central system (somatomotor/salience) and 3 frontoparietal subsystems showed strengthened connectivity with other communities in uMDD but, with the exception of 1 frontoparietal subsystem, returned to control levels in mMDD. These findings provide evidence for reconfiguration of specific cortical functional systems associated with MDD, as well as potential effects of medication in restoring disease-related network alterations, especially those of the FPC system.

Influence of oyster culture on biogeochemistry and bacterial community structure at the sediment-water interface.

PubMed

Azandégbé, Afi; Poly, Franck; Andrieux-Loyer, Françoise; Kérouel, Roger; Philippon, Xavier; Nicolas, Jean-Louis

2012-10-01

Bacterial community structure and some biogeochemical parameters were studied in the sediment of two Pacific oyster farming sites, Aber Benoît (AB) and Rivière d'Auray (RA) in Brittany (France), to examine the ecological impact of oysters and to evaluate the emission of sulfide and ammonia from sediment. At AB, the organic matter accumulated in the sediment beneath the oyster tables was rapidly mineralized, with strong fluxes of ammonia and sulfide that reached 1014 and 215 μmol m(-2) h(-1), respectively, in June 2007. At RA, the fluxes were about half as strong on average and better distributed through the year. The ammonia and sulfide concentrations in the overlying water never reached levels that would be toxic to oysters in either site, nor did hypoxia occur. Total culturable bacteria (TCB) varied greatly according to the temperature: from 1.6 × 10(4) to 9.4 × 10(7) cell g(-1) sediment. Inversely, the bacterial community structure remained surprising stable through the seasons, marginally influenced by the presence of oysters and by temperature. Bacterial communities appeared to be characteristic of the sites, with only one common phylotype, Vibrio aestuarianus, a potential oyster pathogen. These data refine the hypothesis of seawater toxicity to oysters because of ammonia and sulfide fluxes and show that the measured environmental factors had only a weak influence on bacterial community structure. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Patterns of rare and abundant marine microbial eukaryotes.

PubMed

Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angélique; Kooistra, Wiebe H C F; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sébastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A; de Vargas, Colomban; Massana, Ramon

2014-04-14

Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Scale-Free Distribution of Avian Influenza Outbreaks

NASA Astrophysics Data System (ADS)

Small, Michael; Walker, David M.; Tse, Chi Kong

2007-11-01

Using global case data for the period from 25 November 2003 to 10 March 2007, we construct a network of plausible transmission pathways for the spread of avian influenza among domestic and wild birds. The network structure we obtain is complex and exhibits scale-free (although not necessarily small-world) properties. Communities within this network are connected with a distribution of links with infinite variance. Hence, the disease transmission model does not exhibit a threshold and so the infection will continue to propagate even with very low transmissibility. Consequentially, eradication with methods applicable to locally homogeneous populations is not possible. Any control measure needs to focus explicitly on the hubs within this network structure.

Interactions between soil texture, water, and nutrients control patterns of biocrusts abundance and structure

NASA Astrophysics Data System (ADS)

Young, Kristina; Bowker, Matthew; Reed, Sasha; Howell, Armin

2017-04-01

Heterogeneity in the abiotic environment structures biotic communities by controlling niche space and parameters. This has been widely observed and demonstrated in vascular plant and other aboveground communities. While soil organisms are presumably also strongly influenced by the physical and chemical dimensions of the edaphic environment, there are fewer studies linking the development, structure, productivity or function of surface soil communities to specific edaphic gradients. Here, we use biological soil crusts (biocrusts) as a model system to determine mechanisms regulating community structure of soil organisms. We chose soil texture to serve as an edaphic gradient because of soil texture's influence over biocrust distribution on a landscape level. We experimentally manipulated texture in constructed soil, and simultaneously manipulated two main outcomes of texture, water and nutrient availability, to determine the mechanism underlying texture's influence on biocrust abundance and structure. We grew biocrust communities from a field-sourced inoculum on four different soil textures, sieved from the same parent soil material, manipulating watering levels and nutrient additions across soil textures in a full-factorial design over a 5-month period of time. We measured abundance and structure of biocrusts over time, and measured two metrics of function, N2 fixation rates and soil stabilization, at the conclusion of the experiment. Our results showed finer soil textures resulted in faster biocrust community development and dominance by mosses, whereas coarser textures grew more slowly and had biocrust communities dominated by cyanobacteria and lichen. Additionally, coarser textured soils contained cyanobacterial filaments significantly deeper into the soil profile than fine textured soils. N2-fixation values increased with increasing moss cover and decreased with increasing cyanobacterial cover, however, the rate of change depended on soil texture and water amount. Soil shear resistance was highest on finer textured soil with the highest watering treatment, whereas compression resistance was highest on the coarsest textured soils with the highest watering amounts. Nutrient addition did not influence total cover or biocrust function, but did decrease lichen cover. Taken together, these results suggest that interactions between soil texture, water, and to a lesser degree nutrients, create predictable patterns in biocrust assemblage and offers a mechanistic understanding of edaphic controls over biocrust abundance and structure. These insights add to our increasing understanding of how edaphic gradients structure soil communities.

Referee Networks and Their Spectral Properties

NASA Astrophysics Data System (ADS)

Slanina, F.; Zhang, Y.-Ch.

2005-09-01

The bipartite graph connecting products and reviewers of that product is studied empirically in the case of amazon.com. We find that the network has power-law degree distribution on the side of reviewers, while on the side of products the distribution is better fitted by stretched exponential. The spectrum of normalised adjacency matrix shows power-law tail in the density of states. Establishing the community structures by finding localised eigenstates is not straightforward as the localised and delocalised states are mixed throughout the whole support of the spectrum.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

PubMed Central

Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2015-01-01

Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships) according to phyla. Altogether, this study provided valuable clues about the ecological behavior of soil bacterial and archaeal taxa at an agricultural landscape scale and could be useful for developing sustainable strategies of land management. PMID:25922908

An Advanced Professional Pharmacy Experience in a Community Setting Using an Experiential Manual

PubMed Central

Lee, Karen W.; Machado, Matthew R.; Wenzel, Marie M.; Gagnon, James M.; Calomo, Joseph M.

2006-01-01

Objectives To determine the usefulness of a teaching and learning tool used to create structure for advanced pharmacy practice experiences (APPEs) in community pharmacy settings, and to identify differences between respondents' perspectives on the relevance and practicality of implementing specific community pharmacy-related topics during the experience. Design Community practice faculty members designed a manual that outlined a week-by-week schedule of student activities, consistent with the Center for the Advancement of Pharmaceutical Education (CAPE) outcome-based goals, and included associated teaching, documentation, and assessment tools. The manual was distributed to site preceptors and students. Assessment Eighty-six PharmD students responded to a questionnaire upon completion of their community APPE. Student feedback concerning the impact of the manual relative to interactions with site preceptors and their overall learning experience was relatively positive. Conclusion The manual was an effective teaching and learning tool for students completing a community APPE. PMID:17149421

Meso-zooplankton abundance and spatial distribution off Lützow-Holm Bay during austral summer 2007-2008

NASA Astrophysics Data System (ADS)

Makabe, Ryosuke; Tanimura, Atsushi; Tamura, Takeshi; Hirano, Daisuke; Shimada, Keishi; Hashihama, Fuminori; Fukuchi, Mitsuo

2017-06-01

To elucidate spatial differences in mesozooplankton community structure in local scale, vertical hauls using a 60-μm mesh closing net were carried out off Lützow-Holm Bay in January 2008. All of the zooplankton samples collected from three layers (0-100, 100-200, and 200-500 m) at seven stations were dominated by Oithona spp., Oncaea spp., Ctenocalanus citer, Microcalanus pygmaeus, and copepod nauplii. The cluster analysis of mesozooplankton abundances showed three distinct groups according to sampling depth, which appeared to be due to the preferential vertical distribution of dominant copepods. The other cluster analysis on integrated abundance upper 500 m revealed that mesozooplankton community structures at stations located on the western and eastern edges of the observation area (Cluster A) differed from those at the central stations (Cluster B). Abundance of copepod nauplii, Oithona spp., and C. citer differed between Clusters A and B, which was likely caused by differences in recruitment and early development in the dominant copepods, being associated with the timing and duration of ice edge blooms. This suggests that such heterogeneity in abundance and recruitment/development of dominant taxa was likely caused by local heterogeneity in sea ice dynamics. This may affect our understanding of zooplankton distribution.

Shift in the microbial community composition of surface water and sediment along an urban river.

PubMed

Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

2018-06-15

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P < 0.05). The bacterial diversity in sediments was significantly higher than their corresponding water samples. Additionally, archaeal communities showed obvious spatial variability in the surface water. The construction of the hydropower station resulted in increased Cyanobacteria abundance in the upstream (32.2%) compared to its downstream (10.3%). Several taxonomic groups of potential fecal indicator bacteria, like Flavobacteria and Bacteroidia, showed an increasing trend in the urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P < 0.01) and NO 3 - (P < 0.05), and metals (Zn, Fe) (P < 0.05) were the most significant drivers determining the microbial community composition in the urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

Niche specialization of terrestrial archaeal ammonia oxidizers.

PubMed

Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C; James, Phillip; Schloter, Michael; Griffiths, Robert I; Prosser, James I; Nicol, Graeme W

2011-12-27

Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

Visibility graph network analysis of natural gas price: The case of North American market

NASA Astrophysics Data System (ADS)

Sun, Mei; Wang, Yaqi; Gao, Cuixia

2016-11-01

Fluctuations in prices of natural gas significantly affect global economy. Therefore, the research on the characteristics of natural gas price fluctuations, turning points and its influencing cycle on the subsequent price series is of great significance. Global natural gas trade concentrates on three regional markets: the North American market, the European market and the Asia-Pacific market, with North America having the most developed natural gas financial market. In addition, perfect legal supervision and coordinated regulations make the North American market more open and more competitive. This paper focuses on the North American natural gas market specifically. The Henry Hub natural gas spot price time series is converted to a visibility graph network which provides a new direction for macro analysis of time series, and several indicators are investigated: degree and degree distribution, the average shortest path length and community structure. The internal mechanisms underlying price fluctuations are explored through the indicators. The results show that the natural gas prices visibility graph network (NGP-VGN) is of small-world and scale-free properties simultaneously. After random rearrangement of original price time series, the degree distribution of network becomes exponential distribution, different from the original ones. This means that, the original price time series is of long-range negative correlation fractal characteristic. In addition, nodes with large degree correspond to significant geopolitical or economic events. Communities correspond to time cycles in visibility graph network. The cycles of time series and the impact scope of hubs can be found by community structure partition.

