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Sample records for actinobacterial community structure

  1. Actinobacterial Community Structure in Soils Receiving Long-Term Organic and Inorganic Amendments▿ †

    Piao, Zhe; Yang, Linzhang; Zhao, Liping; Yin, Shixue

    2007-01-01

    The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from e...

  2. Actinobacterial community dynamics in long term managed grasslands.

    Jenkins, Sasha N; Waite, Ian S; Blackburn, Adrian; Husband, Rebecca; Rushton, Steven P; Manning, David C; O'Donnell, Anthony G

    2009-05-01

    Palace Leas, a long-term experiment at Cockle Park Farm, Northumberland, UK was established in winter 1896-1897 since when the 13 plots have received regular and virtually unchanged mineral fertiliser and farm yard manure inputs. Fertilisers have had a profound impact on soil pH with the organically fertilised plots showing a significantly higher pH than those receiving mineral fertiliser where ammonium sulphate has led to soil acidification. Here, we investigate the impact of organic and mineral fertilisers on the actinobacterial community structure of these soils using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene analysis. To differentiate fertiliser effects from seasonal variation, soils were sampled three times over one growing season between May and September 2004 and January 2005. Community profiles obtained using T-RFLP were analysed using multivariate statistics to investigate the relationship between community structure, seasonality and fertiliser management. Soil pH was shown to be the most significant edaphic factor influencing actinobacterial communities. Canonical correspondence analysis, used to investigate the relationship between the 16S rRNA gene community profiles and the environmental parameters, showed that actinobacterial communities also responded to soil water content with major changes evident over the summer months between May and September. Quantitative PCR of the actinobacterial and fungal 16S and 18S rRNA genes, respectively suggested that fungal rRNA gene copy numbers were negatively correlated (P = 0.0131) with increasing actinobacterial signals. A similar relationship (P = 0.000365) was also evident when fatty acid methyl esters indicative of actinobacterial biomass (10-methyloctadecanoic acid) were compared with the amounts of fungal octadecadienoic acid (18:2omega9,12). These results show clearly that soil pH is a major driver of change in actinobacterial communities and that genera such as

  3. Characterization of Eubacterial and Actinobacterial communities of contrasting terrestrial soils and sediments

    Hill, P.; Krištůfek, Václav; Bolhuis, H.; Martinez, A. F.; Kroetsch, D.; van Elsas, J.D.

    Newcastle upon Tyne: International Commitee, UK body, University of Newcastle upon Tyne, 2007. s. 185. [International Symposium on the Biology of Actinomycetes /14./. 26.08.2007-30.08.2007, The Sage Gateshead] Institutional research plan: CEZ:AV0Z60660521 Keywords : Eubacterial communities * Actinobacterial communities * contrasting terrestrial soils Subject RIV: EH - Ecology, Behaviour

  4. Actinobacterial community dominated by a distinct clade in acidic soil of a waterlogged deciduous forest

    Kopecký, J.; Kyselková, Martina; Omelka, M.; Čermák, L.; Novotná, J.; Grundmann, G.L.; Moënne-Loccoz, Y.; Ságová-Marečková, M.

    2011-01-01

    Roč. 78, č. 2 (2011), s. 386-394. ISSN 0168-6496 Grant ostatní: GA AVČR(CZ) IAA603020901; GA ČR(CZ) GPP201/11/P290 Institutional research plan: CEZ:AV0Z60660521 Keywords : actinobacterial community * gley soil * soil organic matter Subject RIV: EH - Ecology, Behaviour Impact factor: 3.408, year: 2011

  5. Actinobacterial Flora in Feces of Healthy Cottontail Rabbits (Sylvilagus auduboni).

    Zhang, Yu; Tan, Hongming; Deng, Qingli; Cao, Lixiang

    2015-03-01

    Most known antibiotics from bacteria are produced by Actinobacteria. However, little is known about the community structure and diversity of fecal actinobacteria from rabbit feces. To investigate the actinobacterial community structure in rabbit feces, different actinobacterial-specific primer sets were used to amplify the overlap regions of 16S rRNA genes from the same DNA. At the genus level, 12 actinobacterial genera were detected by the L and S libraries. Arthrobacter, Brachybacterium, Dietzia, Leucobacter, Microbacterium, Promicromonospora and Rhodococcus were detected by L and S libraries. The Nocardioides, Streptomyces and Williamsia were only detected by L library; the Oerskovia and Brevibacterium were only detected by S library. The results indicated that rabbit feces contain diverse nonpathogenic actinobacterial taxa and PCR primer sets could underestimate the actinobacterial diversity besides the DNA extract efficiency. PMID:25424303

  6. An in-depth analysis of actinobacterial communities shows their high diversity in grassland soils along a gradient of mixed heavy metal contamination

    Větrovský, Tomáš; Baldrian, Petr

    2015-01-01

    Roč. 51, č. 7 (2015), s. 827-837. ISSN 0178-2762 R&D Projects: GA AV ČR IAA603020901; GA MŠk LD12048; GA MŠk LD12050; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : Actinobacterial * 16S rDNA * Pyrosequencing Subject RIV: EE - Microbiology, Virology Impact factor: 3.398, year: 2014

  7. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

    Riquelme, Cristina; Marshall Hathaway, Jennifer J.; Enes Dapkevicius, Maria de L. N.; Miller, Ana Z.; Kooser, Ara; Northup, Diana E.; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

    2015-01-01

    Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in

  8. Structuring of Forest Communities

    S. K. Farber

    2014-02-01

    Full Text Available Structuring forest communities is considered as a pre-studying procedure. The paper defines the fundamental structuring terms and describes the theory behind it. Factors hampering forest typology development are discussed. The areas of forest typology promising regarding sustainable and multi-purposed forest management are outlined.

  9. A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

    Finan Christopher L

    2005-03-01

    Full Text Available Abstract Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria. The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope.

  10. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification.

    Yang, Qi; Franco, Christopher M M; Zhang, Wei

    2015-10-01

    Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity. PMID:26245685

  11. Community structure and criminal victimization

    Anzick, Michael A.

    1989-01-01

    This research has attempted to better understand property crime victimization by studying the important role of community structures, while controlling for the following demographic variables: age, gender, race, and income. Three different types of analyses were used: (1) bivariate analysis; (2) multivariate analysis, and (3) path analysis. Bivariate analysis was used in order to gain a better understanding of the following zero-order relationships: (1) the relationship between...

  12. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds.

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-03-26

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents. PMID:26947442

  13. An evolving network model with community structure

    Many social and biological networks consist of communities-groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting community structures in real-world complex networks. In this paper, we propose an evolving network model which exhibits community structure. The network model is based on the inner-community preferential attachment and inter-community preferential attachment mechanisms. The degree distributions of this network model are analysed based on a mean-field method. Theoretical results and numerical simulations indicate that this network model has community structure and scale-free properties

  14. Identifying Community Structures in Dynamic Networks

    Alvari, Hamidreza; Sukthankar, Gita; Lakkaraju, Kiran

    2016-01-01

    Most real-world social networks are inherently dynamic, composed of communities that are constantly changing in membership. To track these evolving communities, we need dynamic community detection techniques. This article evaluates the performance of a set of game theoretic approaches for identifying communities in dynamic networks. Our method, D-GT (Dynamic Game Theoretic community detection), models each network node as a rational agent who periodically plays a community membership game with its neighbors. During game play, nodes seek to maximize their local utility by joining or leaving the communities of network neighbors. The community structure emerges after the game reaches a Nash equilibrium. Compared to the benchmark community detection methods, D-GT more accurately predicts the number of communities and finds community assignments with a higher normalized mutual information, while retaining a good modularity.

  15. Flexible Community Structure Correlates with Stable Community Function in Methanogenic Bioreactor Communities Perturbed by Glucose

    Fernandez, Ana S.; Hashsham, Syed A.; Dollhopf, Sherry L.; Raskin, Lutgarde; Glagoleva, Olga; Dazzo, Frank B.; Hickey, Robert F.; Criddle, Craig S.; Tiedje, James M.

    2000-01-01

    Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDR...

  16. Enhancing community detection by local structural information

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

    2016-01-01

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

  17. Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India and their antimicrobial activities

    Salam eNimaichand

    2015-05-01

    Full Text Available Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups, Micromonospora (4, Amycolatopsis (3, Arthrobacter (3, Kitasatospora (2, Janibacter (1, Nocardia (1, Pseudonocardia (1 and Rhodococcus (1. Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS. The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

  18. Community structure in the phonological network

    Cynthia S. Q. Siew

    2013-08-01

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

  19. Social significance of community structure: Statistical view

    Li, Hui-Jia

    2015-01-01

    Community structure analysis is a powerful tool for social networks, which 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 community structure partitioned is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a novel framework analyzing the significance of social community specially. 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 nodes and their corresponding leaders. Then, using log-likelihood sco...

  20. Matching Community Structure Across Online Social Networks

    Li, Lin

    2016-01-01

    The discovery of community structure in networks is a problem of considerable interest in recent years. In online social networks, often times, users are simultaneously involved in multiple social media sites, some of which share common social relationships. It is of great interest to uncover a shared community structure across these networks. However, in reality, users typically identify themselves with different usernames across social media sites. This creates a great difficulty in detecting the community structure. In this paper, we explore several approaches for community detection across online social networks with limited knowledge of username alignment across the networks. We refer to the known alignment of usernames as seeds. We investigate strategies for seed selection and its impact on networks with a different fraction of overlapping vertices. The goal is to study the interplay between network topologies and seed selection strategies, and to understand how it affects the detected community structu...

  1. Finding local community structure in networks

    Clauset, A

    2005-01-01

    Although the inference of global community structure in networks has recently become a topic of great interest in the physics community, all such algorithms require that the graph be completely known. Here, we define both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time. This algorithm runs in time O(d*k^2) for general graphs when $d$ is the mean degree and k is the number of vertices to be explored. For graphs where exploring a new vertex is time-consuming, the running time is linear, O(k). We show that on computer-generated graphs this technique compares favorably to algorithms that require global knowledge. We also use this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer and show the existence of mesoscopic structure.

  2. Hierarchical community structure in complex (social) networks

    Massaro, Emanuele

    2014-01-01

    The investigation of community structure in networks is a task of great importance in many disciplines, namely physics, sociology, biology and computer science where systems are often represented as graphs. One of the challenges is to find local communities from a local viewpoint in a graph without global information in order to reproduce the subjective hierarchical vision for each vertex. In this paper we present the improvement of an information dynamics algorithm in which the label propagation of nodes is based on the Markovian flow of information in the network under cognitive-inspired constraints \\cite{Massaro2012}. In this framework we have introduced two more complex heuristics that allow the algorithm to detect the multi-resolution hierarchical community structure of networks from a source vertex or communities adopting fixed values of model's parameters. Experimental results show that the proposed methods are efficient and well-behaved in both real-world and synthetic networks.

  3. Impact of Community Structure on Cascades

    Moharrami, Mehrdad; Subramanian, Vijay; Liu, Mingyan; Lelarge, Marc

    2016-01-01

    The threshold model is widely used to study the propagation of opinions and technologies in social networks. In this model individuals adopt the new behavior based on how many neighbors have already chosen it. We study cascades under the threshold model on sparse random graphs with community structure to see whether the existence of communities affects the number of individuals who finally adopt the new behavior. Specifically, we consider the permanent adoption model where nodes that have ado...

  4. Rocky Intertidal Community Structure on Different Substrates

    Osborn, Dawn A.

    2005-01-01

    The extensive anthropogenic armoring of the shoreline in California changes the substrate available to settling invertebrate larvae and algal spores that are passively distributed in the ocean currents. Rock types available to settlers likely influences community structure in the intertidal, as rock characteristics have been shown to favor or inhibit settlement. Much research has been done examining the mechanisms that determine intertidal community patterns, but the role of rock type has bee...

  5. Centrality measures for networks with community structure

    Gupta, Naveen; Singh, Anurag; Cherifi, Hocine

    2016-06-01

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

  6. Finding Community Structures In Social Activity Data

    Peng, Chengbin

    2015-05-19

    Social activity data sets are increasing in number and volume. Finding community structure in such data is valuable in many applications. For example, understand- ing the community structure of social networks may reduce the spread of epidemics or boost advertising revenue; discovering partitions in tra c networks can help to optimize routing and to reduce congestion; finding a group of users with common interests can allow a system to recommend useful items. Among many aspects, qual- ity of inference and e ciency in finding community structures in such data sets are of paramount concern. In this thesis, we propose several approaches to improve com- munity detection in these aspects. The first approach utilizes the concept of K-cores to reduce the size of the problem. The K-core of a graph is the largest subgraph within which each node has at least K connections. We propose a framework that accelerates community detection. It first applies a traditional algorithm that is relatively slow to the K-core, and then uses a fast heuristic to infer community labels for the remaining nodes. The second approach is to scale the algorithm to multi-processor systems. We de- vise a scalable community detection algorithm for large networks based on stochastic block models. It is an alternating iterative algorithm using a maximum likelihood ap- proach. Compared with traditional inference algorithms for stochastic block models, our algorithm can scale to large networks and run on multi-processor systems. The time complexity is linear in the number of edges of the input network. The third approach is to improve the quality. We propose a framework for non- negative matrix factorization that allows the imposition of linear or approximately linear constraints on each factor. An example of the applications is to find community structures in bipartite networks, which is useful in recommender systems. Our algorithms are compared with the results in recent papers and their quality and e

  7. Phylogenetic structure in tropical hummingbird communities

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten;

    2009-01-01

    sustaining an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast......How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic...... composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...

  8. Emergent Community Structure in Social Tagging Systems

    Cattuto, Ciro; Servedio, Vito D P; Loreto, Vittorio

    2008-01-01

    A distributed classification paradigm known as collaborative tagging has been widely adopted in new Web applications designed to manage and share online resources. Users of these applications organize resources (Web pages, digital photographs, academic papers) by associating with them freely chosen text labels, or tags. Here we leverage the social aspects of collaborative tagging and introduce a notion of resource distance based on the collective tagging activity of users. We collect data from a popular system and perform experiments showing that our definition of distance can be used to build a weighted network of resources with a detectable community structure. We show that this community structure clearly exposes the semantic relations among resources. The communities of resources that we observe are a genuinely emergent feature, resulting from the uncoordinated activity of a large number of users, and their detection paves the way for mapping emergent semantics in social tagging systems.

  9. Emergence of structured communities through evolutionary dynamics.

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

    2015-10-21

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

  10. Modelling community structure in freshwater ecosystems

    Lek, S.; Scardi, M.; Verdonschot, P.F.M.; Descy, J.P.; Park, Y.S.

    2005-01-01

    The book presents approaches and methodologies for predicting the structure and diversity of key aquatic communities (namely diatoms, benthic macroinvertebrates and fish), under natural conditions and under man-made disturbance. Such an approach will make it possible to: 1) set up procedures for rob

  11. School, Community Leadership, and Election Structure

    Allen, Ann

    2008-01-01

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

  12. The nested structure of a scavenger community

    Selva, Nuria; Fortuna, Miguel A

    2007-01-01

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

  13. Spatial and temporal changes in Actinobacterial dominance in experimental artificial groundwater recharge.

    Kolehmainen, Reija E; Tiirola, Marja; Puhakka, Jaakko A

    2008-11-01

    Artificial groundwater recharge (AGR) is used in the drinking water industry to supplement groundwater resources and to minimise the use of chemicals in water treatment. This study analysed the spatial and temporal changes of microbial communities in AGR using two test systems: a nutrient-amended fluidized-bed reactor (FBR) and a sand column. Structural changes in the feed lake water (Lake Roine), FBR, and sand column bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) and the length heterogeneity analysis of amplified 16S rRNA genes (LH-PCR). Two clone libraries were created to link the LH-PCR results to the dominant bacterial groups. The lake water bacterial community was relatively stable, with three bands dominating in all LH-PCR products. The most dominant fragment accounted for up to 72% and was derived from Actinobacteria. Based on the clone libraries and LH-PCR data, Actinobacteria also dominated in the unattached bacterial community of the FBR, whereas several Proteobacterial groups were more abundant on the FBR carrier particles. In the stabilised AGR system a major change in the community structure of the lake water bacteria took place during passage within the first 0.6m in the sand column as the community composition shifted from Actinobacteria-dominated populations to a diverse, mainly Proteobacterial communities. Concurrently, most of the dissolved organic carbon (DOC) was removed at this stage. In summary, the study showed that the make-up of microbial communities in experimental AGR systems responded to changes in their environment. LH-PCR showed potential as a method to determine microbial community dynamics in long-term studies at real-scale AGR sites. This is the first step to provide data on microbial community dynamics in AGR for drinking water production. PMID:18757075

  14. Community structure and dynamics in social systems

    Wilkinson, Dennis M.

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

  15. Information transfer in community structured multiplex networks

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

    2015-08-01

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

  16. A preferential attachment approach to community structure and the structure of communities

    Young, Jean-Gabriel; Allard, Antoine; Dubé, Louis J

    2016-01-01

    We introduce an intuitive mechanism to describe both the emergence of community structure and the evolution of the internal structure of communities in social networks. Our idea is based on the simple assumption that each individual can, for every social group to which it belongs, develop connections and introduce new members. Complex behaviors emerge from opposing time scales for the activities of individuals and for the sum of individuals gathered in groups. We show how the resulting model reproduces behaviors observed in real social networks and in the anthropological theory known as Dunbar's number, i.e. the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. Using this growth process, we organically reproduce the micro and mesoscopic structure of social networks. In so doing, we highlight two interesting properties of the community structure of social networks. First, strong correlations between the number of communities to which a node belo...

  17. Walk modularity and community structure in networks

    Mehrle, David; Harkin, Anthony

    2014-01-01

    Modularity maximization has been one of the most widely used approaches in the last decade for discovering community structure in networks of practical interest in biology, computing, social science, statistical mechanics, and more. Modularity is a quality function that measures the difference between the number of edges found within clusters minus the number of edges one would statistically expect to find based on random chance. We present a natural generalization of modularity based on the difference between the actual and expected number of walks within clusters, which we call walk-modularity. Walk-modularity can be expressed in matrix form, and community detection can be performed by finding leading eigenvectors of the walk-modularity matrix. We demonstrate community detection on both synthetic and real-world networks and find that walk-modularity maximization returns significantly improved results compared to traditional modularity maximization.

  18. Distance, dissimilarity index, and network community structure

    Zhou, H

    2003-01-01

    We address the question of finding the community structure of a complex network. In an earlier effort [H. Zhou, {\\em Phys. Rev. E} (2003)], the concept of network random walking is introduced and a distance measure defined. Here we calculate, based on this distance measure, the dissimilarity index between nearest-neighboring vertices of a network and design an algorithm to partition these vertices into communities that are hierarchically organized. Each community is characterized by an upper and a lower dissimilarity threshold. The algorithm is applied to several artificial and real-world networks, and excellent results are obtained. In the case of artificially generated random modular networks, this method outperforms the algorithm based on the concept of edge betweenness centrality. For yeast's protein-protein interaction network, we are able to identify many clusters that have well defined biological functions.

  19. Identifying community structure in complex networks

    Shao, Chenxi; Duan, Yubing

    2015-07-01

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

  20. (Actino)Bacterial "intelligence": using comparative genomics to unravel the information processing capacities of microbes.

    Pinto, Daniela; Mascher, Thorsten

    2016-08-01

    Bacterial genomes encode numerous and often sophisticated signaling devices to perceive changes in their environment and mount appropriate adaptive responses. With their help, microbes are able to orchestrate specific decision-making processes that alter the cellular behavior, but also integrate and communicate information. Moreover and beyond, some signal transducing systems also enable bacteria to remember and learn from previous stimuli to anticipate environmental changes. As recently suggested, all of these aspects indicate that bacteria do, in fact, exhibit cognition remarkably reminiscent of what we refer to as intelligent behavior, at least when referred to higher eukaryotes. In this essay, comprehensive data derived from comparative genomics analyses of microbial signal transduction systems are used to probe the concept of cognition in bacterial cells. Using a recent comprehensive analysis of over 100 actinobacterial genomes as a test case, we illustrate the different layers of the capacities of bacteria that result in cognitive and behavioral complexity as well as some form of 'bacterial intelligence'. We try to raise awareness to approach bacteria as cognitive organisms and believe that this view would enrich and open a new path in the experimental studies of bacterial signal transducing systems. PMID:26852121

  1. Taxonomies of networks from community structure

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

    2012-09-01

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

  2. Community-oriented support and research structures

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

    2009-07-01

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

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

    Chertoprud, M V

    2007-01-01

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

  4. Information transfer in community structured multiplex networks

    Solé-Ribalta, Albert; Gómez, Sergio; Arenas, Alex

    2015-01-01

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

  5. Immunization of networks with community structure

    In this study, an efficient method to immunize modular networks (i.e. networks with community structure) is proposed. The immunization of networks aims at fragmenting networks into small parts with a small number of removed nodes. Its applications include prevention of epidemic spreading, protection against intentional attacks on networks, and conservation of ecosystems. Although preferential immunization of hubs is efficient, good immunization strategies for modular networks have not been established. On the basis of an immunization strategy based on eigenvector centrality, we develop an analytical framework for immunizing modular networks. To this end, we quantify the contribution of each node to the connectivity in a coarse-grained network among modules. We verify the effectiveness of the proposed method by applying it to model and real networks with modular structure.

  6. Community structure in introductory physics course networks

    Traxler, Adrienne L

    2015-01-01

    Student-to-student interactions are foundational to many active learning environments, but are most often studied using qualitative methods. Network analysis tools provide a quantitative complement to this picture, allowing researchers to describe the social interactions of whole classrooms as systems. Past results from introductory physics courses have suggested a sharp division in the formation of social structure between large lecture sections and small studio classroom environments. Extending those results, this study focuses on calculus-based introductory physics courses at a large public university with a heavily commuter and nontraditional student population. Community detection network methods are used to characterize pre- and post-course collaborative structure in several sections, and differences are considered between small and large classes. These results are compared with expectations from earlier findings, and comment on implications for instruction and further study.

  7. Permanence and Community Structure in Complex Networks

    Chakraborty, Tanmoy; Ganguly, Niloy; Mukherjee, Animesh; Bhowmick, Sanjukta

    2016-01-01

    The goal of community detection algorithms is to identify densely-connected units within large networks. An implicit assumption is that all the constituent nodes belong equally to their associated community. However, some nodes are more important in the community than others. To date, efforts have been primarily driven to identify communities as a whole, rather than understanding to what extent an individual node belongs to its community. Therefore, most metrics for evaluating communities, for example modularity, are global. These metrics produce a score for each community, not for each individual node. In this paper, we argue that the belongingness of nodes in a community is not uniform. The central idea of permanence is based on the observation that the strength of membership of a vertex to a community depends upon two factors: (i) the the extent of connections of the vertex within its community versus outside its community, and (ii) how tightly the vertex is connected internally. We discuss how permanence ...

  8. Community Structure in Online Collegiate Social Networks

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

    2009-03-01

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

  9. Bipartite Community Structure of eQTLs.

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

    2016-09-01

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

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

    Smith, Reginald D.

    2006-02-01

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

  11. Phase synchronization on small-world networks with community structure

    In this paper, we propose a simple model that can generate small-world network with community structure. The network is introduced as a tunable community organization with parameter r, which is directly measured by the ratio of inter- to intra-community connectivity, and a smaller r corresponds to a stronger community structure. The structure properties, including the degree distribution, clustering, the communication efficiency and modularity are also analysed for the network. In addition, by using the Kuramoto model, we investigated the phase synchronization on this network, and found that increasing the fuzziness of community structure will markedly enhance the network synchronizability; however, in an abnormal region (r ≤ 0.001), the network has even worse synchronizability than the case of isolated communities (r = 0). Furthermore, this network exhibits a remarkable synchronization behaviour in topological scales: the oscillators of high densely interconnected communities synchronize more easily, and more rapidly than the whole network. (general)

  12. Detecting the overlapping and hierarchical community structure of complex networks

    Lancichinetti, Andrea; Fortunato, Santo; Kertesz, Janos

    2008-01-01

    Many networks in nature, society and technology are characterized by a mesoscopic level of organization, with groups of nodes forming tightly connected units, called communities or modules, that are only weakly linked to each other. Uncovering this community structure is one of the most important problems in the field of complex networks. Networks often show a hierarchical organization, with communities embedded within other communities; moreover, nodes can be shared between different communi...

  13. Temporal abiotic variability structures invertebrate communities in agricultural drainage ditches

    M.H. Whatley; J.A. Vonk; H.G. van der Geest; W. Admiraal

    2015-01-01

    Abiotic variability is known to structure lotic invertebrate communities, yet its influence on lentic invertebrates is not clear. This study tests the hypothesis that variability of nutrients and macro-ions are structuring invertebrate communities in agricultural drainage ditches. This was determine

  14. Investigating Effects of Invasive Species on Plant Community Structure

    Franklin, Wilfred

    2008-01-01

    In this article, the author presents a field study project that explores factors influencing forest community structure and lifts the veil off of "plant blindness." This ecological study consists of three laboratories: (1) preliminary field trip to the study site; (2) plant survey; and (3) analyzing plant community structure with descriptive…

  15. Nash Stability in Additively Separable Hedonic Games and Community Structures

    Olsen, Martin

    2009-01-01

    symmetric   preferences is NP-complete. We motivate our study of the   computational complexity by linking Nash stable partitions in   Additively Separable Hedonic Games to community structures in   networks. Our results formally justify that computing community   structures in general is hard....

  16. Shifting Niches for Community Structure Detection

    Grappiolo, Corrado; Togelius, Julian; Yannakakis, Georgios N.

    2013-01-01

    in complete networks, this approach seems to scale badly due to solutions with the wrong number of communities dominating the population. The new algorithm is based on a niching model, where separate compartments of the population contain candidate solutions with different numbers of communities. We...

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

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

    2007-01-01

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

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

    Chin, Jia Hou; Ratnavelu, Kuru

    2016-01-01

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

  19. Virality Prediction and Community Structure in Social Networks

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

    2013-08-01

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

  20. Assembly and phylogenetic structure of Neotropical palm communities

    Eiserhardt, Wolf L.; Svenning, J.-C.; Balslev, Henrik

    Diversity, composition and dynamics of Neotropical palm communities are receiving an increasing amount of attention due to their economic importance, but also because their high species richness and functional diversity render them valuable model systems for overall forest biodiversity. However, to...... better understand these palm communities, it is crucial to gain insight into the mechanisms responsible for their assembly. These can be dispersal limitation, environmental filtering, or biotic interactions. If the degree of niche conservatism is known for a group of organisms, patterns of community...... phylogenetic structure can be directly traced back to mechanisms of community assembly. We aim to examine this for Neotropical palm communities. Phylogenetic structure will be inferred on different spatial scales and for different community definitions (plot-based and environment-based). To overcome an...

  1. Community structure in traffic zones based on travel demand

    Sun, Li; Ling, Ximan; He, Kun; Tan, Qian

    2016-09-01

    Large structure in complex networks can be studied by dividing it into communities or modules. Urban traffic system is one of the most critical infrastructures. It can be abstracted into a complex network composed of tightly connected groups. Here, we analyze community structure in urban traffic zones based on the community detection method in network science. Spectral algorithm using the eigenvectors of matrices is employed. Our empirical results indicate that the traffic communities are variant with the travel demand distribution, since in the morning the majority of the passengers are traveling from home to work and in the evening they are traveling a contrary direction. Meanwhile, the origin-destination pairs with large number of trips play a significant role in urban traffic network's community division. The layout of traffic community in a city also depends on the residents' trajectories.

  2. Detecting highly overlapping community structure by greedy clique expansion

    Lee, Conrad; McDaid, Aaron; Hurley, Neil

    2010-01-01

    In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms, capable of detecting overlapping communities, perform well only when the extent of community overlap is kept to modest levels. To overcome this limitation, we introduce a new community assignment algorithm called Greedy Clique Expansion (GCE). The algorithm identifies distinct cliques as seeds and expands these seeds by greedily optimizing a local fitness function. We perform extensive benchmarks on synthetic data to demonstrate that GCE's good performance is robust across diverse graph topologies. Significantly, GCE is the only algorithm to perform well on these synthetic graphs, in which every node belongs to multiple communities. Furthermore, when put to the task of identifying functional modules in protein interaction data, and college dorm assignments in Facebook friendship data, we find ...

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

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

  4. Measuring the robustness of network community structure using assortativity

    Shizuka, Daizaburo; Farine, Damien R.

    2016-01-01

    The existence of discrete social clusters, or ‘communities’, is a common feature of social networks in human and nonhuman animals. The level of such community structure in networks is typically measured using an index of modularity, Q. While modularity quantifies the degree to which individuals associate within versus between social communities and provides a useful measure of structure in the social network, it assumes that the network has been well sampled. However, animal social network da...

  5. New spectral approach for community structure analysis on complex networks

    Danila, Bogdan

    2015-01-01

    A simple but efficient spectral approach for analyzing the community structure of complex networks is introduced. It works the same way for all types of networks by spectrally splitting the adjacency matrix into a "unipartite" and a "multipartite" component whose entries provide measures of the affinity or antagonism between the nodes in a manner that clearly reveals the communities and also provides additional information, including a ranking of the links and nodes and the highlighting of the "gateway" links that are important in connecting the communities together. Two algorithms are then proposed to achieve the actual partition into communities. These algorithms can be tuned to discard the overlaps and produce the most meaningful non-overlapping community structure.

  6. Exploring community structure in networks by consensus dynamics

    He, He; Yang, Bo; Hu, Xiaoming

    2016-05-01

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

  7. Community detection using global and local structural information

    Hai-Long Yan; Ju Xiang; Xiao-Yu Zhang; Jun-Feng Fan; Fang Chane; Gen-Yi Fu; Er-Min Guo; Xin-Guang Hu; Ke Hu; Ru-Min Wang

    2013-01-01

    Community detection is of considerable importance for understanding both the structure and function of complex networks. In this paper, we introduced the general procedure of the community detection algorithms using global and local structural information, where the edge betweenness and the local similarity measures respectively based on local random walk dynamics and local cyclic structures were used. The algorithms were tested on artificial and real-world networks. The results clearly show that all the algorithms have excellent performance in the tests and the local similarity measure based on local random walk dynamics is superior to that based on local cyclic structures.

  8. Measuring robustness of community structure in complex networks

    Li, Hui-Jia; Chen, Luonan

    2015-01-01

    The theory of community structure is a powerful tool for real networks, which 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 robustness of community structure is an urgent and important task. In this letter, we employ the critical threshold of resolution parameter in Hamiltonian function, $\\gamma_C$, to measure the robustness of a network. According to spectral theory, a rigorous proof shows that the index we proposed is inversely proportional to robustness of community structure. Furthermore, by utilizing the co-evolution model, we provides a new efficient method for computing the value of $\\gamma_C$. The research can be applied to broad clustering problems in network analysis and data mining due to its solid mathematical basis and experimental effects.

  9. Jellyfish modulate bacterial dynamic and community structure.

    Tinkara Tinta

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

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

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

    2014-03-01

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

  11. Measuring the robustness of network community structure using assortativity

    Shizuka, Daizaburo; Farine, Damien R.

    2016-01-01

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

  12. Analysis of stability of community structure across multiple hierarchical levels

    Li, Hui-Jia

    2015-01-01

    The analysis of stability of community structure is an important problem for scientists from many fields. Here, we propose a new framework to reveal hidden properties of community structure by quantitatively analyzing the dynamics of Potts model. Specifically we model the Potts procedure of community structure detection by a Markov process, which has a clear mathematical explanation. Critical topological information regarding to multivariate spin configuration could also be inferred from the spectral significance of the Markov process. We test our framework on some example networks and find it doesn't have resolute limitation problem at all. Results have shown the model we proposed is able to uncover hierarchical structure in different scales effectively and efficiently.

  13. A benchmark model to assess community structure in evolving networks

    Granell, Clara; Arenas, Alex; Fortunato, Santo; Gómez, Sergio

    2015-01-01

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

  14. Community structures and role detection in music networks

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

    2008-12-01

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

  15. A local algorithm for detecting community structures in dynamic networks

    Massaro, Emanuele; Guazzini, Andrea; Passarella, Andrea; Bagnoli, Franco

    2013-01-01

    The emergence and the global adaptation of mobile devices has influenced human interactions at the individual, community, and social levels leading to the so called Cyber-Physical World (CPW) convergence scenario [1]. One of the most important features of CPW is the possibility of exploiting information about the structure of social communities of users, that manifest through joint movement patterns and frequency of physical co-location: mobile devices of users that belong to the same social community are likely to "see" each other (and thus be able to communicate through ad hoc networking techniques) more frequently and regularly than devices outside of the community. In mobile opportunistic networks, this fact can be exploited, for example, to optimize networking operations such as forwarding and dissemination of messages. In this paper we present a novel local cognitive-inspired algorithm for revealing the structure of these dynamic social networks by exploiting information about physical encounters, logge...

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

    Danila, Bogdan

    2016-02-01

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

  17. Structure of an Anuran community in a Mediterranean area

    Richter Boix, Alexander

    2006-01-01

    [eng] The thesis research concerned evolutionary ecology and community ecology of amphibians in two different areas of a Mediterranean region. The goal of the research was to test how anuran species coexist along a lentic freshwater gradient from ephemeral to permanent ponds. The community structure across the gradient has been explained by different ecological models, based on different trade-offs and inherent properties of the species. To test the different models he used four-year field su...

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

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

    2015-07-01

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

  19. Experimental sulfate amendment alters peatland bacterial community structure.

    Strickman, R J S; Fulthorpe, R R; Coleman Wasik, J K; Engstrom, D R; Mitchell, C P J

    2016-10-01

    As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group. PMID:27267720

  20. Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

    Cretoiu, Mariana Silvia; Korthals, Gerard W.; Visser, Johnny H. M.; van Elsas, Jan Dirk

    2013-01-01

    A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the

  1. Environmental controls over Actinobacteria communities in ecological sensitive Yanshan mountains zone

    hui etang

    2016-03-01

    Full Text Available The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10 on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120 oC for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1. However, there were differences (P < 0.05 from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001 in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites.. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.