On the statistical mechanics of species abundance distributions.

PubMed

Bowler, Michael G; Kelly, Colleen K

2012-09-01

A central issue in ecology is that of the factors determining the relative abundance of species within a natural community. The proper application of the principles of statistical physics to species abundance distributions (SADs) shows that simple ecological properties could account for the near universal features observed. These properties are (i) a limit on the number of individuals in an ecological guild and (ii) per capita birth and death rates. They underpin the neutral theory of Hubbell (2001), the master equation approach of Volkov et al. (2003, 2005) and the idiosyncratic (extreme niche) theory of Pueyo et al. (2007); they result in an underlying log series SAD, regardless of neutral or niche dynamics. The success of statistical mechanics in this application implies that communities are in dynamic equilibrium and hence that niches must be flexible and that temporal fluctuations on all sorts of scales are likely to be important in community structure. Copyright © 2012 Elsevier Inc. All rights reserved.

Effects of storage temperature on bacterial growth rates and community structure in fresh retail sushi.

PubMed

Hoel, S; Jakobsen, A N; Vadstein, O

2017-09-01

This study was conducted to assess the effects of different storage temperatures (4-20°C), on bacterial concentrations, growth rates and community structure in fresh retail sushi, a popular retail product with a claimed shelf life of 2-3 days. The maximum specific growth rate based on aerobic plate count (APC) at 4°C was 0·06 h -1 and displayed a sixfold increase (0·37 h -1 ) at 20°C. Refrigeration resulted in no growth of hydrogen sulphide (H 2 S)-producing bacteria, but this group had the strongest temperature response. The bacterial community structure was determined by PCR/DGGE (denaturing gradient gel electrophoresis). Multivariate analysis based on Bray-Curtis similarities demonstrated that temperature alone was not the major determinant for the bacterial community structure. The total concentration of aerobic bacteria was the variable that most successfully explained the differences between the communities. The dominating organisms, detected by sequencing of DNA bands excised from the DGGE gel, were Brochothrix thermosphacta and genera of lactic acid bacteria (LAB). The relationship between growth rates and storage temperatures clearly demonstrates that these products are sensitive to deviations from optimal storage temperature, possibly resulting in loss of quality during shelf life. Regardless of the storage temperature, the bacterial communities converged towards a similar structure and density, but the storage temperature determined how fast the community reached its carrying capacity. Little information is available on the microbial composition of ready-to-eat food that are prepared with raw fish, subjected to contamination during handling, and susceptible to microbial growth during cold storage. Moreover, the data are a good first possibility to simulate growth of APC, H 2 S-producing bacteria and LAB under different temperature scenarios that might occur during production, distribution or storage. © 2017 The Society for Applied Microbiology.

Ocean plankton. Determinants of community structure in the global plankton interactome.

PubMed

Lima-Mendez, Gipsi; Faust, Karoline; Henry, Nicolas; Decelle, Johan; Colin, Sébastien; Carcillo, Fabrizio; Chaffron, Samuel; Ignacio-Espinosa, J Cesar; Roux, Simon; Vincent, Flora; Bittner, Lucie; Darzi, Youssef; Wang, Jun; Audic, Stéphane; Berline, Léo; Bontempi, Gianluca; Cabello, Ana M; Coppola, Laurent; Cornejo-Castillo, Francisco M; d'Ovidio, Francesco; De Meester, Luc; Ferrera, Isabel; Garet-Delmas, Marie-José; Guidi, Lionel; Lara, Elena; Pesant, Stéphane; Royo-Llonch, Marta; Salazar, Guillem; Sánchez, Pablo; Sebastian, Marta; Souffreau, Caroline; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Gorsky, Gabriel; Not, Fabrice; Ogata, Hiroyuki; Speich, Sabrina; Stemmann, Lars; Weissenbach, Jean; Wincker, Patrick; Acinas, Silvia G; Sunagawa, Shinichi; Bork, Peer; Sullivan, Matthew B; Karsenti, Eric; Bowler, Chris; de Vargas, Colomban; Raes, Jeroen

2015-05-22

Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models. Copyright © 2015, American Association for the Advancement of Science.

Opinion diversity and community formation in adaptive networks

NASA Astrophysics Data System (ADS)

Yu, Y.; Xiao, G.; Li, G.; Tay, W. P.; Teoh, H. F.

2017-10-01

It is interesting and of significant importance to investigate how network structures co-evolve with opinions. In this article, we show that, a simple model integrating consensus formation, link rewiring, and opinion change allows complex system dynamics to emerge, driving the system into a dynamic equilibrium with the co-existence of diversified opinions. Specifically, similar opinion holders may form into communities yet with no strict community consensus; and rather than being separated into disconnected communities, different communities are connected by a non-trivial proportion of inter-community links. More importantly, we show that the complex dynamics may lead to different numbers of communities at the steady state with a given tolerance between different opinion holders. We construct a framework for theoretically analyzing the co-evolution process. Theoretical analysis and extensive simulation results reveal some useful insights into the complex co-evolution process, including the formation of dynamic equilibrium, the transition between different steady states with different numbers of communities, and the dynamics between opinion distribution and network modularity.

Distributions and habitat associations of deep-water corals in Norfolk and Baltimore Canyons, Mid-Atlantic Bight, USA

NASA Astrophysics Data System (ADS)

Brooke, S. D.; Watts, M. W.; Heil, A. D.; Rhode, M.; Mienis, F.; Duineveld, G. C. A.; Davies, A. J.; Ross, S. W.

2017-03-01

A multi-disciplinary study of two major submarine canyons, Baltimore Canyon and Norfolk Canyon, off the US mid-Atlantic coast focused on the ecology and biology of canyon habitats, particularly those supporting deep-sea corals. Historical data on deep-sea corals from these canyons were sparse with less than 750 records for the mid-Atlantic region, with most being soft sediment species. This study substantially increased the number of deep-sea coral records for the target canyons and the region. Large gorgonians were the dominant structure-forming coral taxa on exposed hard substrates, but several species of scleractinians were also documented, including first observations of Lophelia pertusa in the mid-Atlantic Bight region. Coral distribution varied within and between the two canyons, with greater abundance of the octocoral Paragorgia arborea in Baltimore Canyon, and higher occurrence of stony corals in Norfolk Canyon; these observations reflect the differences in environmental conditions, particularly turbidity, between the canyons. Some species have a wide distribution (e.g., P. arborea, Primnoa resedaeformis, Anthothela grandiflora), while others are limited to certain habitat types and/or depth zones (e.g., Paramuricea placomus, L. pertusa, Solenosmilia variabilis). The distribution of a species is driven by a combination of factors, which include availability of appropriate physical structure and environmental conditions. Although the diversity of the structure-forming corals (gorgonians, branching scleractinians and large anemones) was low, many areas of both canyons supported high coral abundance and a diverse coral-associated community. The canyons provide suitable habitat for the development of deep-sea coral communities that is not readily available elsewhere on the sedimented shelf and slope of the Mid-Atlantic Bight.

Understanding the spatial distribution of subtidal reef assemblages in the southern Baltic Sea using towed camera platform imagery

NASA Astrophysics Data System (ADS)

Beisiegel, Kolja; Darr, Alexander; Zettler, Michael L.; Friedland, René; Gräwe, Ulf; Gogina, Mayya

2018-07-01

Quantitative sampling of sessile assemblages on temperate subtidal rocky reefs is expensive and severely time-limited by logistics. However, knowledge about distribution patterns of critical and endangered species and habitats at different spatial scales is needed for effective marine management strategies. To gain information of sessile community distribution on broader spatial scales (>1 km), visual imaging was employed for the first time on a reef complex in the south-western Baltic Sea. Analysis of 3000 images along 6 transects (in total 18 km long) from 10 to 40 m depth revealed high natural variation in reef physical structure, with well-defined changes in sessile species richness, cover and composition. Overall 14 morphological groups could be distinguished by imaging and 4 distinct community groups associated with specific habitat requirements were identified. Depth remained the best descriptor. However, data indicate that light intensity, concentration of organic carbon and suspended particulate matter have an effect on reef community distribution. Compared to fully marine conditions, the study revealed a unique zonation pattern in the circalittoral zone of the Fehmarnbelt brackish transition area, with an unexpected reef habitat in the trench. We conclude that towed camera platform imagery might help to close the information gap regarding rocky reefs in the temperate subtidal. It provides a valuable tool to assess the main distribution patterns of sessile assemblages on rough terrain, potentially applicable for management and conservation planning.

Explaining local-scale species distributions: relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage

USGS Publications Warehouse

Mattsson, Brady J.; Zipkin, Elise F.; Gardner, Beth; Blank, Peter J.; Sauer, John R.; Royle, J. Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition.

Explaining local-scale species distributions: relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage.

PubMed

Mattsson, Brady J; Zipkin, Elise F; Gardner, Beth; Blank, Peter J; Sauer, John R; Royle, J Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition.

Explaining Local-Scale Species Distributions: Relative Contributions of Spatial Autocorrelation and Landscape Heterogeneity for an Avian Assemblage

PubMed Central

Mattsson, Brady J.; Zipkin, Elise F.; Gardner, Beth; Blank, Peter J.; Sauer, John R.; Royle, J. Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition. PMID:23393564

Dominant predators mediate the impact of habitat size on trophic structure in bromeliad invertebrate communities.

PubMed

Petermann, Jana S; Farjalla, Vinicius F; Jocque, Merlijn; Kratina, Pavel; MacDonald, A Andrew M; Marino, Nicholas A C; De Omena, Paula M; Piccoli, Gustavo C O; Richardson, Barbara A; Richardson, Michael J; Romero, Gustavo Q; Videla, Martin; Srivastava, Diane S

2015-02-01

Local habitat size has been shown to influence colonization and extinction processes of species in patchy environments. However, species differ in body size, mobility, and trophic level, and may not respond in the same way to habitat size. Thus far, we have a limited understanding of how habitat size influences the structure of multitrophic communities and to what extent the effects may be generalizable over a broad geographic range. Here, we used water-filled bromeliads of different sizes as a natural model system to examine the effects of habitat size on the trophic structure of their inhabiting invertebrate communities. We collected composition and biomass data from 651 bromeliad communities from eight sites across Central and South America differing in environmental conditions, species pools, and the presence of large-bodied odonate predators. We found that trophic structure in the communities changed dramatically with changes in habitat (bromeliad) size. Detritivore : resource ratios showed a consistent negative relationship with habitat size across sites. In contrast, changes in predator: detritivore (prey) ratios depended on the presence of odonates as dominant predators in the regional pool. At sites without odonates, predator: detritivore biomass ratios decreased with increasing habitat size. At sites with odonates, we found odonates to be more frequently present in large than in small bromeliads, and predator: detritivore biomass ratios increased with increasing habitat size to the point where some trophic pyramids became inverted. Our results show that the distribution of biomass amongst food-web levels depends strongly on habitat size, largely irrespective of geographic differences in environmental conditions or detritivore species compositions. However, the presence of large-bodied predators in the regional species pool may fundamentally alter this relationship between habitat size and trophic structure. We conclude that taking into account the response and multitrophic effects of dominant, mobile species may be critical when predicting changes in community structure along a habitat-size gradient.

Graptolite community responses to global climate change and the Late Ordovician mass extinction.

PubMed

Sheets, H David; Mitchell, Charles E; Melchin, Michael J; Loxton, Jason; Štorch, Petr; Carlucci, Kristi L; Hawkins, Andrew D

2016-07-26

Mass extinctions disrupt ecological communities. Although climate changes produce stress in ecological communities, few paleobiological studies have systematically addressed the impact of global climate changes on the fine details of community structure with a view to understanding how changes in community structure presage, or even cause, biodiversity decline during mass extinctions. Based on a novel Bayesian approach to biotope assessment, we present a study of changes in species abundance distribution patterns of macroplanktonic graptolite faunas (∼447-444 Ma) leading into the Late Ordovician mass extinction. Communities at two contrasting sites exhibit significant decreases in complexity and evenness as a consequence of the preferential decline in abundance of dysaerobic zone specialist species. The observed changes in community complexity and evenness commenced well before the dramatic population depletions that mark the tipping point of the extinction event. Initially, community changes tracked changes in the oceanic water masses, but these relations broke down during the onset of mass extinction. Environmental isotope and biomarker data suggest that sea surface temperature and nutrient cycling in the paleotropical oceans changed sharply during the latest Katian time, with consequent changes in the extent of the oxygen minimum zone and phytoplankton community composition. Although many impacted species persisted in ephemeral populations, increased extinction risk selectively depleted the diversity of paleotropical graptolite species during the latest Katian and early Hirnantian. The effects of long-term climate change on habitats can thus degrade populations in ways that cascade through communities, with effects that culminate in mass extinction.

Graptolite community responses to global climate change and the Late Ordovician mass extinction

NASA Astrophysics Data System (ADS)

Sheets, H. David; Mitchell, Charles E.; Melchin, Michael J.; Loxton, Jason; Štorch, Petr; Carlucci, Kristi L.; Hawkins, Andrew D.

2016-07-01

Mass extinctions disrupt ecological communities. Although climate changes produce stress in ecological communities, few paleobiological studies have systematically addressed the impact of global climate changes on the fine details of community structure with a view to understanding how changes in community structure presage, or even cause, biodiversity decline during mass extinctions. Based on a novel Bayesian approach to biotope assessment, we present a study of changes in species abundance distribution patterns of macroplanktonic graptolite faunas (˜447-444 Ma) leading into the Late Ordovician mass extinction. Communities at two contrasting sites exhibit significant decreases in complexity and evenness as a consequence of the preferential decline in abundance of dysaerobic zone specialist species. The observed changes in community complexity and evenness commenced well before the dramatic population depletions that mark the tipping point of the extinction event. Initially, community changes tracked changes in the oceanic water masses, but these relations broke down during the onset of mass extinction. Environmental isotope and biomarker data suggest that sea surface temperature and nutrient cycling in the paleotropical oceans changed sharply during the latest Katian time, with consequent changes in the extent of the oxygen minimum zone and phytoplankton community composition. Although many impacted species persisted in ephemeral populations, increased extinction risk selectively depleted the diversity of paleotropical graptolite species during the latest Katian and early Hirnantian. The effects of long-term climate change on habitats can thus degrade populations in ways that cascade through communities, with effects that culminate in mass extinction.

An experimental test of a fundamental food web motif.

PubMed

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Living in the branches: population dynamics and ecological processes in dendritic networks

USGS Publications Warehouse

Grant, E.H.C.; Lowe, W.H.; Fagan, W.F.

2007-01-01

Spatial structure regulates and modifies processes at several levels of ecological organization (e.g. individual/genetic, population and community) and is thus a key component of complex systems, where knowledge at a small scale can be insufficient for understanding system behaviour at a larger scale. Recent syntheses outline potential applications of network theory to ecological systems, but do not address the implications of physical structure for network dynamics. There is a specific need to examine how dendritic habitat structure, such as that found in stream, hedgerow and cave networks, influences ecological processes. Although dendritic networks are one type of ecological network, they are distinguished by two fundamental characteristics: (1) both the branches and the nodes serve as habitat, and (2) the specific spatial arrangement and hierarchical organization of these elements interacts with a species' movement behaviour to alter patterns of population distribution and abundance, and community interactions. Here, we summarize existing theory relating to ecological dynamics in dendritic networks, review empirical studies examining the population- and community-level consequences of these networks, and suggest future research integrating spatial pattern and processes in dendritic systems.

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

PubMed Central

Bryant, Jessica A.; Lamanna, Christine; Morlon, Hélène; Kerkhoff, Andrew J.; Enquist, Brian J.; Green, Jessica L.

2008-01-01

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ. PMID:18695215

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

PubMed Central

Hathaway, Jennifer J.M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Young, Jesse M.; Read, Kaitlyn J.H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens. PMID:29093998

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits.

PubMed

Winter, Ara S; Hathaway, Jennifer J M; Kimble, Jason C; Buecher, Debbie C; Valdez, Ernest W; Porras-Alfaro, Andrea; Young, Jesse M; Read, Kaitlyn J H; Northup, Diana E

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

USGS Publications Warehouse

Winter, Ara S.; Hathaway, Jennifer J. M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Porras-Alfaro, Andrea; Young, Jesse M.; Read, Kaitlyn J. H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

[Dung beetles (Coleoptera: Scarabaeinae) of the northwestern slope of the Sierra Nevada of Santa Marta, Colombia].

PubMed

Martínez, Neis J; García, Héctor; Pulido, Luz A; Ospino, Deibi; Harváez, Juan C

2009-01-01

The community structure of dung beetles in the middle and lower river basin of the Gaira river, Sierra Nevada de Santa Marta, Colombia, is described. Four sites were selected along an altitudinal gradient of 50-940 m for sampling from June to October, 2004. Dung beetles were captured using modified pitfall traps and manual recollections. We captured 7,872 individuals belonging to 29 species, distributed in 15 genera and five tribes of Scarabaeinae. Canthon and Onthophagus were the most diverse genera, each represented by six species. The sampled sites shared the following species: Onthophagus acuminatus Harold, O. clypeatus Blanchard, O. marginicollis Harold. Bocatoma was the most diverse site with 23 species; whereas Port Mosquito presented the highest abundance, with 3,262 individuals. Seven species represented 89% of all captures: Canthidium sp., Dichotomius sp., Uroxys sp. 1, Uroxys sp. 2, O. marginicollis, O. clypeatus and O. acuminatus. Of the 29 captured species, 17 belonged to the functional group of diggers and 10 were ball-rollers. We did not observe significant among-site differences in community structure. Abiotic factors such as altitude, temperature and humidity cannot explain observed variation in community structure across sites, indicating other variables such as vegetation cover, density of the vegetation and soil type may play a role in the community structure of these insects.

Callous-Unemotional Traits in a Community Sample of Adolescents

ERIC Educational Resources Information Center

Essau, Cecilia A.; Sasagawa, Satoko; Frick, Paul J.

2006-01-01

This study examined the structure, distribution, and correlates of a new measure of self-reported callous-unemotional (CU) traits in 1,443 adolescents (774 boys, 669 girls) between the ages of 13 to 18 years. The Inventory of Callous-Unemotional Traits was subjected to exploratory factor analysis and confirmatory factor analysis. Exploratory…

MODIS-Aqua Reveals Evolving Phytoplankton Community Structure During the Arabian Sea Northeast Monsoon

NASA Technical Reports Server (NTRS)

Werdell, P. Jeremy; Roesler, Collin S.; Goes, Joaquim I.

2016-01-01

Applying a bio-optical model designed to identify the mixotrophic dinoflagellate Noctiluca miliaris to MODIS-Aqua revealed (1) patterns in its spatial distribution not previously seen (including its appearance in places not previously sampled), and (2) the surprising disassociation of total chlorophyll biomass with the presence of N. miliaris.

Community structure of Aspergillus flavus and A. parasiticus in major almond producing areas of California, United States

USDA-ARS?s Scientific Manuscript database

Several nut crops including almonds, pistachios, and walnuts can become contaminated with mycotoxins. Of greatest economic significance are aflatoxins, which are mainly produced by members of Aspergillus section Flavi. The distribution of the two sclerotial-size morphotypes of A. flavus (i.e. S and ...

Bayesian calibration of the Community Land Model using surrogates

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

Ray, Jaideep; Hou, Zhangshuan; Huang, Maoyi

2014-02-01

We present results from the Bayesian calibration of hydrological parameters of the Community Land Model (CLM), which is often used in climate simulations and Earth system models. A statistical inverse problem is formulated for three hydrological parameters, conditional on observations of latent heat surface fluxes over 48 months. Our calibration method uses polynomial and Gaussian process surrogates of the CLM, and solves the parameter estimation problem using a Markov chain Monte Carlo sampler. Posterior probability densities for the parameters are developed for two sites with different soil and vegetation covers. Our method also allows us to examine the structural errormore » in CLM under two error models. We find that surrogate models can be created for CLM in most cases. The posterior distributions are more predictive than the default parameter values in CLM. Climatologically averaging the observations does not modify the parameters' distributions significantly. The structural error model reveals a correlation time-scale which can be used to identify the physical process that could be contributing to it. While the calibrated CLM has a higher predictive skill, the calibration is under-dispersive.« less

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety.