  2. Quantum Probabilistic Structures in Competing Lizard Communities

    Aerts, Diederik; Kuna, Maciej; Sinervo, Barry; Sozzo, Sandro

    2012-01-01

    Almost two decades of research on the use of the mathematical formalism of quantum theory as a modeling tool for entities and their dynamics in domains different from the micro-world has now firmly shown the systematic appearance of quantum structures in aspects of human behavior and thought, such as in cognitive processes of decision-making, and in the way concepts are combined into sentences. In this paper, we extend this insight to animal behavior showing that a quantum probabilistic structure models the mating competition of three side-blotched lizard morphs. We analyze a set of experimental data collected from 1990 to 2011 on these morphs, whose territorial behavior follows a cyclic rock-paper-scissors (RPS) dynamics. Consequently we prove that a single classical Kolmogorovian space does not exist for the lizard's dynamics, and elaborate an explicit quantum description in Hilbert space faithfully modeling the gathered data. This result is relevant for population dynamics as a whole, since many systems, e...

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

    Park, Sangki

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

  4. Relating methanogen community structure and anaerobic digester function.

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

    2015-03-01

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

  5. Changes in Age Structure and Rural Community Growth.

    McGranahan, David A.

    1985-01-01

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

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

    Hoffmann, John P.

    2002-01-01

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

  7. Mass Media Influence Spreading in Social Networks with Community Structure

    Candia, Julián; Mazzitello, Karina I.

    2008-01-01

    We study an extension of Axelrod's model for social influence, in which cultural drift is represented as random perturbations, while mass media are introduced by means of an external field. In this scenario, we investigate how the modular structure of social networks affects the propagation of mass media messages across the society. The community structure of social networks is represented by coupled random networks, in which two random graphs are connected by intercommunity links. Considerin...

  8. Community structure and multi-modal oscillations in complex networks.

    Henry Dorrian

    Full Text Available In many types of network, the relationship between structure and function is of great significance. We are particularly interested in community structures, which arise in a wide variety of domains. We apply a simple oscillator model to networks with community structures and show that waves of regular oscillation are caused by synchronised clusters of nodes. Moreover, we show that such global oscillations may arise as a direct result of network topology. We also observe that additional modes of oscillation (as detected through frequency analysis occur in networks with additional levels of topological hierarchy and that such modes may be directly related to network structure. We apply the method in two specific domains (metabolic networks and metropolitan transport demonstrating the robustness of our results when applied to real world systems. We conclude that (where the distribution of oscillator frequencies and the interactions between them are known to be unimodal our observations may be applicable to the detection of underlying community structure in networks, shedding further light on the general relationship between structure and function in complex systems.

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

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

    2016-01-01

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

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

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

    2015-12-01

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

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

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

    2016-01-01

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

  12. A framework for solving ill-structured community problems

    Keller, William Cotesworth

    A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.

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

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

    2016-05-01

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

  14. Are Gay Communities Dying or Just in Transition? Results from an International Consultation Examining Structural Change in Gay Communities

    Simon Rosser, B. R.; West, William; Weinmeyer, Richard

    2008-01-01

    This study sought to identify how urban gay communities are undergoing structural change, reasons for that change, and implications for HIV prevention planning. Key informants (N=29) at the AIDS Impact Conference from 17 cities in 14 countries completed surveys and participated in a facilitated structured dialog about how gay communities are changing. In all cities, the virtual gay community was identified as now larger than the offline physical community. Most cities identified that while th...

  15. Router-level community structure of the Internet Autonomous Systems

    Beiró, Mariano G; Alvarez-Hamelin, J Ignacio

    2015-01-01

    The Internet is composed of routing devices connected between them and organized into independent administrative entities: the Autonomous Systems. The existence of different types of Autonomous Systems (like large connectivity providers, Internet Service Providers or universities) together with geographical and economical constraints, turns the Internet into a complex modular and hierarchical network. This organization is reflected in many properties of the Internet topology, like its high degree of clustering and its robustness. In this work, we study the modular structure of the Internet router-level graph in order to assess to what extent the Autonomous Systems satisfy some of the known notions of community structure. We show that the modular structure of the Internet is much richer than what can be captured by the current community detection methods, which are severely affected by resolution limits and by the heterogeneity of the Autonomous Systems. Here we overcome this issue by using a multiresolution d...

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

    Crumrine, P. W.

    2005-05-01

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

  17. Community structure benefits the fixation of cooperation under strong selection

    Wu, Zhi-Xi; Yang, Han-Xin

    2014-01-01

    Recent empirical studies suggest that heavy-tailed distributions of human activities are universal in real social dynamics [Muchnik, \\emph{et al.}, Sci. Rep. \\textbf{3}, 1783 (2013)]. On the other hand, community structure is ubiquitous in biological and social networks [M.~E.~J. Newman, Nat. Phys. \\textbf{8}, 25 (2012)]. Motivated by these facts, we here consider the evolutionary Prisoner's dilemma game taking place on top of a real social network to investigate how the community structure and the heterogeneity in activity of individuals affect the evolution of cooperation. In particular, we account for a variation of the birth-death process (which can also be regarded as a proportional imitation rule from social point of view) for the strategy updating under both weak- and strong-selection (meaning the payoffs harvested from games contribute either slightly or heavily to the individuals' performance). By implementing comparative studies, where the players are selected either randomly or in terms of their ac...

  18. Phytoplankton community structure and its succession in Dianshan Lake

    Liqing Wang; Rong Shi; Gaohua Ji; Zhifeng Fan; Jinglei Cheng

    2011-01-01

    Phytoplankon samples were collected monthly in Dianshan Lake, the largest natural freshwater lake in Shanghai during 2004–2006, to assay the phytoplankton community structure and ascertain the rela-tionship between its succession and the eutrophication for the lake. Two hundred and five species from 84 genera were identified in Dianshan Lake, with Chlorophyta (50%), Bacillariophyta (20%), Cyanophyta (13%) and Euglenophyta (13%) being the main phyla. The monthly similarity index of species was...

  19. Resource variation and the structure of British bird communities

    Lister, Bradford C.

    1980-01-01

    Data on the foraging microhabitats of British birds are reanalyzed with the aim of understanding how fluctuations in resource abundance affect niche relationships and community structure. At Marley Wood, overlap in the foraging sites of resident bird species increased during the late spring and summer and decreased during the fall and winter. Among bird species coexisting in the pine forests at Thetford Chase, spatial overlap and spatial niche widths were positively correlated with food abund...

  20. Comparison and validation of community structures in complex networks

    Gustafsson, M; Lombardi, A; Gustafsson, Mika; Hornquist, Michael; Lombardi, Anna

    2006-01-01

    The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples f...

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

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

    2014-10-01

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

  2. Bacterial community structure in aquifers corresponds to stratigraphy

    Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

    2014-05-01

    So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

  3. Making the links between community structure and individual well-being: community quality of life in Riverdale, Toronto, Canada.

    Raphael, D; Renwick, R; Brown, I; Steinmetz, B; Sehdev, H; Phillips, S

    2001-09-01

    An inquiry into community quality of life was carried out within a framework that recognizes the complex relationship between community structures and individual well-being. Through use of focus groups and key informant interviews, community members, service providers, and elected representatives in a Toronto community considered aspects of their community that affected quality of life. Community members identified strengths of access to amenities, caring and concerned people, community agencies, low-cost housing, and public transportation. Service providers and elected representatives recognized diversity, community agencies and resources, and presence of culturally relevant food stores and services as strengths. At one level, findings were consistent with emerging concepts of social capital. At another level, threats to the community were considered in relation to the hypothesized role neo-liberalism plays in weakening the welfare state. PMID:11439254

  4. Competition for space and the structure of ecological communities

    Yodzis, Peter

    1978-01-01

    This volume is an investigation of interspecific competition for space, particularly among sessile organisms, both plant and animal, and its consequences for community structure. While my own contribu­ tion ----and the bulk of this volume --- lies in mathematical analysis of the phenomenon, I have also tried to summarize the most important natural historical aspects of these communities, and have devoted much effort to relating the mathematical results to observations of the natural world. Thus, the volume has both a synthetic and an analytic aspect. On the one hand, I have been struck by certain similarities among many communities, from forests to mussel beds, in which spatial com­ petition is important. On the other hand, I have analyzed this pheno­ menon by means of reaction-dispersal models. Finally, the mathematical analysis has suggested a conceptual framework for these communities which, I believe, further unifies and illuminates the field data. A focal perception of this work is that, just as niche...

  5. Community structure characteristics of phytoplankton in zhalong wetland, china

    In autumn 2010, the phytoplankton samples were collected in Zhalong Wetland. A total of 347 species belonging to 78 genera,6 phyla were identified, Chlorophyta and Bacillariophyta were dominated phytoplankton communities, including 143 species of Chlorophyta, 116 species of Bacillariophyta, 45 species of Cyanophyta, 39 species of Euglenophyta, 3 species of Pyrrophyta, 1 species of Chrysophyta. In the core area 66 genera, 222 species were identified, in the buffer area 63 genera, 210 species were identified, in the experiment area 63 genera, 167 species were identified. The dominant species in Zhalong Wetland included Cyclotella meneghiniana, Chlorella vulgaris, Trachelomonas volvocina, Nitzschia sp.. The average phytoplankton density was 12.13*10/sup 6/ in Zhalong Wetland, the phytoplankton density of Bacillariophyta was highest (32.82*10/sup 6/ ind L/sup -1/), and then Chlorophyta (23.73*10/sup 6/ ind L/sup -1/) and Cyanophyta (11.43*106 ind L-1), respectively. The results of cluster analysis showed that phytoplankton community structure could be divided into three types, and within-group similarities of phytoplankton community structure was not high, but inter-group non-similarity was high. Based on the species composition, phytoplankton density, phytoplankton pollution indicator, it suggested that Zhalong Wetland was mesotrophic state. (author)

  6. Structure and Dynamics of North-western Mediterranean Rocky Benthic Communities along a Depth Gradient

    Garrabou, J.; Ballesteros, E.; Zabala, M.

    2002-09-01

    The structure and dynamics of four Mediterranean communities along a depth gradient (5 to 20 m depth) were investigated. The main environmental factors relevant to the organization of benthic communities varied predictably with depth, decreasing both in magnitude and in temporal variability. The following hypotheses were tested on the organization of communities as depth increases: (1) community structure increases in complexity, (2) community dynamics decrease, and (3) temporal (seasonal) variations both in community structure and dynamics become dampened. A series of photographs (310 cm2 each) of 12 permanent plots were taken monthly over a 2-year period. Plots belonged to one of four communities, two algal- and two animal-dominated by animals. In the analysis of photographs, a novel methodological approach was employed using techniques borrowed from landscape ecology. Community structure was quantified using three landscape pattern indices: number of patches, mean patch size and Shannon's diversity index. Community dynamics were measured by calculating spatially explicit area changes over time by overlaying drawings corresponding to different sampling times. The results support the hypotheses tested. Firstly, the shallower, algae-dominated communities, had, in general, significantly lower structure (i.e. patch-mosaics were less heterogeneous), than were deeper communities dominated by animals. Secondly, community dynamics were significantly larger in shallower communities than in deeper communities. Thirdly, temporal changes in community structure and dynamics were generally dampened with depth showing, in some cases, significant temporal patterns in structure and dynamics, which were consistent with seasonal variations. These depth-related trends in community structure and dynamics in subtidal Mediterranean communities may respond to strong changes in community determining factors (nutrient availability, physical disturbance, predation). Finally, it is

  7. Interlinking backscatter, grain size and benthic community structure

    McGonigle, Chris; Collier, Jenny S.

    2014-06-01

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

  8. Analysis of community structure in networks of correlated data

    Gomez, S.; Jensen, P.; Arenas, A.

    2008-12-25

    We present a reformulation of modularity that allows the analysis of the community structure in networks of correlated data. The new modularity preserves the probabilistic semantics of the original definition even when the network is directed, weighted, signed, and has self-loops. This is the most general condition one can find in the study of any network, in particular those defined from correlated data. We apply our results to a real network of correlated data between stores in the city of Lyon (France).

  9. Habitat structure and fish communities of warmwater streams

    Karr, J.R.; Schlosser, I.J.; Angermeier, P.L.

    1983-09-01

    The basic goal of recent clean water legislation is to restore and maintain the chemical, physical, and biological integrity of the nation's waters. A research program was initiated to evaluate the role of physical habitat in regulating the structure of fish communities in warmwater streams in east-central Illinois. An empirical approach involving observations of fish in relatively natural conditions was combined with studies of stream areas that have been subjected to extensive modification by human society. This report is a summary of the work relating to this research.

  10. Trophic structure and community stability in an overfished ecosystem

    Utne-Palm, Anne Christine

    2010-07-15

    Since the collapse of the pelagic fisheries off southwest Africa in the late 1960s, jellyfish biomass has increased and the structure of the Benguelan fish community has shifted, making the bearded goby (Sufflogobius bibarbatus) the new predominant prey species. Despite increased prédation pressure and a harsh environment, the gobies are thriving. Here we show that physiological adaptations and antipredator and foraging behaviors underpin the success of these fish. In particular, body-tissue isotope signatures reveal that gobies consume jellyfish and sulphidic diatomaceous mud, transferring "dead-end" resources back into the food chain.

  11. Comparison of adult mosquito community structure on various habitats

    ZHONG-CHENGYAN; HARRYZHONG

    2005-01-01

    The community structure of adult mosquitoes was compared from New Jersey light trap collections in six different types of habitats in Citrus County, Florida, USA. From October 1998 to December 2000, mosquitoes were collected three times a week from the following habitats (swamps, swamps and freshwater marshes, pine fiat-woods, pine fiat-woods and scrub, salt marshes, and salt marshes and mangroves). Mosquito density was highest in the swamps and freshwater marshes habitat, with an average of 95.65 specimens per trap.Density was lowest in the flatwoods and scrub habitat, with an average of 14.38 specimens per trap. Species dominance differed among habitats. Salt marshes produced the greatest aggregation index, while pine flatwoods produced the lowest. Conversely, diversity analysis showed that pine flatwoods had the greatest diversity, while salt marshes the lowest diversity. Similarity indices indicated that the adult mosquito communities from pine flatwoods and pine flatwoods and scrub were very similar (0.8583). The adult mosquito community of salt marshes was different from that of swamps and freshwater marshes (the similar index was 0.0217).

  12. [Structure of parasitic arthropod communities in forest small mammals].

    Balashov, Iu S

    2004-01-01

    Species composition and structure of ectoparasite arthropod communities were examined all year round six years in the bank vole Clethrionomys glareolus, Ural wood mouse Apodemus uralensis and the common shrew Sorex araneus in forests of the Ilmen'-Volkhov depression. In total, 4500 host samples have been examined and all ectoparasites have been collected. The species composition of ectoparasite community in small mammal species are as follows: the bank vole--29 insect, tick and mite species, the common shrew--23 species, the Ural wood mouse--16 species. In forest biotopes, many temporary ectoparasitic species occur on several host species living in the same habitats under a forest canopy and contacting each other. A parasitic supracommunity in the ecosystem examined has a pool of temporary ectoparasites, which is available for all the community of small mammals. A role of different rodent and shrew species are hosts of insects and ticks changes depending on a density of potential host populations and numerous other environment factors. PMID:15656091

  13. Impact of oil on bacterial community structure in bioturbated sediments.

    Magalie Stauffert

    Full Text Available Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment, the common burrowing organism Hediste (Nereis diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by

  14. Impact of oil on bacterial community structure in bioturbated sediments.

    Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

    2013-01-01

    Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria

  15. Mass media influence spreading in social networks with community structure

    Candia, Julián; Mazzitello, Karina I.

    2008-07-01

    We study an extension of Axelrod's model for social influence, in which cultural drift is represented as random perturbations, while mass media are introduced by means of an external field. In this scenario, we investigate how the modular structure of social networks affects the propagation of mass media messages across a society. The community structure of social networks is represented by coupled random networks, in which two random graphs are connected by intercommunity links. Considering inhomogeneous mass media fields, we study the conditions for successful message spreading and find a novel phase diagram in the multidimensional parameter space. These findings show that social modularity effects are of paramount importance for designing successful, cost-effective advertising campaigns.

  16. Using Model-based Overlapping Seed Expansion to detect highly overlapping community structure

    McDaid, Aaron F

    2010-01-01

    As research into community finding in social networks progresses, there is a need for algorithms capable of detecting overlapping community structure. Many algorithms have been proposed in recent years that are capable of assigning each node to more than a single community. The performance of these algorithms tends to degrade when the ground-truth contains a more highly overlapping community structure, with nodes assigned to more than two communities. Such highly overlapping structure is likely to exist in many social networks, such as Facebook friendship networks. In this paper we present a scalable algorithm, MOSES, based on a statistical model of community structure, which is capable of detecting highly overlapping community structure, especially when there is variance in the number of communities each node is in. In evaluation on synthetic data MOSES is found to be superior to existing algorithms, especially at high levels of overlap. We demonstrate MOSES on real social network data by analyzing the netwo...

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

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

    2013-01-01

    Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter−1) or high (25 mg liter−1) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerp...

  18. The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale

    Zhang, Binglin; Wu, Xiukun; Zhang, Gaosen; Li, Shuyan; Zhang, Wei; Chen, Ximing; Sun, Likun; Zhang, Baogui; Liu, Guangxiu; Chen, Tuo

    2016-05-01

    Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the distribution and biogeography of Actinobacteria in glacier forelands. Therefore, we investigated the patterns of diversity and the biogeography of actinobacterial communities of the inhabited forefields of 5 glaciers in China. Of the bacteria, the mean relative abundance of Actinobacteria was 13.1%, and 6 classes were identified in the phylum Actinobacteria. The dominant class was Actinobacteria (57%), which was followed in abundance by Acidimicrobiia (19%) and Thermoleophilia (19%). When combined, the relative abundance of the other three classes, the MB-A2-108, Nitriliruptoria and Rubrobacteria, was only 2.4%. A biogeographic pattern in the forelands of the 5 glaciers in China was not detected for actinobacterial communities. Compared with 7 other actinobacterial communities found in the forelands of glaciers globally, those in the Southern Hemisphere were significantly different from those in the Northern Hemisphere. Moreover, the communities were significantly different on the separate continents of the Northern Hemisphere. The dissimilarity of the actinobacterial communities increased with geographic distance (r = 0.428, p = 0.0003). Because of environmental factors, the effect of geography was clear when the distance exceeded a certain continent-level threshold. With the analysis of indicator species, we found that each genus had a geographic characteristic, which could explain why the communities with greater diversity were more strongly affected by biogeography.

  19. Tricholoma matsutake Dominates Diverse Microbial Communities in Different Forest Soils▿†

    Vaario, Lu-Min; Fritze, Hannu; Spetz, Peter; Heinonsalo, Jussi; Hanajík, Peter; Pennanen, Taina

    2011-01-01

    Fungal and actinobacterial communities were analyzed together with soil chemistry and enzyme activities in order to profile the microbial diversity associated with the economically important mushroom Tricholoma matsutake. Samples of mycelium-soil aggregation (shiro) were collected from three experimental sites where sporocarps naturally formed. PCR was used to confirm the presence and absence of matsutake in soil samples. PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and d...

  20. Community structure and composition of the Cambrian Chengjiang biota

    2010-01-01

    Based on previously published species data(228 species in over 18 phyla) and field sampling(114 species and 18406 individuals) in the Chengjiang-Haikou-Anning area,we analyzed quantitatively the paleocommunity composition and structure of the Cambrian Chengjiang biota(Cambrian Series 2,eastern Yunnan,China).Arthropods dominate the community both in species diversity(species:37%) and in abundance(individuals:51.8%).Priapulids(individuals:22.6%) and brachiopods(individuals:16.3%) follow in abundance rank.The arthropod Kunmingella douvillei(26.2%),the priapulid Cricocosmia jinning-ensis(15.4%),and the brachiopod Diandongia pista(11%) are the three most abundant species.Ecological analyses show that the community was dominated by epifaunal organisms(species:63%,individuals:68.4%) followed by infaunal organisms(species:11.9%,individuals:25.9%),nektobenthic organisms(species:11.5%,individuals:2.6%),and pelagic organisms(species:5.3%,individuals:3.1%).The diverse feeding strategies,dominated by suspension feeders(species:35.6%,individuals:26.1%) and hunter/scavengers(species:31.1%,individuals:40.4%),indicate the former existence of a complex food chain and intense competition.Epifaunal vagrant omnivores(28.2%),infaunal vagrant hunter/scavengers(19.8%),epifaunal sessile suspension feeders(17.7%),and epifaunal vagrant hunter/scavengers(15.3%) were the most abundant ecological groups,represented primarily by arthropods,poriferans,priapulids,and brachiopods.Ecological group analyses reveal that the early Cambrian Chengjiang biota is similar in community patterns and functional relations to modern biotas in shallow marine settings.

  1. Predator foraging altitudes reveal the structure of aerial insect communities.

    Helms, Jackson A; Godfrey, Aaron P; Ames, Tayna; Bridge, Eli S

    2016-01-01

    The atmosphere is populated by a diverse array of dispersing insects and their predators. We studied aerial insect communities by tracking the foraging altitudes of an avian insectivore, the Purple Martin (Progne subis). By attaching altitude loggers to nesting Purple Martins and collecting prey delivered to their nestlings, we determined the flight altitudes of ants and other insects. We then tested hypotheses relating ant body size and reproductive ecology to flight altitude. Purple Martins flew up to 1,889 meters above ground, and nestling provisioning trips ranged up to 922 meters. Insect communities were structured by body size such that species of all sizes flew near the ground but only light insects flew to the highest altitudes. Ant maximum flight altitudes decreased by 60% from the lightest to the heaviest species. Winged sexuals of social insects (ants, honey bees, and termites) dominated the Purple Martin diet, making up 88% of prey individuals and 45% of prey biomass. By transferring energy from terrestrial to aerial food webs, mating swarms of social insects play a substantial role in aerial ecosystems. Although we focus on Purple Martins and ants, our combined logger and diet method could be applied to a range of aerial organisms. PMID:27352817

  2. Generalized method for finding community structures in networks

    Chang, Chang

    2013-01-01

    To date, most algorithms aiming to find community structures in networks mainly focus on unipartite or bipartite networks. However, to our knowledge, there is no algorithm specifically designed for the mixture network, a third type defined in our paper that represents a wide range of real-world networks. Interestingly, unipartite and bipartite networks can be viewed as limiting cases of a mixture network, suggesting that the mixture network can be considered as a general condition. Based on this observation, we propose a probabilistic model based on the link community model for a unipartite, undirected network [B. Ball, B. Karrer, and M. E. Newman, Phys. Rev. E 84, 036103 (2011)] by redefining this model in the context of a bipartite network and generalizing the bipartite network version model to a mixture network, the general condition, which can be used to find modules in unipartite, bipartite, and mixture networks in a unified framework. We show that both the model of Ball et al. (unipartite, undirected ne...

  3. Aquifer community structure in dependence of lithostratigraphy in groundwater reservoirs.

    Beyer, Andrea; Rzanny, Michael; Weist, Aileen; Möller, Silke; Burow, Katja; Gutmann, Falko; Neumann, Stefan; Lindner, Julia; Müsse, Steffen; Brangsch, Hanka; Stoiber-Lipp, Jennifer; Lonschinski, Martin; Merten, Dirk; Büchel, Georg; Kothe, Erika

    2015-12-01

    Groundwater microbiology with respect to different host rocks offers new possibilities to describe and map the habitat harboring approximately half of Earths' biomass. The Thuringian Basin (Germany) contains formations of the Permian (Zechstein) and Triassic (Muschelkalk and Buntsandstein) with outcrops and deeper regions at the border and central part. Hydro(geo)chemistry and bacterial community structure of 11 natural springs and 20 groundwater wells were analyzed to define typical patterns for each formation. Widespread were Gammaproteobacteria, while Bacilli were present in all wells. Halotolerant and halophilic taxa were present in Zechstein. The occurrence of specific taxa allowed a clear separation of communities from all three lithostratigraphic groups. These specific taxa could be used to follow fluid movement, e.g., from the underlying Zechstein or from nearby saline reservoirs into Buntsandstein aquifers. Thus, we developed a new tool to identify the lithostratigraphic origin of sources in mixed waters. This was verified with entry of surface water, as species not present in the underground Zechstein environments were isolated from the water samples. Thus, our tool shows a higher resolution as compared to hydrochemistry, which is prone to undergo fast dilution if water mixes with other aquifers. Furthermore, the bacteria well adapted to their respective environment showed geographic clustering allowing to differentiate regional aquifers. PMID:26002361

  4. Assessing the structure and temporal dynamics of seabird communities: the challenge of capturing marine ecosystem complexity

    Moreno, Rocio; Stowasser, Gabriele; McGill, Rona A.R.; Bearhop, Stuart; Phillips, Richard A.

    2016-01-01

    Summary 1.Understanding interspecific interactions, and the influences of anthropogenic disturbance and environmental change on communities, are key challenges in ecology. Despite the pressing need to understand these fundamental drivers of community structure and dynamics, only 17% of ecological studies conducted over the past three decades have been at the community level. 2.Here, we assess the trophic structure of the procellariiform community breeding at South Georgia, to identify ...

  5. A Statistical Analysis of the Community Structure of a Weighted Collaboration Network Among Rappers

    Smith, R D

    2006-01-01

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

  6. Are gay communities dying or just in transition? Results from an international consultation examining possible structural change in gay communities.

    Simon Rosser, B R; West, William; Weinmeyer, Richard

    2008-05-01

    This study sought to identify how urban gay communities are undergoing structural change, reasons for that change, and implications for HIV prevention planning. Key informants (N=29) at the AIDS Impact Conference from 17 cities in 14 countries completed surveys and participated in a facilitated structured dialog about if gay communities are changing, and if so, how they are changing. In all cities, the virtual gay community was identified as currently larger than the offline physical community. Most cities identified that while the gay population in their cities appeared stable or growing, the gay community appeared in decline. Measures included greater integration of heterosexuals into historically gay-identified neighborhoods and movement of gay persons into suburbs, decreased number of gay bars/clubs, less attendance at gay events, less volunteerism in gay or HIV/AIDS organizations, and the overall declining visibility of gay communities. Participants attributed structural change to multiple factors including gay neighborhood gentrification, achievement of civil rights, less discrimination, a vibrant virtual community, and changes in drug use. Consistent with social assimilation, gay infrastructure, visibility, and community identification appears to be decreasing across cities. HIV prevention planning, interventions, treatment services, and policies need to be re-conceptualized for MSM in the future. Four recommendations for future HIV prevention and research are detailed. PMID:18484330

  7. Iterated tabu search for identifying community structure in complex networks

    Lü, Zhipeng; Huang, Wenqi

    2009-08-01

    This paper presents an iterated tabu search (denoted by ITS) algorithm for optimizing the modularity of community structure in complex networks. The proposed algorithm follows a general framework composed of two phases: basic optimization and postrefinement. When the basic optimization cannot improve the modularity any more, a postrefinement procedure is employed to further optimize the objective function with a global view. For both these two phases, iterated tabu search algorithm is employed to optimize the objective function. Computational results show the high effectiveness of the proposed ITS algorithm compared with six state-of-the-art algorithms in the literature. In particular, our ITS algorithm improves the previous best known modularity for several small and medium size networks.

  8. Measuring and Modeling Bipartite Graphs with Community Structure

    Aksoy, Sinan; Pinar, Ali

    2016-01-01

    Network science is a powerful tool for analyzing complex systems in fields ranging from sociology to engineering to biology. This paper is focused on generative models of bipartite graphs, also known as two-way graphs. We propose two generative models that can be easily tuned to reproduce the characteristics of real-world networks, not just qualitatively, but quantitatively. The measurements we consider are the degree distributions and the bipartite clustering coefficient, which we refer to as the metamorphosis coefficient. We define edge, node, and degreewise metamorphosis coefficients, enabling a more detailed understand of the bipartite community structure. Our proposed bipartite Chung-Lu model is able to reproduce real-world degree distributions, and our proposed bipartite "BTER" model reproduces both the degree distributions as well as the degreewise metamorphosis coefficients. We demonstrate the effectiveness of these models on several real-world data sets.

  9. Effect of power plant emissions on plant community structure

    Singh, J.; Agrawal, M.; Narayan, D. (Banaras Hindu University, Varanasi (India))

    1994-06-01

    A field study was conducted around two coal-fired thermal power plants (TPP) to analyse the impact of their emission on the structure of herbaceous communities in a dry tropical area. Phytosociological studies reflected that Cassia tora, Cynodon dactylon and Dichanthium annulatum dominate at heavily polluted sites. Alsycarpus monilifer, Convolvulus pluricaulis, and Desmodium triflorum are uniformly distributed, whereas Paspalidium flavidum, Phyllanthus simplex, and Rungia repens are dominant at less polluted sites. On the basis of Importance Value Index, the species were classified as sensitive, intermediate and resistant to TPP emissions. Shannon-Wiener Index of species diversity, species richness and evenness were inversely related to the pollution load in the area. Significant negative correlation between ambient SO[sub 2] concentration and species diversity suggested selective elimination of sensitive species from the heavily polluted sites.

  10. ORGANIC VS CONVENTIONAL: SOIL NEMATODE COMMUNITY STRUCTURE AND FUNCTION.

    Kapp, C; Storey, S G; Malan, A P

    2014-01-01

    Global increases in human population are creating an ever-greater need for food production. Poor soil management practices have degraded soil to such an extent that rapidly improved management practices is the only way to ensure future food demands. In South Africa, deciduous fruit producers are realising the need for soil health, and for an increased understanding of the benefits of soil ecology, to ensure sustainable fruit production. This depends heavily on improved orchard management. Conventional farming relies on the addition of artificial fertilizers, and the application of chemicals, to prevent or minimise, the effects of the soil stages of pest insects, and of plant-parasitic nematodes. Currently, there is resistance toward conventional farming practices, which, it is believed, diminishes biodiversity within the soil. The study aimed to establish the soil nematode community structure and function in organically, and conventionally, managed deciduous fruit orchards. This was done by determining the abundance, the diversity, and the functionality of the naturally occurring free-living, and plant-parasitic, nematodes in deciduous fruit orchards in the Western Cape province of South Africa. The objective of the study was to form the basis for the use of nematodes as future indicators of soil health in deciduous fruit orchards. Orchards from neighbouring organic, and conventional, apricot farms, and from an organic apple orchard, were studied. All the nematodes were quantified, and identified, to family level. The five nematode-classified trophic groups were found at each site, while 14 families were identified in each orchard, respectively. Herbivores were dominant in all the orchards surveyed. Organic apples had the fewest herbivores and fungivores, with the highest number of carnivores. When comparing organic with conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic apricot orchards. The Maturity Index (MI

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

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

    2008-09-01

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

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

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

    2008-01-01

    In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living oil sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitins pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITSI)....

  13. Microzooplankton herbivory and community structure in the Amundsen Sea, Antarctica

    Yang, Eun Jin; Jiang, Yong; Lee, SangHoon

    2016-01-01

    We examined microzooplankton abundance, community structure, and grazing impact on phytoplankton in the Amundsen Sea, Western Antarctica, during the early austral summer from December 2010 to January 2011. Our study area was divided into three regions based on topography, hydrographic properties, and trophic conditions: (1) the Oceanic Zone (OZ), with free sea ice and low phytoplankton biomass dominated by diatoms; (2) the Sea Ice Zone (SIZ), covered by heavy sea ice with colder water, lower salinity, and dominated by diatoms; and (3) the Amundsen Sea Polynya (ASP), with high phytoplankton biomass dominated by Phaeocystis antarctica. Microzooplankton biomass and communities associated with phytoplankton biomass and composition varied among regions. Heterotrophic dinoflagellates (HDF) were the most significant grazers in the ASP and OZ, whereas ciliates co-dominated with HDF in the SIZ. Microzooplankton grazing impact is significant in our study area, particularly in the ASP, and consumed 55.4-107.6% of phytoplankton production (average 77.3%), with grazing impact increasing with prey and grazer biomass. This result implies that a significant proportion of the phytoplankton production is not removed by sinking or other grazers but grazed by microzooplankton. Compared with diatom-based systems, Phaeocystis-based production would be largely remineralized and/or channeled through the microbial food web through microzooplankton grazing. In these waters the major herbivorous fate of phytoplankton is likely mediated by the microzooplankton population. Our study confirms the importance of herbivorous protists in the planktonic ecosystems of high latitudes. In conclusion, microzooplankton herbivory may be a driving force controlling phytoplankton growth in early summer in the Amundsen Sea, particularly in the ASP.

  14. [Effect of environmental factors on fish community structure in the Huntai River Basin at multiple scales].