PubMed

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety

PubMed Central

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health. PMID:29312177

Knowledge representation of rock plastic deformation

NASA Astrophysics Data System (ADS)

Davarpanah, Armita; Babaie, Hassan

2017-04-01

The first iteration of the Rock Plastic Deformation (RPD) ontology models the semantics of the dynamic physical and chemical processes and mechanisms that occur during the deformation of the generally inhomogeneous polycrystalline rocks. The ontology represents the knowledge about the production, reconfiguration, displacement, and consumption of the structural components that participate in these processes. It also formalizes the properties that are known by the structural geology and metamorphic petrology communities to hold between the instances of the spatial components and the dynamic processes, the state and system variables, the empirical flow laws that relate the variables, and the laboratory testing conditions and procedures. The modeling of some of the complex physio-chemical, mathematical, and informational concepts and relations of the RPD ontology is based on the class and property structure of some well-established top-level ontologies. The flexible and extensible design of the initial version of the RPD ontology allows it to develop into a model that more fully represents the knowledge of plastic deformation of rocks under different spatial and temporal scales in the laboratory and in solid Earth. The ontology will be used to annotate the datasets related to the microstructures and physical-chemical processes that involve them. This will help the autonomous and globally distributed communities of experimental structural geologists and metamorphic petrologists to coherently and uniformly distribute, discover, access, share, and use their data through automated reasoning and enhanced data integration and software interoperability.

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

Meter scale variation in shrub dominance and soil moisture structure Arctic arthropod communities

PubMed Central

Hansen, Oskar Liset Pryds; Bowden, Joseph J.; Treier, Urs A.; Normand, Signe; Høye, Toke

2016-01-01

The Arctic is warming at twice the rate of the rest of the world. This impacts Arctic species both directly, through increased temperatures, and indirectly, through structural changes in their habitats. Species are expected to exhibit idiosyncratic responses to structural change, which calls for detailed investigations at the species and community level. Here, we investigate how arthropod assemblages of spiders and beetles respond to variation in habitat structure at small spatial scales. We sampled transitions in shrub dominance and soil moisture between three different habitats (fen, dwarf shrub heath, and tall shrub tundra) at three different sites along a fjord gradient in southwest Greenland, using yellow pitfall cups. We identified 2,547 individuals belonging to 47 species. We used species richness estimation, indicator species analysis and latent variable modeling to examine differences in arthropod community structure in response to habitat variation at local (within site) and regional scales (between sites). We estimated species responses to the environment by fitting species-specific generalized linear models with environmental covariates. Species assemblages were segregated at the habitat and site level. Each habitat hosted significant indicator species, and species richness and diversity were significantly lower in fen habitats. Assemblage patterns were significantly linked to changes in soil moisture and vegetation height, as well as geographic location. We show that meter-scale variation among habitats affects arthropod community structure, supporting the notion that the Arctic tundra is a heterogeneous environment. To gain sufficient insight into temporal biodiversity change, we require studies of species distributions detailing species habitat preferences. PMID:27478709

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

PubMed

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

2017-06-01

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

Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

USGS Publications Warehouse

Kidd, Haack S.; Garchow, H.; Odelson, D.A.; Forney, L.J.; Klug, M.J.

1994-01-01

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

Implementing a Healthy Food Distribution Program: A Supply Chain Strategy to Increase Fruit and Vegetable Access in Underserved Areas.

PubMed

DeFosset, Amelia R; Kwan, Allison; Rizik-Baer, Daniel; Gutierrez, Luis; Gase, Lauren N; Kuo, Tony

2018-05-24

Increasing access to fresh produce in small retail venues could improve the diet of people in underserved communities. However, small retailers face barriers to stocking fresh produce. In 2014, an innovative distribution program, Community Markets Purchasing Real and Affordable Foods (COMPRA), was launched in Los Angeles with the aim of making it more convenient and profitable for small retailers to stock fresh produce. Our case study describes the key processes and lessons learned in the first 2 years of implementing COMPRA. Considerable investments in staff capacity and infrastructure were needed to launch COMPRA. Early successes included significant week-to-week increases in the volume of produce distributed. Leveraging partnerships, maintaining a flexible operational and funding structure, and broadly addressing store owners' needs contributed to initial gains. We describe key challenges and next steps to scaling the program. Lessons learned from implementing COMPRA could inform other jurisdictions considering supply-side approaches to increase access to healthy food.

45 CFR 2517.600 - How are funds for community-based service-learning programs distributed?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 4 2010-10-01 2010-10-01 false How are funds for community-based service-learning... (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COMMUNITY-BASED SERVICE-LEARNING PROGRAMS Distribution of Funds § 2517.600 How are funds for community-based service-learning programs distributed? All...

45 CFR 2517.600 - How are funds for community-based service-learning programs distributed?

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 4 2011-10-01 2011-10-01 false How are funds for community-based service-learning... (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COMMUNITY-BASED SERVICE-LEARNING PROGRAMS Distribution of Funds § 2517.600 How are funds for community-based service-learning programs distributed? All...

Population Structure of Two Rabies Hosts Relative to the Known Distribution of Rabies Virus Variants in Alaska

PubMed Central

Goldsmith, Elizabeth W.; Renshaw, Benjamin; Clement, Christopher J.; Himschoot, Elizabeth A.; Hundertmark, Kris J.; Hueffer, Karsten

2015-01-01

For pathogens that infect multiple species the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We test the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (V. vulpes) in order to possibly distinguish reservoir and spill over hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found 2 groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising 2 regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the artic fox Therefore we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. PMID:26661691

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska.

PubMed

Goldsmith, Elizabeth W; Renshaw, Benjamin; Clement, Christopher J; Himschoot, Elizabeth A; Hundertmark, Kris J; Hueffer, Karsten

2016-02-01

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. © 2015 John Wiley & Sons Ltd.

Long‐term monitoring reveals differing impacts of elephants on elements of a canopy shrub community.

PubMed

Landman, Marietjie; Schoeman, David S; Hall-Martin, Anthony J; Kerley, Graham I H

The conservation management of southern Africa's elephants focuses on identifying and mitigating the extent and intensity of impacts on biological diversity. However, variation in the intensity of elephant effects between elements of biodiversity is seldom explored, which limits our ability to interpret the scale of the impacts. Our study quantifies >50 years of impacts in the succulent thickets of the Addo Elephant National Park, South Africa, contrasting hypotheses for the resilience of the canopy shrubs (a key functional guild) to elephants with those that argue the opposite. We also assess the impacts between elements of the community, ranging from community composition and structure to the structure of individual canopy species. We show the vulnerability of the canopy shrubs to transformation as the accumulated influences of elephants alter community composition and structure. The pattern of transformation is similar to that caused by domestic herbivores, which leads us to predict that elephants will eventually bring about landscape-level degradation and a significant loss of biodiversity. While we expected the canopy species to show similar declining trends in structure, providing insight into the response of the community as a whole, we demonstrate an uneven distribution of impacts between constituent elements; most of the canopy dominants exhibited little change, resisting removal. This implies that these canopy dominants might not be useful indicators of community change in thickets, a pattern that is likely repeated among the canopy trees of savanna systems. Our findings suggest that predicting elephant impacts, and finding solutions to the so-called “elephant problem,” require a broader and more integrated understanding of the mechanisms driving the changes between elements of biodiversity at various spatial and temporal scales.

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

PubMed

Filker, Sabine; Sommaruga, Ruben; Vila, Irma; Stoeck, Thorsten

2016-05-01

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures. © 2016 John Wiley & Sons Ltd.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Environmental Drivers of the Canadian Arctic Megabenthic Communities

PubMed Central

Roy, Virginie; Iken, Katrin; Archambault, Philippe

2014-01-01

Environmental gradients and their influence on benthic community structure vary over different spatial scales; yet, few studies in the Arctic have attempted to study the influence of environmental gradients of differing spatial scales on megabenthic communities across continental-scales. The current project studied for the first time how megabenthic community structure is related to several environmental factors over 2000 km of the Canadian Arctic, from the Beaufort Sea to northern Baffin Bay. Faunal trawl samples were collected between 2007 and 2011 at 78 stations from 30 to 1000 m depth and patterns in biomass, density, richness, diversity, and taxonomic composition were examined in relation to indirect/spatial gradients (e.g., depth), direct gradients (e.g., bottom oceanographic variables), and resource gradients (e.g., food supply proxies). Six benthic community types were defined based on their biomass-based taxonomic composition. Their distribution was significantly, but moderately, associated with large-scale (100–1000 km) environmental gradients defined by depth, physical water properties (e.g., bottom salinity), and meso-scale (10–100 km) environmental gradients defined by substrate type (hard vs. soft) and sediment organic carbon content. We did not observe a strong decline of bulk biomass, density and richness with depth or a strong increase of those community characteristics with food supply proxies, contrary to our hypothesis. We discuss how local- to meso-scale environmental conditions, such as bottom current regimes and polynyas, sustain biomass-rich communities at specific locations in oligotrophic and in deep regions of the Canadian Arctic. This study demonstrates the value of considering the scales of variability of environmental gradients when interpreting their relevance in structuring of communities. PMID:25019385

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities. PMID:26943622

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Effects of brine contamination from energy development on wetland macroinvertebrate community structure in the Prairie Pothole Region

USGS Publications Warehouse

Preston, Todd M.; Borgreen, Michael J.; Ray, Andrew M.

2018-01-01

Wetlands in the Prairie Pothole Region (PPR) of North America support macroinvertebrate communities that are integral to local food webs and important to breeding waterfowl. Macroinvertebrates in PPR wetlands are primarily generalists and well adapted to within and among year changes in water permanence and salinity. The Williston Basin, a major source of U.S. energy production, underlies the southwest portion of the PPR. Development of oil and gas results in the coproduction of large volumes of highly saline, sodium chloride dominated water (brine) and the introduction of brine can alter wetland salinity. To assess potential effects of brine contamination on macroinvertebrate communities, 155 PPR wetlands spanning a range of hydroperiods and salinities were sampled between 2014 and 2016. Brine contamination was documented in 34 wetlands with contaminated wetlands having significantly higher chloride concentrations, specific conductance and percent dominant taxa, and significantly lower taxonomic richness, Shannon diversity, and Pielou evenness scores compared to uncontaminated wetlands. Non-metric multidimensional scaling found significant correlations between several water quality parameters and macroinvertebrate communities. Chloride concentration and specific conductance, which can be elevated in naturally saline wetlands, but are also associated with brine contamination, had the strongest correlations. Five wetland groups were identified from cluster analysis with many of the highly contaminated wetlands located in a single cluster. Low or moderately contaminated wetlands were distributed among the remaining clusters and had macroinvertebrate communities similar to uncontaminated wetlands. While aggregate changes in macroinvertebrate community structure were observed with brine contamination, systematic changes were not evident, likely due to the strong and potentially confounding influence of hydroperiod and natural salinity. Therefore, despite the observed negative response of macroinvertebrate communities to brine contamination, macroinvertebrate community structure alone is likely not the most sensitive indicator of brine contamination in PPR wetlands.