    Li, Yan-li; Li, Yan-fen; Xu, Zong-xue

    2014-09-01

    In June 2012, fishes was investigated at 65 sampling sites in the Huntai River basin in Northeast of China. Forty species were collected, belonging to 9 orders, 14 families,33 genera. Cobitidae and Cyprinidae were the dominant fishes in the community structure in the Huntai River basin, accounting for 13. 21% and 65. 83% of the fish community, respectively. There were two types of spatial distribution of fish community, one was distributed in the head water and tributaries in the upstream, and the other was in the plain rivers. Nemachilus nudus, Cobitis granoei and Phoxinus lagowskii dominated the local community in the upper reaches of the Dahuofang Reservoir and shenwo River, while Carassius ayratus and Hemiculter leucisculdus dominated the local community in the plain rivers. CCA (canonical correspondence analysis) was used to distinguish the primary environmental variables that affected the fish community structure. The results indicated fish community was mainly affected by environment factors at watershed and reach scales. Proportions of woodland and urban land, and altitude were three important environmental factors affecting the fish community at the watershed scale. Dissolved oxygen, total nitrogen, pH and habitat inhomogeneity significantly affected the fish community at the reach scale, whereas substrate didn't show significant influence at the microhabitat scale. Environmental factors at watershed scale explained 7. 66% of the variation of fish community structure, environmental factors at reach scale explained 10. 57% of the variation of fish community structure. Environmental factors at reach scale influenced the fish community more significantly. PMID:25518673

  15. Interspecific associations and community structure: A local survey and analysis in a grass community

    WenJun Zhang

    2014-09-01

    Full Text Available Interspecific associations in the plant community may help to understand the self-organizing assembly and succession of the community. In present study, Pearson correlation, net correlation, Spearman rank correlation, and point correlation were used to detect the interspecific (inter-family associations of grass species (families using the sampling data collected in a grass community of Zhuhai, China. We found that most associations between grass species (families were positive associations. The competition/interference/niche separation between grass species (families was not significant. A lot of pairs of grass species and families with statistically significant interspecific (inter-family associations based on four correlation measures were discovered. Cluster trees for grass species/families were obtained by using cluster analysis. Relationship among positive/negative associations, interspecific relationship and community succession/stability/robustness was discussed. I held that species with significant positive or negative associations are generally keystone species in the community. Although both negative and positive associations occur in the community succession, the adaptation and selection will finally result in the successful coexistence of the species with significant positive associations in the climax community. As the advance of community succession, the significant positive associations increase and maximize in climax community, and the significant negative associations increase to a maximum and then decline into climax community. Dominance of significant positive associations in the climax community means the relative stablility and equilibrium of the community. No significant associations usually account for the majority of possible interspecific associations at each phase of community succession. They guarantee the robustness of community. They are candidates of keystone species. Lose of some existing keystone species might be

  16. Community Structure, Biodiversity, and Ecosystem Services in Treeline Whitebark Pine Communities: Potential Impacts from a Non-Native Pathogen

    Diana F. Tomback

    2016-01-01

    Full Text Available 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 generally as an important keystone and foundation species. In the Rocky Mountains, whitebark pine facilitates the development of krummholz conifer communities in the alpine-treeline ecotone (ATE, and thus potentially provides capacity for critical ecosystem services such as snow retention and soil stabilization. The invasive, exotic pathogen Cronartium ribicola, which causes white pine blister rust, now occurs nearly rangewide in whitebark pine communities, to their northern limits. Here, we synthesize data from 10 studies to document geographic variation in structure, conifer species, and understory plants in whitebark pine treeline communities, and examine the potential role of these communities in snow retention and regulating downstream flows. Whitebark pine mortality is predicted to alter treeline community composition, structure, and function. Whitebark pine losses in the ATE may also alter response to climate warming. Efforts to restore whitebark pine have thus far been limited to subalpine communities, particularly through planting seedlings with potential blister rust resistance. We discuss whether restoration strategies might be appropriate for treeline communities.

  17. Microbial Community Structure of Casing Soil During Mushroom Growth

    CAI Wei-Ming; YAO Huai-Ying; FENG Wei-Lin; JIN Qun-Li; LIU Yue-Yan; LI Nan-Yi; ZHENG Zhong

    2009-01-01

    The culturable bacterial population and phospholipid fatty acid (PLFA)profile of casing soil were investigated at different mushroom (Agaricus bisporusI cropping stages.The change in soil bacterial PLFAs was always accompanied by a change in the soil culturable bacterial population in the first flush.Comparatively higher culturable bacterial population and bacterial PLFAs were found in the casing soil at the primordia formation stage of the first flush.There was a significant increase in the ratio of fungal to bacterial PLFAs during mushroom growth.Multivariate analysis of PLFA data demonstrated that the mushroom cropping stage could considerably affect the microbial community structure of the casing soil.The bacterial population increased significantly from casing soil application to the primordia formation stage of the first flush.Casing soil application resulted in an increase in the ratio of gram-negative bacterial PLFAs to gram-positive bacterial PLFAs,suggesting that some gram-negative bacteria might play an important role in mushroom sporophore initiation.

  18. Nonequilibrium plankton community structures in an ecohydrodynamic model system

    H. Malchow

    1994-01-01

    Full Text Available Due to the local and global impacts of algae blooms and patchiness on water quality, carbon cycling and climate, models of plankton dynamics are of current interest. In this paper, the temporal and spatial patterns in natural plankton communities are interpreted as transient and stationary nonequilibrium solutions of dynamical nonlinear interaction-diffusion-advection systems. A simple model of phytoplankton-zooplankton dynamics (Scheffer, 1991 is presented in space and time. After summarizing the local properties as multiple stability and oscillations, the emergence of spatial and spatio- temporal patterns is considered, accounting also for diffusion and weak advection. In order to study the emergence and stability of these structures under hydrodynamic forcing, the interaction- diffusion-advection model is coupled to the hydrodynamic equations. It is shown, that the formation of nonequilibrium spatio-temporal density patterns due to the interplay of the deterministic nonlinear biological interactions and physical processes is a rare occurrence in rapidly flowing waters. The two-timing perturbation technique is applied to problems with very rapid single-directed steady flows. A channel under tidal forcing serves as and example for a system with a relatively high detention time of matter. Generally, due to the different time and length scales of planktic interactions, diffusion and transport, initial nonequilibrium plankton patches are simply moved through the system unless the strong hydrodynamic forces do not destroy them before.

  19. Microbial community structure in the rhizosphere of rice plants

    Björn eBreidenbach; Judith ePump; Marc Gregory Dumont

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized...

  20. Microbial Community Structure in the Rhizosphere of Rice Plants

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

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized...

  1. Interspecific associations and community structure: A local survey and analysis in a grass community

    WenJun Zhang

    2014-01-01

    Interspecific associations in the plant community may help to understand the self-organizing assembly and succession of the community. In present study, Pearson correlation, net correlation, Spearman rank correlation, and point correlation were used to detect the interspecific (inter-family) associations of grass species (families) using the sampling data collected in a grass community of Zhuhai, China. We found that most associations between grass species (families) were positive association...

  2. Strong influence of regional species pools on continent-wide structuring of local communities

    Lessard, Jean-Philippe; Borregaard, Michael K.; Fordyce, James A.; Rahbek, Carsten; Weiser, Michael D.; Dunn, Robert R.; Sanders, Nathan J

    2011-01-01

    There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that...

  3. Structure in Community College Career-Technical Programs: A Qualitative Analysis. CCRC Working Paper No. 50

    Van Noy, Michelle; Weiss, Madeline Joy; Jenkins, Davis; Barnett, Elisabeth A.; Wachen, John

    2012-01-01

    Using data obtained from interviews and program websites at Washington community and technical colleges, the authors of this study examine the structure of community college career-technical programs in allied health, business and marketing, computer and information studies, and mechanics and repair. A framework for structure with four…

  4. Human exploitation and benthic community structure on a tropical intertidal mudflat

    Boer, de W.F.; Prins, H.H.T.

    2002-01-01

    Human exploitation of intertidal marine invertebrates is known to alter benthic community structure. This study describes the impact that harvesting by women and children has on the intertidal community structure of the mudflats of the Saco on Inhaca Island, Mozambique, by comparing the benthic comm

  5. Human exploitation and benthic community structure on a tropical intertidal flat

    de Boer, WF; Prins, HHT

    2002-01-01

    Human exploitation of intertidal marine invertebrates is known to alter benthic community structure. This study describes the impact that harvesting by women and children has on the intertidal community structure of the mudflats of the Saco on Inhaca Island, Mozambique, by comparing the benthic comm

  6. [Community Structure of Aquatic Community and Evaluation of Water Quality in Laovingyan Section of Dadu River].

    Huang, You-you; Zeng, Yu; Liu, Shou-jiang; Ma, Yong-hong; Xu, Xiao

    2016-01-15

    In order to understand the aquatic community structure in the Laoyingyan section of the Dadu River, we collected samples from 9 aquatic sampling points along that section, and studied the phycophyta, zooplankton, benthic invertebrate and fish in them; we also used expert scoring method based on the actual situation of the river to weigh different biome. The water quality was evaluated using comprehensive evaluation of water quality index ( CEWI). The results showed that: (1) there were a total of 105 phycophyta species, belonging to 6 phyla,31 families, and 56 genera in the Laoyingyan section of the Dadu River, among which, diatom species had a higher richness than the others. The mean cell density of the phycophyta was 17.997 8 x 10(4) ind x L(-1), the mean biomass was 0.4463 mg x L(-1), and the highest population density sites were LTS, LYH and XSH. (2) there were a total of 26 zooplankton species, belonging to 3 phyla, 11 families, and 12 genera, among which, Protozoa had a higher richness than the others, accounting for 80.77% of all the zooplankton species; The mean density of the phycophyta was 40.89 ind x L(-1), and the mean biomass was 13.26 x 10(-3) mg x L(-1). The whole community composition was simple, characterized by few species and small population size. (3) there were a total of 14 benthic invertebrate species, belonging to 6 phyla,14 families, and 14 genera, among which, insecta had a higher richness than the others, accounting for 57.16% of the benthic invertebrate species. Benthic invertebrate had higher population densities in LYH and XSH. (4) The mean CEWI of the whole river water was 2. 698 28, characterized by slightly polluted water quality. The CEWI value between every collection point and the individual water quality evaluation index showed a significant positive correlation, manifesting a high consistency. In addition, the water quality of SLH and NYH was mesosaprobic (1 3), among which the worst was SLH with a lowest CEWI of 1.6207, and

  7. Strong influence of regional species pools on continent-wide structuring of local communities

    Lessard, Jean-Philippe; Borregaard, Michael Krabbe; Fordyce, James A.; Rahbek, Carsten; Weiser, Michael D.; Dunn, Robert R.; Sanders, Nate

    2012-01-01

    There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species...... a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the...... that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong....

  8. The Organization and Structure of Community Education Offerings in Community Colleges

    Miller, Michael; Grover, Kenda S.; Kacirek, Kit

    2014-01-01

    One of the key services community colleges provide is community education, meaning those programs and activities that are often offered for leisure or self-improvement and not for credit. Programs of this nature are increasingly challenged to be self-financing, whether through user fees or externally funded grants. The current study explored 75…

  9. Discovery of Opinion Leader Community Via Multilayer Structure based Time-dividing Approach

    Yan Liu

    2013-07-01

    Full Text Available With the advent of web 3.0, social network has become an important way to disclosure and spread the public sentiment. Opinion leaders play an important role in leading the direction of the public opinion. In this paper, due to the structure of the community in the network, we extracted the community by replies of each post in BBS, and we came up with an opinion leader community mining method based on level structure. In this way the communities each other have a better overlap result. Thus, communities can have more relations. Then, we analyzed the revolution of the communities after we got the structure of the opinion leader communities and we put forward a time-dividing method, and divided the whole communities into different pieces based on the character of the post and the duration of the time and we came up with the suitable measurement parameter to get the evolution result of the communities. Finally, experiments prove the efficiency of the opinion leader community mining method and we summarize the properties of the opinion leader community in revolution.

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

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

    2015-01-01

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

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

    Gözdereliler, Erkin; Boon, Nico; Aamand, Jens;

    2013-01-01

    Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter−1) or high (25 mg liter−1) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different...... community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and pyrosequencing. The communities also differed in their MCPA-mineralizing activities. The...... enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low-nucleic acid-content bacteria (LNA bacteria) was correlated with mineralization...

  12. Reef community structure, Sand Island, Oahu HI, (NODC Accession 0000177)

    National Oceanic and Atmospheric Administration, Department of Commerce — These reports provide the results of nine years (1990-98) of an annual quantitative monitoring of shallow marine communities inshore of the Sand Island Ocean...

  13. Macrofouling community structure in Kanayama Bay, Kii Peninsula (Japan)

    Raveendran, T.V.; Harada, E.

    of fouling organisms were monitored at monthly intervals. Fortnightly variations in hydrographic parameters were also noted simultaneously. The fouling community at this bay was a complex assemblage of bryozoans, ascidians, polychaetes and barnacles...

  14. Biofilm diatom community structure: Influence of temporal and substratum variability

    Patil, J.S.; Anil, A.C.

    occasions, the influence of planktonic blooms was also seen on the biofilm community. A comparative study of biofilms formed on the two substrata revealed significant differences in density and diversity. However species composition was almost constant...

  15. Macrozoobenthic community structure and dynamics in Cerna River (western Romania)

    Cosmina-Simona Răescu; Mălina Dumbravă-Dodoacă; Milca Petrovici

    2011-01-01

    In order to determine water quality in Cerna River, researchers carried out analyses into thestructure and dynamics of benthic macroinvertebrates communities as well as into the physical-chemicalfactors. 12 Groups of macroinvertebrates were identified. Density, abundance and frequency values recordedfor benthic communities varied according to the physical-chemical conditions specific to each samplecollecting station. Researchers noticed a direct influence of Băile Herculane town and dam upon ...

  16. Impact of oil on bacterial community structure in bioturbated sediments

    Stauffert, Magali; Cravo-Laureau, Cristiana; Jezequel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

    2013-01-01

    Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In t...

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

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

    2013-01-01

    It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral...

  18. Cooperation and punishment in community-structured populations with migration.

    Kaiping, G A; Cox, S J; Sluckin, T J

    2016-09-21

    The stable presence of punishing strategies in various cooperative species is a persistent puzzle in the study of the evolution of cooperation. To investigate the effect of group competition, we study the evolutionary dynamics of the Public Goods Game with punishment in a metapopulation that consists of separate communities. In addition to (a) well-mixed non-interacting communities, we model three distinct types of interaction between communities, (b) Migration independent of fitness; (c) Competition between whole communities, where entire communities replace each other depending on average fitness; (d) Migration where the probability of an offspring replacing an individual in another community depends on fitness. We use stochastic simulations to study the long-run frequencies of strategies with these interactions, subject to high mutation and migration rates. In cases (a) and (b), the transition between cooperation/punishment and defection regimes occurs for similar parameter values; with migration (b), the transitions are steeper due to higher total mixing. Fitness-based migration (d) by contrast can help support cooperation, changing the locations of transitions, but while group selection (c) does stabilise cooperation over much of the parameter space, fitness-based migration (d) acts as a proxy for group selection only in a smaller region. PMID:26796223

  19. Impact of metal pollution on fungal diversity and community structures.

    Op De Beeck, Michiel; Lievens, Bart; Busschaert, Pieter; Rineau, Francois; Smits, Mark; Vangronsveld, Jaco; Colpaert, Jan V

    2015-06-01

    The impact of metal pollution on plant communities has been studied extensively in the past, but little is known about the effects of metal pollution on fungal communities that occur in metal-polluted soils. Metal-tolerant ecotypes of the ectomycorrhizal fungus Suillus luteus are frequently found in pioneer pine forests in the Campine region in Belgium on metal-polluted soils. We hypothesized that metal pollution would play an important role in shaping below-ground fungal communities that occur in these soils and that Suillus luteus would be a dominant player. To test these hypotheses, the fungal communities in a young pine plantation in soil polluted with zinc, and cadmium were studied using 454 amplicon pyrosequencing. Results show that zinc, cadmium and soil organic matter content were strongly correlated with the fungal community composition, but no effects on fungal diversity were observed. As hypothesized, S. luteus was found to be a dominant member of the studied fungal communities. However, other dominant fungal species, such as Sistotrema sp., Wilcoxina mikolae and Cadophora finlandica were found as well. Their presence in metal-polluted sites is discussed. PMID:24947496

  20. Overlapping communities reveal rich structure in large-scale brain networks during rest and task conditions.

    Najafi, Mahshid; McMenamin, Brenton W; Simon, Jonathan Z; Pessoa, Luiz

    2016-07-15

    Large-scale analysis of functional MRI data has revealed that brain regions can be grouped into stable "networks" or communities. In many instances, the communities are characterized as relatively disjoint. Although recent work indicates that brain regions may participate in multiple communities (for example, hub regions), the extent of community overlap is poorly understood. To address these issues, here we investigated large-scale brain networks based on "rest" and task human functional MRI data by employing a mixed-membership Bayesian model that allows each brain region to belong to all communities simultaneously with varying membership strengths. The approach allowed us to 1) compare the structure of disjoint and overlapping communities; 2) determine the relationship between functional diversity (how diverse is a region's functional activation repertoire) and membership diversity (how diverse is a region's affiliation to communities); 3) characterize overlapping community structure; 4) characterize the degree of non-modularity in brain networks; 5) study the distribution of "bridges", including bottleneck and hub bridges. Our findings revealed the existence of dense community overlap that was not limited to "special" hubs. Furthermore, the findings revealed important differences between community organization during rest and during specific task states. Overall, we suggest that dense overlapping communities are well suited to capture the flexible and task dependent mapping between brain regions and their functions. PMID:27129758

  1. Microarthropod community structures (Oribatei and Collembola) in Tam Dao National Park, Vietnam

    Quang Manh Vu; Tri Tien Nguyen

    2000-12-01

    A study on the microarthropod community with special reference to species diversity of Oribatid and Collembola communities (Microarthropoda: Oribatei and Collembola) in Tam Dao National Park of Vietnam, a subtropical evergreen broad leaf alpine forest, was undertaken with the aim to explain how they are related to forest decline, and whether they can be used as bioindicators of forest plant succession. The results have shown that microarthropod community structures, particularly species diversity of oribatid and collembolan communities, are related to forest decline. Therefore they can be used as bioindicators of forest plant succession. In Tam Dao National Park, there was an inverse relation between species diversity of the oribatid and collembola communities. The species diversity of the oribatid community gradually decreased with forest decline whereas the species diversity of the collembola community gradually increased.

  2. Metastable Chimera States in Community-Structured Oscillator Networks

    Shanahan, Murray

    2010-01-01

    A system of symmetrically coupled identical oscillators with phase lag is presented, which is capable of generating a large repertoire of transient (metastable) "chimera" states in which synchronisation and desynchronisation co-exist. The oscillators are organised into communities, such that each oscillator is connected to all its peers in the same community and to a subset of the oscillators in other communities. Measures are introduced for quantifying metastability, the prevalence of chimera states, and the variety of such states a system generates. By simulation, it is shown that each of these measures is maximised when the phase lag of the model is close, but not equal, to pi/2. The relevance of the model to a number of fields is briefly discussed, with particular emphasis on brain dynamics.

  3. Macrozoobenthic community structure and dynamics in Cerna River (western Romania

    Cosmina-Simona Răescu

    2011-01-01

    Full Text Available In order to determine water quality in Cerna River, researchers carried out analyses into thestructure and dynamics of benthic macroinvertebrates communities as well as into the physical-chemicalfactors. 12 Groups of macroinvertebrates were identified. Density, abundance and frequency values recordedfor benthic communities varied according to the physical-chemical conditions specific to each samplecollecting station. Researchers noticed a direct influence of Băile Herculane town and dam upon thecommunity submitted to study, the maximum density and percentage numerical abundance beingestablished for Oligochaeta and Diptera, benthic groups tolerant to changes in aquatic ecosystemsqualitative parameters. The community of organisms including Ephemeroptera, Trichoptera, Plecoptera,Odonata and Coleoptera was characterized by a decrease in density and abundance values upstream -downstream as water quality is more and more degraded. This deterioration is also emphasized by the bioticindex EPT/Ch values.

  4. The reconstruction of complex networks with community structure

    Zhang, Peng; Wang, Futian; Wang, Xiang; Zeng, An; Xiao, Jinghua

    2015-12-01

    Link prediction is a fundamental problem with applications in many fields ranging from biology to computer science. In the literature, most effort has been devoted to estimate the likelihood of the existence of a link between two nodes, based on observed links and nodes’ attributes in a network. In this paper, we apply several representative link prediction methods to reconstruct the network, namely to add the missing links with high likelihood of existence back to the network. We find that all these existing methods fail to identify the links connecting different communities, resulting in a poor reproduction of the topological and dynamical properties of the true network. To solve this problem, we propose a community-based link prediction method. We find that our method has high prediction accuracy and is very effective in reconstructing the inter-community links.

  5. Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

    Acácio Aparecido Navarrete; Rodrigo Gouvêa Taketani; Lucas William Mendes; Fabiana de Souza Cannavan; Fatima Maria de Souza Moreira; Siu Mui Tsai

    2011-01-01

    The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 a...

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

    Easson, Cole G.; Thacker, Robert W.

    2014-01-01

    Sponges (Porifera) can host diverse and abundant communities of microbial symbionts that make crucial contributions to host metabolism. Although these communities are often host-specific and hypothesized to co-evolve with their hosts, correlations between host phylogeny and microbiome community structure are rarely tested. As part of the Earth Microbiome Project (EMP), we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range. W...

  7. Geochip: A high throughput genomic tool for linking community structure to functions

    Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe; Zhou, Jizhong

    2009-01-30

    GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis.

  8. Disturbance Alters the Phylogenetic Composition and Structure of Plant Communities in an Old Field System

    Russell Dinnage

    2009-01-01

    The changes in phylogenetic composition and structure of communities during succession following disturbance can give us insights into the forces that are shaping communities over time. In abandoned agricultural fields, community composition changes rapidly when a field is plowed, and is thought to reflect a relaxation of competition due to the elimination of dominant species which take time to re-establish. Competition can drive phylogenetic overdispersion, due to phylogenetic conservation o...

  9. Community Structure Detection for Overlapping Modules through Mathematical Programming in Protein Interaction Networks

    Bennett, L; Kittas, A.; Liu, S; Papageorgiou, L. G.; Tsoka, S.

    2014-01-01

    Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non lin...

  10. Can artificial reefs mimic natural reef communities? The roles of structural features and age.

    Perkol-Finkel, S; Shashar, N; Benayahu, Y

    2006-03-01

    In light of the deteriorating state of coral reefs worldwide, the need to rehabilitate marine environments has greatly increased. Artificial reefs (ARs) have been suggested as a tool for reef conservation and rehabilitation. Although successions of AR communities have been thoroughly studied, current understanding of the interactions between artificial and natural reefs (NRs) is poor and a fundamental question still to be answered is that of whether AR communities can mimic adjacent NR communities. We suggest three alternative hypotheses: Neighboring ARs and NRs will (1) achieve a similar community structure given sufficient time; (2) be similar only if they possess similar structural features; (3) always differ, regardless of age or structural features. We examined these hypotheses by comparing the community structure on a 119-year old shipwreck to a neighboring NR. Fouling organisms, including stony and soft corals, sponges, tunicates, sea anemones and hydrozoans were recorded and measured along belt transects. The ahermatypic stony coral Tubastrea micrantha dominated vertical AR regions while the soft corals Nephthea sp. and Xenia sp. dominated both artificial and natural horizontal surfaces. Our results support the second hypothesis, indicating that even after a century an AR will mimic its adjacent NR communities only if it possesses structural features similar to those of the natural surroundings. However, if the two differ structurally, their communities will remain distinct. PMID:16198411

  11. The Impact of Differential Communication Structures on Rural Community Development Efforts.

    Voth, Donald E.; And Others

    1982-01-01

    Posits that increased communication of community leaders involving relatively short communications paths should lead to program success. However, measures of connectivity and average distance in the communications structure reveal no significant relationships. Suggests other factors which may be more important to rural community development…

  12. Microbial Community Structure and Enzyme Activities in a Sequence of Copper-Polluted Soils

    GE Chao-Rong; ZHANG Qi-Chun

    2011-01-01

    The microbial community structure and enzyme activities of seven paddy soils with different Cu concentrations were investigated in the vicinity of a Cu smelter in Fuyang County, Zhejiang Province in Southeast China. The microbial community structure was analyzed using the phospholipid fatty acid (PLFA) and multiplex-terminal restriction fragment length polymorphism (M-TRFLP)techniques. There was no clear dose-response relationship between Cu pollution and soil enzyme activity except for urease. Both PLFA and M-TRFLP methods showed that Cu contamination had a large effect on the soil microbial community structure. PLFA indicators of Gram-positive bacteria (16:0i, 15:0i) and fungi (18:2w6,9) relatively decreased with increasing Cu concentration, whereas indicators of Gram-negative bacteria (19:0cy, 16:1w7) increased. The M-TRFLP results suggested that there was a dose-dependent response between Cu pollution and bacterial community or fungal community. The fungal community was more sensitive to Cu pollution than the bacterial community. Therewere no significant differences in archaeal community structure between the different Cu pollution plots and archaea might be more tolerant to Cu pollution than both bacteria and fungi.

  13. The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters.

    Kaur, Mandeep; Bowman, John P; Stewart, Doug C; Evans, David E

    2015-12-23

    Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria. PMID:26340674

  14. Microbial community structure in three deep-sea carbonate crusts

    Heijs, S. K.; Aloisi, G.; Bouloubassi, I.; Pancost, R. D.; Pierre, C.; Damste, J. S. Sinninghe; Gottschal, J. C.; van Elsas, J. D.; Forney, L. J.

    2006-01-01

    Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eas

  15. Creating Communities of Professionalism: Addressing Cultural and Structural Barriers

    Murphy, Joseph

    2015-01-01

    Purpose: The goal of this narrative synthesis is twofold. The purpose of this paper is to understand the barriers and constraints that hinder or prevent the growth of professional community. The author also want to form an empirical understanding of how educators can be successful in meeting these challenges. In both cases, the author wish to grow…

  16. Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil

    Ning Hu; Hui Li; Zheng Tang; Zhongfang Li; Jing Tian; Yilai Lou; Jianwei Li; Guichun Li; Xiaomin Hu

    2016-01-01

    We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H′), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nem...

  17. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae)

    Narit Thaochan; Richard A.I. Drew; Anuchit Chinajariyawong; Anurag Sunpapao; Chaninun Pornsuriya

    2015-01-01

    The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering) and Bactrocera tryoni (Froggatt), was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria w...

  18. Macrobenthic community structure and distribution in the Zwin nature reserve (Belgium and the Netherlands)

    Van Colen, C.; Snoeck, F.; Struyf, K.; Vincx, M.; Degraer, S.

    2009-01-01

    Distribution and structure of intertidal macrobenthic communities in the Zwin nature reserve, a lagoonal inlet consisting of marsh and tidal flat habitats, was investigated using univariate and multivariate analyses. Macrobenthos community structure was related to environmental characteristics and discussed in the framework of the implemented extension of the nature reserve.Based on explorative multivariate techniques, five different sample groups (SGs) were distinguished, which were, in gene...

  19. Modeling Risk Perception in Networks with Community Structure

    Bagnoli, Franco; Guazzini, Andrea; Massaro, Emanuele; Rudolph, Stefan

    2012-01-01

    We study the influence of global, local and community-level risk perception on the extinction probability of a disease in several models of social networks. In particular, we study the infection progression as a susceptible-infected-susceptible (SIS) model on several modular networks, formed by a certain number of random and scale-free communities. We find that in the scale-free networks the progression is faster than in random ones with the same average connectivity degree. For what concerns the role of perception, we find that the knowledge of the infection level in one's own neighborhood is the most effective property in stopping the spreading of a disease, but at the same time the more expensive one in terms of the quantity of required information, thus the cost/effectiveness optimum is a tradeoff between several parameters.

  20. Disturbance drives phylogenetic community structure in coastal dune vegetation

    Brunbjerg, A.K.; Borchsenius, Finn; Eiserhardt, Wolf L.;

    2012-01-01

    It has long been thought that environmental factors determine plant community assembly, but it is now increasingly argued that geographic spatial processes such as dispersal may also matter. Notably, the metacommunity framework considers local communities to be linked by dispersal and different...... theories hereunder assign varying importance to dispersal limitation and local environmental species sorting. At present the relative importance of these factors across habitats, geographic regions, and spatial scales remains unclear. The present study assessed the relative importance of species sorting by......) to estimate the relative importance of local environment and multi-scale random geographic factors as determinants of floristic gradients. In addition, we assessed the dependence of species composition on local environment and geographic distance using Mantel tests. The LME analyses found local...

  1. Pentachlorophenol (PCP) degradation microorganism community structure under microaeration condition

    Chen Yuancai; Hao Yuan; Fu Shiyu; Zhan Huaiyu

    2007-01-01

    The comparison of pentachlorophenol (PCP)degradation was conducted under micro-aeration and anaerobic condition with three series of batch experiment,results of which indicated that during micro-aeration condition co-immobilized of anaerobic granular sludge and isolated aerobic bacterial species could enhance the efficiency of PCP reduction through the synergism of aerobes and anaerobes reductive dechlorination and exchange of metabolites within the co-immobilized granular sludge.While during anaerobic condition,there was no great difference in the three series.The specific activities experiment further confirmed that strict anaerobes were not affected over the presence of micro aeration environment.Microorganism community construction of co-immobilized anaerobic granular sludge and the mixed isolated aerobic community was also deduced.By the efficient cooperation of aerobes and anaerobes,the high efficiency removal rate of PCP was implemented.

  2. Convergent evolution of modularity in metabolic networks through different community structures

    Zhou Wanding

    2012-09-01

    Full Text Available Abstract Background It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. Results In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxomony. Conclusions We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct enzymes in the organism’s metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability. Further, our results

  3. Microbial community structure affects marine dissolved organic matter composition

    Elizabeth B Kujawinski

    2016-04-01

    Full Text Available Marine microbes are critical players in the global carbon cycle, affecting both the reduction of inorganic carbon and the remineralization of reduced organic compounds back to carbon dioxide. Members of microbial consortia all depend on marine dissolved organic matter (DOM and in turn, affect the molecules present in this heterogeneous pool. Our understanding of DOM produced by marine microbes is biased towards single species laboratory cultures or simplified field incubations, which exclude large phototrophs and protozoan grazers. Here we explore the interdependence of DOM composition and bacterial diversity in two mixed microbial consortia from coastal seawater: a whole water community and a <1.0-μm community dominated by heterotrophic bacteria. Each consortium was incubated with isotopically-labeled glucose for 9 days. Using stable-isotope probing techniques and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry, we show that the presence of organisms larger than 1.0-μm is the dominant factor affecting bacterial diversity and low-molecular-weight (<1000 Da DOM composition over this experiment. In the <1.0-μm community, DOM composition was dominated by compounds with lipid and peptide character at all time points, confirmed by fragmentation spectra with peptide-containing neutral losses. In contrast, DOM composition in the whole water community was nearly identical to that in the initial coastal seawater. These differences in DOM composition persisted throughout the experiment despite shifts in bacterial diversity, underscoring an unappreciated role for larger microorganisms in constraining DOM composition in the marine environment.

  4. Mapping scientific literature. Structuring scientific communities through scientometrics

    Riviera,

    2013-01-01

    A sociologically integrated approach suggesting an interpretation of bibliometric indicators and maps is developed in this work. The programmatic element of the thesis is the integration of the constructivist perspective relating to the re-production of scientific community with the metric program in Bibliometrics. The accomplishment of the main purposes introduced above is realised through the following goals, which can be listed according to the level of generality. First of all, this work ...

  5. Predator foraging altitudes reveal the structure of aerial insect communities

    Helms, Jackson A.; Aaron P. Godfrey; Tayna Ames; Bridge, Eli S.

    2016-01-01

    The atmosphere is populated by a diverse array of dispersing insects and their predators. We studied aerial insect communities by tracking the foraging altitudes of an avian insectivore, the Purple Martin (Progne subis). By attaching altitude loggers to nesting Purple Martins and collecting prey delivered to their nestlings, we determined the flight altitudes of ants and other insects. We then tested hypotheses relating ant body size and reproductive ecology to flight altitude. Purple Martins...

  6. Insidious Power: The Structure of Community College Course Placement Counseling

    Maldonado, Carlos

    2015-01-01

    Past research has shown slightly mixed results about the relationship between community college academic counseling and Latino student experiences. Latino student experiences with academic counseling have been shown to be positive within the context of a special program. However, researchers have not examined how academic counseling is related to course access for Latino students. Given limitations of past research, this dissertation sought to examine counselor and Latino student perceptions ...

  7. Activity and structure of methanotrophic communities in landfill cover soils.

    Gebert, Julia; Singh, Brajesh Kumar; Pan, Yao; Bodrossy, Levente

    2009-10-01

    The composition of the methanotrophic community in soil covers on five landfills in Northern and Eastern Germany was investigated by means of diagnostic microarray and terminal restriction fragment length polymorphism (T-RFLP), both targeting the pmoA gene of methanotrophs. Physical and chemical properties of the 15 sampled soil profiles varied greatly, thus providing for very different environmental conditions. The potential methane oxidation activity, assessed using undisturbed soil cores, varied between 0.2 and 28 µg CH4 gdw (-1)  h(-1) , the latter amounting to 426 g CH4 m(-2)  h(-1) . Total nitrogen was found to be the soil variable correlating most strongly with methanotrophic activity. Explaining close to 50% of the observed variability, this indicates that on the investigated sites activity and thus abundance of methanotrophs may have been nitrogen-limited. Variables that enhance organic matter and thus nitrogen accumulation, such as field capacity, also positively impacted methanotrophic activity. In spite of the great variability of soil properties and different geographic landfill location, both microarray and T-RFLP analysis suggested that the composition of the methanotrophic community on all five sites, in all profiles and across all depths was similar. Methylocystis, Methylobacter and Methylococcus species, including Methylococcus-related uncultivated methanotrophs, were predominantly detected among type II, Ia and Ib methanotrophs, respectively. This indicates that the high methane fluxes typical for landfill environments may be the most influential driver governing the community composition, or other variables not analysed in this study. Principal component analysis suggested that community diversity is most influenced by the site from which the samples were taken and second, from the location on the individual sites, i.e. the soil profile. Landfill and individual profiles reflect the combined impact of all effective variables, including

  8. [Structural characteristics of Hemiptelea davidii community on Kerqin sandy land].

    Bai, Yun-Peng; Han, Da-Yong; Dong, Yan-Hong; Zhao, Yu-Jing; Li, Jian-Dong

    2008-02-01

    An investigation was made on the species composition and eco-type of Hemiptelea davidii community on Kerqin sandy land. The results showed that in study area, no shrub layer existed in H. davidii forest, while arbor layer could be divided into two sub-layers, with a height of 4.05-7.86 m for the upper layer, and of 2.05-3.20 m for the lower layer. In the community, there were 32 herbal species belonging to 27 genera of 13 families and dominant by Poaceae, Fabaceae and Compositae, and 11 areal types, among which, the species number in Mongolian-Northeastern China-Dahuricia-North China areal type was the highest (34.38%), followed by that in Northeastern China-North China areal type (12.5%). Among three water ecological types, mesophytes occupied 59.37% of the total, and mesoxerophytes and xerophytes occupied 25% and 15.63%, respectively. Hemicryptophytes had a larger amount in six life forms, accounting for 31.25% of the total. H. davidii community had the typical life form characteristics of temperate steppe. PMID:18464628

  9. [The ethiology structure of community-acquried pneumonia of young adults in closed communities].

    Nosach, E S; Skryl', S V; Kulakova, N V; Martynova, A V

    2012-01-01

    Despite of success in ethiology evaluation of community-acquired pneumonia (CAP) and instant improvement of diagnostic methods microbiological spectrum of CAP is still remaining underestimated and is still the problem for the routine clinical practice. In our study we estimated the role of fastidious bacteria which cause atypical CAP such as Chlamydophilla pneumoniae, Mycoplasma pneumoniae, Legionella pneumophila. Furthermore we also defined the role of viral pathogens in ethiology of CAP. PMID:23013002

  10. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity.

    Badin, Anne-Laure; Mustafa, Tarfa; Bertrand, Cédric; Monier, Armelle; Delolme, Cécile; Geremia, Roberto A; Bedell, Jean-Philippe

    2012-08-01

    This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils. PMID:22404135

  11. Evaluation of community structure and community function after exposure to the turbine fuel jet-A

    The underlying premises of the Mixed Flask Culture (MFC), an aquatic microcosm design, include (1) that the effects of a perturbation to an aquatic community may be monitored through the measurement of its functional parameters (i.e. pH and productivity/respiration ratio) and (2) these measurements will be similar between different wild-derived communities given the same perturbation. Two MFC experiments were conducted to assess these two premises. The treatment groups in both experiments consisted of 0%, 1%, 5%, and 15% WSF Jet-A with six replicates respectively. The experimental designs reflected both the MFC and the Standard Aquatic Microcosm (SAM); this hybrid design resulted in following a MFC protocol, but incorporated the SAM specified laboratory cultured organisms. Beaker homogeneity via cross inoculation and reinoculation was encouraged in the first experiment prior to dosing. Beaker heterogeneity was encouraged in the first experiment prior to dosing. Beaker heterogeneity was encouraged in the second experiment by not cross inoculating or reinoculating. The differences between the two experiments was designed to indicate if differently derived communities react similarly to an identical perturbation. Do the microcosms within each treatment group resemble each other functionally throughout the experiment, or is the within group deviation greater than the between group deviation?

  12. Distribution and structure of zooplankton communities in the austral summer in the Prydz Bay, Antarctica

    2001-01-01

    As a structure linking the ecosystem and population, community plays an important role in the marine ecology. Abundance of different species and development stages were used in our classification to the sampling stations with clustering-analysis and multi-dimension scaling, through which three geographic communities were marked out, respectively as following: the Salp community characterized by presence of Salp thompni in the northern area, the Near-shore community by Euphausia crystallorophias in the south and the main ocean community located between the above two communities. Indicator species method was then carried out between every two communities to findout which species or stages differ most. It tells that Rhincalanus gigas, adult cheatognath, late stages of Metridia gerlachei and calyptopis of Euphausiidae are indicators between Salp and neritic communities, between Krill and Salp communities are Salp thompni, adult and larvae of Cheatognath and R. gigas, and the most notable indicator between the Krill and the neritic communities are E. crystallorophias, then nauplii of Euphausiidae and Onceae conifera with less evidence.

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

    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. PMID:23004823

  14. Community Structure of Urban Forest and Disposition Characteristics of Trees in Hefei Ring Park

    WUZemin; WANGYuan; ZHANGShaojie; YANGHaiyan; XUYinbi

    2004-01-01

    The methods of vegetation ecology were used to analyze the community structure of Hefei Ring Park, and species composition, distribution pattern of tree height and DBH were described. Through calculation of tree growth index and association correlation of component species, the community structures were analyzed. The results showed that community structures are complex, there are 22 pairs of species with positive association, and tree individual in the following communities grow well and are more stable, the major are Platycladus orientalis-Prunus cerasifera fatropurpurea-Osmanthus fragrans, Robinia pseduacacia-Ligustrum lucidum, Robinia pseudoacacia-Ginkgo biloba-Photinia serrulata, Populus cadadensis-Ligustrum lucidum-Osmanthus fragrans, Sophora japonica-Ligustrum lucidum-Buxus sinica, Cyclobalanopsis glauca-Distylium racemosum.

  15. Structure and seasonality in a Malaysian mudflat community

    Broom, M. J.

    1982-08-01

    An assessment of community composition and the functional roles of the dominant species has been carried out in two intertidal areas of Malaysian mudflat dominated by natural populations of the arcid bivalve mollusc Anadara granosa. In addition to A. granosa, organisms of numerical importance are the venerid bivalve Pelecyora trigona, the neogastropod Plicarcularia leptospira, the mesogastropods Stenothyra glabrata and Cerithidea cingulata and the hermit crab Diogenes sp. The mesogastropod Natica maculosa and the neogastropod Thais carinifera may be of some importance to community organization but they are not numerically dominant. Annelids are conspicuous by their absence. The following trophic roles are ascribed to specific members of the community: A. granosa—facultative surface deposit feeder; P. trigona—suspension feeder; P. leptospira—scavenger; C. cingulata—deposit feeder/grazer; S. glabrata—deposit feeder/grazer; N. maculosa—predator; T. carinifera—predator; Diogenes sp.—scavenger/predator. S. glabrata is of particular interest because it appears to fill the niche occupied by mud snails of the genus Hydrobia in temperate mudflat systems. There is evidence of seasonality on the mudflats which points to a spawning of certain forms triggered by the major annual salinity depression at the time of the onset of the north-east monsoon in October/November. Concentrations of benthic chlorophyll a show no obvious signs of a seasonal fluctuation and the seasonality of the primary consumers is not thought to be related to food abundance. However there is some evidence of seasonality of reproduction in N. maculosa which preys on the seasonally reproducing bivalves.

  16. Determinants of community structure of zooplankton in heavily polluted river ecosystems

    Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

    2016-02-01

    River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

  17. Can microcystins affect zooplankton structure community in tropical eutrophic reservoirs?

    Paes, T A S V; Costa, I A S; Silva, A P C; Eskinazi-Sant'Anna, E M

    2016-06-01

    The aim of our study was to assess whether cyanotoxins (microcystins) can affect the composition of the zooplankton community, leading to domination of microzooplankton forms (protozoans and rotifers). Temporal variations in concentrations of microcystins and zooplankton biomass were analyzed in three eutrophic reservoirs in the semi-arid northeast region of Brazil. The concentration of microcystins in water proved to be correlated with the cyanobacterial biovolume, indicating the contributions from colonial forms such as Microcystis in the production of cyanotoxins. At the community level, the total biomass of zooplankton was not correlated with the concentration of microcystin (r2 = 0.00; P > 0.001), but in a population-level analysis, the biomass of rotifers and cladocerans showed a weak positive correlation. Cyclopoid copepods, which are considered to be relatively inefficient in ingesting cyanobacteria, were negatively correlated (r2 = - 0.01; P > 0.01) with the concentration of cyanotoxins. Surprisingly, the biomass of calanoid copepods was positively correlated with the microcystin concentration (r2 = 0.44; P > 0.001). The results indicate that allelopathic control mechanisms (negative effects of microcystin on zooplankton biomass) do not seem to substantially affect the composition of mesozooplankton, which showed a constant and high biomass compared to the microzooplankton (rotifers). These results may be important to better understand the trophic interactions between zooplankton and cyanobacteria and the potential effects of allelopathic compounds on zooplankton. PMID:26959954

  18. Effects of large river dam regulation on bacterioplankton community structure.

    Ruiz-González, Clara; Proia, Lorenzo; Ferrera, Isabel; Gasol, Josep M; Sabater, Sergi

    2013-05-01

    Large rivers are commonly regulated by damming, yet the effects of such disruption on prokaryotic communities have seldom been studied. We describe the effects of the three large reservoirs of the Ebro River (NE Iberian Peninsula) on bacterioplankton assemblages by comparing several sites located before and after the impoundments on three occasions. We monitored the abundances of several bacterial phylotypes identified by rRNA gene probing, and those of two functional groups (picocyanobacteria and aerobic anoxygenic phototrophic bacteria-AAPs). Much greater numbers of particles colonized by bacteria were found in upstream waters than downstream sites. Picocyanobacteria were found in negligible numbers at most sites, whereas AAPs constituted up to 14% of total prokaryotes, but there was no clear effect of reservoirs on the spatial dynamics of these two groups. Instead, damming caused a pronounced decline in Betaproteobacteria, Gammaproteobacteria and Bacteroidetes from upstream to downstream sites, whereas Alphaproteobacteria and Actinobacteria significantly increased after the reservoirs. Redundancy analysis revealed that conductivity, temperature and dissolved inorganic nitrogen were the environmental predictors that best explained the observed variability in bacterial community composition. Our data show that impoundments exerted significant impacts on bacterial riverine assemblages and call attention to the unforeseen ecological consequences of river regulation. PMID:23278359

  19. The structure and functions of bacterial communities in an agrocenosis

    Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

  20. Seasonal dynamics and community structure of bacterioplankton in upper Paraná River floodplain.

    Chiaramonte, Josiane Barros; Roberto, Maria do Carmo; Pagioro, Thomaz Aurélio

    2013-11-01

    Knowing the bacterial community, as well as understanding how it changes during a hydrological pulse, is very important to understand nutrient cycles in floodplain systems. The bacterial community structure was analyzed in the 12 sites of upper Paraná River floodplain, and its changes during a flood pulse were described. In order to understand how high and low water phases change bacterial community by changing abiotical variables, the bacterial community distribution was determined in superficial water of 12 different sampling stations, every 3 months, from December 2010 to September 2011. The bacterial community structure and diversity was analyzed by fluorescent in situ hybridization, considering the main domains Bacteria and Archaea and the subdivisions of the phylum Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and the Cytophaga-Flavobacterium cluster. Smaller densities were observed on ebb and low water periods and the highest density was observed in March 2011. The high water period caused a decrease in diversity because of the lost of equitability. The highest values of Shannon-Wiener index were found on December 2010 and September 2011. The nutrients runoff to the aquatic environments of the floodplain promoted an increase in the total bacterial density during the high water phase as well as changes in bacterial community composition. The bacterial community presented both spatial and temporal differences. Yet, temporal changes in limnological characteristics of the floodplain were the most important predictor of bacterial community and also influenced its diversity. PMID:24046074

  1. The network structure of human personality according to the NEO-PI-R: matching network community structure to factor structure.

    Rutger Goekoop

    Full Text Available INTRODUCTION: Human personality is described preferentially in terms of factors (dimensions found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. AIM: To directly compare the ability of network community detection (NCD and principal component factor analysis (PCA to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R. METHODS: 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. RESULTS: At facet level, NCS showed a best match (96.2% with a 'confirmatory' 5-FS. At item level, NCS showed a best match (80% with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with 'confirmatory' 5-FS and 'exploratory' 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. CONCLUSION: We present the first optimized network graph of personality traits according to the NEO-PI-R: a 'Personality Web'. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network.

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

    W. K. Balasooriya

    2008-02-01

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

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

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

    2008-02-01

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

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

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

    2015-03-01

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

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

    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

  6. Community structure and regeneration types of Betula dahurica forest in Badaling forest center of Beijing

    Zhang Yong; Zheng Zhi-hua; Zhang Zhi-xiang

    2007-01-01

    Using plant community analysis methods, we analyzed the floristic characteristics, species composition, community structure, population structure, and spatial distribution patterns of a Betula dahurica forest on the "1238" mountain of Badaling in Beijing, China. The results show that: 1) There are 33 plant species in the B. dahurica community, including 18 woody plant species. The B. dahurica forest is a monodominant community with 75.9% dominance. 2) Based on diameter at breast height (DBH)size class distribution, the population structure of B. dahurica and Acer mono-two heliophyllous and pioneer tree species is cascade-type, with both in an increasing stage. The population structure of Tilia mandshurica and T. mongolica, two shade-tolerant tree species, is inverse-J type, and they have more young seedling individuals and regenerate more stably. They are associated species of the pioneer tree species. The population structure of Quercus mongolica, as the associated species of climax species in the community, is sporadic, and its regeneration is fluctuating and random. Fraxinus rhynchophylla is a shade-tolerant tree species which has a unibar population structure and climax characteristics of pioneer tree species. The relative frequency of young seedlings reached 0.4.3) The dominant species B. dahurica is still in an increasing stage, and the regeneration of other species is steady or partly influences the community, putting the community in the pioneer species stage. From the population structure and distribution frequency ofF. rhynchophylla, the B. dahurica forest will approach to a climax state in the future.

  7. The management of a sexually charged clinical problem: social structural and psychoanalytic functionalist approaches in a therapeutic community.

    James, O W

    1986-03-01

    An event in a therapeutic community is examined from the perspectives of the structuralism of Durkheim and the functionalism of psychoanalysis. Although these two approaches might appear theoretically contradictory, analysis of the evidence shows them to be clinically complementary. The role of social structure in therapeutic communities requires deliberate conceptualization if such communities are to be demonstrably therapeutic. PMID:3964583

  8. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes?

    Emily B. Graham

    2016-02-01

    Full Text Available Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  9. Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

    Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

    2016-01-01

    Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

  10. Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439.

    He, Jingxuan; Van Treeck, Briana; Nguyen, Han B; Melançon, Charles E

    2016-02-19

    Many Actinobacteria, most notably Streptomyces, produce structurally diverse bioactive natural products, including ribosomally synthesized peptides, by multistep enzymatic pathways. The use of site-specific genetic incorporation of unnatural amino acids to investigate and manipulate the functions of natural product biosynthetic enzymes, enzyme complexes, and ribosomally derived peptides in these organisms would have important implications for drug discovery and development efforts. Here, we have designed, constructed, and optimized unnatural amino acid systems capable of incorporating p-iodo-l-phenylalanine and p-azido-l-phenylalanine site-specifically into proteins in the model natural product producer Streptomyces venezuelae ATCC 15439. We observed notable differences in the fidelity and efficiency of these systems between S. venezuelae and previously used hosts. Our findings serve as a foundation for using an expanded genetic code in Streptomyces to address questions related to natural product biosynthesis and mechanism of action that are relevant to drug discovery and development. PMID:26562751

  11. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  12. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  13. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Thomas H A Haverkamp

    Full Text Available Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm sediment communities are affected by local conditions within the sediment.

  14. Family and Community Services. Module XII: The Family: Functions and Structure.

    Petrich, Beatrice

    This twelfth of 14 curriculum modules in the Family and Community Services Occupational Education Modules series deals with functions and structure of the family. Definitions of the family are compared, and students are helped to understand various forms, functions, and structures of families. The developmental stages of the family life cycle and…

  15. Dynamical origins of the community structure of multi-layer societies

    Klimek, Peter; Eguiluz, Victor; Miguel, Maxi San; Thurner, Stefan

    2016-01-01

    Social structures emerge as a result of individuals managing a variety of different of 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 network layers in the multiplex. Community size distributions are either similar to a power-law 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. Depending on link- and node fluctuation rates, the model exhibits an anomalous shattered fragmentation transition, where one layer frag...

  16. The community seismic network and quake-catcher network: enabling structural health monitoring through instrumentation by community participants

    Kohler, Monica D.; Heaton, Thomas H.; Cheng, Ming-Hei

    2013-04-01

    A new type of seismic network is in development that takes advantage of community volunteers to install low-cost accelerometers in houses and buildings. The Community Seismic Network and Quake-Catcher Network are examples of this, in which observational-based structural monitoring is carried out using records from one to tens of stations in a single building. We have deployed about one hundred accelerometers in a number of buildings ranging between five and 23 stories in the Los Angeles region. In addition to a USB-connected device which connects to the host's computer, we have developed a stand-alone sensor-plug-computer device that directly connects to the internet via Ethernet or wifi. In the case of the Community Seismic Network, the sensors report both continuous data and anomalies in local acceleration to a cloud computing service consisting of data centers geographically distributed across the continent. Visualization models of the instrumented buildings' dynamic linear response have been constructed using Google SketchUp and an associated plug-in to matlab with recorded shaking data. When data are available from only one to a very limited number of accelerometers in high rises, the buildings are represented as simple shear beam or prismatic Timoshenko beam models with soil-structure interaction. Small-magnitude earthquake records are used to identify the first set of horizontal vibrational frequencies. These frequencies are then used to compute the response on every floor of the building, constrained by the observed data. These tools are resulting in networking standards that will enable data sharing among entire communities, facility managers, and emergency response groups.

  17. Diversity and community structure of epibenthic invertebrates and fish in the North Sea

    Callaway, R.; Alsväg, J.; de Boois, I.;

    2002-01-01

    The structure of North Sea benthic invertebrate and fish communities is an important indicator of anthropogenic and environmental impacts. Although North Sea fish stocks are monitored regularly, benthic fauna are not. Here, we report the results of a survey carried out in 2000, in which five...... nations sampled the epibenthic and fish fauna at 270 stations throughout the North Sea. The aim of the survey was to investigate the diversity and community structure of epibenthic and fish communities and to identify relationships with environmental factors, including the frequency of commercial otter...... and beam trawling disturbance. Epibenthic species diversity was lower in the southern North Sea than in central and northern areas. Fish, conversely, were more diverse in the south. The 50 m, 100 m and 200 m depth contours broadly defined the boundaries of benthic and fish communities. The abundance...

  18. Assessing the structure and temporal dynamics of seabird communities: the challenge of capturing marine ecosystem complexity.

    Moreno, Rocío; Stowasser, Gabriele; McGill, Rona A R; Bearhop, Stuart; Phillips, Richard A

    2016-01-01

    Understanding interspecific interactions, and the influences of anthropogenic disturbance and environmental change on communities, are key challenges in ecology. Despite the pressing need to understand these fundamental drivers of community structure and dynamics, only 17% of ecological studies conducted over the past three decades have been at the community level. Here, we assess the trophic structure of the procellariiform community breeding at South Georgia, to identify the factors that determine foraging niches and possible temporal changes. We collected conventional diet data from 13 sympatric species between 1974 and 2002, and quantified intra- and inter-guild, and annual variation in diet between and within foraging habits. In addition, we tested the reliability of stable isotope analysis (SIA) of seabird feathers collected over a 13-year period, in relation to those of their potential prey, as a tool to assess community structure when diets are diverse and there is high spatial heterogeneity in environmental baselines. Our results using conventional diet data identified a four-guild community structure, distinguishing species that mainly feed on crustaceans; large fish and squid; a mixture of crustaceans, small fish and squid; or carrion. In total, Antarctic krill Euphausia superba represented 32%, and 14 other species a further 46% of the combined diet of all 13 predators, underlining the reliance of this community on relatively few types of prey. Annual variation in trophic segregation depended on relative prey availability; however, our data did not provide evidence of changes in guild structure associated with a suggested decline in Antarctic krill abundance over the past 40 years. Reflecting the differences in δ(15) N of potential prey (crustaceans vs. squid vs. fish and carrion), analysis of δ(15) N in chick feathers identified a three-guild community structure that was constant over a 13-year period, but lacked the trophic cluster representing

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

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

    1999-01-01

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

  20. The Structure of Psychopathology in a Community Sample of Preschoolers

    Strickland, Jennifer; Keller, Jennifer; Lavigne, John V.; Gouze, Karen; Hopkins, Joyce; LeBailly, Susan

    2011-01-01

    Despite growing interest in the development of alternative diagnostic classification systems for psychopathology in young children, little is known about the adequacy of the DSM symptom structure for describing psychopathology in this population. This paper examines the fit of the DSM-IV emotional (ED) and disruptive behavior disorder (DD) symptom…

  1. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.

    Roling, W.F.M.; Breukelen, van, R.; Braster, M; Lin, B.; Verseveld, van, Marloes

    2001-01-01

    Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic cont...

  2. Structure, organization and dynamics of a Sardinian sand dune plant community

    Cusseddu, Valentina

    2016-01-01

    Coastal sand dunes have attracted the attention of plant ecologists for over a century, but have largely relied on correlations to explain striking dune plant community organization. We experimentally examined longstanding hypotheses that sand binding, interspecific interactions, abiotic factors and seedling recruitment are drivers of sand dune plant community structure in Sardinia, Italy. Removing foundation species from the fore, middle and back dune over 3 years led to erosion and habitat ...

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

    Garland, J. L.

    1994-11-01

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

  4. Community structure and the evolution of interdisciplinarity in Slovenia's scientific collaboration network

    Lužar, Borut; Levnajić, Zoran; Povh, Janez; Perc, Matjaž

    2014-01-01

    Interaction among the scientific disciplines is of vital importance in modern science. Focusing on the case of Slovenia, we study the dynamics of interdisciplinary sciences from 1960 to 2010. Our approach relies on quantifying the interdisciplinarity of research communities detected in the coauthorship network of Slovenian scientists over time. Examining the evolution of the community structure, we find that the frequency of interdisciplinary research is only proportional with the overall gro...

  5. Biogeographical Boundaries, Functional Group Structure and Diversity of Rocky Shore Communities along the Argentinean Coast

    Wieters, Evie A.; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; SERGIO A NAVARRETE

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10′s km) and local (10′s m) scales, could be associated to species diversity within and among these groups. Functional community structu...

  6. Field-based experimental acidification alters fouling community structure and reduces diversity.

    Brown, Norah E M; Therriault, Thomas W; Harley, Christopher D G

    2016-09-01

    Increasing levels of CO2 in the atmosphere are affecting ocean chemistry, leading to increased acidification (i.e. decreased pH) and reductions in calcium carbonate saturation state. Many species are likely to respond to acidification, but the direction and magnitude of these responses will be based on interspecific and ontogenetic variation in physiology and the relative importance of calcification. Differential responses to ocean acidification (OA) among species will likely result in important changes in community structure and diversity. To characterize the potential impacts of OA on community composition and structure, we examined the response of a marine fouling community to experimental CO2 enrichment in field-deployed flow-through mesocosm systems. Acidification significantly altered the community structure by altering the relative abundance of species and reduced community variability, resulting in more homogenous biofouling communities from one experimental tile to the next both among and within the acidified mesocosms. Mussel (Mytilus trossulus) recruitment was reduced by over 30% in the elevated CO2 treatment compared to the ambient treatment by the end of the experiment. Strong differences in mussel cover (up to 40% lower in acidified conditions) developed over the second half of the 10-week experiment. Acidification did not appear to affect the mussel growth, as average mussel sizes were similar between treatments at the end of the experiment. Hydroid (Obelia dichotoma) cover was significantly reduced in the elevated CO2 treatment after 8 weeks. Conversely, the percentage cover of bryozoan colonies (Mebranipora membranacea) was higher under acidified conditions with differences becoming apparent after 6 weeks. Neither recruitment nor final size of barnacles (Balanus crenatus) was affected by acidification. By the end of the experiment, diversity was 41% lower in the acidified treatment relative to ambient conditions. Overall, our findings support the

  7. Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm

    Gieseke, Armin; Purkhold, Ulrike; Wagner, Michael; Amann, Rudolf; Schramm, Andreas

    2001-01-01

    The microbial community structure and activity dynamics of a phosphate-removing biofilm from a sequencing batch biofilm reactor were investigated with special focus on the nitrifying community. O2, NO2−, and NO3− profiles in the biofilm were measured with microsensors at various times during the nonaerated-aerated reactor cycle. In the aeration period, nitrification was oxygen limited and restricted to the first 200 μm at the biofilm surface. Additionally, a delayed onset of nitrification aft...

  8. Stream invertebrate communities of Mongolia: current structure and expected changes due to climate change

    Maasri, Alain; Gelhaus, Jon

    2012-01-01

    Background Mongolia’s riverine landscape is divided into three watersheds, differing in extent of permafrost, amount of precipitation and in hydrological connectivity between sub-drainages. In order to assess the vulnerability of macroinvertebrate communities to ongoing climate change, we consider the taxonomic and functional structures of stream communities in two major watersheds: The Central Asian Internal Watershed (CAIW) and the Arctic Ocean Watershed (AOW), together covering 86.1% of Mo...

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

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

    2011-01-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus'...

  10. COMMUNITY STRUCTURE OF THE TINTINNIDS (CILIOPHORA: SPIROTRICHEA) IN THE REGION OF ABROLHOS (BAHIA, BRAZIL)

    Alejandro Esteweson Santos Faustino da Costa; Sigrid Neumann-Leitão; Fabiano Lopes Thompson; Pedro Augusto Mendes de Castro Melo; Jana Ribeiro de Santana

    2015-01-01

    The tintinnid community in the region of Abrolhos (Bahia, Brazil) was studied during February 2012. We hypothesized that the tintinnid community structure varies significantly over a short temporal scale (photoperiod), as well as spatially over a short scale (on and away from the reefs), and a broad scale (distance of the reef area from the coast). Three areas in Abrolhos were studied. Two sampling points were delimited in each area, where the tintinnids were collected by horizontal subsurfac...

  11. Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

    Lucas William Mendes

    2014-12-01

    Full Text Available Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%, which presented differences according to the depth, where the classes Betaproteobacteria (21% and Deltaproteobacteria (16% were abundant at 10 cm and Epsilonproteobacteria (35% was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively, Chloroflexi (2.8% and 0.75%, and Acidobacteria (2.75% and 0.57% according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

  12. A thermal flux-diffusing model for complex networks and its applications in community structure detection

    Shen Yi

    2013-01-01

    We introduce a thermal flux-diffusing model for complex networks.Based on this model,we propose a physical method to detect the communities in the complex networks.The method allows us to obtain the temperature distribution of nodes in time that scales linearly with the network size.Then,the local community enclosing a given node can be easily detected for the reason that the dense connections in the local communities lead to the temperatures of nodes in the same community being close to each other.The community structure of a network can be recursively detected by randomly choosing the nodes outside the detected local communities.In the experiments,we apply our method to a set of benchmarking networks with known pre-determined community structures.The experiment results show that our method has higher accuracy and precision than most existing globe methods and is better than the other existing local methods in the selection of the initial node.Finally,several real-world networks are investigated.

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

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

    2015-11-22

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

  14. Structure of marine predator and prey communities along environmental gradients in a glaciated fjord

    Renner, Martin; Arimitsu, Mayumi L.; Piatt, John F.

    2012-01-01

    Spatial patterns of marine predator communities are influenced to varying degrees by prey distribution and environmental gradients. We examined physical and biological attributes of an estuarine fjord with strong glacier influence to determine the factors that most influence the structure of predator and prey communities. Our results suggest that some species, such as walleye pollock (Theragra chalcogramma), black-legged kittiwake (Rissa tridactyla), and glaucous-winged gull (Larus glaucescens), were widely distributed across environmental gradients, indicating less specialization, whereas species such as capelin (Mallotus villosus), harbor seal (Phoca vitulina), and Kittlitz's murrelet (Brachyramphus brevirostris) appeared to have more specialized habitat requirements related to glacial influence. We found that upper trophic level communities were well correlated with their mid trophic level prey community, but strong physical gradients in photic depth, temperature, and nutrients played an important role in community structure as well. Mid-trophic level forage fish communities were correlated with the physical gradients more closely than upper trophic levels were, and they showed strong affinity to tidewater glaciers. Silica was closely correlated with the distribution of fish communities, the mechanisms of which deserve further study.

  15. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile

    Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

    2006-01-01

    Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.

  16. Structuring Community Care using Multi-Agent Systems

    Beer, Martin D.

    Community care is a complex operation that requires the interaction of large numbers of dedicated individuals, managed by an equally wide range of organisations. They are also by their nature highly mobile and flexible, moving between clients in whatever order person receiving care is that they receive what they expect regularly, reliably and when they expect to receive it. Current systems are heavily provider focused on providing the scheduled care with as high apparent cost effectiveness as possible. Unfortunately, the lack of focus on the client often leads to inflexibility with expensive services being provided when they are not needed, large scale duplication of effort or inadequate flexibility to change the care regime to meet changing circumstances. Add to this the problems associated with the lack of integration of emergency and routing care and the extensive support given by friends and family and many opportunities exist to improve both the levels of support and the efficiency of care. The move towards Individual Care Plans requires much closer monitoring to ensure that the care specified for each individual is actually delivered and when linked with smart home technology in conjunction with appropriate sensors allows a much richer range of services to be offered which can be customised to meet the needs of each individual, giving them the assurance to continue to live independently.

  17. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  18. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  19. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-06-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production. PMID:26585859

  20. Error and attack tolerance of synchronization in Hindmarsh–Rose neural networks with community structure

    Synchronization is one of the most important features observed in large-scale complex networks of interacting dynamical systems. As is well known, there is a close relation between the network topology and the network synchronizability. Using the coupled Hindmarsh–Rose neurons with community structure as a model network, in this paper we explore how failures of the nodes due to random errors or intentional attacks affect the synchronizability of community networks. The intentional attacks are realized by removing a fraction of the nodes with high values in some centrality measure such as the centralities of degree, eigenvector, betweenness and closeness. According to the master stability function method, we employ the algebraic connectivity of the considered community network as an indicator to examine the network synchronizability. Numerical evidences show that the node failure strategy based on the betweenness centrality has the most influence on the synchronizability of community networks. With this node failure strategy for a given network with a fixed number of communities, we find that the larger the degree of communities, the worse the network synchronizability; however, for a given network with a fixed degree of communities, we observe that the more the number of communities, the better the network synchronizability.

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

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

    2006-12-01

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

  2. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

    Xiaohui Wang

    Full Text Available BACKGROUND: Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. AIMS: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs and to understand the effects of environmental factors on their structure. METHODS: 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. RESULTS: High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO, ammonia concentrations and loading rate of chemical oxygen demand (COD. Based on the variance partitioning analyses (VPA, a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25% and operational parameters (23%, respectively. CONCLUSIONS: This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

  3. Correlation between microbial community structure and biofouling as determined by analysis of microbial community dynamics.

    Guo, Xuechao; Miao, Yu; Wu, Bing; Ye, Lin; Yu, Haiyan; Liu, Su; Zhang, Xu-Xiang

    2015-12-01

    Three lab-scale membrane bioreactors (MBRs) were continuously operated to treat saline wastewater under 0%, 0.75% and 1.5% NaCl stress. 0.75% and 1.5% NaCl reduced the COD and NH4(+)-N removal at the beginning, while the removal efficiencies could be recovered along with the operation of MBRs. Also, the polysaccharide in extracellular polymeric substances (EPS) and soluble microbial products (SMP) played an important role in the membrane fouling. Illumina sequencing of 16S rRNA gene showed that the increasing level of salinity reduced the diversity of the microbial community, and a higher salinity stimulated the growth of Bacteroidetes. At genus level, Flavobacterium, Aequorivita, Gelidibacter, Microbacterium, and Algoriphagus increased with the increase of salinity, which are shown to be highly salt tolerant. The strength of salinity or the duration of salinity could stimulate the microorganisms with similar functions, and the changes of polysaccharide in EPS and SMP were closely related to the membrane fouling rate as well as correlated with some saline-resistance genera. PMID:26318928

  4. Potential Networks, Contagious Communities, and Understanding Social Network Structure

    Schoenebeck, Grant

    2013-01-01

    In this paper we study how the network of agents adopting a particular technology relates to the structure of the underlying network over which the technology adoption spreads. We develop a model and show that the network of agents adopting a particular technology may have characteristics that differ significantly from the social network of agents over which the technology spreads. For example, the network induced by a cascade may have a heavy-tailed degree distribution even if the original n...

  5. Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

    Xue, Zheng

    2014-07-15

    Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community. © 2014 © 2014 Taylor & Francis.

  6. Uncovering the overlapping community structure of complex networks in nature and society

    Pálla, G; Farkas, I; Vicsek, T; Palla, Gergely; Derenyi, Imre; Farkas, Illes; Vicsek, Tamas

    2005-01-01

    Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of...

  7. Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community.

    Xue, Zheng; Lu, Huijie; Liu, Wen-Tso

    2014-01-01

    Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community. PMID:25115516

  8. Hierarchical mutual information for the comparison of hierarchical community structures in complex networks

    Perotti, Juan Ignacio; Caldarelli, Guido

    2015-01-01

    The quest for a quantitative characterization of community and modular structure of complex networks produced a variety of methods and algorithms to classify different networks. However, it is not clear if such methods provide consistent, robust and meaningful results when considering hierarchies as a whole. Part of the problem is the lack of a similarity measure for the comparison of hierarchical community structures. In this work we give a contribution by introducing the {\\it hierarchical mutual information}, which is a generalization of the traditional mutual information, and allows to compare hierarchical partitions and hierarchical community structures. The {\\it normalized} version of the hierarchical mutual information should behave analogously to the traditional normalized mutual information. Here, the correct behavior of the hierarchical mutual information is corroborated on an extensive battery of numerical experiments. The experiments are performed on artificial hierarchies, and on the hierarchical ...

  9. Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link.