Influence of habitat heterogeneity on the community structure of deep-sea harpacticoid communities from a canyon and an escarpment site on the continental rise off California

NASA Astrophysics Data System (ADS)

Thistle, David; Sedlacek, Linda; Carman, Kevin R.; Barry, James P.

2017-05-01

The sediment-covered deep-sea floor was initially thought to be environmentally homogeneous. Recent work has shown otherwise, and deep-sea ecologists have been searching for ecologically important environmental heterogeneities on different spatial and temporal scales, with particular interest in canyons. Here we report results for harpacticoid copepods from a site at 3262 m depth in the axis of Monterey Canyon and one on an escarpment 46 km away at 3090 m depth. Multivariate community analyses revealed significant differences between sites in community structure. Absolute abundance, the ratio of subadult copepodites to adults, species density, the proportion of the harpacticoid individuals that emerged, and the proportion that lived in tubes were significantly lower at the canyon site than at the escarpment site. The proportion of the harpacticoid individuals that belonged to the surface-dweller life-style group was significantly higher than at the escarpment site. These marked differences imply that ecologically important environmental heterogeneities exist. We speculate that differences between the sites in food conditions and sediment grain-size distributions are among them.

Spatial Patterns in the Efficiency of the Biological Pump: What Controls Export Ratios at the Global Scale?

NASA Astrophysics Data System (ADS)

Moore, J. K.

2016-02-01

The efficiency of the biological pump is influenced by complex interactions between chemical, biological, and physical processes. The efficiency of export out of surface waters and down through the water column to the deep ocean has been linked to a number of factors including biota community composition, production of mineral ballast components, physical aggregation and disaggregation processes, and ocean oxygen concentrations. I will examine spatial patterns in the export ratio and the efficiency of the biological pump at the global scale using the Community Earth System Model (CESM). There are strong spatial variations in the export efficiency as simulated by the CESM, which are strongly correlated with new nutrient inputs to the euphotic zone and their impacts on phytoplankton community structure. I will compare CESM simulations that include dynamic, variable export ratios driven by the phytoplankton community structure, with simulations that impose a near-constant export ratio to examine the effects of export efficiency on nutrient and surface chlorophyll distributions. The model predicted export ratios will also be compared with recent satellite-based estimates.

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics.

PubMed

Niederdorfer, Robert; Peter, Hannes; Battin, Tom J

2016-10-03

Small-scale hydraulics affects microbial behaviour at the cell level 1 , trophic interactions in marine aggregates 2 and the physical structure and function of stream biofilms 3,4 . However, it remains unclear how hydraulics, predictably changing from small streams to large rivers, impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we present experimental evidence unveiling hydraulics as a hitherto poorly recognized control of microbial lifestyle differentiation in fluvial ecosystems. Exposing planktonic source communities from stream and floodplain ecosystems to different hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Only a few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous resident taxa characterized aggregate communities. Our findings unveil fundamental differences between biofilms and aggregates and build the basis for a mechanistic understanding of how hydraulics drives the distribution of microbial diversity along the fluvial continuum 5-7 .

Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China.

PubMed

Hu, Weigang; Zhang, Qi; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2014-12-01

While a vast number of studies have addressed the prokaryotic diversity in permafrost, characterized by subzero temperatures, low water activity, and extremely low rates of nutrient and metabolite transfer, fungal patterns have received surprisingly limited attention. Here, the fungal diversity and community structure were investigated by culture-dependent technique combined with cloning-restriction fragment length polymorphism (RFLP) analysis of sediments in a 10-m-long permafrost core from the Qinghai-Tibet Plateau of China. A total of 62 fungal phylotypes related to 10 distinct classes representing three phyla were recovered from 5031 clones generated in 13 environmental gene libraries. A large proportion of the phylotypes (25/62) that were distantly related to described fungal species appeared to be novel diversity. Ascomycota was the predominant group of fungi, with respect to both clone and phylotype number. Our results suggested there was the existence of cosmopolitan psychrophilic or psychrotolerant fungi in permafrost sediments, the community composition of fungi varied with increasing depth, while these communities largely distributed according to core layers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reservoirs override seasonal variability of phytoplankton communities in a regulated Mediterranean river.

PubMed

Tornés, E; Pérez, M C; Durán, C; Sabater, S

2014-03-15

Water hydrology, temperature and transparency, as well as nutrient retention downstream of the reservoirs alter the temporal and spatial distribution patterns of phytoplankton communities in regulated rivers. The seasonal dynamics of phytoplankton communities in the Ebro was analysed in contrasting water flow periods in sections upstream and downstream of three large reservoirs, as well as in an intermediate site. Phytoplankton communities changed in response to seasonal variations in the areas not influenced by the reservoirs, but the phytoplankton distribution downstream of the reservoirs was driven by their particular hydrodynamics. The change in environmental conditions promoted by reservoirs influenced the pattern of replacement between diatoms and green algae of the upstream section. Differences in the phytoplankton community structure, abundance and environmental variables between upstream and downstream sites were maximal during low flow periods. Chlorophytes and dinoflagellates were present during low flow periods upstream of the reservoirs and in the intermediate site. Cocconeis cf. placentula characterized the downstream section, associated to the presence of macrophytes in that section. The present study sheds light on the consequences of river regulation under potential scenarios of climate change, and results could be used to anticipate ecological problems in large regulated rivers under these circumstances. Copyright © 2013 Elsevier B.V. All rights reserved.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce.

PubMed

Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-28

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

[Effects of different fertilization regimes on weed communities in wheat fields under rice-wheat cropping system].

PubMed

Yuan, Fang; Li, Yong; Li, Fen-hua; Sun, Guo-jun; Han, Min; Zhang, Hai-yan; Ji, Zhong; Wu, Chen-yu

2016-01-01

To reveal the effects of different fertilization regimes on weed communities in wheat fields under a rice-wheat rotation system, a survey was conducted before wheat harvest in 2014 after a 4-year long-term recurrent fertilization scheme. Weed species types, density, height and diversity index under different fertilization and straw-returning schemes in wheat fields were studied and complemented with a canonical correspondence analysis on weed community distribution and soil nutrient factors. Twenty weed species were recorded among 36 wheat fields belonging to 19 genera and 11 families. Beckmannia syzigachne, Hemistepta lyrata, Malachium aquaticum and Cnidium monnieri were widely distributed throughout the sampled area. Long-term fertilization appeared to reduce weed species richness and density, particularly for broadleaf weeds, but increased weed height. Diversity and evenness indices of weed communities were lower and dominance indices were higher in fields where chemical fertilizers were applied alone or combined with organic fertilizers, especially, where organic-inorganic compound fertilizer was used, in which it readily caused the outbreak of a dominant species and severe damage. Conversely, diversity and evenness indices of weed communities were higher and dominance indices were lower when the straw was returned to the field combined with chemical or organic fertilizers, in which weed community structures were complex and stable with lower weed density. Under these conditions weeds only caused slight reduction of wheat growth.

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce

NASA Astrophysics Data System (ADS)

Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-01

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3--N, and NH4+-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

Distribution of phytobenthos in the Yakima River basin, Washington, in relation to geology, land use, and other environmental factors

USGS Publications Warehouse

Leland, Harry V.

1995-01-01

Benthic-algal distributions in the Yakima River, Washington, basin were, examined in relation to geology, land use, water chemistry, and stream habitat using indicator-species classification (TWINSPAN) and canonical correspondence analysis (CCA). Algal assemblages identified byTWINSPAN were each associated with a narrow range of water-quality conditions. In the Cascade geologic province, where timber harvest and grazing are the dominant land uses, differences in community structure (CCA site scores) and concentrations of major ions (Ca and Mg) and nutrients (solute P, SiO2 and inorganic N) varied with dominant rock type of the basin. In agricultural areas of the Columbia Plateau province, differences in phytobenthos structure were based primarily on the degree of enrichment of dissolved solids, inorganic N, and solute P from irrigation-return flows and subsurface drainage. Habitat characteristics strongly correlated with community structure included reach altitude, turbidity, substratum embeddedness (Columbia Plateau), large woody-debris density (Cascade Range), and composition and density of the riparian vegetation. Algal biomass (AFDM) correlated with composition and density of the riparian vegetation but not with measured chemical-constituent concentrations. Nitrogen limitation in streams of the Cascade Range favored nitrogen-fixing blue-green algae and diatoms with endosymbiotic blue-greens, whereas nitrogen heterotrophs were abundant in agricultural areas of the Columbia Plateau.

Distribution of phytobenthos in the Yakima River basin, Washington, in relation to geology, land use and other environmental factors

USGS Publications Warehouse

Leland, Harry V.

1995-01-01

Benthic-algal distributions in the Yakima River, Washington, basin were, examined in relation to geology, land use, water chemistry, and stream habitat using indicator-species classification (TWINSPAN) and canonical correspondence analysis (CCA). Algal assemblages identified byTWINSPAN were each associated with a narrow range of water-quality conditions. In the Cascade geologic province, where timber harvest and grazing are the dominant land uses, differences in community structure (CCA site scores) and concentrations of major ions (Ca and Mg) and nutrients (solute P, SiO2 and inorganic N) varied with dominant rock type of the basin. In agricultural areas of the Columbia Plateau province, differences in phytobenthos structure were based primarily on the degree of enrichment of dissolved solids, inorganic N, and solute P from irrigation-return flows and subsurface drainage. Habitat characteristics strongly correlated with community structure included reach altitude, turbidity, substratum embeddedness (Columbia Plateau), large woody-debris density (Cascade Range), and composition and density of the riparian vegetation. Algal biomass (AFDM) correlated with composition and density of the riparian vegetation but not with measured chemical-constituent concentrations. Nitrogen limitation in streams of the Cascade Range favored nitrogen-fixing blue-green algae and diatoms with endosymbiotic blue-greens, whereas nitrogen heterotrophs were abundant in agricultural areas of the Columbia Plateau.

Archaeobotanical evidence for climate as a driver of ecological community change across the anthropocene boundary.