    Souza-Alonso, Pablo; Guisande, Alejandra; González, Luís

    2015-01-01

    Triclopyr is a commonly used herbicide in the control of woody plants and can exhibit toxic effects to soil microorganisms. However, the impact on soils invaded by plant exotics has not yet been addressed. Here, we present the results of an 18-month field study conducted to evaluate the impact of triclopyr on the structure of fungal and bacterial communities in soils invaded by Acacia dealbata Link, through the use of denature gradient gel electrophoresis. After triclopyr application, analyses of bacterial fingerprints suggested a change in the structure of the soil bacterial community, whereas the structure of the soil fungal community remained unaltered. Bacterial density and F:B ratio values changed across the year but were not altered due to herbicide spraying. On the contrary, fungal diversity was increased in plots sprayed with triclopyr 5 months after the first application. Richness and diversity (H') of both bacteria and fungi were not modified after triclopyr application. PMID:25602151

  10. Analysis of community properties and node properties to understand the structure of the bus transport network

    Sun, Yeran; Mburu, Lucy; Wang, Shaohua

    2016-05-01

    Akin to most infrastructures, intraurban bus networks are large and highly complex. Understanding the composition of such networks requires an intricate decomposition of the network into modules, taking into account the manner in which network links are distributed among the nodes. There exists for each set of highly interlinked nodes little connectivity with the next set of highly interlinked nodes. This inherent property of nodes makes community detection a popular approach for analyzing the structure of complex networks. In this study, we attempt to understand the structure of the intraurban bus network of Ireland's capital city, Dublin in a two-step approach. We first analyze the modular structure of the network by identifying potential communities. Secondly, we assess the prominence of each network node by examining the module-based topological properties of the nodes. Results of this empirical study reveal a clear pattern of independent communities, indicating thus, an implicit multi-community structure of the intraurban bus network. Examination of the geographic characteristics of the identified communities shows a degree of socio-economic divisions of the Dublin city. Furthermore, a large majority of the important nodes (vital transportation hubs) are located at the city center, implying that most of the bus lines in Dublin city tend to intersect the city's core.

  11. Force-Based Incremental Algorithm for Mining Community Structure in Dynamic Network

    Bo Yang; Da-You Liu

    2006-01-01

    Community structure is an important property of network. Being able to identify communities can provide invaluable help in exploiting and understanding both social and non-social networks. Several algorithms have been developed up till now. However, all these algorithms can work well only with small or moderate networks with vertexes of order 104.Besides, all the existing algorithms are off-line and cannot work well with highly dynamic networks such as web, in which web pages are updated frequently. When an already clustered network is updated, the entire network including original and incremental parts has to be recalculated, even though only slight changes are involved. To address this problem, an incremental algorithm is proposed, which allows for mining community structure in large-scale and dynamic networks. Based on the community structure detected previously, the algorithm takes little time to reclassify the entire network including both the original and incremental parts. Furthermore, the algorithm is faster than most of the existing algorithms such as Girvan and Newman's algorithm and its improved versions. Also, the algorithm can help to visualize these community structures in network and provide a new approach to research on the evolving process of dynamic networks.

  12. Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest.

    Yanqiu Hu

    Full Text Available We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1 forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2 soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3 a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting.

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

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

    2014-01-01

    A number of recent studies have shown that intraspecific genetic variation of plants may have a profound effect on the herbivorous communities which depend on them. However less is known about the relative importance of intraspecific variation compared to other ecological factors, for example environmental variation or the effects of herbivore damage. We randomly selected 22 Betula pendula genotypes from a local population (block) variation on a local scale, while on a regional scale, genotypic and environmental (site) variation accounted for 4-14% of the arthropod community structure. The genetic effects were modified by environmental variation on both a local and regional scale over one study year, and locally, the largest part of the variation (38%) could be explained by the genotype × environment (block) interactions. Suppression of insect herbivores during one growing season led to changed arthropod community structure in the following growing season, but this effect was minimal and could explain only 4% of the total variation in insect community structure. Our results suggest that both genetic and environmental factors are important determinants of the community structure of herbivorous insects. Together these mechanisms appear to maintain the high diversity of insects in B. pendula forest ecosystems. PMID:24715977

  14. Does the edge effect influence plant community structure in a tropical dry forest?

    Diogo Gallo de Oliveira; Ana Paula do Nascimento Prata; Leandro de Sousa Souto; Robério Anastácio Ferreira

    2013-01-01

    Edge effects are considered a key factor in regulating the structure of plant communities in different ecosystems. However, regardless to few studies, edge influence does not seem to be decisive in semiarid regions such as the Brazilian tropical dry forest known as Caatinga but this issue remains inconclusive. The present study tests the null hypothesis that the plant community of shrubs and trees does not change in its structure due to edge effects. Twenty-four plots (20 x 20 m) were set up ...

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

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

    2015-09-01

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

  16. Effects of application of corn straw on soil microbial community structure during the maize growing season.

    Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

    2015-01-01

    This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. PMID:24652702

  17. Structural and cultural sources of community in American congregations.

    Stroope, Samuel; Baker, Joseph O

    2014-05-01

    Religious institutions are among the deepest reservoirs of social belonging in America, but what determines whether belonging is cultivated in these institutions? Previous research shows that individuals' social network composition is a primary predictor of feelings of belonging. However, less is known about how group characteristics condition the influence of social networks on belonging. We use data from the 2001 U.S. Congregational Life Survey and multilevel modeling to examine how organizational characteristics such as group size, in-group network density, and aggregate ideological uniformity moderate the effects of individual social networks on sense of belonging. Results indicate that both structural (network density, church size) and cultural (ideology) characteristics of groups significantly condition the effects of individual social networks on belonging. Smaller group size, network density, and ideological unity cultivate contexts that amplify the relationship between personal networks and belonging. PMID:24576623

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

    BongkeunSong

    2014-09-01

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

  19. Detectability Thresholds and Optimal Algorithms for Community Structure in Dynamic Networks

    Ghasemian, Amir; Zhang, Pan; Clauset, Aaron; Moore, Cristopher; Peel, Leto

    2016-07-01

    The detection of communities within a dynamic network is a common means for obtaining a coarse-grained view of a complex system and for investigating its underlying processes. While a number of methods have been proposed in the machine learning and physics literature, we lack a theoretical analysis of their strengths and weaknesses, or of the ultimate limits on when communities can be detected. Here, we study the fundamental limits of detecting community structure in dynamic networks. Specifically, we analyze the limits of detectability for a dynamic stochastic block model where nodes change their community memberships over time, but where edges are generated independently at each time step. Using the cavity method, we derive a precise detectability threshold as a function of the rate of change and the strength of the communities. Below this sharp threshold, we claim that no efficient algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this threshold. The first uses belief propagation, which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the belief propagation equations. These results extend our understanding of the limits of community detection in an important direction, and introduce new mathematical tools for similar extensions to networks with other types of auxiliary information.

  20. Detectability thresholds and optimal algorithms for community structure in dynamic networks

    Ghasemian, Amir; Clauset, Aaron; Moore, Cristopher; Peel, Leto

    2015-01-01

    We study the fundamental limits on learning latent community structure in dynamic networks. Specifically, we study dynamic stochastic block models where nodes change their community membership over time, but where edges are generated independently at each time step. In this setting (which is a special case of several existing models), we are able to derive the detectability threshold exactly, as a function of the rate of change and the strength of the communities. Below this threshold, we claim that no algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this limit. The first uses belief propagation (BP), which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the BP equations. We verify our analytic and algorithmic results via numerical simulation, and close with a brief discussion of extensions and open questions.

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

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

    2016-09-01

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

  2. Effects of community structure on the dynamics of random threshold networks

    Wang, Rui-Sheng; Albert, Réka

    2013-01-01

    Random threshold networks (RTNs) have been widely used as models of neural or genetic regulatory networks. Network topology plays a central role in the dynamics of these networks. Recently it has been shown that many social and biological networks are scale-free and also exhibit community structure, in which autonomous modules are wired together to perform relatively independent functions. In this study we use both synchronous and asynchronous models of RTNs to systematically investigate how community structure affects the dynamics of RTNs with scale-free topology. Extensive simulation experiments show that RTNs with high modularity have more attractors than those RTNs with low modularity, and RTNs with smaller communities tend to have more attractors. Damage resulting from perturbation of initial conditions spreads less effectively in RTNs with higher modularity and RTNs with smaller communities. In addition, RTNs with high modularity can coordinate their internal dynamics better than RTNs with low modularity under the synchronous update scheme, and it is the other way around under the asynchronous update. This study shows that community structure has a strong effect on the dynamics of RTNs.

  3. [Analysis of Prokaryotic Community Structure in River Waters of the Ningbo Sanjiang Mouth].

    Hu, An-yi; Li, Jiang-wei; Yang, Xiao-yong; Wang, Hong-jie; Yu, Chang-ping

    2015-07-01

    The prokaryotic community structure in river waters of the Ningbo Sanjiang Mouth was analyzed for the first time using 16S rRNA gene based-Illumina Miseq high-throughput sequencing. A total of 215 504 high-quality sequences were obtained, and the results of alpha-diversity analysis revealed that Yongjiang River Watershed (YRW) harbored high diversity and richness of prokaryotic communities. Taxonomic assignment analysis indicated that β-Proteobacterium, Actinobacteria and Bacteroidetes dominated in the river water of YRW, and accounted for 78. 88% of the total prokaryotic communities. Hydrological condition may play an important role in influencing the composition and structure of YRW prokaryotic community. In addition, several kinds of sewer- and fecal-pollution indicator bacterial groups were observed in this area with the highest abundance of pollution indicator bacteria occurring in the water sample of Yuyao River, implying that the Yuyao River might have a high potential risk of sewer- and fecal-pollution. Moreover, a total of 76 species and 18 subspecies of potential pathogenic bacteria, which accounted for 2. 19% and 0. 40% of total sequences respectively, were identified using BLASTN analysis with a local pathogenic bacteria database. Overall, this study provided an important basic data for shedding light on the structure and ecological function of YRW prokaryotic community. PMID:26489316

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

    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

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

    Benny Kwok Kan Chan

    Full Text Available 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.

  6. Compositional divergence and convergence in local communities and spatially structured landscapes.

    Tancredi Caruso

    Full Text Available Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence than, less dissimilar (convergence than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect. The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community

  7. Is benthic food web structure related to diversity of marine macrobenthic communities?

    Sokołowski, A.; Wołowicz, M.; Asmus, H.; Asmus, R.; Carlier, A.; Gasiunaité, Z.; Grémare, A.; Hummel, H.; Lesutiené, J.; Razinkovas, A.; Renaud, P. E.; Richard, P.; Kędra, M.

    2012-08-01

    Numerical structure and the organisation of food webs within macrozoobenthic communities has been assessed in the European waters (Svalbard, Barents Sea, Baltic Sea, North Sea, Atlantic Ocean and the Mediterranean Sea) to address the interactions between biodiversity and ecosystem functioning. Abundance and classical species diversity indices (S, H', J) of macrofaunal communities were related to principal attributes of food webs (relative trophic level and food chain length, FCL) that were determined from carbon and nitrogen stable isotope values. Structure of marine macrobenthos varies substantially at a geographical scale; total abundance ranges from 63 ind. m-2 to 34,517 ind. m-2, species richness varies from 3 to 166 and the Shannon-Weaver diversity index from 0.26 to 3.26 while Pielou's evenness index is below 0.73. The major source of energy for macrobenthic communities is suspended particulate organic matter, consisting of phytoplankton and detrital particles, sediment particulate organic matter, and microphytobenthos in varying proportions. These food sources support the presence of suspension- and deposit-feeding communities, which dominate numerically on the sea floor. Benthic food webs include usually four to five trophic levels (FCL varies from 3.08 to 4.86). Most species are assigned to the second trophic level (primary consumers), fewer species are grouped in the third trophic level (secondary consumers), and benthic top predators are the least numerous. Most species cluster primarily at the lowest trophic level that is consistent with the typical organization of pyramidal food webs. Food chain length increases with biodiversity, highlighting a positive effect of more complex community structure on food web organisation. In more diverse benthic communities, energy is transferred through more trophic levels while species-poor communities sustain a shorter food chain.

  8. Gastropod diversification and community structuring processes in ancient Lake Ohrid: a metacommunity speciation perspective

    Hauffe, T.; Albrecht, C.; Wilke, T.

    2015-09-01

    The Balkan Lake Ohrid is the oldest and most speciose freshwater lacustrine system in Europe. However, it remains unclear whether the diversification of its endemic taxa is mainly driven by neutral processes, environmental factors, or species interactions. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics. Such a unifying framework - the metacommunity speciation model - considers how community assembly affects diversification and vice versa by assessing the relative contribution of the three main community assembly processes, dispersal limitation, environmental filtering, and species interaction. The current study therefore used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process based metacommunity analyses. Specifically, the study aimed at (i) identifying the relative importance of the three community assembly processes and (ii) to test whether the importance of these individual processes changes gradually with lake depth or whether they are distinctively related to eco-zones. Based on specific simulation steps for each of the three processes, it could be demonstrated that dispersal limitation had the strongest influence on gastropod community structures in Lake Ohrid. However, it was not the exclusive assembly process but acted together with the other two processes - environmental filtering, and species interaction. In fact, the relative importance of the three community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter. The study thus corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community structure) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental

  9. [Macrobenthic community structure and bioassessment for water quality of Banqiao Reservoir in Huaihe River basin].

    Sun, Wei-sheng; Gu, Qian-hong; Dong, Jing; Cheng, Qing-qing; Li, Xue-jun; Zhang, Man

    2015-09-01

    In order to demonstrate macrobenthic community structure dynamics and conduct a biological evaluation of water quality in Banqiao Reservoir, we collected seasonal samples from January to November 2014 across 15 sampling sites. A total of 17 species belonging to five families, four classes, and 3 phyla were identified, including 8 chironomidae, 4 oligochaeta and 5 mollusc. Bellamya aeruginosa, Corbicula fluminea, Branchiura sowerbyi, Pelopia sp. and Glyptotendipes sp. were the important species in Banqiao Reservoir. The total density, biomass and biodiversity of marobenthos showed significant spatial and temporal differences. ANOSIM analysis indicated that the macrobenthic community structure also differed significantly among regions and seasons, and the main contributing species were Glyptotendipes sp., Pelopia sp. and B. sowerbyi. The abundance-biomass comparison curves (ABC curves) indicated that the current macrobenthic community in Banqiao Reservoir was stable. Combined with the biodiversity index, biological pollution index (BPI) and Hilsenhoff biotic index (BI), it was suggested that Banqiao Reservoir suffered slight pollution. PMID:26785570

  10. The ecology of unhealthy places: violence, birthweight, and the importance of territoriality in structurally disadvantaged communities.

    Kane, Robert J

    2011-12-01

    The present study tested the relationships between macro-level violence and birthweight in structurally disadvantaged communities in the District of Columbia. The study hypothesized that both rates of violence and violence "uncertainty" (the latter was operationalized as within-census tract residual change scores in violence), should be inversely associated with birthweight among all live singleton births in DC from 2000 to 2002. Using mixed models, the study found that (1) patterns of violence and violence uncertainty were significantly associated with birthweight among mothers residing in structurally disadvantaged communities, and (2) these findings held for Black and Hispanic, but not white, mothers. The study argues that urban ecological researchers should begin to consider not just how rates (or levels) of violence influence health and other social outcomes in communities, but also the effects of violence uncertainty as a source of unpredictable risk and territorial disruption. PMID:22001230

  11. Assessment of nematode community structure as a bioindicator in river monitoring

    Nematode communities from river water and sediments were assessed for the abundance, feeding types, maturity indices and nematode channel ratio (NCR). The sampling sites studied included different levels of pollution and contamination from agricultural, industrial and sewage sources. The nematode abundance found in the sediment samples was more than that in the water samples. The lowest nematode abundance in sediment samples and the lowest NCR in water samples were both found at the industrial pollution site. Water samples showed positive correlation between the NCR and river pollution index (RPI). Mean maturity indices in sediment samples were inversely correlated with RPI. The pollutant source determined the relationship between NCR and pollution level, while maturity index always showed negative correlation with pollutant level regardless of the pollutant sources. The nematode abundance and its community structure were both reliable bioindicators for monitoring long-term river pollution in both qualitative and quantitative aspects. - Nematode community structure in rivers is related to the contamination source and level.

  12. Assessment of nematode community structure as a bioindicator in river monitoring

    Wu, H.C.; Chen, P.C. [Department of Plant Pathology, National Chung Hsing University, 250 Kuo Kuan Rd, Taichung 402, Taiwan (China); Tsay, T.T., E-mail: tttsay@nchu.edu.t [Department of Plant Pathology, National Chung Hsing University, 250 Kuo Kuan Rd, Taichung 402, Taiwan (China)

    2010-05-15

    Nematode communities from river water and sediments were assessed for the abundance, feeding types, maturity indices and nematode channel ratio (NCR). The sampling sites studied included different levels of pollution and contamination from agricultural, industrial and sewage sources. The nematode abundance found in the sediment samples was more than that in the water samples. The lowest nematode abundance in sediment samples and the lowest NCR in water samples were both found at the industrial pollution site. Water samples showed positive correlation between the NCR and river pollution index (RPI). Mean maturity indices in sediment samples were inversely correlated with RPI. The pollutant source determined the relationship between NCR and pollution level, while maturity index always showed negative correlation with pollutant level regardless of the pollutant sources. The nematode abundance and its community structure were both reliable bioindicators for monitoring long-term river pollution in both qualitative and quantitative aspects. - Nematode community structure in rivers is related to the contamination source and level.

  13. Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting.

    Chen, Yuxiang; Zhang, Yufen; Zhang, Quanguo; Xu, Lixin; Li, Ran; Luo, Xiaopei; Zhang, Xin; Tong, Jin

    2015-11-01

    In the present study, maize stover was vermicomposted with the epigeic earthworm Eisenia fetida. The results showed that, during vermicomposting process, the earthworms promoted decomposition of maize stover. Analysis of microbial communities of the vermicompost by high-throughput pyrosequencing showed more complex bacterial community structure in the substrate treated by the earthworms than that in the control group. The dominant microbial genera in the treatment with the earthworms were Pseudoxanthomonas, Pseudomonas, Arthrobacter, Streptomyces, Cryptococcus, Guehomyces, and Mucor. Compared to the control group, the relative abundance of lignocellulose degradation microorganisms increased. The results indicated that the earthworms modified the structure of microbial communities during vermicomposting process, activated the growth of lignocellulose degradation microorganisms, and triggered the lignocellulose decomposition. PMID:26139410

  14. Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil.

    Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

    2016-01-01

    We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H'), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments. PMID:27311984

  15. Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil

    Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

    2016-06-01

    We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H‧), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments.

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

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

    2016-08-01

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

  17. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    Bowman, Jeff S.; Rasmussen, Simon; Blom, Nikolaj;

    2011-01-01

    community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than...

  18. Importance of structure and density of macroalgae communities (Fucus serratus) for photosynthetic production and light utilisation

    Binzer, Thomas; Sand-Jensen, Kaj

    2002-01-01

    a natural day-night cycle is attained at an LAI of 5 to 6. Maximum gross production was about 3-fold lower in F. serratus communities than in terrestrial communities in forests, grasslands and crops. Manipulating F. serratus communities to a more vertical structure increased light penetration and...

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

    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.

  20. Linking microbial community structure and microbial processes: an empirical and conceptual overview.

    Bier, Raven L; Bernhardt, Emily S; Boot, Claudia M; Graham, Emily B; Hall, Edward K; Lennon, Jay T; Nemergut, Diana R; Osborne, Brooke B; Ruiz-González, Clara; Schimel, Joshua P; Waldrop, Mark P; Wallenstein, Matthew D

    2015-10-01

    A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009-13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them. PMID:26371074

  1. Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

    Acácio Aparecido Navarrete

    2011-10-01

    Full Text Available The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure and ammonia-oxidizing Archaea (richness and community composition were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009 from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old, agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA of Archaea (306 sequences, the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366, followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715, crops (H' = 1.4613; D = 0.3309 and secondary forest (H' = 0.8633; D = 0.5405. All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 % previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

  2. Threadfin shad impacts phytoplankton and zooplankton community structures in channel catfish ponds

    Plankton community structure and chlorophyll a concentration were compared in 12 0.1-ha earthen ponds co-stocked with channel catfish (Ictalurus punctatus Rafinesque, 1818) in multiple-batch culture (initial biomass = 5,458 kg ha-1) and a planktivore, threadfin shad (Dorosoma petenense Güther, 1867;...

  3. Confronting different models of community structure to species-abundance data: a Bayesian model comparison

    Etienne, R.S.; Olff, H.

    2005-01-01

    Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species-abundance data that yields a full joint probability distribution of each model's parameter

  4. Confronting different models of community structure to species-abundance data : a Bayesian model comparison

    Etienne, RS; Olff, H

    2005-01-01

    Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species-abundance data that yields a full joint probability distribution of each model's parameter

  5. Structure of the Phytoplankton Community and Its Relationship to Water Quality in Donghu Lake, Wuhan, China

    An-Ping LEI; Zhang-Li HU; Jian WANG; Zhi-Xin SHI; Fung-Yee Nora TAM

    2005-01-01

    The phytoplankton community structure, in terms of species composition, total standing crop,and abundance of the dominant algal species, at four stations in Donghu Lake, Wuhan, China, was investigated monthly from January 1994 to December 1996. A total of 260 taxa was observed, of which Chlorophyta (106 taxa) contributed the highest portion of the total number of taxa, followed by Bacillariophyta (82 taxa)and Cyanophyta (32 taxa). The total standing crop measured by means of chlorophyll a content, cell density,and cell biovolume, as well as the abundance of the dominant species, declined in the order of Station I to Station Ⅳ. Seasonal changes of the standing crop varied greatly among the four stations. Although the cell density at the four stations showed a single peak within a year, the peak density varied from July to November, dependent on the sampling year and the station. For chlorophyll a content and cell biovolume,multiple peaks were observed at Stations Ⅰ and Ⅱ, but a single peak was found at Stations Ⅲ and Ⅳ. The phytoplankton community structure indicated that the trophic status was the highest at Station Ⅰ (most eutrophic), followed by Station Ⅱ; Stations Ⅲ and Ⅳ were the least trophic areas. The long-term changes in phytoplankton community structure further suggested that changes in phytoplankton community structure were correlated with water quality, and eutrophication of Donghu Lake had been aggravated since the 1950s.

  6. Heavy metals pollution influence the community structure of Cyanobacteria in nutrient rich tropical estuary

    Anas, A.; Jasmin, C.; Sheeba V.A.; Gireeshkumar, T.R.; Nair, S.

    . The level of dissolved Zn was higher in stations near river head during dry (130 µg L-1) and wet seasons (105 µg L-1). The community structure of cyanobacteria was higher in CE during wet season (H’ index: 1.4 to 3.1) compared to that in dry season (H’ index...

  7. Measuring Institutional Effectiveness of California Community Colleges through Existing Governance Structures and External Funding Efforts

    Jameson-Meledy, Kathryn

    2013-01-01

    The purpose of this research was to compare the differing structures of governance within the California Community College (CCC) system in relation to resource development and grant management. This is to explain how governance may impact the effectiveness of institutions to strengthen services to students with funding resources secured through…

  8. Bacterial community structure of a full-scale biofilter treating pig house exhaust air

    Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær; Nielsen, Lars Peter; Nielsen, Jeppe Lund; Schramm, Andreas

    2011-01-01

    Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter...

  9. Changes in bacterial community structure in a full-scale membrane bioreactor for municipal wastewater treatment.

    Hashimoto, Kurumi; Tsutsui, Hirofumi; Takada, Kazuki; Hamada, Hiroshi; Sakai, Kousuke; Inoue, Daisuke; Sei, Kazunari; Soda, Satoshi; Yamashita, Kyoko; Tsuji, Koji; Hashimoto, Toshikazu; Ike, Michihiko

    2016-07-01

    This study investigated changes in the structure and metabolic capabilities of the bacterial community in a full-scale membrane bioreactor (MBR) treating municipal wastewater. Microbial monitoring was also conducted for a parallel-running conventional activated sludge (CAS) process treating the same influent. The mixed-liquor suspended solid concentration in the MBR reached a steady-state on day 73 after the start-up. Then the MBR maintained higher rates of removal of organic compounds and nitrogen than the CAS process did. Terminal restriction fragment length polymorphism analysis revealed that the bacterial community structure in the MBR was similar to that in the CAS process at the start-up, but it became very different from that in the CAS process in the steady state. The bacterial community structure of the MBR continued to change dynamically even after 20 months of the steady-state operation, while that of the CAS process was maintained in a stable condition. By contrast, Biolog assay revealed that the carbon source utilization potential of the MBR resembled that of the CAS process as a whole, although it declined transiently. Overall, the results indicate that the bacterial community of the MBR has flexibility in terms of its phylogenetic structure and metabolic activity to maintain the high wastewater treatment capability. PMID:26811223

  10. Influence of Detritus on the Structure of the Invertebrate Community in a Small Portuguese Stream

    González, M.; Graça, Manuel A. S.

    2005-01-01

    This study tests if the coarse particulate organic matter (CPOM) mass was related to the invertebrate community structure in riffles and sandy pools of a fourth-order reach of a stream after partialling out the effects of physical characteristics of the sampled patches. Diversity and structure of the assemblages differed between habitats. In both, CPOM mass was positively correlated with total density and with all functional feeding groups excepting filterers. Redundancy analyses and variance...

  11. Community structure and microhabitat preferences of harpacticoid copepods in a tropical reef lagoon (Zanzibar Island, Tanzania)

    Gheerardyn, Hendrik; De Troch, Marleen; Ndaro, SGM; Raes, Maarten; Vincx, Magda; Vanreusel, Ann

    2008-01-01

    Three microhabitat types (dead coral fragments, coral gravel and coral sand) were distinguished and sampled at two locations (Matemwe and Makunduchi) in a tropical lagoon (Zanzibar Island, Tanzania), and the community structure, habitat preferences and biodiversity of the associated harpacticoid copepod fauna was investigated. The harpacticoid fauna is affected by sediment granulometry and by the structural differences between coral and both gravel and sediment. The coral fragments contained ...

  12. Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil

    ZHANG Huiwen; ZHOU Qixing; ZHANG Qianru; ZHANG Chenggang

    2005-01-01

    The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOGGN system analysis method as well as two conventional methods(DHA and SIR). All results of DGGE banding fingerprint patterns(amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition,the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the bacterial community. The effects of the single factors with lower concentrations on the communiy structure were weaker than those with higher concentrations. Moreover, the bacterial community structures under the combined stresses of methamidophos and copper were significantly different from those of control and their corresponding single factors. The change of DHA and carbon source substrate utilizing fingerprint patterns based on BIOLOGGNsystem were two relatively sensitive directors corresponding to the stress presented in this study. Between methamodophos and copper, there happened the significant joint-toxic actions when they were used in combination on DHA and carbon source substrate utilizing fingerprint patterns of soil bacterial communities. The DHA of soil under the combined stresses was lower than that of the control and that under the single factors, and the BIOLOGGN substrate utilizing patterns of soil treated by combinations were distinctively

  13. Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

    Pischedda, Laura; Militon, Cécile; Gilbert, Franck; Cuny, Philippe

    2011-01-01

    Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. S...

  14. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure.

    Hill, Richard; Saetnan, Eli R; Scullion, John; Gwynn-Jones, Dylan; Ostle, Nick; Edwards, Arwyn

    2016-06-01

    Microbial responses to Arctic climate change could radically alter the stability of major stores of soil carbon. However, the sensitivity of plot-scale experiments simulating climate change effects on Arctic heathland soils to potential confounding effects of spatial and temporal changes in soil microbial communities is unknown. Here, the variation in heathland soil bacterial communities at two survey sites in Sweden between spring and summer 2013 and at scales between 0-1 m and, 1-100 m and between sites (> 100 m) were investigated in parallel using 16S rRNA gene T-RFLP and amplicon sequencing. T-RFLP did not reveal spatial structuring of communities at scales changes were striking. Amplicon sequencing corroborated shifts from r- to K-selected taxon-dominated communities, influencing in silico predictions of functional potential. Network analyses reveal temporal keystone taxa, with a spring betaproteobacterial sub-network centred upon a Burkholderia operational taxonomic unit (OTU) and a reconfiguration to a summer sub-network centred upon an alphaproteobacterial OTU. Although spatial structuring effects may not confound comparison between plot-scale treatments, temporal change is a significant influence. Moreover, the prominence of two temporally exclusive keystone taxa suggests that the stability of Arctic heathland soil bacterial communities could be disproportionally influenced by seasonal perturbations affecting individual taxa. PMID:26259508

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

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

    2016-03-01

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

  16. Structure Changes of Macrobenthic Community on Rocky Shores After the Hebei Spirit Oil Spill

    Yun-Hwan Jung

    2013-09-01

    Full Text Available In Korea, more than 300 oil spill accidents occur every year. Despite the frequency, only a small pool of data is available on the initial effect of oil spill on macrobenthic fauna inhabiting rocky shores. The aim of this study was to analyze the variation of macrobenthic fauna composition and community structure on rocky shores, and understand the impact of oil on rocky shore organisms after the Hebei Spirit oil spill. Field surveys were carried out in five regions dose to the wreck site in January, April and September 2008. Polluted sites after the Hebei Spirit oil spill showed that biological index consistently decreased for 9 months limited to breeding and recruitment of organisms by spilled oil. Macrobenthic community was subdivided into 3 groups by species elimination and differences between density of major dominant species: enriched biota community under a relatively stable environment, the second with relatively low ecological index and the last with poor community. In this study, species number did not clearly reflect the effect of oil on the rare and mobile species. However, mean density, biomass and community structure showed the effect of oil by considering breeding activity, decline in recruitment and variation pattern with time.

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

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

    2016-01-01

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

  18. Characterisation of the bacterial community structures in the intestine of Lampetra morii.

    Li, Yingying; Xie, Wenfang; Li, Qingwei

    2016-07-01

    The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response. PMID:27180095

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

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

    2011-12-01

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

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

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

    2015-11-01

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

  1. Variations in soil microbial community structure induced by the conversion from paddy fields to upland fields

    Dai, X.

    2015-12-01

    Land-use conversion is an important factor influencing the carbon and nitrogen gas exchange between land and atmosphere, and soil microorganisms is main driver of soil carbon and nitrogen gas production. Understanding the effect of land-use conversion on soil microbial communities and its influencing factor is important for greenhouse gas emission reduction and soil organic carbon and nitrogen sequestration and stability. The influence of land use conversion on soil process was undergoing a dynamic change, but little research has been done to understand the effect on soil microbial communities during the initial years after land conversion. In the study, the influences of land-use conversion from double rice cropping (RR) to maize-maize (MM) and soybean-peanut (SP) double cropping systems on soil physical and chemical properties, and microbial community structure was studied after two years of the conversion in southern China. The results showed that land use conversion significantly changed soil properties, microbial communities and biomass. Soil pH significantly decreased by 0.50 and 0.52 after conversion to MM and SP, respectively. Soil TN and NH4-N also significantly decreased by 9%-15% and 60% after conversion to upland fields, respectively. The total PLFAs, bacterial, gram-positive bacterial (G+), gram-negative bacterial (G-) and actinomycetic PLFAs decreased significantly. The ng g-1 soil concentration of monounsaturated chain PLFAs 16:1ω7c and 18:1ω9t were significantly higher at paddy fields than at upland fields. No significant differences in soil properties, microbial communities and biomass were found between conversed MM and SP. Our results indicated that land use conversion, not crop type conversed had a significant effects on soil properties and microbial communities at the initial of land conversion. And soil pH was the key factor regulating the variations in soil microbial community structure after land use conversion from paddy to upland fields.