PubMed

Ellis, Christopher J; Yahr, Rebecca; Belinchón, Rocío; Coppins, Brian J

2014-07-01

The biodiversity response to climate change is a major focus in conservation research and policy. Predictive models that are used to project the impact of climate change scenarios - such as bioclimatic envelope models - are widely applied and have come under severe scrutiny. Criticisms of such models have focussed on at least two problems. First, there is an assumption that climate is the primary driver of observed species distributions ('climatic equilibrium'), when other biogeographical controls are often reliably established. Second, a species' sensitivity to macroclimate may become less relevant when impacts are down-scaled to a local level, incorporating a modifying effect of species interactions structuring communities. This article examines the role of different drivers (climate, pollution and landscape habitat structure) in explaining spatial community variation for a widely applied bioindicator group: lichen epiphytes. To provide an analysis free of 'legacy effects' (e.g. formerly higher pollution loads), the study focused on hazel stems as a relatively short-lived and recently colonized substratum. For communities during the present day, climate is shown to interact with stem size/age as the most likely explanation of community composition, thus coupling a macroclimatic and community-scale effect. The position of present-day communities was projected into ordination space for eight sites in England and compared to the position of historical epiphyte communities from the same sites, reconstructed using preserved hazel wattles dating mainly to the 16th Century. This comparison of community structure for the late- to post-Mediaeval period, with the post-Industrial period, demonstrated a consistent shift among independent sites towards warmer and drier conditions, concurrent with the end of the Little Ice Age. Long-term temporal sensitivity of epiphyte communities to climate variation thus complements spatial community patterns. If more widely applied, preserved lichen epiphytes have potential to generate new baseline conditions of environment and biodiversity for preindustrial lowland Europe. © 2014 John Wiley & Sons Ltd.

[Diversity and community structure of endophytic fungi from Taxus chinensis var. mairei].

PubMed

2014-07-01

A total of 628 endophytic fungi were isolated from 480 tissue segments of needles and branches of Taxus chinensis var. mairei. According to morphological characteristics and ITS sequences, they represented 43 taxa in 28 genera, of which 10 Hyphomycetes, 20 Coelomycetes, 12 Ascomycetes and 1 unknown fungus. Phomopsis mali was confirmed as the dominant species. In accordance with relative frequency, Alternaria alternata, Aureobasidium pullulans, Colletotrichum boninense, C. gloeosporioides, Epicoccum nigrum , Fungal sp., Fusarium lateritium, Glomerella cingulata, Magnaporthales sp. , Nigrospora oryzae, Pestalotiopsis maculiformans, P. microspora, Peyronellaea glomerata and Xylaria sp. 1 were more common in T. chinensis var. mairei. T. chinensis var. mairei were severely infected by endophytic fungi. Endophytic fungi were found in 81 percent of plant tissues with a high diversity. Distribution ranges of endophytic fungi were influenced by tissue properties. The colonization rate, richness, diversity of endophytic fungi in needles were obviously lower than in branches, and kinds of endophytic fungi between branches were more similar than those in needles, thus endophytic fungi had tissue preference. In addition, tissue age influenced the community structure of endophytic fungi. The elder branch tissues were, the higher colonization rate, richness, diversity of endophytic fungi were. Systematic studying the diversity and community structure of endophytic fungi in T. chinensis var. mairei and clarifying their distribution regularity in plant tissues would offer basic data and scientific basis for their development and utilization. Discussing the presence of fungal pathogens in healthy plant tissues would be of positive significance for source protection of T. chinensis var. mairei.

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system.

PubMed

Satler, Jordan D; Zellmer, Amanda J; Carstens, Bryan C

2016-01-01

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

An experimental analysis of granivory in a desert ecosystem: Progress report

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

Brown, J.H.

1987-03-01

Controlled, replicated experiments are revealing the network of interactions that determine structure, dynamics, and energy transfer in a desert community that is functionally interconnected by the consumption of seeds (granivory). This community includes seed-eating rodents, ants, and birds, seed-producing annual and perennial plants, and other kinds of organisms that interact with these. The experiments entail removal of important species or functional groups of granivores or plants and supplementation of seed resources. The results demonstrate a large number of direct and indirect interactions that have important effects on the abundance of species and functional groups, the structure of the community, andmore » the dynamics of energy flow. The results suggest that networks of interaction are structured with sufficient overlap in resource requirements and interconnections through indirect pathways that community- and ecosystem-level processes, such as energy flow, are relatively insensitive to major perturbations in the abundance of particular species or functional groups. This preliminary finding has important implications for understanding the response of ecosystems to natural and human-caused perturbations, for the management of agricultural and other human-modified ecosystems, and for the design of perturbation-resistant networks for acquisition and distribution of human resources such energy and information. 44 refs.« less

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

PubMed

Bracco, Mariana; Cascales, Jimena; Hernández, Julián Cámara; Poggio, Lidia; Gottlieb, Alexandra M; Lia, Verónica V

2016-08-26

Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure. Bayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models. Our results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.

Benthic infaunal community structuring in an acidified tropical estuarine system.

PubMed

Hossain, M Belal; Marshall, David J

2014-01-01

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). 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 and community structuring is more strongly influenced by sediment particle characteristics than by the chemical properties of the water (pH and salinity). Infaunal estuarine communities, which are typically adapted to survive relatively acidic conditions, may be less exposed, less sensitive, and less vulnerable than epibenthic or pelagic communities to further acidification of above-sediment waters. These data question the extent to which all marine infaunal communities, including oceanic communities, are likely to be affected by future global CO2-driven acidification.

Signatures of ecological processes in microbial community time series.

PubMed

Faust, Karoline; Bauchinger, Franziska; Laroche, Béatrice; de Buyl, Sophie; Lahti, Leo; Washburne, Alex D; Gonze, Didier; Widder, Stefanie

2018-06-28

Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection. We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model. We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield.

PubMed

Rime, Thomas; Hartmann, Martin; Brunner, Ivano; Widmer, Franco; Zeyer, Josef; Frey, Beat

2015-03-01

Spatial patterns of microbial communities have been extensively surveyed in well-developed soils, but few studies investigated the vertical distribution of micro-organisms in newly developed soils after glacier retreat. We used 454-pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils. © 2014 John Wiley & Sons Ltd.

SOMWeb: a semantic web-based system for supporting collaboration of distributed medical communities of practice.

PubMed

Falkman, Göran; Gustafsson, Marie; Jontell, Mats; Torgersson, Olof

2008-08-26

Information technology (IT) support for remote collaboration of geographically distributed communities of practice (CoP) in health care must deal with a number of sociotechnical aspects of communication within the community. In the mid-1990s, participants of the Swedish Oral Medicine Network (SOMNet) began discussing patient cases in telephone conferences. The cases were distributed prior to the conferences using PowerPoint and email. For the technical support of online CoP, Semantic Web technologies can potentially fulfill needs of knowledge reuse, data exchange, and reasoning based on ontologies. However, more research is needed on the use of Semantic Web technologies in practice. The objectives of this research were to (1) study the communication of distributed health care professionals in oral medicine; (2) apply Semantic Web technologies to describe community data and oral medicine knowledge; (3) develop an online CoP, Swedish Oral Medicine Web (SOMWeb), centered on user-contributed case descriptions and meetings; and (4) evaluate SOMWeb and study how work practices change with IT support. Based on Java, and using the Web Ontology Language and Resource Description Framework for handling community data and oral medicine knowledge, SOMWeb was developed using a user-centered and iterative approach. For studying the work practices and evaluating the system, a mixed-method approach of interviews, observations, and a questionnaire was used. By May 2008, there were 90 registered users of SOMWeb, 93 cases had been added, and 18 meetings had utilized the system. The introduction of SOMWeb has improved the structure of meetings and their discussions, and a tenfold increase in the number of participants has been observed. Users submit cases to seek advice on diagnosis or treatment, to show an unusual case, or to create discussion. Identified barriers to submitting cases are lack of time, concern about whether the case is interesting enough, and showing gaps in one's own knowledge. Three levels of member participation are discernable: a core group that contributes most cases and most meeting feedback; an active group that participates often but only sometimes contribute cases and feedback; and a large peripheral group that seldom or never contribute cases or feedback. SOMWeb is beneficial for individual clinicians as well as for the SOMNet community. The system provides an opportunity for its members to share both high quality clinical practice knowledge and external evidence related to complex oral medicine cases. The foundation in Semantic Web technologies enables formalization and structuring of case data that can be used for further reasoning and research. Main success factors are the long history of collaboration between different disciplines, the user-centered development approach, the existence of a "champion" within the field, and nontechnical community aspects already being in place.

SOMWeb: A Semantic Web-Based System for Supporting Collaboration of Distributed Medical Communities of Practice

PubMed Central

Gustafsson, Marie; Jontell, Mats; Torgersson, Olof

2008-01-01

Background Information technology (IT) support for remote collaboration of geographically distributed communities of practice (CoP) in health care must deal with a number of sociotechnical aspects of communication within the community. In the mid-1990s, participants of the Swedish Oral Medicine Network (SOMNet) began discussing patient cases in telephone conferences. The cases were distributed prior to the conferences using PowerPoint and email. For the technical support of online CoP, Semantic Web technologies can potentially fulfill needs of knowledge reuse, data exchange, and reasoning based on ontologies. However, more research is needed on the use of Semantic Web technologies in practice. Objectives The objectives of this research were to (1) study the communication of distributed health care professionals in oral medicine; (2) apply Semantic Web technologies to describe community data and oral medicine knowledge; (3) develop an online CoP, Swedish Oral Medicine Web (SOMWeb), centered on user-contributed case descriptions and meetings; and (4) evaluate SOMWeb and study how work practices change with IT support. Methods Based on Java, and using the Web Ontology Language and Resource Description Framework for handling community data and oral medicine knowledge, SOMWeb was developed using a user-centered and iterative approach. For studying the work practices and evaluating the system, a mixed-method approach of interviews, observations, and a questionnaire was used. Results By May 2008, there were 90 registered users of SOMWeb, 93 cases had been added, and 18 meetings had utilized the system. The introduction of SOMWeb has improved the structure of meetings and their discussions, and a tenfold increase in the number of participants has been observed. Users submit cases to seek advice on diagnosis or treatment, to show an unusual case, or to create discussion. Identified barriers to submitting cases are lack of time, concern about whether the case is interesting enough, and showing gaps in one’s own knowledge. Three levels of member participation are discernable: a core group that contributes most cases and most meeting feedback; an active group that participates often but only sometimes contribute cases and feedback; and a large peripheral group that seldom or never contribute cases or feedback. Conclusions SOMWeb is beneficial for individual clinicians as well as for the SOMNet community. The system provides an opportunity for its members to share both high quality clinical practice knowledge and external evidence related to complex oral medicine cases. The foundation in Semantic Web technologies enables formalization and structuring of case data that can be used for further reasoning and research. Main success factors are the long history of collaboration between different disciplines, the user-centered development approach, the existence of a “champion” within the field, and nontechnical community aspects already being in place. PMID:18725355

Core-periphery structure requires something else in the network

NASA Astrophysics Data System (ADS)

Kojaku, Sadamori; Masuda, Naoki

2018-04-01

A network with core-periphery structure consists of core nodes that are densely interconnected. In contrast to a community structure, which is a different meso-scale structure of networks, core nodes can be connected to peripheral nodes and peripheral nodes are not densely interconnected. Although core-periphery structure sounds reasonable, we argue that it is merely accounted for by heterogeneous degree distributions, if one partitions a network into a single core block and a single periphery block, which the famous Borgatti–Everett algorithm and many succeeding algorithms assume. In other words, there is a strong tendency that high-degree and low-degree nodes are judged to be core and peripheral nodes, respectively. To discuss core-periphery structure beyond the expectation of the node’s degree (as described by the configuration model), we propose that one needs to assume at least one block of nodes apart from the focal core-periphery structure, such as a different core-periphery pair, community or nodes not belonging to any meso-scale structure. We propose a scalable algorithm to detect pairs of core and periphery in networks, controlling for the effect of the node’s degree. We illustrate our algorithm using various empirical networks.