  2. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    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

  3. Associations between leaf structure, orientation, and sunlight exposure in five Western Australian communities

    Five plant communities in Western Australia, as well as selected desert and Rocky Mountain species of the western USA, were surveyed to evaluate associations among leaf structure, orientational properties, and the sunlight exposure and precipitation characteristic of each community. Selected leaf structural features have been associated previously with photosynthetic function and included shape, thickness, the ratio of thickness to width, stomatal distribution, leaf surface coloration, and the number and distribution of palisade cell layers. Decreases in annual precipitation (<4 to over 15 cm/yr) and increases in total daily sunlight (4.2 to 29.2 mol photons/m1) corresponded strongly to an increase in the percentage of species in a given community with more inclined (more inclined than +/- 45 degrees from horizontal) or thicker leaf mesophyll (>0.4 mm) leaves. Also, the percentage of species with a leaf thickness to width ratio >0.1, which were amphistomatous, or which had palisade cell layers beneath both leaf surfaces, increased from >20% in the highest rainfall and lowest sunlight community to >80% in the community with least rainfall but greatest sunlight exposure. Over 70% of the species in the most mesic, shaded community had lighter abaxial than adaxial leaf surfaces (leaf bicoloration). All of the above structural features were positively associated with a more inclined leaf orientation (r2 = 0.79), except for leaf bicoloration, which was negatively associated (r2 = 0.75). The ratio of adaxial to abaxial light was more strongly associated with leaf bicoloration (r2 = 0.83) and the presence of multiple adaxial and isobilateral palisade cell layers(r2 = 0.80) than with total incident sunlight on just the adaxial leaf surface (r2 = 0.69 and 0.73, respectively). These results provide field evidence that leaf orientation and structure may have evolved in concert to produce a photosynthetic symmetry in leaf structure in response to the amount of sunlight and

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

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

    2016-01-01

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

  5. Effect of agricultural management regime on Burkholderia community structure in soil.

    Salles, J F; van Elsas, J D; van Veen, J A

    2006-08-01

    The main objective of this study was to determine the Burkholderia community structure associated with areas under different agricultural management and to evaluate to which extent this community structure is affected by changes in agricultural management. Two fields with distinct soil history (arable land and permanent grassland) were exposed to three agricultural management regimes (crop rotation, maize monoculture, and grassland). By using a culture-independent approach, based on a Burkholderia-specific polymerase chain reaction-denaturing gradient gel electrophoresis system, it was possible to observe the conversion of Burkholderia communities typical for permanent grassland to those of arable land after four consecutive years. However, the time needed to achieve the reverse transition, i.e., converting the Burkholderia community associated with arable land to that of grassland, was beyond the duration of the field experiment. In addition, by applying principal response curves, the direction and extent of the conversion from grassland to arable land (maize monoculture and to crop rotation) were determined. Hence, the results suggested that agricultural practices, such as fertilization and tillage, were more effective in changing the Burkholderia community structure than agricultural management regime. To determine the effect of agricultural management on the Burkholderia population with biocontrol abilities, the culturable fraction of the Burkholderia community was assessed. The areas under permanent grassland and grassland converted to maize monoculture had the highest percentages of Burkholderia strains with antagonistic activity against Rhizoctonia solani AG-3, mainly Burkholderia pyrrocinia and Burkholderia sp. LMG 22929. The isolation frequency of antagonistic isolates from arable land was extremely low. Our results indicate that (changes in) agricultural management, mainly crop rotation, affect the frequency of isolation of antagonistic Burkholderia

  6. Disturbance alters the phylogenetic composition and structure of plant communities in an old field system.

    Russell Dinnage

    Full Text Available The changes in phylogenetic composition and structure of communities during succession following disturbance can give us insights into the forces that are shaping communities over time. In abandoned agricultural fields, community composition changes rapidly when a field is plowed, and is thought to reflect a relaxation of competition due to the elimination of dominant species which take time to re-establish. Competition can drive phylogenetic overdispersion, due to phylogenetic conservation of 'niche' traits that allow species to partition resources. Therefore, undisturbed old field communities should exhibit higher phylogenetic dispersion than recently disturbed systems, which should be relatively 'clustered' with respect to phylogenetic relationships. Several measures of phylogenetic structure between plant communities were measured in recently plowed areas and nearby 'undisturbed' sites. There was no difference in the absolute values of these measures between disturbed and 'undisturbed' sites. However, there was a difference in the 'expected' phylogenetic structure between habitats, leading to significantly lower than expected phylogenetic diversity in disturbed plots, and no difference from random expectation in 'undisturbed' plots. This suggests that plant species characteristic of each habitat are fairly evenly distributed on the shared species pool phylogeny, but that once the initial sorting of species into the two habitat types has occurred, the processes operating on them affect each habitat differently. These results were consistent with an analysis of correlation between phylogenetic distance and co-occurrence indices of species pairs in the two habitat types. This study supports the notion that disturbed plots are more clustered than expected, rather than 'undisturbed' plots being more overdispersed, suggesting that disturbed plant communities are being more strongly influenced by environmental filtering of conserved niche traits.

  7. Disturbance alters the phylogenetic composition and structure of plant communities in an old field system.

    Dinnage, Russell

    2009-01-01

    The changes in phylogenetic composition and structure of communities during succession following disturbance can give us insights into the forces that are shaping communities over time. In abandoned agricultural fields, community composition changes rapidly when a field is plowed, and is thought to reflect a relaxation of competition due to the elimination of dominant species which take time to re-establish. Competition can drive phylogenetic overdispersion, due to phylogenetic conservation of 'niche' traits that allow species to partition resources. Therefore, undisturbed old field communities should exhibit higher phylogenetic dispersion than recently disturbed systems, which should be relatively 'clustered' with respect to phylogenetic relationships. Several measures of phylogenetic structure between plant communities were measured in recently plowed areas and nearby 'undisturbed' sites. There was no difference in the absolute values of these measures between disturbed and 'undisturbed' sites. However, there was a difference in the 'expected' phylogenetic structure between habitats, leading to significantly lower than expected phylogenetic diversity in disturbed plots, and no difference from random expectation in 'undisturbed' plots. This suggests that plant species characteristic of each habitat are fairly evenly distributed on the shared species pool phylogeny, but that once the initial sorting of species into the two habitat types has occurred, the processes operating on them affect each habitat differently. These results were consistent with an analysis of correlation between phylogenetic distance and co-occurrence indices of species pairs in the two habitat types. This study supports the notion that disturbed plots are more clustered than expected, rather than 'undisturbed' plots being more overdispersed, suggesting that disturbed plant communities are being more strongly influenced by environmental filtering of conserved niche traits. PMID:19763265

  8. Human Impact Assessment on the Subtidal Macrobenthic Community Structure in the Mondego Estuary (Western Portugal)

    Marques, J. C.; Maranhão, P.; Pardal, M. A.

    1993-10-01

    The Mondego Estuary consists of two arms, north and south. The north arm is deeper, while the south arm is largely silted up, which causes the freshwater to flow primarily by the north arm. Human impact is significant, due to harbour activities, salt-works, aquaculture farms, and nutrient and chemical discharge from agricultural areas. From December 1989 to September 1990 a reference study on the subtidal macrofauna was carried out, in order to characterize the community structure in relation to physicochemical environmental factors. The subtidal macrofauna in the Mondego Estuary appears to be clearly impoverished compared to a reference Portuguese estuary, the Mira, which has been much less exposed to human impacts. The south arm macrobenthic community consists mainly of infaunal species and appears to be more stable and structured, presenting a higher macrofauna abundance. The north arm community is mainly characterized by sparse mobile epibenthic species populations, exhibiting a lower biodiversity and an impoverished macrofuna, compared to the south arm. The subtidal communities appear to be physically controlled, with emphasis on the type of sediment, salinity and currents. Biologically, due to their distinct physicochemical characteristics, the two arms of the estuary constitute different subsystems. Dredging takes place twice a year along the north arm, and time intervals between dredging operations appear to be inadequate to allow macrofauna recovery. Although structurally more stable, the south arm community, due to the feeble water circulation, may be more exposed to environmental changes. Benthic monitoring of the Mondego Estuary biological communities is clearly necessary in order to assess temporal trends and to establish if the apparent environmental changes are reversible.

  9. Dissolved nitrogen transformations and microbial community structure in the organic layer of forest soils in Olkiluoto in 2006

    Carbon (C) and nitrogen (N) cycles in the ecosystem are strongly coupled. Biomass, structure and activity of the bacterial and fungal community are the key factors influencing C and N cycles. Changes in the function of soil microbial community can be a signal of plant responses to environmental changes. Dissolved N compounds, microbial biomass, microbial activity, fungal community structure and functional diversity of microbial communities were measured in September 2006 from five monitoring plots on Olkiluoto to assess information about soil microbial community structure and activity. High within and between variation in the studied plots were detected. However, in this study the values and their variation in the level of N mineralisation, dissolved N compounds, fungal biomass and microbial community structure in the studied plots were within a normal range in comparison with other published data of similar forest types in Finland. (orig.)

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

    Raeymaekers, J. A. M.; Huyse, T.; Maelfait, H.; Hellemans, B.; Volckaert, F.A.M.

    2008-01-01

    In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living on sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitius pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITS1). ...

  11. Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

    Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

    2015-04-01

    Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary

  12. The reemergence of Vietnam's ethnic Chinese community through local, national, and transnational structures

    Yu, LiAnne Sandra

    2006-01-01

    This dissertation is an examination of how the ethnic Chinese community in Vietnam, the Hoa, re-built their economic and social structures after the persecution they faced post-1975. In the decade after the fall of Saigon to Communist forces, the wealthiest and most powerful Hoa were forced out of their positions, and over half a million people from that community left Vietnam as refugees. By the mid-1980's, it seemed that Cholon, once the thriving center of Vietnam's Hoa entrepreneurial acti...

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

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

    2016-06-01

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

  14. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

    Hirakata, Yuga; Oshiki, Mamoru; Kuroda, Kyohei; Hatamoto, Masashi; Kubota, Kengo; Yamaguchi, Takashi; Harada, Hideki; Araki, Nobuo

    2016-01-01

    Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates—ciliates frequently found in anoxic ecosystems—on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885–3,190 and 2,387–2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function. PMID:27431197

  15. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  16. Conservation of acquired morphology and community structure in aged biofilms after facing environmental stress.

    Saur, T; Escudié, R; Santa-Catalina, G; Bernet, N; Milferstedt, K

    2016-01-01

    The influence of growth history on biofilm morphology and microbial community structure is poorly studied despite its important role for biofilm development. Here, biofilms were exposed to a change in hydrodynamic conditions at different growth stages and we observed how biofilm age affected the change in morphology and bacterial community structure. Biofilms were developed in two bubble column reactors, one operated under constant shear stress and one under variable shear stress. Biofilms were transferred from one reactor to the other at different stages in their development by withdrawing and inserting the support medium from one reactor to the other. The developments of morphology and microbial community structure were followed by image analysis and molecular tools. When transferred early in biofilm development, biofilms adapted to the new hydrodynamic conditions and adopted features of the biofilm already developed in the receiving reactor. Biofilms transferred at a late state of biofilm development continued their initial trajectories of morphology and community development even in a new environment. These biofilms did not immediately adapt to their new environment and kept features acquired during their early growth phase, a property we called memory effect. PMID:26492343

  17. The structure and dynamics of a rhinolophid bat community of Latium (Central Italy (Chiroptera

    Pierangelo Crucitti

    1998-12-01

    Full Text Available Abstract The present paper summarizes the results of 3 years of observation made at six month intervals for six months at a time (18 field surveys in a man-made cave in Northern Latium (Central Italy from April 1992 to April 1995. Its aim is to analyze the main structural and dynamic features of a bat community which hibernates at the shelter. Rhinolophus ferrumequinum and especially Rhinolophus euryale are the most abundant species. Population dynamics of both species as well as that of Rhinoluphus hipposideros show higher levels of abundance between December and February of each semester. In mid-winter, large and sometimes mixed aggregations of Rhinolophus ferrumequinum and Rhinolophus euryale in deep hypothermia occur. A small number of Rhinolophus hipposideros, mainly adult males, was observed. The paper compares the structure of this community to the structure of another community of the same district which has been previously analyzed, in which Vespertilionidae, especially Miniopterus schreibersi, are much more abundant. Despite the difference in species composition, body size was found to be a significant and common feature (as highlighted by forearm length, of the dominant species in both communities, Rhinolophus euryale and Miniopterus schreibersi respectively.

  18. Measuring The Social Relations: Social Distance in Social Structure - A Study of Prison Community

    Social relations and their influence on various phenomena are one of the key issues not only in sociology. The crucial problem, however, is how to measure the social relations and their implications in society. We try to adapt a physical perspective to the ''typical'' sociological analysis and to measure the qualitative nature of human community adapting the category of social distance. This category is used to explore the properties of social relations in the structure and the communication system of prison community. The issues that are discussed: the specific properties of social relations as the constitutive factors for different type of group structure and type of communication. How the elementary social networks (short-range group structures) form the dynamics of prison community? What is the role of the numerical force of the group for prison community? Is there the interplay between the microstructures and macrostructures? The work is based on our research carried out in 17 prisons in Poland in 2003, 2004 and 2005. There were about 2000 prisoners in the sample. (author)

  19. Link prediction based on hyperbolic mapping with community structure for complex networks

    Wang, Zuxi; Wu, Yao; Li, Qingguang; Jin, Fengdong; Xiong, Wei

    2016-05-01

    Link prediction is becoming a concerned topic in the complex network field in recent years. However, the existing link prediction methods are unsatisfactory for processing topological information and have high time complexity. This paper presents a novel method of Link Prediction with Community Structure (LPCS) based on hyperbolic mapping. Different from the existing link prediction methods, to utilize global structure information of the network, LPCS deals with the network from an overall perspective. LPCS takes full advantage of the community structure and its hierarchical organization to map networks into hyperbolic space, and obtains the hyperbolic coordinates which depict the global structure information of the network, then uses hyperbolic distance to describe the similarity between the nodes, finally predicts missing links according to the degree of the similarity between unconnected node pairs. The combination of the hyperbolic geometry framework and the community structure makes LPCS perform well in predicting missing links, and the time complexity of LPCS is linear, which makes LPCS can be applied to handle large scale networks in acceptable time. LPCS outperforms many state-of-the-art link prediction methods in the networks obeying power-law degree distribution.

  20. Multi-scale community organization of the human structural connectome and its relationship with resting-state functional connectivity

    Betzel, Richard F.; Griffa, Alessandra; Avena-Koenigsberger, Andrea; Goñi, Joaquín; Thiran, Jean-Phillippe; Hagmann, Patric; Sporns, Olaf

    2013-01-01

    The human connectome has been widely studied over the past decade. A principal finding is that it can be decomposed into communities of densely interconnected brain regions. This result, however, may be limited methodologically. Past studies have often used a flawed modularity measure in order to infer the connectome's community structure. Also, these studies relied on the intuition that community structure is best defined in terms of a network's static topology as opposed to a more dynamical...

  1. Canopy structural alterations to nitrogen functions of the soil microbial community in a Quercus virginiana forest

    Moore, L. D.; Van Stan, J. T., II; Rosier, C. L.; Gay, T. E.; Wu, T.

    2014-12-01

    Forest canopy structure controls the timing, amount and chemical character of precipitation supply to soils through interception and drainage along crown surfaces. Yet, few studies have examined forest canopy structural connections to soil microbial communities (SMCs), and none have measured how this affects SMC N functions. The maritime Quercus virginiana Mill. (southern live oak) forests of St Catherine's Island, GA, USA provide an ideal opportunity to examine canopy structural alterations to SMCs and their functioning, as their throughfall varies substantially across space due to dense Tillandsia usneoides L. (spanish moss) mats bestrewn throughout. To examine the impact of throughfall variability on SMC N functions, we examined points along the canopy coverage continuum: large canopy gaps (0%), bare canopy (50-60%), and canopy of heavy T. usneoides coverage (>=85%). Five sites beneath each of the canopy cover types were monitored for throughfall water/ions and soil leachates chemistry for one storm each month over the growing period (7 months, Mar-2014 to Sep-2014) to compare with soil chemistry and SMC communities sampled every two months throughout that same period (Mar, May, Jul, Sep). DGGE and QPCR analysis of the N functioning genes (NFGs) to characterize the ammonia oxidizing bacterial (AOB-amoA), archaea (AOA-amoA), and ammonification (chiA) communities were used to determine the nitrification and decomposition potential of these microbial communities. PRS™-probes (Western Ag Innovations Inc., Saskatoon, Canada) were then used to determine the availability of NO3-N and NH4+N in the soils over a 6-week period to evaluate whether the differing NFG abundance and community structures resulted in altered N cycling.

  2. Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms

    A.-S. Roy

    2012-09-01

    Full Text Available The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord and nine mesocosms, with pCO2 range from ~145 to ~1420 μatm. Samples collected at nine time points (t-1, t1, t5, t7, t12, t14, t22, t26 to t28 in seven treatments (ambient fjord (~145, 2×~185, ~270, ~685, ~820, ~1050 μatm were analysed for "free-living" and "particle associated" microbial community composition using 16S rRNA amplicon sequencing. This high-throughput sequencing analysis produced ~20 000 000 16S rRNA V4 reads, which comprised 7000 OTUs. The main variables structuring these communities were, sample origin (fjord or mesocosms and the filter size fraction (free-living or particle associated. The community was significantly different between the fjord and both the control and elevated 2 mesocosms (which were not significant different after nutrients were added to the mesocosms; suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The size fraction was the second most important factor for community structure; separating free-living from particle-associated bacteria. When free-living and particle-associated bacteria were analysed separately at different time points, the only taxon pCO2 was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO2 treatment was found to be significantly correlated (non-linear with 15 rare taxa, most of which increased in abundance with higher CO2.

  3. Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus.

    Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Teotonio, Thais L; Minbiole, Kevin P C; Belden, Lisa K

    2015-01-01

    The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection. PMID:26445500

  4. Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus.

    Jenifer B Walke

    Full Text Available The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd. In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum, or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection.

  5. The community structure of the European network of interlocking directorates 2005-2010.

    Heemskerk, Eelke M; Daolio, Fabio; Tomassini, Marco

    2013-01-01

    The boards of directors at large European companies overlap with each other to a sizable extent both within and across national borders. This could have important economic, political and management consequences. In this work we study in detail the topological structure of the networks that arise from this phenomenon. Using a comprehensive information database, we reconstruct the implicit networks of shared directorates among the top 300 European firms in 2005 and 2010, and suggest a number of novel ways to explore the trans-nationality of such business elite networks. Powerful community detection heuristics indicate that geography still plays an important role: there exist clear communities and they have a distinct national character. Nonetheless, from 2005 to 2010 we observe a densification of the boards interlocks network and a larger transnational orientation in its communities. Together with central actors and assortativity analyses, we provide statistical evidence that, at the level of corporate governance, Europe is getting closer. PMID:23894318

  6. The community structure of the European network of interlocking directorates 2005-2010.

    Eelke M Heemskerk

    Full Text Available The boards of directors at large European companies overlap with each other to a sizable extent both within and across national borders. This could have important economic, political and management consequences. In this work we study in detail the topological structure of the networks that arise from this phenomenon. Using a comprehensive information database, we reconstruct the implicit networks of shared directorates among the top 300 European firms in 2005 and 2010, and suggest a number of novel ways to explore the trans-nationality of such business elite networks. Powerful community detection heuristics indicate that geography still plays an important role: there exist clear communities and they have a distinct national character. Nonetheless, from 2005 to 2010 we observe a densification of the boards interlocks network and a larger transnational orientation in its communities. Together with central actors and assortativity analyses, we provide statistical evidence that, at the level of corporate governance, Europe is getting closer.

  7. Community Structure in Large Networks: Natural Cluster Sizes and the Absence of Large Well-Defined Clusters

    Leskovec, Jure; Dasgupta, Anirban; Mahoney, Michael W

    2008-01-01

    A large body of work has been devoted to defining and identifying clusters or communities in social and information networks. We explore from a novel perspective several questions related to identifying meaningful communities in large social and information networks, and we come to several striking conclusions. We employ approximation algorithms for the graph partitioning problem to characterize as a function of size the statistical and structural properties of partitions of graphs that could plausibly be interpreted as communities. In particular, we define the network community profile plot, which characterizes the "best" possible community--according to the conductance measure--over a wide range of size scales. We study over 100 large real-world social and information networks. Our results suggest a significantly more refined picture of community structure in large networks than has been appreciated previously. In particular, we observe tight communities that are barely connected to the rest of the network ...

  8. Class structure refactoring of object-oriented softwares using community detection in dependency networks

    Weifeng PAN; Bing LI; Yutao MA; Jing LIU; Yeyi QIN

    2009-01-01

    The quality of a software system is largely de-termined by its internal structures which always degrade over the software evolution. Therefore, the structures have to be reconditioned from time to time. However, the ex-isting methods are very complex and resource-consuming when doing this task. In this paper, we present an approach to recondition the class structures of object-otiented (OO) software systems. It uses attribute-method networks and method-method networks to represent attributes, methods and dependencies between them; It proposes a guided com-munity detection algorithm to obtain the optimized commu-nity structures in the method-method networks, which also correspond to the optimized class structures; It also provides a list of refactorings by comparing the optimized class struc-tures with the real class structure in software systems and inspecting the attribute-method networks. The approach is evaluated using the open-source case study, JHotDraw 5.1, and the advantages of our approach are illustrated in com-parison with existing methods.

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

    Cole G Easson

    2014-10-01

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

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

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

    2002-12-01

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

  11. Ectomycorrhizal community structure and function in relation to forest residue harvesting and wood ash applications

    Ectomycorrhizal fungi form symbiotic associations with tree roots and assist in nutrient-uptake and -cycling in forest ecosystems, thereby constituting a most significant part of the microbial community. The aims of the studies described in this thesis were to evaluate the potential of DNA-based molecular methods in below-ground ectomycorrhizal community studies and to investigate changes in ectomycorrhizal communities on spruce roots in sites with different N deposition, and in sites subjected to harvesting of forest residues or application of wood ash. The ability of selected ectomycorrhizal fungi to mobilise nutrients from wood ash and to colonise root systems in the presence and absence of ash was also studied. In total 39 ectomycorrhizal species were detected in the experimental forests located in southern Sweden. At each site five to six species colonised around 60% of the root tips. The dominant species, common to the sites, were Tylospora fibrillosa, Thelephora terrestris and Cenococcum geophilum. Differences between two sites with differing levels of N deposition suggested that community structure may be influenced by N deposition, although site history, location and degree of isolation may also influence species composition. Repeated harvesting of forest residues reduced numbers of mycorrhizal roots in the humus layer to approximately 50% of that in control plots but no shift in the ectomycorrhizal community could be detected. At another site, application of granulated wood ash induced a shift in ectomycorrhizal community structure and three ectomycorrhizal fungi ('ash fungi') were found to colonise ash granules. Two 'ash fungi' showed a superior ability to solubilise stabilised wood ash in laboratory experiments compared to other ectomycorrhizal isolates from the same site. In laboratory microcosms containing intact mycorrhizal mycelia, colonisation of wood ash patches by one 'ash fungus' was good whereas colonisation by Piloderma croceum was poor. In a

  12. Denitrification in agriculturally impacted streams: seasonal changes in structure and function of the bacterial community.

    Erin Manis

    Full Text Available Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage, whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3- and that seasonal drying of stream channels has a negative impact on NO3- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change

  13. Can benthic community structure be used to predict the process of bioturbation in real ecosystems?

    Queirós, Ana M.; Stephens, Nicholas; Cook, Richard; Ravaglioli, Chiara; Nunes, Joana; Dashfield, Sarah; Harris, Carolyn; Tilstone, Gavin H.; Fishwick, James; Braeckman, Ulrike; Somerfield, Paul J.; Widdicombe, Stephen

    2015-09-01

    Disentangling the roles of environmental change and natural environmental variability on biologically mediated ecosystem processes is paramount to predict future marine ecosystem functioning. Bioturbation, the biogenic mixing of sediments, has a regulating role in marine biogeochemical processes. However, our understanding of bioturbation as a community level process and of its environmental drivers is still limited by loose use of terminology, and a lack of consensus about what bioturbation is. To help resolve these challenges, this empirical study investigated the links between four different attributes of bioturbation (bioturbation depth, activity and distance, and biodiffusive transport); the ability of an index of bioturbation (BPc) to predict each of them; and their relation to seasonality, in a shallow coastal system - the Western Channel Observatory, UK. Bioturbation distance depended on changes in benthic community structure, while the other three attributes were more directly influenced by seasonality in food availability. In parallel, BPc successfully predicted bioturbation distance but not the other attributes of bioturbation. This study therefore highlights that community bioturbation results from this combination of processes responding to environmental variability at different time-scales. However, community level measurements of bioturbation across environmental variability are still scarce, and BPc is calculated using commonly available data on benthic community structure and the functional classification of invertebrates. Therefore, BPc could be used to support the growth of landscape scale bioturbation research, but future uses of the index need to consider which bioturbation attributes the index actually predicts. As BPc predicts bioturbation distance, estimated here using a random-walk model applicable to community settings, studies using either of the metrics should be directly comparable and contribute to a more integrated future for

  14. Impact of organic and inorganic nanomaterials in the soil microbial community structure

    In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6–V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO2), titanium silicon oxide (TiSiO4), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO2, CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: ► Organic and inorganic nanomaterials on soil microbial community. ► Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. ► All the organic nanomaterials, TiO2 and gold nanorods significantly affected the structural diversity.

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

    Richard R Rodrigues

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

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

    Antony Meunier

    2015-11-01

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

  17. Conservation of forest birds: evidence of a shifting baseline in community structure.

    Chadwick D Rittenhouse

    Full Text Available BACKGROUND: Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance. METHODOLOGY/PRINCIPAL FINDINGS: We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period and modest losses in abundance (-28.7 - -10.2 individuals per route that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States. CONCLUSIONS/SIGNIFICANCE: Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., approximately 22 years. Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary

  18. Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer.

    Medihala, P G; Lawrence, J R; Swerhone, G D W; Korber, D R

    2012-09-01

    Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon's richness (H') and Pielou's evenness (J') indices revealed a varied microbial diversity (H' = 1.488-2.274) and an even distribution of microbial communities within the aquifer (J' = 0.811-0.917). Overall, these analyses revealed that the aquifer's microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling. PMID:22913282

  19. Community structure and spatial distribution of macrobenthos in the shelf area of the Bering Sea

    WANG Jianjun; HE Xuebao; LIN Heshan; LIN Junhui; HUANG Yaqin; ZHENG Chengxing; ZHENG Fengwu; LI Rongguan; JIANG Jinxiang

    2014-01-01

    Field investigations of marine macrobenthos were conducted at ten sites in the Bering Sea in July 2010. Alto-gether 90 species of macrobenthos belonging to 59 families and 78 genera were identified. Among them, 41 polychaetes, 16 mollusks, 23 crustaceans, three echinoderms, two cnidarians, one nemertean, one priapu-lid, two sipunculids, and one echiuran were identified. The average density and biomass of total macrob-enthos were 984 ind./m2 and 1 207.1 g/m2 of wet weight, respectively. The predominant species in the study area were Scoloplos armiger, Eudorella pacifica, Ophiura sarsii, Heteromastus filiformis, Ennucula tenuis, and Harpiniopsis vadiculus by abundance, while the predominant species in this area was Echinarachnius parma by biomass. Hierarchical cluster analysis (Bray-Curtis similarity measure) revealed that two impor-tant benthic assemblages in the study area were Community A and Community B. Community A was stable and Community B was unstable, as shown by the Abundance/Biomass Comparisons (ABC) approach. The macrobenthic community structure in the shelf of the Bering Sea was characterized by its high abundance and biomass, high productivity but great heterogeneity.

  20. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

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

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

    2016-03-01

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

  2. COMMUNITY STRUCTURE OF THE TINTINNIDS (CILIOPHORA: SPIROTRICHEA IN THE REGION OF ABROLHOS (BAHIA, BRAZIL

    Alejandro Esteweson Santos Faustino da Costa

    2015-03-01

    Full Text Available The tintinnid community in the region of Abrolhos (Bahia, Brazil was studied during February 2012. We hypothesized that the tintinnid community structure varies significantly over a short temporal scale (photoperiod, as well as spatially over a short scale (on and away from the reefs, and a broad scale (distance of the reef area from the coast. Three areas in Abrolhos were studied. Two sampling points were delimited in each area, where the tintinnids were collected by horizontal subsurface plankton net (20 μm mesh-size hauls. Sampling was undertaken every 6 hours, during 24 hours in each area. 24 species were found, all of which are of neritic, cosmopolitan, and of warm-water distribution. The only hypothesis that is not rejected is that related to variability on an extensive spatial scale. There are significant differences between the samples collected in the three areas studied (ANOVA p = 0.017. The clustering of the species highlights a continent-ocean gradient. There is one community typical of the internal arc, composed mainly of neritic agglutinated tintinnids, and another community typical of the external arc, composed mainly of hyaline warm-water and cosmopolitan tintinnids. The factor which exercises the greatest influence on the tintinnid community in the Abrolhos region is the distance from the coast.

  3. Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems.

    Ferrari, Belinda C; Bissett, Andrew; Snape, Ian; van Dorst, Josie; Palmer, Anne S; Ji, Mukan; Siciliano, Steven D; Stark, Jonathon S; Winsley, Tristrom; Brown, Mark V

    2016-06-01

    Landscape heterogeneity impacts community assembly in animals and plants, but it is not clear if this ecological concept extends to microbes. To examine this question, we chose to investigate polar soil environments from the Antarctic and Arctic, where microbes often form the major component of biomass. We examined soil environments that ranged in connectivity from relatively well-connected slopes to patchy, fragmented landforms that comprised isolated frost boils. We found landscape connectedness to have a significant correlation with microbial community structure and connectivity, as measured by co-occurrence networks. Soils from within fragmented landforms appeared to exhibit less local environmental heterogeneity, harboured more similar communities, but fewer biological associations than connected landforms. This effect was observed at both poles, despite the geographical distances and ecological differences between them. We suggest that microbial communities inhabiting well-connected landscape elements respond consistently to regional-scale gradients in biotic and edaphic factors. Conversely, the repeated freeze thaw cycles that characterize fragmented landscapes create barriers within the landscape and act to homogenize the soil environment within individual frost boils and consequently the microbial communities. We propose that lower microbial connectivity in the fragmented landforms is a function of smaller patch size and continual disturbances following soil mixing. PMID:26310523

  4. Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere.

    Erika Yashiro

    Full Text Available We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65% was greater than at sprayed orchards (mean of 50% (P = 0.0271. For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R = -0.104, P = 0.655. Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.

  5. Impact of ocean acidification on the structure of future phytoplankton communities

    Dutkiewicz, Stephanie; Morris, J. Jeffrey; Follows, Michael J.; Scott, Jeffery; Levitan, Orly; Dyhrman, Sonya T.; Berman-Frank, Ilana

    2015-11-01

    Phytoplankton form the foundation of the marine food web and regulate key biogeochemical processes. These organisms face multiple environmental changes, including the decline in ocean pH (ocean acidification) caused by rising atmospheric pCO2 (ref. ). A meta-analysis of published experimental data assessing growth rates of different phytoplankton taxa under both ambient and elevated pCO2 conditions revealed a significant range of responses. This effect of ocean acidification was incorporated into a global marine ecosystem model to explore how marine phytoplankton communities might be impacted over the course of a hypothetical twenty-first century. Results emphasized that the differing responses to elevated pCO2 caused sufficient changes in competitive fitness between phytoplankton types to significantly alter community structure. At the level of ecological function of the phytoplankton community, acidification had a greater impact than warming or reduced nutrient supply. The model suggested that longer timescales of competition- and transport-mediated adjustments are essential for predicting changes to phytoplankton community structure.

  6. Does the edge effect influence plant community structure in a tropical dry forest?

    Diogo Gallo Oliveira

    2013-04-01

    Full Text Available Edge effects are considered a key factor in regulating the structure of plant communities in different ecosystems. However, regardless to few studies, edge influence does not seem to be decisive in semiarid regions such as the Brazilian tropical dry forest known as Caatinga but this issue remains inconclusive. The present study tests the null hypothesis that the plant community of shrubs and trees does not change in its structure due to edge effects. Twenty-four plots (20 x 20 m were set up in a fragment of Caatinga, in which 12 plots were in the forest edges and 12 plots were inside the fragment. Tree richness, abundance and species composition did not differ between edge and interior plots. The results of this study are in agreement with the pattern previously found for semiarid environments and contrasts with previous results obtained in different environments such as Rainforests, Savanna and Forest of Araucaria, which indicate abrupt differences between the border and interior of the plant communities in these ecosystems, and suggest that the community of woody plants of the Caatinga is not ecologically affected by the presence of edges.

  7. Structure of the epiphyte community in a tropical montane forest in SW China.

    Mingxu Zhao

    Full Text Available Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site environmental factors were investigated. Epiphyte diversity was strongly correlated with host size (DBH, diameter at breast height, while within hosts the highest epiphyte diversity was in the middle canopy and epiphyte diversity was significantly higher in sites with canopy soil or a moss mat than on bare bark. DBH, elevation and stem height explained 22% of the total variation in the epiphyte species assemblage among hosts, and DBH was the most important factor which alone explained 6% of the variation. Within hosts, 51% of the variation in epiphyte assemblage composition was explained by canopy position and substrate, and the most important single factor was substrate which accounted for 16% of the variation. Analysis of network properties indicated that the epiphyte host community was highly nested, with a low level of epiphyte specialization, and an almost even interaction strength between epiphytes and host trees. Together, these results indicate that large trees harbor a substantial proportion of the epiphyte community in this forest.

  8. The Effect of Perfluorooctane Sulfonate, Exposure Time, and Chemical Mixtures on Methanogenic Community Structure and Function.

    McNamara, Patrick J; LaPara, Timothy M; Novak, Paige J

    2015-01-01

    A plethora of organic micropollutant mixtures are found in untreated municipal wastewater. Anaerobic digesters receive large loadings of hydrophobic micropollutants that sorb to wastewater biosolids. Despite micropollutants being pervasive as mixtures, little research is available to explain the impact that mixtures of compounds, as well as exposure time, have on microbial communities in anaerobic digesters. Perfluorooctane sulfonate (PFOS) was added to anaerobic enrichment cultures in both short-term (14 days) and long-term (140 days) studies to determine the impact of exposure time. Additionally, triclosan was added during the experiments to investigate the impact of mixtures on community structure and function. PFOS did not alter methane production in short-term studies, but in long-term studies, methane production increased, consistent with our hypothesis that PFOS may act as a metabolic uncoupler. The impact of triclosan on methane production was exacerbated when PFOS was already present in the anaerobic enrichment cultures. Triclosan also had greater impacts on microbial community structures in the bottles that had been exposed to PFOS long-term. These results demonstrate that both chemical mixtures and exposure time are important parameters to address when trying to define the impacts of micropollutants on anaerobic microbial communities. PMID:26462249

  9. The Effect of Perfluorooctane Sulfonate, Exposure Time, and Chemical Mixtures on Methanogenic Community Structure and Function

    McNamara, Patrick J; LaPara, Timothy M; Novak, Paige J

    2015-01-01

    A plethora of organic micropollutant mixtures are found in untreated municipal wastewater. Anaerobic digesters receive large loadings of hydrophobic micropollutants that sorb to wastewater biosolids. Despite micropollutants being pervasive as mixtures, little research is available to explain the impact that mixtures of compounds, as well as exposure time, have on microbial communities in anaerobic digesters. Perfluorooctane sulfonate (PFOS) was added to anaerobic enrichment cultures in both short-term (14 days) and long-term (140 days) studies to determine the impact of exposure time. Additionally, triclosan was added during the experiments to investigate the impact of mixtures on community structure and function. PFOS did not alter methane production in short-term studies, but in long-term studies, methane production increased, consistent with our hypothesis that PFOS may act as a metabolic uncoupler. The impact of triclosan on methane production was exacerbated when PFOS was already present in the anaerobic enrichment cultures. Triclosan also had greater impacts on microbial community structures in the bottles that had been exposed to PFOS long-term. These results demonstrate that both chemical mixtures and exposure time are important parameters to address when trying to define the impacts of micropollutants on anaerobic microbial communities. PMID:26462249

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

    Huirong Lin

    2015-01-01

    Full Text Available 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.

  11. The effect of salinity levels on the structure of zooplankton communities

    Paturej Ewa

    2015-01-01

    Full Text Available The objective of this study was to determine the qualitative and quantitative structure of zooplankton communities in the Vistula Lagoon and to establish whether zooplankton abundance and biodiversity are affected by salinity levels. Samples for biological analyses were collected in the summer (June-September of 2007-2011 at eleven sampling sites. Statistical analysis revealed a significant correlation between salinity levels and the number of species (r= -0.2020, abundance (r= 0.1967 and biomass (r= 0.3139 of zooplankton. No significant correlations were found between salinity and the biodiversity of zooplankton. The results of the study suggest that salinity affects the abundance and structure, but not the diversity of zooplankton communities in the Vistula Lagoon.

  12. Influence of toxic cyanobacteria on community structure and microcystin accumulation of freshwater molluscs

    Community structure and microcystin accumulation of freshwater molluscs were studied before and after cyanobacterial proliferations, in order to assess the impact of toxic blooms on molluscs and the risk of microcystin transfer in food web. Observed decrease in mollusc abundance and changes in species richness in highly contaminated waters were not significant; however, relative abundances of taxa (prosobranchs, pulmonates, bivalves) were significantly different before and after cyanobacterial bloom. Pulmonates constituted the dominant taxon, and bivalves never occurred after bloom. Microcystin accumulation was significantly higher in molluscs from highly (versus lowly) contaminated waters, in adults (versus juveniles) and in pulmonates (versus prosobranchs and bivalves). Results are discussed according to the ecology of molluscs, their sensitivity and their ability to detoxify. - Proliferations of toxic cyanobacteria may alter the structure of mollusc communities with cyanotoxin accumulation depending on age and taxon

  13. Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management

    Wayne Houston; Jones, Alison M.; Ray Berkelmans

    2011-01-01

    In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species that build the structural framework of the reef. In this study, we investigate key coral diversity and environmental attributes of an inshore reef system surrounding the Keppel Bay Islan...

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

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

    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 diffe...

  15. The Effects of Marenzelleria spp on the Benthic Macro Fauna Community Structure in the Isefjord

    Olsen, Jeppe; Reyhe, Tore; Happel, Elisabeth; Kayikci, Ozan

    2008-01-01

    In environmental biology, the interspecies interactions are always interesting and much studied as these relations may change the destiny and life of individuals and gradually the community structure in the given area. In addition to some regular relationships, such as symbiosis, commensalism, prey - predator and etc. there is also the term “invasive species”. The effect of such invasive species, Marenzellaria spp. is investigated in this survey. Marenzelleria spp. belongs to the Phylum A...

  16. Viruses in the marine environment: community dynamics, phage-host interactions and genomic structure

    Lara de la Casa, Elena

    2014-01-01

    [EN] There are an estimated 1030 viruses in the world oceans, the majority of which are phages (viruses that infect bacteria). Extensive research has demonstrated the significant influence of marine phages on microbial abundance, community structure, genetic exchange and global biogeochemical cycles. In this thesis, we contribute to increase the knowledge about the ecological role of viruses in marine systems, but also we aimed to provide a better understanding about the interactions between ...

  17. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure (α-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  18. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-07-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure ({alpha}-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  19. Impacts Of Bleaching On Coral Communities On Artificial Reef Structures In Maldives

    Clark, S.

    2000-01-01

    A research programme to evaluate the feasibility of using artificial reef structures (ARS) to rehabilitate degraded reefs was conducted in Maldives between 1990-1994. Detailed monitoring and analysis of coral recruitment patterns on the ARS over a period of 3.5 years demonstrated that a diverse community of branching corals developed within three years with a similar composition to adjacent reef flats. A warm water anomaly of +3° C occurred in Maldives between late April and May1998 resulting...

  20. Alternative Stable States in Size-Structured Communities : Patterns, Processes, and Mechanisms

    Schröder, Arne

    2008-01-01

    Alternative stable states have been, based on theoretical findings, predicted to be common in ecological systems. Empirical data from a number of laboratory and natural studies strongly suggest that alternative stable states also occur in real populations, communities and ecosystems. Potential mechanisms involve population size-structure and food-dependent individual development. These features can lead to ontogenetic niche shifts, juvenile recruitment bottlenecks and emergent Allee effects; ...

  1. Community structure in large-scale cortical networks during motor acts

    Highlights: ► Estimate of large-scale functional brain networks from standard scalp EEG signals. ► Community structure detection in brain network during baseline and motor execution. ► Higher inter-module and inter-hemispheric connectivity during motor execution. - Abstract: The purpose of the present work is to evaluate the community structure of the cortical network subserving the neurophysiologic processes in simple motor acts. To this end, we studied the topological properties of the functional brain connectivity in the frequency domain. The functional networks were estimated by means of the imaginary coherence from a dataset of high-resolution EEG recordings (4094 cortical sources) in a group of healthy subjects (n = 10) during a finger extension task. The analysis of the community structure was addressed through a particular detection algorithm that optimizes the modularity, a function related to the level of internal clustering inside the communities in the network. The principal results indicate that the cortical network changes its structural organization during the motor execution with respect to a baseline condition. Notably in the Beta band (12.5–30 Hz), the level of intra-module connectivity decreases, while inter-module connectivity increases reflecting the need for a neural integration of distant regions. Notably, this distributed interaction involves anatomical regions belonging to both the hemispheres including pre-motor and primary motor areas in the frontal and central part of the cortex as well as parietal associative regions, which are related to the planning, selection and execution of actions.

  2. Physiology and microbial community structure in soil at extreme water content

    Uhlířová, Eva; Elhottová, Dana; Tříska, Jan; Šantrůčková, Hana

    2005-01-01

    Roč. 50, č. 2 (2005), s. 161-166. ISSN 0015-5632 R&D Projects: GA ČR(CZ) GA206/99/1410; GA ČR(CZ) GA526/99/P033 Institutional research plan: CEZ:AV0Z6066911 Keywords : microbial community structure * soils * extreme water content Subject RIV: EH - Ecology, Behaviour Impact factor: 0.918, year: 2005

  3. Structure of a toothed cetacean community around a tropical island (Mayotte, Mozambique Channel)

    Kiszka, Jeremy; Ersts, Peter; Ridoux, Vincent

    2010-01-01

    International audience We describe the structure of a toothed cetacean community around the island of Mayotte (South-West Indian Ocean, 45°10'E, 12°50'S), using data collected from small boat-based surveys conducted between July 2004 and June 2006. In all, 16 odontocete species were recorded. Diversity (Shannon-Weaver index) was particularly high along the outer slope of the barrier reef. Patterns of spatial distribution underscore the existence of three main cetacean habitat types: the in...

  4. Species diversity and community structure in trap-nesting bees in Southern Brazil

    Luisa Tunes Buschini, Maria

    2006-01-01

    International audience The species diversity and community structure of trap-nesting bees in the Parque Municipal das Araucárias in Southern Brazil was studied during 2 years. Three different habitats (Araucaria forest, swamp and grassland) were investigated in terms of abundance, richness, diversity and similarity of bee communicites. A total of 120 nests of 11 species were collected. The largest abundance of individuals and species richness was found for the family Megachilidae. The most...

  5. Structural and functional diversity of bacterial communities of bloom-forming freshwater cyanobacterial phycosphere

    Louati, Imen

    2015-01-01

    Potentially toxic cyanobacteria blooms often occur in eutrophic aquatic ecosystems. While many studies have been published on their ecology and toxicity, few have investigated the interactions between cyanobacteria and their associated chimiotrophic bacteria within the phycosphere. This latter is the subject of this thesis. Using both natural ecosystems and laboratory approaches, we show that the structure and composition of bacterial communities (BC) associated with cyanobacteria are differe...

  6. Influence of phosphorus availability on the community structure and physiology of cultured biofilms.

    Li, Shuangshuang; Wang, Chun; Qin, Hongjie; Li, Yinxia; Zheng, Jiaoli; Peng, Chengrong; Li, Dunhai

    2016-04-01

    Biofilms have important effects on nutrient cycling in aquatic ecosystems. However, publications about the community structure and functions under laboratory conditions are rare. This study focused on the developmental and physiological properties of cultured biofilms under various phosphorus concentrations performed in a closely controlled continuous flow incubator. The results showed that the biomass (Chl a) and photosynthesis of algae were inhibited under P-limitation conditions, while the phosphatase activity and P assimilation rate were promoted. The algal community structure of biofilms was more likely related to the colonization stage than with the phosphorus availability. Cyanobacteria were more competitive than other algae in biofilms, particularly when cultured under low P levels. A dominance shift occurred from non-filamentous algae in the early stage to filamentous algae in the mid and late stages under P concentrations of 0.01, 0.1 and 0.6mg/L. However, the total N content, dry weight biomass and bacterial community structure of biofilms were unaffected by phosphorus availability. This may be attributed to the low respiration rate, high accumulation of extracellular polymeric substances and high alkaline phosphatase activity in biofilms when phosphorus availability was low. The bacterial community structure differed over time, while there was little difference between the four treatments, which indicated that it was mainly affected by the colonization stage of the biofilms rather than the phosphorus availability. Altogether, these results suggested that the development of biofilms was influenced by the phosphorus availability and/or the colonization stage and hence determined the role that biofilms play in the overlying water. PMID:27090691

  7. Change in Phylogenetic Community Structure during Succession of Traditionally Managed Tropical Rainforest in Southwest China

    Xiao-Xue Mo; Ling-Ling Shi; Yong-Jiang Zhang; Hua Zhu; Ferry Slik, J. W.

    2013-01-01

    Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old grow...

  8. Microgastrinae (Hymenoptera: Braconidae) in the Forest State of Artikutza (Navarra: Spain): Diversity and Community Structure

    Francisco Javier Peris-Felipo; Ricardo Jiménez-Peydró; Teresa Oltra-Moscardó; Jesica Pérez-Rodríguez

    2013-01-01

    Microgastrinae is one of the largest subfamilies of the Braconidae with about 2,000 described species worldwide. These wasps are of enormous ecological interest due to their role in controlling the caterpillar populations. This study analyses diversity and community structure within the Microgastrinae in the Artikutza Forest, located in the Peñas de Aia Natural Park, western Pyrenees, Spain. The specimens were collected in two different habitats: mixed forest and beech forest. A total of 524 ...

  9. Biodiversity and community structure of freeliving marine nematodes from the Larsemann Ice Shelf, East Antarctica

    Ingole, B.S.; Singh, R.

    IN SOUTHERN OCEAN CURRENT SCIENCE, VOL. 99, NO. 10, 25 NOVEMBER 2010 1413 *For correspondence. (e-mail: baban@nio.org) Biodiversity and community structure of free- living marine nematodes from the Larsemann Ice Shelf, East Antarctica Baban Ingole... Boris Petrov with a 25 × 25 × 40 cm VSNL SPECIAL SECTION: CURRENT SCIENCE, VOL. 99, NO. 10, 25 NOVEMBER 2010 1414 Table 1. Details of the sampling locations in the Larsmann Ice Shelf area, East Antarctica Water Core Core section studied...

  10. Effects of grassland conversion and tillage intensities on soil microbial biomass, residues and community structure

    Murugan, Rajasekaran

    2013-01-01

    Agricultural intensification has a strong impact on level of soil organic matter (SOM), microbial biomass stocks and microbial community structure in agro-ecosystems. The size of the microbial necromass C pool could be about 40 times that of the living microbial biomass C pool in soils. Due to the specificity, amino sugar analysis gives more important information on the relative contribution of fungal and bacterial residues to C sequestration potential of soils. Meanwhile, the relationship be...

  11. Quantifying heterogeneous responses of fish community size structure using novel combined statistical techniques.

    Marshall, Abigail M; Bigg, Grant R; van Leeuwen, Sonja M; Pinnegar, John K; Wei, Hua-Liang; Webb, Thomas J; Blanchard, Julia L

    2016-05-01

    To understand changes in ecosystems, the appropriate scale at which to study them must be determined. Large marine ecosystems (LMEs) cover thousands of square kilometres and are a useful classification scheme for ecosystem monitoring and assessment. However, averaging across LMEs may obscure intricate dynamics within. The purpose of this study is to mathematically determine local and regional patterns of ecological change within an LME using empirical orthogonal functions (EOFs). After using EOFs to define regions with distinct patterns of change, a statistical model originating from control theory is applied (Nonlinear AutoRegressive Moving Average with eXogenous input - NARMAX) to assess potential drivers of change within these regions. We have selected spatial data sets (0.5° latitude × 1°longitude) of fish abundance from North Sea fisheries research surveys (spanning 1980-2008) as well as of temperature, oxygen, net primary production and a fishing pressure proxy, to which we apply the EOF and NARMAX methods. Two regions showed significant changes since 1980: the central North Sea displayed a decrease in community size structure which the NARMAX model suggested was linked to changes in fishing; and the Norwegian trench region displayed an increase in community size structure which, as indicated by NARMAX results, was primarily linked to changes in sea-bottom temperature. These regions were compared to an area of no change along the eastern Scottish coast where the model determined the community size structure was most strongly associated to net primary production. This study highlights the multifaceted effects of environmental change and fishing pressures in different regions of the North Sea. Furthermore, by highlighting this spatial heterogeneity in community size structure change, important local spatial dynamics are often overlooked when the North Sea is considered as a broad-scale, homogeneous ecosystem (as normally is the case within the political

  12. Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure.

    Le Roux, Xavier; Poly, Franck; Currey, Pauline; Commeaux, Claire; Hai, Brigitte; Nicol, Graeme W; Prosser, James I; Schloter, Michael; Attard, Eléonore; Klumpp, Katja

    2008-02-01

    The influence of switches in grassland management to or from grazing on the dynamics of nitrifier activity, as well as the abundance of ammonia-oxidizing bacteria, AOB and ammonia-oxidizing archeae, AOA, was analyzed for two years after changing management. Additionally community structure of AOB was surveyed. Four treatments were compared in mesocosms: grazing on previously grazed grassland (G-G); no grazing on ungrazed grassland (U-U); grazing on ungrazed grassland (U-G) and cessation of grazing on grazed grassland (G-U). Nitrifier activity and abundance were always higher for G-G than U-U treatments and AOB community structure differed between these treatments. AOA abundance was in the same range as AOB abundance and followed the same trend. Grazing led to a change in AOB community structure within <5 months and a subsequent (5-12 months) increase in nitrifier activity and abundance. In contrast, cessation of grazing led to a decrease in nitrifier activity and abundance within <5 months and to a later (5-12 months) change in AOB community structure. Activity in G-U and U-G was similar to that in U-U and G-G, respectively, after 12 months. Sequence analysis of 16S rRNA gene clones showed that AOB retrieved from soils fell within the Nitrosospira lineage and percentages of AOB related to known Nitrosospira groups were affected by grazing. These results demonstrate that AOB and AOA respond quickly to changes in management. The selection of nitrifiers adapted to novel environmental conditions was a prerequisite for nitrification enhancement in U-G, whereas nitrification decrease in G-U was likely due to a partial starvation and decrease in the abundance of nitrifiers initially present. The results also suggest that taxonomic affiliation does not fully infer functional traits of AOB. PMID:18049458

  13. Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations▿†

    Shanks, Orin C.; Kelty, Catherine A.; Archibeque, Shawn; Jenkins, Michael; Newton, Ryan J.; McLellan, Sandra L; Susan M. Huse; Sogin, Mitchell L.

    2011-01-01

    The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal mi...

  14. Effects of a bactericide on the structure and survival of benthic diatom communities

    Morin, S.; Proia, L.; Ricart, M.; Bonnineau, C.; Geiszinger, A.; Ricciardi, F.; Guasch, H.; Romani, A.M.; Sabater, S.

    2010-01-01

    We studied the adverse effects of triclosan, a widely used biocide commonly reported in surface waters, on the structure and function of benthic diatom communities. Laboratory-grown biofilms were exposed (i) to chronic contamination by increasing concentrations of triclosan and (ii) to a short-pulse of sublethal triclosan concentrations followed by a 2-week recuperation period. The first experiment was performed using 6 nominal concentrations ranging from 0.05 to 500 µg/L triclosan to obtain ...

  15. Gastropod diversification and community structuring processes in ancient Lake Ohrid: a metacommunity speciation perspective

    T. Hauffe

    2015-09-01

    Full Text Available The Balkan Lake Ohrid is the oldest and most speciose freshwater lacustrine system in Europe. However, it remains unclear whether the diversification of its endemic taxa is mainly driven by neutral processes, environmental factors, or species interactions. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics. Such a unifying framework – the metacommunity speciation model – considers how community assembly affects diversification and vice versa by assessing the relative contribution of the three main community assembly processes, dispersal limitation, environmental filtering, and species interaction. The current study therefore used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process based metacommunity analyses. Specifically, the study aimed at (i identifying the relative importance of the three community assembly processes and (ii to test whether the importance of these individual processes changes gradually with lake depth or whether they are distinctively related to eco-zones. Based on specific simulation steps for each of the three processes, it could be demonstrated that dispersal limitation had the strongest influence on gastropod community structures in Lake Ohrid. However, it was not the exclusive assembly process but acted together with the other two processes – environmental filtering, and species interaction. In fact, the relative importance of the three community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter. The study thus corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community structure and generating endemic biodiversity (via its influence on diversification processes. However, according to the metacommunity speciation model, the inferred importance of

  16. Macrozoobenthic community structure in two Portuguese estuaries: Relationship with organic enrichment and nutrient gradients

    Mucha, Ana Paula; Costa, Maria Helena

    1999-07-01

    The aim of this work consists in the study of the structural and functional aspects of the macrozoobenthic communities and their relationships with the organic enrichment and nutrient gradients in water and sediment. The study was carried out in two coastal ecosystems under strong anthropogenic pressure: the Sado estuary and the Aveiro Lagoon. Samples were collected at four stations between October 1994 and April 1995. The results obtained allowed us to state that spatial variability, both horizontal and vertical, was higher than the temporal variability. This was due to local hydrodynamism, organic load and granulometric structure of the sediment. Comparing the community structure at the different stations, it was possible to observe the existence of disturbance cases not directly related to organic enrichment gradients. The interpretation of the functional role of the macrozoobenthic communities at the water-sediment interface was based on the trophodynamic group classification. This approach allowed us to state that the sensitivity of different groups to organic enrichment, confirming the role of burrower subsurface-deposit feeders as opportunists associated with organic enrichment and, on the other hand, the influence of certain trophodynamic groups in the nutrient transfer processes, particularly the association between tube-builder omnivores and burrower carnivore and nitrate content in interstitial water.

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

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

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

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

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

    2014-12-01

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

  19. Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China.

    Mo, Xiao-Xue; Shi, Ling-Ling; Zhang, Yong-Jiang; Zhu, Hua; Slik, J W Ferry

    2013-01-01

    Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old growth forests, old secondary forests (∼200-years after slash and burn), and young secondary forests (15-50-years after slash and burn). We found that tree phylogenetic community structure changed from clustering to over-dispersion from early to late successional forests and finally became random in old-growth forest. We also found that the phylogenetic structure of the tree overstorey and understorey responded differentially to change in environmental conditions during succession. In addition, we show that slash and burn agriculture (swidden cultivation) can increase landscape level plant community evolutionary information content. PMID:23936268

  20. Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China.

    Xiao-Xue Mo

    Full Text Available Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old growth forests, old secondary forests (∼200-years after slash and burn, and young secondary forests (15-50-years after slash and burn. We found that tree phylogenetic community structure changed from clustering to over-dispersion from early to late successional forests and finally became random in old-growth forest. We also found that the phylogenetic structure of the tree overstorey and understorey responded differentially to change in environmental conditions during succession. In addition, we show that slash and burn agriculture (swidden cultivation can increase landscape level plant community evolutionary information content.

  1. Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8.

    Ibrahim F Farag

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

  2. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

    Fang, Hua; Lian, Jianjun; Wang, Huifang; Cai, Lin; Yu, Yunlong

    2015-04-01

    Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils. PMID:25603295

  3. The role of macrobiota in structuring microbial communities along rocky shores

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  4. Diversity and network structure of invertebrate communities associated to Heliconia species in natural and human disturbed tropical rain forests

    Julieta Benítez-Malvido; Ana Paola Martínez-Falcón; Wesley Dáttilo; Ek Del Val

    2014-01-01

    We analyzed the influence of natural and anthropogenic habitat disturbance on the structure of invertebrate communities living on two species of Heliconia herbs. We compared the invertebrate community structure associated to both species growing in natural forest gaps, on road edges for H. latispatha, and in riparian vegetation for H. collinsiana. We assessed the topological structure of individual-based Heliconia–invertebrate networks. Species richness was greater in H. collinsiana inhabitin...

  5. Patterns of the benthic community structure in coral reefs of the north western Caribbean

    Borges-Souza, J.M.; Chávez, E.A.

    2007-01-01

    Data on the benthic community structure of six coral reefs of the Mexican portion of the Mesoamerican Barrier Reef System using the photographic-transect method, aimed to describe the structural patterns in each reef, and comparing differences between shallow and deep reefs. In the shallow stratum (Colombia 6-7m, Chankanaab 6m, Majahual 1-6m and Akumal 8m) hexacorals, sponges and algae dominated, with 38%, 34.6% and 14.5% of abundance, respectively. The species most commonly found were: Monta...

  6. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Cody S Sheik

    Full Text Available Extensive use of chromium (Cr and arsenic (As based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI. Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

  7. Vertical stratification of ichneumonid wasp communities: the effects of forest structure and life-history traits.

    Di Giovanni, Filippo; Cerretti, Pierfilippo; Mason, Franco; Minari, Emma; Marini, Lorenzo

    2015-10-01

    Parasitoid wasp communities of the canopy of temperate forests are still largely unexplored. Very little is known about the community composition of parasitoids between canopy and understory and how much of this difference is related to forest structure or parasitoid biological strategies. In this study we investigated upon the difference in the community composition of the parasitic wasps Ichneumonidae between canopy and understory in a lowland temperate forest in northern Italy. We used general linear models to test whether parasitic strategy modifies species vertical stratification and the effect of forest structure. We also tested differences in β-diversity between canopy and understory traps and over time within single forest layers. We found that stand basal area was positively related to species richness, suggesting that the presence of mature trees can influence local wasp diversity, providing a higher number of microhabitats and hosts. The ichneumonid community of the canopy was different from that of the understory, and the β-diversity analysis showed higher values for the canopy, due to a higher degree of species turnover between traps. In our analyses, the vertical stratification was different between groups of ichneumonids sharing different parasitic strategies. Idiobiont parasitoids of weakly or deeply concealed hosts were more diverse in the understory than in the canopy while parasitoids of spiders were equally distributed between the two layers. Even though the ichneumonid community was not particularly species-rich in the canopy of the temperate forests, the extension of sampling to that habitat significantly increased the number of species recorded. PMID:24996133

  8. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Sheik, Cody S; Mitchell, Tyler W; Rizvi, Fariha Z; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J; Krumholz, Lee R

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  9. Mangrove community in an abandoned brick kiln: A structural and association analysis

    Sumit Manna

    2012-03-01

    Full Text Available Background: The presence of brick kiln along the Hoogly rever sites of lower Bengal is very usual and this phenomenon is not only restricted to India alone but also to the other south Asian countries. The abandoned brick Kiln are important habitat for the formation of mangrove community due to tidal action, loose silty substratum and less anthropogenic interference. In this context, the aim of the present study is to visualize how the structural and association pattern regulate the community dynamics of a mangrove ecosystem. Materials and Methods: The entire study area was divided into 37 units (Quadrats of 27.31 sq m. Structural parameters like density, relative density, abundance, relative abundance, frequency, relative basal area were measured based on vegetation map, prepared through satellite image and ground truthing. Association indices (Ochiai, Dice and Jaccard were measured based on 2X2 contingency/species association table. Results: Out of 10 species under 10 genera and 9 families found in the present habitat, Sonneratia caseolaris is the only mangrove tree species with 155 individuals along with other mangrove associates like Cryptocoryne ciliata, Crinum viviparum, Acanthus ilicifolius and Derris scandens. The high importance value index of Sonneratia caseolaris, Cryptocoryne ciliata, and Crinum viviparum indicated their significant role in community formation. The strong positive association of these 3 species also suggests to help in developing community in stressed environment. Conclusion: Identification of such potential mangrove habitat and study of their community dynamics would be helpful to find out the nature of mangrove establishment for future afforestation programme of threatened mangrove species.

  10. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots

    Bourdel, Guillaume; Roy-Bolduc, Alice; St-Arnaud, Marc; Hijri, Mohamed

    2016-01-01

    Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous pattern of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs) retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of pollution reduce fungal

  11. Structure of parasite component communities of didelphid marsupials: insights from a comparative study.

    Jiménez, F Agustín; Catzeflis, François; Gardner, Scott L

    2011-10-01

    chance, in the structuring of parasite communities in marsupials. PMID:21506798

  12. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots.

    Bourdel, Guillaume; Roy-Bolduc, Alice; St-Arnaud, Marc; Hijri, Mohamed

    2016-01-01

    Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous pattern of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs) retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of pollution reduce fungal

  13. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

    Le, Huong T; Ho, Cuong T; Trinh, Quan H; Trinh, Duc A; Luu, Minh T N; Tran, Hai S; Orange, Didier; Janeau, Jean L; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

    2016-01-01

    Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

  14. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

    Penton, C Ryan; Gupta, V V S R; Tiedje, James M; Neate, Stephen M; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K

    2014-01-01

    Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. PMID:24699870

  15. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

    C Ryan Penton

    Full Text Available Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

  16. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

    Le, Huong T.; Ho, Cuong T.; Trinh, Quan H.; Trinh, Duc A.; Luu, Minh T. N.; Tran, Hai S.; Orange, Didier; Janeau, Jean L.; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

    2016-01-01

    Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

  17. Community structure and seasonal variation of an inshore demersal fish community at Goa, West Coast of India

    Ansari, Z. A.; Chatterji, A.; Ingole, B. S.; Sreepada, R. A.; Rivonkar, C. U.; Parulekar, A. H.

    1995-11-01

    Structure and seasonal variation of an inshore demersal fish assemblage have been described from 52 trawl samples collected between November 1988-November 1989 from Aguada and Marmugao Bays at Goa (west coast of India). A total of 12 519 individuals belonging to 59 species were collected. There was a clear seasonal fluctuation in relative abundance, biomass, species occurrence and species dominance. Families such as Sciaenidae, Leiognathidae, Cynoglossidae, Clupeidae and Ariidae dominated the demersal fish community, both in abundance and in biomass over the two areas. About 50% of the recorded species regularly occurred in the two areas. Density and biomass were high during post- and pre-monsoon seasons and low during the monsoon seasons. The species assemblages at the two sites were similar and showed much overlap of dominant species. Resident and quasi-resident species were dominant throughout the year and the overall population consisted mainly of marine coastal species. Cluster analysis showed species segregation into seasonal groups and intense association among different species groups. There was seasonal fluctuation in diversity indices and a marginal increase in species richness in Aguada bay was noticed. The dominance of juveniles in the catches indicate that the two areas serve as nursery grounds for the juveniles of several commercially important marine teleosts.

  18. Community Structure of a Mental Health Internet Support Group: Modularity in User Thread Participation

    Reynolds, Julia; Bennett, Kylie; Bennett, Anthony; Cunningham, John Alastair; Griffiths, Kathleen Margaret

    2016-01-01

    Background Little is known about the community structure of mental health Internet support groups, quantitatively. A greater understanding of the factors, which lead to user interaction, is needed to explain the design information of these services and future research concerning their utility. Objective A study was conducted to determine the characteristics of users associated with the subgroup community structure of an Internet support group for mental health issues. Methods A social network analysis of the Internet support group BlueBoard (blueboard.anu.edu.au) was performed to determine the modularity of the community using the Louvain method. Demographic characteristics age, gender, residential location, type of user (consumer, carer, or other), registration date, and posting frequency in subforums (depression, generalized anxiety, social anxiety, panic disorder, bipolar disorder, obsessive compulsive disorder, borderline personality disorder, eating disorders, carers, general (eg, “chit chat”), and suggestions box) of the BlueBoard users were assessed as potential predictors of the resulting subgroup structure. Results The analysis of modularity identified five main subgroups in the BlueBoard community. Registration date was found to be the largest contributor to the modularity outcome as observed by multinomial logistic regression. The addition of this variable to the final model containing all other factors improved its classification accuracy by 46.3%, that is, from 37.9% to 84.2%. Further investigation of this variable revealed that the most active and central users registered significantly earlier than the median registration time in each group. Conclusions The five subgroups resembled five generations of BlueBoard in distinct eras that transcended discussion about different mental health issues. This finding may be due to the activity of highly engaged and central users who communicate with many other users. Future research should seek to determine

  19. Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

    Martins, Monica [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Faleiro, Maria Leonor [IBB - Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Chaves, Sandra; Tenreiro, Rogerio [Universidade de Lisboa, Faculdade de Ciencias, Centro de Biodiversidade, Genomica Integrativa e Funcional (BioFIG), Campus de FCUL, Campo Grande 1749-016 Lisboa (Portugal); Santos, Erika [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, Maria Clara, E-mail: mcorada@ualg.pt [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

    2010-04-15

    Several microbial communities, obtained from uranium contaminated and non-contaminated samples, were investigated for their ability to remove uranium (VI) and the cultures capable for this removal were further assessed on their efficiency for chromium (VI) removal. The highest efficiency for removal of both metals was observed on a consortium from a non-contaminated soil collected in Monchique thermal place, which was capable to remove 91% of 22 mg L{sup -1} U(VI) and 99% of 13 mg L{sup -1} Cr(VI). This study revealed that uranium (VI) removing communities have also ability to remove chromium (VI), but when uranium (VI) was replaced by chromium (VI) several differences in the structure of all bacterial communities were observed. TGGE and phylogenetic analysis of 16S rRNA gene showed that the uranium (VI) removing bacterial consortia are mainly composed by members of Rhodocyclaceae family and Clostridium genus. On the other hand, bacteria from Enterobacteriaceae family were detected in the community with ability for chromium (VI) removal. The existence of members of Enterobacteriaceae and Rhodocyclaceae families never reported as chromium or uranium removing bacteria, respectively, is also a relevant finding, encouraging the exploitation of microorganisms with new abilities that can be useful for bioremediation.

  20. Activity and community structure of methane-oxidising bacteria in a wet meadow soil.

    Horz, Hans-Peter; Raghubanshi, Akhilesh S; Heyer, Jürgen; Kammann, Claudia; Conrad, Ralf; Dunfield, Peter F

    2002-09-01

    The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137-300 nM CH(4), a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (10(5)-10(7) cells g(-1) d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses. PMID:19709259

  1. Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands.

    Zhang, Dan; Wang, Chuan; Zhang, Liping; Xu, Dong; Liu, Biyun; Zhou, Qiaohong; Wu, Zhenbin

    2016-06-01

    Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable. PMID:27266297

  2. Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

    Several microbial communities, obtained from uranium contaminated and non-contaminated samples, were investigated for their ability to remove uranium (VI) and the cultures capable for this removal were further assessed on their efficiency for chromium (VI) removal. The highest efficiency for removal of both metals was observed on a consortium from a non-contaminated soil collected in Monchique thermal place, which was capable to remove 91% of 22 mg L-1 U(VI) and 99% of 13 mg L-1 Cr(VI). This study revealed that uranium (VI) removing communities have also ability to remove chromium (VI), but when uranium (VI) was replaced by chromium (VI) several differences in the structure of all bacterial communities were observed. TGGE and phylogenetic analysis of 16S rRNA gene showed that the uranium (VI) removing bacterial consortia are mainly composed by members of Rhodocyclaceae family and Clostridium genus. On the other hand, bacteria from Enterobacteriaceae family were detected in the community with ability for chromium (VI) removal. The existence of members of Enterobacteriaceae and Rhodocyclaceae families never reported as chromium or uranium removing bacteria, respectively, is also a relevant finding, encouraging the exploitation of microorganisms with new abilities that can be useful for bioremediation.

  3. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  4. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition

  5. Plant growth and soil microbial community structure of legumes and grasses grown in monoculture or mixture

    CHEN Meimei; CHEN Baodong; MARSCHNER Petra

    2008-01-01

    A greenhouse pot experiment was conducted to investigate the influence of soil moisture eontent on plant growth and the rhizospheremicrobial community structure of four plant species (white clover, alfalfa, sudan grass, tall fescue), grown individually or in a mixture.The soil moisture content was adjusted to 55% or 80% water holding capacity (WHC). The results indicated that the total plant biomassof one pot was lower at 55% WHC. At a given soil moisture, the total plant biomass of white clover and tall fescue in the mixture waslower than that in a monoculture, indicating their poor competitiveness. For leguminous plants, the decrease in soil moisture reducedthe total microbial biomass, bacterial biomass, fungal biomass, and fungal/baeterial ratio in soil as assessed by the phospholipid fattyacid analysis, whereas, lower soil moisture increased those parameters in the tall fescue. The microbial biomass in the soil with legumeswas higher than that in the soil with grasses and the two plant groups differed in soil microbial community composition. At high soilmoisture content, microbial communities of the plant mixture were similar to those of the legume monoculture, and the existenceof legumes in the mixture enhanced the bacterial and fungal biomass in the soil compared to the grasses grown in the monoculture,indicating that legumes played a dominant role in the soil microbial community changes in the plant mixture.