Distributed computing for macromolecular crystallography

PubMed Central

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Ballard, Charles

2018-01-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community. PMID:29533240

Distributed computing for macromolecular crystallography.

PubMed

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Winn, Martyn; Ballard, Charles

2018-02-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community.

An Analysis of Artificial Reef Fish Community Structure along the Northwestern Gulf of Mexico Shelf: Potential Impacts of “Rigs-to-Reefs” Programs

PubMed Central

Ajemian, Matthew J.; Wetz, Jennifer J.; Shipley-Lozano, Brooke; Shively, J. Dale; Stunz, Gregory W.

2015-01-01

Artificial structures are the dominant complex marine habitat type along the northwestern Gulf of Mexico (GOM) shelf. These habitats can consist of a variety of materials, but in this region are primarily comprised of active and reefed oil and gas platforms. Despite being established for several decades, the fish communities inhabiting these structures remain poorly investigated. Between 2012 and 2013 we assessed fish communities at 15 sites using remotely operated vehicles (ROVs). Fish assemblages were quantified from standing platforms and an array of artificial reef types (Liberty Ships and partially removed or toppled platforms) distributed over the Texas continental shelf. The depth gradient covered by the surveys (30–84 m) and variability in structure density and relief also permitted analyses of the effects of these characteristics on fish richness, diversity, and assemblage composition. ROVs captured a variety of species inhabiting these reefs from large transient piscivores to small herbivorous reef fishes. While structure type and relief were shown to influence species richness and community structure, major trends in species composition were largely explained by the bottom depth where these structures occurred. We observed a shift in fish communities and relatively high diversity at approximately 60 m bottom depth, confirming trends observed in previous studies of standing platforms. This depth was also correlated with some of the largest Red Snapper captured on supplementary vertical longline surveys. Our work indicates that managers of artificial reefing programs (e.g., Rigs-to-Reefs) in the GOM should carefully consider the ambient environmental conditions when designing reef sites. For the Texas continental shelf, reefing materials at a 50–60 m bottom depth can serve a dual purpose of enhancing diving experiences and providing the best potential habitat for relatively large Red Snapper. PMID:25954943

Recommendations for scale-up of community-based misoprostol distribution programs.

PubMed

Robinson, Nuriya; Kapungu, Chisina; Carnahan, Leslie; Geller, Stacie

2014-06-01

Community-based distribution of misoprostol for prevention of postpartum hemorrhage (PPH) in resource-poor settings has been shown to be safe and effective. However, global recommendations for prenatal distribution and monitoring within a community setting are not yet available. In order to successfully translate misoprostol and PPH research into policy and practice, several critical points must be considered. A focus on engaging the community, emphasizing the safe nature of community-based misoprostol distribution, supply chain management, effective distribution, coverage, and monitoring plans are essential elements to community-based misoprostol program introduction, expansion, or scale-up. Copyright © 2014 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Impact of climate variability on ichthyoplankton communities: An example of a small temperate estuary

NASA Astrophysics Data System (ADS)

Primo, Ana Lígia; Azeiteiro, Ulisses Miranda; Marques, Sónia Cotrim; Pardal, Miguel Ângelo

2011-03-01

Recent variations in the precipitation regime across southern Europe have led to changes in river fluxes and salinity gradients affecting biological communities in most rivers and estuaries. A sampling programme was developed in the Mondego estuary, Portugal, from January 2003 to December 2008 at five distinct sampling stations to evaluate spatial, seasonal and inter-annual distributions of fish larvae. Gobiidae was the most abundant family representing 80% of total catch and Pomatoschistus spp. was the most important taxon. The fish larval community presented a clear seasonality with higher abundances and diversities during spring and summer seasons. Multivariate analysis reinforced differences among seasons but not between years or sampling stations. The taxa Atherina presbyter, Solea solea, Syngnathus abaster, Crystallogobius linearis and Platichthys flesus were more abundant during spring/summer period while Ammodytes tobianus, Callionymus sp., Echiichthys vipera and Liza ramada were more abundant in autumn/winter. Temperature, chlorophyll a and river flow were the main variation drivers observed although extreme drought events (year 2005) seemed not to affect ichthyoplankton community structure. Main changes were related to a spatial displacement of salinity gradient along the estuarine system which produced changes in marine species distribution.

Microbial community structure and diversity in the soil spatial profile of 5-year-old Robinia pseudoacacia 'Idaho,' determined by 454 sequencing of the 16S RNA gene.

PubMed

Chang, Yanping; Bu, Xiangpan; Niu, Weibo; Xiu, Yu; Wang, Huafang

2013-01-01

Relatively little information is available regarding the variability of microbial communities inhabiting deeper soil layers. We investigated the distribution of soil microbial communities down to 1.2 m in 5-year-old Robinia pseudoacacia 'Idaho' soil by 454 sequencing of the 16S RNA gene. The average number of sequences per sample was 12,802. The Shannon and Chao 1 indices revealed various relative microbial abundances and even distribution of microbial diversity for all evaluated sample depths. The predicted diversity in the topsoil exceeded that of the corresponding subsoil. The changes in the relative abundance of the major soil bacterial phyla showed decreasing, increasing, or no consistent trends with respect to sampling depth. Despite their novelty, members of the new candidate phyla OD1 and TM7 were widespread. Environmental variables affecting the bacterial community within the environment appeared to differ from those reported previously, especially the lack of detectable effect from pH. Overall, we found that the overall relative abundance fluctuated with the physical and chemical properties of the soil, root system, and sampling depth. Such information may facilitate forest soil management.

Effect of long-term mechanical perturbation on intertidal soft-bottom meiofaunal community spatial structure

NASA Astrophysics Data System (ADS)

Boldina, Inna; Beninger, Peter G.; Le Coz, Maïwen

2014-01-01

Situated at the interface of the microbial and macrofaunal compartments, soft-bottom meiofauna accomplish important ecological functions. However, little is known of their spatial distribution in the benthic environment. To assess the effects of long-term mechanical disturbance on soft-bottom meiofaunal spatial distribution, we compared a site subjected to long-term clam digging to a nearby site untouched by such activities, in Bourgneuf Bay, on the Atlantic coast of France. Six patterned replicate samples were taken at 3, 6, 9, 12, 15, 18, 21 and 24 cm lags, all sampling stations being separated by 5 m. A combined correlogram-variogram approach was used to enhance interpretation of the meiofaunal spatial distribution; in particular, the definition of autocorrelation strength and its statistical significance, as well as the detailed characteristics of the periodic spatial structure of nematode assemblages, and the determination of the maximum distance of their spatial autocorrelation. At both sites, nematodes and copepods clearly exhibited aggregated spatial structure at the meso scale; this structure was attenuated at the impacted site. The nematode spatial distribution showed periodicity at the non-impacted site, but not at the impacted site. This is the first explicit report of a periodic process in meiofaunal spatial distribution. No such cyclic spatial process was observed for the more motile copepods at either site. This first study to indicate the impacts of long-term anthropogenic mechanical perturbation on meiofaunal spatial structure opens the door to a new dimension of mudflat ecology. Since macrofaunal predator search behaviour is known to be strongly influenced by prey spatial structure, the alteration of this structure may have important consequences for ecosystem functioning.

Effects of haze pollution on microbial community changes and correlation with chemical components in atmospheric particulate matter.

PubMed

Sun, Yujiao; Xu, Shangwei; Zheng, Danyang; Li, Jie; Tian, Hezhong; Wang, Yong

2018-05-10

In this study, particulate matter (PM) with aerodynamic diameters of ≤2.5 and ≤10 μm (PM 2.5 and PM 10 , respectively), which was found at different concentrations in spring, was collected in Beijing. The chemical composition and bacterial community diversity of PM were determined, and the relationship between them was studied by 16S rRNA sequencing and mathematical statistics. Chemical composition analysis revealed greater relative percentages of total organic compounds (TOC) and secondary ions (NO 3 - , SO 4 2- , and NH 4 + ). The concentrations of Ca 2+ , Na + , Mg 2+ , K + and SO 4 2- increased in high-concentration PM, which was associated with the contribution of soil, dust and soot. Microbiological analysis revealed 1191 operational taxonomic units. Microbial community structure was stable at the phylum level. The most abundant phyla were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Community clustering analysis at the genus level showed that the difference in bacterial community structure between different PM concentrations (clean air vs. smog) was greater than that between different particle sizes. The dominant genera varied in different concentrations of PM. An unclassified genus of Cyanobacteria and Comamonadaceae were most abundant in low- and high-concentration PM, respectively. The microbial community structure was dynamic at the genus level due to different environmental factors. The dominant bacteria in high-concentration PM were widely distributed in soils, indicating that the soil contributed more to the increase in the PM. The individual microbes that were detected did not increase significantly as the PM concentration increased. The bacterial community structure was strongly correlated with K + , Ca 2+ , Na + , Mg 2+ , SO 4 2- and TOC in high-concentration PM and had a good correlation with NO 3 - , Cl - , NH 4 + and TIC in low-concentration PM. Soil and dust contributed to the increase in the concentration of the particles, and the relevant chemical components also produced differences in the bacterial community structure in different concentrations of PM. Copyright © 2018. Published by Elsevier B.V.

Fine-scale spatial patterns in the demersal fish and invertebrate community in a northwest Atlantic ecosystem

NASA Astrophysics Data System (ADS)

Malek, Anna J.; Collie, Jeremy S.; Gartland, James

2014-06-01

The abundance, biomass, diversity, and species composition of the demersal fish and invertebrate community in Rhode Island Sound and Block Island Sound, an area identified for offshore renewable energy development, were evaluated for spatial and seasonal structure. We conducted 58 otter trawls and 51 beam trawls in the spring, summer and fall of 2009-2012, and incorporated additional data from 88 otter trawls conducted by the Northeast Area Monitoring and Assessment Program. We used regionally-grouped abundance, biomass, diversity, and size spectra to assess spatial patterns in the aggregate fish community, and hierarchical cluster analysis to evaluate trends in species assemblages. Our analyses revealed coherent gradients in fish community biomass, diversity and species composition extending from inshore to offshore waters, as well as patterns related to the differing bathymetry of Rhode Island and Block Island Sounds. The fish communities around Block Island and Cox's Ledge are particularly diverse, suggesting that the proximity of hard bottom habitat may be important in structuring fish communities in this area. Species assemblages in Rhode Island and Block Island Sounds are characterized by a combination of piscivores (silver hake, summer flounder, spiny dogfish), benthivores (American lobster, black sea bass, Leucoraja spp. skates, scup) and planktivores (sea scallop), and exhibit geographic patterns that are persistent from year to year, yet variable by season. Such distributions reflect the cross-shelf migration of fish and invertebrate species in the spring and fall, highlighting the importance of considering seasonal fish behavior when planning construction schedules for offshore development projects. The fine spatial scale (10 s of kms) of this research makes it especially valuable for local marine spatial planning efforts by identifying local-scale patterns in fish community structure that will enable future assessment of the ecological impacts of offshore development. As such, this knowledge of the spatial and temporal structure of the demersal fish community in Rhode Island and Block Island Sounds will help to guide the placement of offshore structures so as to preserve the ecological and economic value of the area.

Dual-Carbon sources fuel the OCS deep-reef Community, a stable isotope investigation

USGS Publications Warehouse

Sulak, Kenneth J.; Berg, J.; Randall, Michael T.; Dennis, George D.; Brooks, R.A.

2008-01-01

The hypothesis that phytoplankton is the sole carbon source for the OCS deep-reef community (>60 m) was tested. Trophic structure for NE Gulf of Mexico deep reefs was analyzed via carbon and nitrogen stable isotopes. Carbon signatures for 114 entities (carbon sources, sediment, fishes, and invertebrates) supported surface phytoplankton as the primary fuel for the deep reef. However, a second carbon source, the macroalga Sargassum, with its epiphytic macroalgal associate, Cladophora liniformis, was also identified. Macroalgal carbon signatures were detected among 23 consumer entities. Most notably, macroalgae contributed 45 % of total carbon to the 13C isotopic spectrum of the particulate-feeding reef-crest gorgonian Nicella. The discontinuous spatial distribution of some sessile deep-reef invertebrates utilizing pelagic macroalgal carbon may be trophically tied to the contagious distribution of Sargassum biomass along major ocean surface features.

Effect of Rice Cultivation Systems on Indigenous Arbuscular Mycorrhizal Fungal Community Structure

PubMed Central

Watanarojanaporn, Nantida; Boonkerd, Nantakorn; Tittabutr, Panlada; Longtonglang, Aphakorn; Young, J. Peter W.; Teaumroong, Neung

2013-01-01

Arbuscular mycorrhizal fungi (AMF) in an agricultural ecosystem are necessary for proper management of beneficial symbiosis. Here we explored how the patterns of the AMF community in rice roots were affected by rice cultivation systems (the system of rice intensification [SRI] and the conventional rice cultivation system [CS]), and by compost application during growth stages. Rice plants harvested from SRI-managed plots exhibited considerably higher total biomass, root dry weight, and seed fill than those obtained from conventionally managed plots. Our findings revealed that all AMF sequences observed from CS plots belonged (only) to the genus Glomus, colonizing in rice roots grown under this type of cultivation, while rice roots sown in SRI showed sequences belonging to both Glomus and Acaulospora. The AMF community was compared between the different cultivation types (CS and SRI) and compost applications by principle component analysis. In all rice growth stages, AMF assemblages of CS management were not separated from those of SRI management. The distribution of AMF community composition based on T-RFLP data showed that the AMF community structure was different among four cultivation systems, and there was a gradual increase of Shannon-Weaver indices of diversity (H′) of the AMF community under SRI during growth stages. The results of this research indicated that rice grown in SRI-managed plots had more diverse AMF communities than those grown in CS plots. PMID:23719585

Copepod distribution and biodiversity patterns from the surface to the deep sea along a latitudinal transect in the eastern Atlantic Ocean (24°N to 21°S)

NASA Astrophysics Data System (ADS)

Bode, Maya; Hagen, Wilhelm; Cornils, Astrid; Kaiser, Patricia; Auel, Holger

2018-02-01

Vertical distribution, community structure and diversity of calanoid copepods were studied at six stations along a latitudinal transect from 24°N to 21°S in the eastern Atlantic Ocean, resolving nine discrete depth layers to 2000 m. Total copepod abundances integrated from 0 to 2000 m ranged from 148,000 to 197,000 ind m-2. Usually, abundance and biomass were highest in the upper 100 m, exponentially decreasing with increasing depth. Only at the northern- and southernmost stations, a deeper biomass maximum was observed at 100-200 m and 200-400 m, respectively. In total, 26 families, 79 genera and at least 172 species were identified among calanoid copepods. Although there were certain regional differences in species composition between tropical and subtropical stations from north to south, depth had the strongest impact on the community structure of calanoids, resulting in statistically distinct communities in different depth zones. Maximum diversity of calanoids was observed between 100-200 m in the tropical zone and between 400-700 m in subtropical regions. Various interacting mechanisms such as vast spatial extent of the ecosystem, physical stability, avoidance from predators under dim light, small population sizes and high biologically generated heterogeneity possibly contribute to the biodiversity maxima in the twilight zone.

Biofilm structures (EPS and bacterial communities) in drinking water distribution systems are conditioned by hydraulics and influence discolouration.

PubMed

Fish, K; Osborn, A M; Boxall, J B

2017-09-01

High-quality drinking water from treatment works is degraded during transport to customer taps through the Drinking Water Distribution System (DWDS). Interactions occurring at the pipe wall-water interface are central to this degradation and are often dominated by complex microbial biofilms that are not well understood. This study uses novel application of confocal microscopy techniques to quantify the composition of extracellular polymeric substances (EPS) and cells of DWDS biofilms together with concurrent evaluation of the bacterial community. An internationally unique, full-scale, experimental DWDS facility was used to investigate the impact of three different hydraulic patterns upon biofilms and subsequently assess their response to increases in shear stress, linking biofilms to water quality impacts such as discolouration. Greater flow variation during growth was associated with increased cell quantity but was inversely related to EPS-to-cell volume ratios and bacterial diversity. Discolouration was caused and EPS was mobilised during flushing of all conditions. Ultimately, biofilms developed under low-varied flow conditions had lowest amounts of biomass, the greatest EPS volumes per cell and the lowest discolouration response. This research shows that the interactions between hydraulics and biofilm physical and community structures are complex but critical to managing biofilms within ageing DWDS infrastructure to limit water quality degradation and protect public health. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Physical Habitat and Energy Inputs Determine Freshwater Invertebrate Communities in Reference and Cranberry Farm Impacted Northeastern Coastal Zone Streams

NASA Astrophysics Data System (ADS)

Lander, D. M. P.; McCanty, S. T.; Dimino, T. F.; Christian, A. D.

2016-02-01

The River Continuum Concept (RCC) predicts stream biological communities based on dominant physical structures and energy inputs into streams and predicts how these features and corresponding communities change along the stream continuum. Verifying RCC expectations is important for creating valid points of comparison during stream ecosystem evaluation. These reference expectations are critical for restoration projects, such as the restoration of decommissioned cranberry bogs. Our research compares the physical habitat and freshwater invertebrate functional feeding groups (FWIFFG) of reference, active cranberry farming, and cranberry farm passive restoration sites in Northeastern Coastal Zone streams of Massachusetts to the specific RCC FWIFFG predictions. We characterized stream physical habitat using a semi-quantitative habitat characterization protocol and sampled freshwater invertebrates using the U.S. EPA standard 20-jab multi-habitat protocol. We expected that stream habitat would be most homogeneous at active farming stations, intermediate at restoration stations, and most heterogeneous at reference stations. Furthermore, we expected reference stream FWIFFG would be accurately predicted by the RCC and distributions at restoration and active sites would vary significantly. Habitat data was analyzed using a principle component analysis and results confirmed our predictions showing more homogeneous habitat for the active and reference stations, while showing a more heterogeneous habitat at the reference stations. The FWIFFG chi-squared analysis showed significant deviation from our specific RCC FWIFFG predictions. Because published FWIFFG distributions did not match our empirical values for a least disturbed Northeastern Coastal Zone headwater stream, using our data as a community structure template for current and future restoration projects is not recommend without further considerations.

Homophyly/kinship hypothesis: Natural communities, and predicting in networks

NASA Astrophysics Data System (ADS)

Li, Angsheng; Li, Jiankou; Pan, Yicheng

2015-02-01

It has been a longstanding challenge to understand natural communities in real world networks. We proposed a community finding algorithm based on fitness of networks, two algorithms for prediction, accurate prediction and confirmation of keywords for papers in the citation network Arxiv HEP-TH (high energy physics theory), and the measures of internal centrality, external de-centrality, internal and external slopes to characterize the structures of communities. We implemented our algorithms on 2 citation and 5 cooperation graphs. Our experiments explored and validated a homophyly/kinship principle of real world networks. The homophyly/kinship principle includes: (1) homophyly is the natural selection in real world networks, similar to Darwin's kinship selection in nature, (2) real world networks consist of natural communities generated by the natural selection of homophyly, (3) most individuals in a natural community share a short list of common attributes, (4) natural communities have an internal centrality (or internal heterogeneity) that a natural community has a few nodes dominating most of the individuals in the community, (5) natural communities have an external de-centrality (or external homogeneity) that external links of a natural community homogeneously distributed in different communities, and (6) natural communities of a given network have typical structures determined by the internal slopes, and have typical patterns of outgoing links determined by external slopes, etc. Our homophyly/kinship principle perfectly matches Darwin's observation that animals from ants to people form social groups in which most individuals work for the common good, and that kinship could encourage altruistic behavior. Our homophyly/kinship principle is the network version of Darwinian theory, and builds a bridge between Darwinian evolution and network science.