  6. Community Structure of a Bank-Firm Credit Network in Japan

    Iyetomi, Hiroshi; Matsuura, Yuki

    2014-03-01

    We study temporal change of community structure in a Japanese credit network formed by banks and listed firms through their financial relations over the last 30 years. The credit connectedness is regarded as a potenital source of systemic risk. Our network is a bipartite graph consisting of two species of nodes connected with bidirectional links. The direction of links is identified with that of risk flows and their weights are relative credit/loan with respect to the targets. In a partial credit network obtained only with the links pointing from firms toward banks, the city banks forms one major community in most of the time period to share risk when firms go wrong. On the other hand, a partial network only with the links from banks toward firms is decomposed into communities of similar size each of which has its own city bank, reflecting the main-bank system in Japan. Finally we take overlapping parts of the two community sets to find cores of the risk concentration in the credit network. This work was supported by JSPS KAKENHI Grant Number 22300080.

  7. Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord.

    Gutiérrez, Marcelo H; Galand, Pierre E; Moffat, Carlos; Pantoja, Silvio

    2015-10-01

    Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords. PMID:25856307

  8. Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil.

    Shade, Ashley; Klimowicz, Amy K; Spear, Russell N; Linske, Matthew; Donato, Justin J; Hogan, Clifford S; McManus, Patricia S; Handelsman, Jo

    2013-11-01

    Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria. PMID:23974143

  9. Community structure of shallow rocky shore fish in a tropical bay of the southwestern Atlantic

    Camilo Moitinho Ferreira

    2015-12-01

    Full Text Available Abstract Southwestern Atlantic Ocean rocky shores sustain important reef fish communities. However, those communities in tropical regions are not well understood, especially in Brazil. In this present article we assess community parameters of reef fishes such as composition, trophic organization and their relationships with physical and biological factors on four tropical rocky shores in Todos os Santos Bay, southwestern Atlantic. During six months, a total of 80 visual censuses were performed, in which 3,582 fish belonging to 76 species were recorded. Territorial herbivorous fish and turf algae were dominant at all the sites. The spatial variability of fish community structure was related to the benthic cover composition and depth. The high abundance of territorial herbivores and mobile invertebrate feeders could be associated with high levels of turf cover, low wave exposure and shallow waters. Moreover, this fact could be a consequence of the low density of roving herbivores and large carnivores probably due to the pressure of intense fishing activity. Thus complementary studies are needed to evaluate the actual conservation status of these rocky shore reefs, singularly located habitats connecting inner and outer reefs in Todos os Santos Bay.

  10. 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.

    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. PMID:26626912

  11. Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern Gulf of Mexico

    GaryMKing; BradleyTolar

    2013-01-01

    16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤ 100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤ 100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Th...

  12. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas. PMID:27446035

  13. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas. PMID:27446035

  14. Influence of black carbon addition on phenanthrene dissipation and microbial community structure in soil

    Biodegradation processes and changes in microbial community structure were investigated in black carbon (BC) amended soils in a laboratory experiment using two soils (black soil and red soil). We applied different percentages of charcoal as BC (0%, 0.5% and 1% by weight) with 100 mg kg−1 of phenanthrene. Soil samples were collected at different incubation times (0, 7, 15, 30, 60, 120 d). The amendment with BC caused a marked decrease in the dissipation (ascribed to mainly degradation and/or sequestration) of phenanthrene residues from soil. Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil, 0.5% BC amendments were higher. There were significant changes in the PLFA pattern in phenanthrene-spiked soils with time but BC had little effect on the microbial community structure of phenanthrene-spiked soils, as indicated by principal component analysis (PCA) of the PLFA signatures. - Highlights: ► Extracted phenanthrene increased substantially as the BC amount increased. ► Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil. ► BC caused a marked decrease in the dissipation of phenanthrene from soil. ► PLFA pattern in phenanthrene-spiked soils with time had significant changes. - BC amendments on phenanthrene extraction were different for two soils and time was a more effective factor in microbial community changes.

  15. Habitat heterogeneity determines climate impact on zooplankton community structure and dynamics.

    Saskia A Otto

    Full Text Available Understanding and predicting species distribution in space and time and consequently community structure and dynamics is an important issue in ecology, and particularly in climate change research. A crucial factor determining the composition and dynamics of animal populations is habitat heterogeneity, i.e., the number of structural elements in a given locality. In the marine pelagic environment habitat heterogeneity is represented by the distribution of physical oceanographic parameters such as temperature, salinity and oxygen that are closely linked to atmospheric conditions. Little attention has been given, however, to the role of habitat heterogeneity in modulating the response of animal communities to external climate forcing. Here we investigate the long-term dynamics of Acartia spp., Temora longicornis, and Pseudocalanus acuspes, three dominant zooplankton species inhabiting different pelagic habitats in the Central Baltic Sea (CBS. We use the three copepods as indicator species for changes in the CBS zooplankton community and apply non-linear statistical modeling techniques to compare spatial population trends and to identify their drivers. We demonstrate that effects of climate variability and change depend strongly on species-specific habitat utilization, being more direct and pronounced at the upper water layer. We propose that the differential functional response to climate-related drivers in relation to strong habitat segregation is due to alterations of the species' environmental niches. We stress the importance of understanding how anticipated climate change will affect ecological niches and habitats in order to project spatio-temporal changes in species abundance and distribution.

  16. Dynamic changes in microbial activity and community structure during biodegradation of petroleum compounds: A laboratory experiment

    2007-01-01

    With 110-d incubation experiment in laboratory, the responses of microbial quantity, soil enzymatic activity, and bacterial community structure to different amounts of diesel fuel amendments were studied to reveal whether certain biological and biochemical characteristics could serve as reliable indicators of petroleum hydrocarbons contamination in meadow-brown soil, and use these indicators to evaluate the actual ecological impacts of 50-year petroleum-refining wastewater irrigation on soil function in Shenfu irrigation area. Results showed that amendments of ≤1000 mg/kg diesel fuel stimulated the growth of aerobic heterotrophic bacteria, and increased the activity of soil dehydrogenase, hydrogenperoxidase, polyphenol oxidase and substrate-induced respiration. Soil bacterial diversity decreased slightly during the first 15 d of incubation and recovered to the control level on day 30. The significant decrease of the colony forming units of soil actinomyces and filamentous fungi can be taken as the sensitive biological indicators of petroleum contamination when soil was amended with ≥5000 mg/kg diesel fuel. The sharp decrease in urease activity was recommended as the most sensitive biochemical indicator of heavy diesel fuel contamination. The shifts in community structure to a community documented by Sphingomonadaceae within α-subgroup of Proteobacteria could be served as a sensitive and precise indicator of diesel fuel contamination. Based on the results described in this paper, the soil function in Shenfu irrigation area was disturbed to some extent.

  17. Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.

    Coban, Halil; Ertekin, Emine; Ince, Orhan; Turker, Gokhan; Akyol, Çağrı; Ince, Bahar

    2016-07-01

    The effect of veterinary antibiotics in anaerobic digesters is a concern where methane production efficiency is highly dependent on microbial community structure. In this study, both anaerobic degradation of a common veterinary antibiotic, oxytetracycline (OTC), and its effects on an anaerobic digester microbial community were investigated. Qualitative and quantitative molecular tools were used to monitor changes in microbial community structure during a 60-day batch incubation period of cow manure with the addition of different concentrations of the antibiotic. Molecular data were interpreted by a further redundancy analysis as a multivariate statistics approach. At the end of the experiment, approximately 48, 33, and 17 % of the initially added 50, 100, and 200 mg l(-1) of OTC was still present in the serum bottles which reduced the biogas production via accumulation of some of the volatile fatty acids (VFAs). Biogas production was highly correlated with Methanobacteriales and Methanosarcinales gene copy numbers, and those parameters were negatively affected with oxytetracycline and VFA concentrations. PMID:26974525

  18. Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

    Ai-dong Ruan

    2015-10-01

    Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.

  19. Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil

    Jakub eRidl

    2016-06-01

    Full Text Available Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microbial guilds which are adapted to ephemeral carbon inputs are enriched in the vegetated soil.. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism, differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

  20. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes).

    Wood, Jamie R; Wilmshurst, Janet M; Richardson, Sarah J; Rawlence, Nicolas J; Wagstaff, Steven J; Worthy, Trevor H; Cooper, Alan

    2013-10-15

    Knowledge of extinct herbivore community structuring is essential for assessing the wider ecological impacts of Quaternary extinctions and determining appropriate taxon substitutes for rewilding. Here, we demonstrate the potential for coprolite studies to progress beyond single-species diet reconstructions to resolving community-level detail. The moa (Aves: Dinornithiformes) of New Zealand are an intensively studied group of nine extinct herbivore species, yet many details of their diets and community structuring remain unresolved. We provide unique insights into these aspects of moa biology through analyses of a multispecies coprolite assemblage from a rock overhang in a montane river valley in southern New Zealand. Using ancient DNA (aDNA), we identified 51 coprolites, which included specimens from four sympatric moa species. Pollen, plant macrofossils, and plant aDNA from the coprolites chronicle the diets and habitat preferences of these large avian herbivores during the 400 y before their extinction (∼1450 AD). We use the coprolite data to develop a paleoecological niche model in which moa species were partitioned based on both habitat (forest and valley-floor herbfield) and dietary preferences, the latter reflecting allometric relationships between body size, digestive efficiency, and nutritional requirements. Broad ecological niches occupied by South Island giant moa (Dinornis robustus) and upland moa (Megalapteryx didinus) may reflect sexual segregation and seasonal variation in habitat use, respectively. Our results show that moa lack extant ecological analogs, and their extinction represents an irreplaceable loss of function from New Zealand's terrestrial ecosystems. PMID:24082104

  1. SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF SUCKING LICE IN YUNNAN, CHINA

    Xian-guoGuo; Ti-junQian; Li-junGuo; JingWang; Wen-geDong; LiZhang; Zhi-minMa; andWeiLi

    2004-01-01

    On the basis of investigating 9 counties (towns) in Yunnan Province of China, the species diversity and community structure of sucking lice on the body surface of small mammal hosts are studied in the paper. Species richness (S) is used to stand for the species diversity. The calculation of community diversity index and evenness are based on Shannon-Wiener's method. 2745 small mammals captured from the investigated sites belong to 10 families, 25 genera and 41 species in 5 orders (Rodentia, Insectivora, Scandentia, Logomorpha and Carnivora) while 18165 individuals of sucking lice collected from the body surface of the small mammal hosts are identified into 4 families, 6 genera and 22 species. The species of sucking lice are much less than the species of their hosts. Most species of small mammals have their fixed sucking lice on their body surface. One species of small mammals usually have few species of sucking lice (1 to 4 species). The close species of the hosts in the taxonomy are found to have the same or similar dominant species of sucking lice on their body surface. The results reveal that the species diversity of sucking lice on small mammals is very low with a very simple community structure. The results also imply there may be a close co-evolution relationship between the lice and the hosts.

  2. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  3. Land management practices interactively affect wetland beetle ecological and phylogenetic community structure.

    Kelly, Sandor L; Song, Hojun; Jenkins, David G

    2015-06-01

    Management practices can disturb ecological communities in grazing lands, which represent one-quarter of land surface. But three knowledge gaps exist regarding disturbances: disturbances potentially interact but are most often studied singly; experiments with multiple ecosystems as treatment units are rare; and relatively new metrics of phylogenetic community structure have not been widely applied. We addressed all three of these needs with a factorial experiment; 40 seasonal wetlands embedded in a Florida ranch were treated with pasture intensification, cattle exclosure, and prescribed fire. Treatment responses were evaluated through four years for aquatic beetle (Coleoptera: Adephaga) assemblages using classic ecological metrics (species richness, diversity) and phylogenetic community structure (PCS) metrics. Adephagan assemblages consisted of 23 genera representing three families in a well-resolved phylogeny. Prescribed fire significantly reduced diversity one year post-fire, followed by a delayed pasture X fire interaction. Cattle exclosure significantly reduced one PCS metric after one year and a delayed pasture x fence x fire interaction was detected with another PCs metric. Overall, effects of long-term pasture intensification were modified by cattle exclosure and prescribed fire. Also, PCS metrics revealed effects otherwise undetected by classic ecological metrics. Management strategies (e.g., "flash grazing," prescribed fires) in seasonal wetlands may successfully balance economic gains from high forage quality with ecological benefits of high wetland diversity in otherwise simplified grazing lands. Effects are likely taxon specific; multiple taxa should be similarly evaluated. PMID:26465031

  4. Change and recovery of coastal mesozooplankton community structure during the Deepwater Horizon oil spill

    The response of mesozooplankton community structure to the Deepwater Horizon oil spill in the northern Gulf of Mexico was investigated using data from a long-term plankton survey off the coast of Alabama (USA). Environmental conditions observed in the study area during the oil spill (2010) were compared to historical observations (2005–2009), to support the contention that variations observed in zooplankton assemblage structure may be attributed to the oil spill, as opposed to natural climatic or environmental variations. Zooplankton assemblage structure observed during the oil spill period (May–August) in 2010 was then compared to historical observations from the same period (2005–2009). Significant variations were detected in assemblage structure in May and June 2010, but these changes were no longer significant by July 2010. The density of ostracods, cladocerans and echinoderm larvae were responsible for most of the differences observed, but patterns differed depending on taxa and months. Many taxa had higher densities during the oil spill year, including calanoid and cyclopoid copepods, ostracods, bivalve larvae and cladocerans, among others. Although this result is somewhat surprising, it is possible that increased microbial activity related to the infusion of oil carbon may have stimulated secondary production through microbial-zooplankton trophic linkages. Overall, results suggest that, although changes in zooplankton community composition were observed during the oil spill, variations were weak and recovery was rapid. (letter)

  5. Ecological assessment of an intermitent Mediterranean river using community structure and function: evaluating the role of different organism groups

    Hughes, Samantha Jane; Santos, José Maria; Ferreira, Maria Teresa; Caraça, Rute; Mendes, Ana M.

    2009-01-01

    1. Reliable lotic ecological monitoring requires knowledge of river typology, environmental factors, the effect of stressors known here as ‘pressures’ and appropriate indicators of anthropogenically induced change. We sampled benthic macroinvertebrate, fish, bird and macrophyte communities along an intermittent Mediterranean river and analysed community structure (relative abundance) and function (metrics) relative to environmental and pressure gradients in order to identify su...

  6. EFFECTS OF COVER CROPPING AND PLASTICULTURE ON SOIL AND RHIZOSPHERE MICROBIAL COMMUNITY STRUCTURE IN TOMATO PRODUCTION SYSTEMS

    In a previous study (Carrera et al., submitted for publication) we found that soil microbial community structure was distinctly different under plasticulture than under hairy vetch cover crops in tomato production systems. In order to determine the major factors affecting microbial communities we se...

  7. An evaluation of the influence of environment and biogeography on community structure: the case of Holarctic mammals

    Rodríguez, J.; Hortal, Joaquín; Nieto, M.

    2006-01-01

    Aim To evaluate the influence of environment and biogeographical region, as a proxy for historical influence, on the ecological structure of Holarctic communities from similar environments. It is assumed that similarities among communities from similar environments in different realms are the res...

  8. Complex networks from experimental horizontal oil–water flows: Community structure detection versus flow pattern discrimination

    We propose a complex network-based method to distinguish complex patterns arising from experimental horizontal oil–water two-phase flow. We first use the adaptive optimal kernel time–frequency representation (AOK TFR) to characterize flow pattern behaviors from the energy and frequency point of view. Then, we infer two-phase flow complex networks from experimental measurements and detect the community structures associated with flow patterns. The results suggest that the community detection in two-phase flow complex network allows objectively discriminating complex horizontal oil–water flow patterns, especially for the segregated and dispersed flow patterns, a task that existing method based on AOK TFR fails to work. - Highlights: • We combine time–frequency analysis and complex network to identify flow patterns. • We explore the transitional flow behaviors in terms of betweenness centrality. • Our analysis provides a novel way for recognizing complex flow patterns. • Broader applicability of our method is demonstrated and articulated

  9. Effects of thermal constancy and seasonal temperature displacement on community structure of stream macroinvertebrates

    Diurnal and seasonal thermal constancy, a greatly delayed seasonal temperature maximum, and summer cool and winter warm conditions characterize the stream environment below a deep-release dam in Colorado. Low diversity index and equitability values and changes in macroinvertebrate species composition may result from failure of the temperature regime to provide the thermal stimuli essential for various life-cycle phenomena. It is hypothesized that the following sublethal effects, directly or indirectly resulting from the modified temperature regime, may further alter macroinvertebrate community structure: reduction of niche overlap and a shift toward an equilibrium community as a consequence of reduced environmental fluctuation; more intense competition associated with greater productivity; elimination of major invertebrate predators; and failure of the limited temperature range to provide optimal temperatures for various physiological processes. Effects of the temperature regime on diversity patterns should be considered in dam construction and operation

  10. Community structure and the evolution of interdisciplinarity in Slovenia's scientific collaboration network.

    Lužar, Borut; Levnajić, Zoran; Povh, Janez; Perc, Matjaž

    2014-01-01

    Interaction among the scientific disciplines is of vital importance in modern science. Focusing on the case of Slovenia, we study the dynamics of interdisciplinary sciences from 1960 to 2010. Our approach relies on quantifying the interdisciplinarity of research communities detected in the coauthorship network of Slovenian scientists over time. Examining the evolution of the community structure, we find that the frequency of interdisciplinary research is only proportional with the overall growth of the network. Although marginal improvements in favor of interdisciplinarity are inferable during the 70s and 80s, the overall trends during the past 20 years are constant and indicative of stalemate. We conclude that the flow of knowledge between different fields of research in Slovenia is in need of further stimulation. PMID:24728345

  11. Composition of the metazooplankton community and structure across the continental shelf off tropical NW Australia

    Jaspers, Cornelia; Nielsen, Torkel Gissel; Maar, Marie

    This talk focuses on the distribution pattern and grazing impact of different functional metazooplankton groups in a tropical marine ecosystem. We studied the metazooplankton distribution across the continental shelf from eutrophic mangrove areas to the oligotrophic deep blue ocean off NW Australia....... Small size classes <200 μm dominated the zooplankton and e.g. 80 % of the larvacean community belonged to the micro-size fraction. We show that gelatinous zooplankton is of key importance for the carbon cycling in this tropical area. Larvaceans exceeded the copepod grazing impact on the primary...... producers especially in oligotrophic areas. The metazooplankton community structure and production reflect biotic and abiotic conditions of the system. We show that small size classes, especially larvaceans, have a higher contribution to secondary production and carbon cycling in tropical oligotrophic areas...

  12. The impact of coastal urbanization on the structure of phytobenthic communities in southern Brazil.

    Martins, Cintia D L; Arantes, Noele; Faveri, Caroline; Batista, Manuela B; Oliveira, Eurico C; Pagliosa, Paulo R; Fonseca, Alessandra L; Nunes, José Marcos C; Chow, Fungyi; Pereira, Sonia B; Horta, Paulo A

    2012-04-01

    The anthropogenic pressures on coastal areas represent important factors affecting local, regional, and even global patterns of distribution and abundance of benthic organisms. This report undertakes a comparative analysis of the community structure of rocky shore intertidal phytobenthos in both pristine like environments (PLE) and urbanized environments (UBE) in southern Brazil, characterizing variations on different spatial scales. Multivariate analysis of variance indicated that the PLE is characterized by a larger number of taxa and an increased occurrence of Rhodophyta species in relation to UBE. In contrast, UBE were dominated by opportunistic algae, such as Cladophora and Ulva spp. Significance tests further indicated higher species richness and Shannon-Wiener diversity on the PLE in relation to UBE. Here we provide data showing the magnitude of seaweed biodiversity loss and discuss direct and indirect consequences of unplanned urbanization on these communities. PMID:22341882

  13. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta.

    Damashek, Julian; Smith, Jason M; Mosier, Annika C; Francis, Christopher A

    2014-01-01

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic

  14. Structure of dung beetle communities in an altitudinal gradient of neotropical dry forest.

    Domínguez, D; Marín-Armijos, D; Ruiz, C

    2015-02-01

    To understand the effects of global warming in tropical insect communities, it is necessary to comprehend how such communities respond to different abiotic factors that covariate with altitude. In this study, we partially answer this question applied to dung beetle communities distributed along an altitudinal gradient. The sampling was conducted in seven stations 100 m apart each in altitude in a dry mountain scrub in southern Ecuador. A total of 7422 individuals belonging to six species were captured. Canthon balteatus Boheman was the most abundant with 6502 individuals, and Onoreidium ohausi (Arrow) was the least abundant with 20 individuals. We found significant changes in the structure of the dung beetle communities with altitude. Two abiotic factors showed a relationship with the abundance pattern for all species (altitude, Z = 0.011, p < 0.01, and temperature, Z = 0.859, p < 0.01). Canthon balteatus Boheman showed a positive relationship with altitude (Z = 1.422, p < 0.001) and temperature (Z = 1.121, p < 0.001), Dichotomius problematicus (Lüederwaldt) a positive relationship with precipitation (Z = 0.113, p < 0.001), and Malagoniella cupreicollis (Waterhouse) a positive relationship with temperature (Z = 0.668, p < 0.001) and negative with precipitation (Z = -0.189, p < 0.001). Phanaeus achilles Boheman, Onthophagus sp., and O. ohausi (Arrow) did not show any relationship with the studied variables, nor was the richness correlated with the studied variables. These results suggest that the effects of global warming over dung beetle communities will be difficult to predict because of species-specific responses to global warming. PMID:26013011

  15. Differential response of high-elevation planktonic bacterial community structure and metabolism to experimental nutrient enrichment.

    Craig E Nelson

    Full Text Available Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient

  16. Benthic Ammonia Oxidizers Differ in Community Structure and Biogeochemical Potential Across a Riverine Delta

    Julian eDamashek

    2015-01-01

    Full Text Available Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California’s Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the massive discharge of ammonium into the Sacramento River has altered this ecosystem by increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (encoding the α-subunit of ammonia monooxygenase. There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB outnumbering ammonia-oxidizing archaea (AOA only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The community structure and biogeochemical function of benthic ammonia oxidizers appears related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

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

    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. PMID:27449214

  18. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

    Lindemann, Stephen R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moran, James J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stegen, James C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Renslow, Ryan S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cole, Jessica K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dohnalkova, Alice [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tremblay, Julien [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Singh, Kanwar [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Malfatti, Stephanie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chen, Feng [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Beyenal, Haluk [Washington State Univ., Pullman, WA (United States); Fredrickson, Jim K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-11-13

    Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2-4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

  19. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

    Aslam, Zubair; Yasir, Muhammad; Yoon, Hwan Sik; Jeon, Che Ok; Chung, Young Ryun

    2013-12-01

    Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera. PMID:24385351

  20. Measuring medical students' sense of community and satisfaction with a structured advising program

    Rachel B. Levine

    2011-11-01

    Full Text Available Objectives: The purpose of this study was to assess changes in students' perceptions of the medical school sense of community and their satisfaction with advising following the initiation of a structured advising program at the Johns Hopkins University School of Medicine. Methods: Participants included School of Medicine graduates from 2006 to 2009. Total sample size was 471. The response rate was 367/471 (81. A cross-sectional survey design was utilized to assess students' perceived differences in advising and sense of community. Scales were developed to assess these constructs. Scale scores and responses to individual items were compared by graduation year. Results: Statistically significant increases over time were noted on the Advising Satisfaction (F (3,363 = 6.54; p≤0.001 and the Relational Community (F(3,363 = 2.76; p=0.042 scales. Using simple logistic regression, unadjusted Odds Ratios show that students graduating in 2009 report higher quality of advising during their clinical years (OR 2.87, 95CI=1.56-5.28, around academics (OR 2.54, 95CI=1.41-4.60, career planning (OR 1.87, 95CI=1.03-3.38, stress management (OR 2.88, 95CI=1.56-5.30, and an enhanced sense of community (OR 2.55, 95CI=1.40-4.64, and social integration (OR 2.07, 95CI=1.15-3.71 compared to 2006 graduates. Conclusions: We found, that students were more satisfied with advising and the medical school environment over the four years of maturation of the Program. A structured advising program that fosters meaningful, longitudinal relationships between students and advisors may enhance students' experiences during medical school

  1. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.

    Röling, W F; van Breukelen, B M; Braster, M; Lin, B; van Verseveld, H W

    2001-10-01

    Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria and Archaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the beta subclass of the class Proteobacteria (beta-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of delta-proteobacteria strongly increased and beta-proteobacteria reappeared. The beta-proteobacteria (Acidovorax, Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the family Geobacteraceae made a strong contribution to the microbial communities. Because the only known

  2. Effects of fungicides and biofungicides on population density and community structure of soil oribatid mites.

    Al-Assiuty, Abdel-Naieem I M; Khalil, Mohamed A; Ismail, Abdel-Wahab A; van Straalen, Nico M; Ageba, Mohamed F

    2014-01-01

    To compare the side-effects of chemical versus biofungicides on non-target organisms in agricultural soil, a study of population structure, spatial distribution and fecundity of oribatid mites, a diverse and species-rich group of microarthropods indicative of decomposer activity in soil was done. Plots laid out in agricultural fields of a research station in Egypt, were cultivated with cucumber and treated with two chemical fungicides: Ridomil Plus 50% wp (active ingredients=metalaxyl and copper oxychloride) and Dithane M-45 (active ingredient=mancozeb), and two biofungicides: Plant Guard (containing the antagonistic fungus Trichoderma harzianum) and Polyversum (containing the fungi-parasitic oomycete Pythium oligandrum). All treatments were done using both low-volume and high-volume spraying techniques to check whether any effects were dependent on the method of application. Oribatid mite communities were assessed from soil core samples collected during the growing season. Total abundance of oribatids was not different across the plots, but some species decreased in number, while one species increased. Species diversity and community equitability decreased with the application of chemical and biofungicides especially when using high-volume spraying. In control plots most oribatid species showed a significant degree of aggregation, which tended to decrease under fungicide treatment. Ridomil Plus, Plant Guard and Polyversum had a negative effect on the gravid/ungravid ratio of some species. Egg number averaged over the whole adult population was not directly related to the application of chemical and biofungicides but it showed a species-specific relationship with population density. In general biofungicides had a smaller effect on population size and community structure of oribatid mite species than chemical fungicides. The results indicate that biofungicides may be the preferred option when aiming to prevent side-effects on sensitive groups among the species

  3. [Impact of Mikania micrantha invasion on soil meso- and micro-invertebrate community structure].

    Quan, Guo-ming; Zhang, Jia-en; Xie, Jun-fang; Mao, Dan-juan; Xu, Hua-qin; Jiang, Wan-bing; Wen, Du-juan

    2011-07-01

    Mikania micrantha, a notorious exotic weed of Asteraceae family, has invaded successfully in southern China, and caused serious damages to native ecosystems. In this paper, a field survey was conducted in the Huolushan Forest Park of Guangzhou, China, aimed to understand the impact of M. micrantha invasion on the soil meso- and micro-invertebrate community. Three sampling sites were installed, including M. micrantha-invaded site, ecotone, and native vegetation site. Through four samplings in 2009, a total of 5206 soil meso- and micro-invertebrate individuals were collected, belonging to 4 phyla, 10 classes, and 19 orders, among which, Nematoda was the dominant group, and Acarina, Collembolan, and Rotifera were the common groups. M. micrantha invasion altered the characteristics of soil meso- and micro-invertebrate community structure. Compared with those at the other two sampling sites, the numbers of total individuals, Nematoda, and Acarina at M. micrantha-invaded site increased significantly, but the groups of soil meso- and micro-invertebrates had less change. At M. micrantha-invaded site, the density-group index (DG) of soil meso- and micro-invertebrates was significantly higher, Margalef richness index (D) and Simpson dominance index (C) tended to ascend, but Pielou evenness index (E) and Shannon index (H') tended to descend. The similarity coefficient of soil meso- and micro-invertebrate community between M. micrantha-invaded site and ecotone was higher than that between M. micrantha-invaded site and native vegetation site. The changes of local climate conditions, plant litters, root secretions, and soil physical-chemical properties caused by M. micrantha invasion could be the major contributing factors that altered the community structure of soil meso- and micro-invertebrates at M. micrantha-invaded site. PMID:22007466

  4. Local and regional effects on community structure of dung beetles in a mainland-island scenario.

    Pedro Giovâni da Silva

    Full Text Available Understanding the ecological mechanisms driving beta diversity is a major goal of community ecology. Metacommunity theory brings new ways of thinking about the structure of local communities, including processes occurring at different spatial scales. In addition to new theories, new methods have been developed which allow the partitioning of individual and shared contributions of environmental and spatial effects, as well as identification of species and sites that have importance in the generation of beta diversity along ecological gradients. We analyzed the spatial distribution of dung beetle communities in areas of Atlantic Forest in a mainland-island scenario in southern Brazil, with the objective of identifying the mechanisms driving composition, abundance and biomass at three spatial scales (mainland-island, areas and sites. We sampled 20 sites across four large areas, two on the mainland and two on the island. The distribution of our sampling sites was hierarchical and areas are isolated. We used standardized protocols to assess environmental heterogeneity and sample dung beetles. We used spatial eigenfunctions analysis to generate the spatial patterns of sampling points. Environmental heterogeneity showed strong variation among sites and a mild increase with increasing spatial scale. The analysis of diversity partitioning showed an increase in beta diversity with increasing spatial scale. Variation partitioning based on environmental and spatial variables suggests that environmental heterogeneity is the most important driver of beta diversity at the local scale. The spatial effects were significant only at larger spatial scales. Our study presents a case where environmental heterogeneity seems to be the main factor structuring communities at smaller scales, while spatial effects are more important at larger scales. The increase in beta diversity that occurs at larger scales seems to be the result of limitation in species dispersal

  5. Structure and phylogenetic diversity of post-fire ectomycorrhizal communities of maritime pine.

    Rincón, A; Santamaría, B P; Ocaña, L; Verdú, M

    2014-02-01

    Environmental disturbances define the diversity and assemblage of species, affecting the functioning of ecosystems. Fire is a major disturbance of Mediterranean pine forests. Pines are highly dependent on the ectomycorrhizal (EM) fungal symbiosis, which is critical for tree recruitment under primary succession. To determine the effects of time since fire on the structure and recovery of EM fungal communities, we surveyed the young Pinus pinaster regenerate in three sites differing in the elapsed time after the last fire event. Pine roots were collected, and EM fungi characterized by sequencing the internal transcribed spacer (ITS) and the large subunit (LSU) regions of the nuclear ribosomal (nr)-DNA. The effects of the elapsed time after fire on the EM community structure (richness, presence/absence of fungi, phylogenetic diversity) and on soil properties were analysed.Fungal richness decreased with the elapsed time since the fire; although, the phylogenetic diversity of the EM community increased. Soil properties were different depending on the elapsed time after fire and particularly, the organic matter, carbon-to-nitrogen (C/N) ratio, nitrogen and iron significantly correlated with the assemblage of fungal species. Ascomycetes, particularly Tuberaceae and Pezizales, were significantly over-represented on saplings in the burned site. On seedlings, a significant over-representation of Rhizopogonaceae and Atheliaceae was observed in the most recently burned site, while other fungi (i.e. Cortinariaceae) were significantly under-represented. Our results are consistent with the hypothesis that fire can act as a selective agent by printing a phylogenetic signal on the EM fungal communities associated with naturally regenerated pines, pointing out to some groups as potential fire-adapted fungi. PMID:23955264

  6. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    Diallo, MD.

    2015-01-01

    Full Text Available Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB community composition and nitrogen (N availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. The aim of this study was to determine the influence of leaf litter decomposition on N mineralization. The specific objectives of this study were to evaluate the influence of the litter biochemistry of five plants species (Faidherbia albida A.Chev., Azadirachta indica A.Juss., Casuarina equisetifolia L., Andropogon gayanus Kunth and Eragrostis tremula Hochst. ex Steud. on N mineralization in a tropical ferrous soil (Lixisol, nitrification, and genetic diversity of ammonia-oxidizing bacteria. Denaturing gradient gel electrophoresis (DGGE of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of leaf litter in soils. Method. Community structure of AOB was determined at two time periods: day 0 and day 140. Ten strains were tested and each of these strains produced a single band. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. Plant secondary compounds such as polyphenols are purported to influence nutrient cycling by affecting organic matter degradation, mineralization rates, N availability and humus formation. In a laboratory study, we investigated the influence of six phenolic acids (ferulic, gallic, vanillic, syringic, p-coumaric and p-HBA acids commonly found in the plant residues on N mineralization and NH4+ and NO3- production in soils. Results. The results showed that litter type did affect soil nitrification. Faidherbia albida litter was associated with

  7. Ectomycorrhizal community structure and function in relation to forest residue harvesting and wood ash applications

    Mahmood, Shahid

    2000-05-01

    Ectomycorrhizal fungi form symbiotic associations with tree roots and assist in nutrient-uptake and -cycling in forest ecosystems, thereby constituting a most significant part of the microbial community. The aims of the studies described in this thesis were to evaluate the potential of DNA-based molecular methods in below-ground ectomycorrhizal community studies and to investigate changes in ectomycorrhizal communities on spruce roots in sites with different N deposition, and in sites subjected to harvesting of forest residues or application of wood ash. The ability of selected ectomycorrhizal fungi to mobilise nutrients from wood ash and to colonise root systems in the presence and absence of ash was also studied. In total 39 ectomycorrhizal species were detected in the experimental forests located in southern Sweden. At each site five to six species colonised around 60% of the root tips. The dominant species, common to the sites, were Tylospora fibrillosa, Thelephora terrestris and Cenococcum geophilum. Differences between two sites with differing levels of N deposition suggested that community structure may be influenced by N deposition, although site history, location and degree of isolation may also influence species composition. Repeated harvesting of forest residues reduced numbers of mycorrhizal roots in the humus layer to approximately 50% of that in control plots but no shift in the ectomycorrhizal community could be detected. At another site, application of granulated wood ash induced a shift in ectomycorrhizal community structure and three ectomycorrhizal fungi ('ash fungi') were found to colonise ash granules. Two 'ash fungi' showed a superior ability to solubilise stabilised wood ash in laboratory experiments compared to other ectomycorrhizal isolates from the same site. In laboratory microcosms containing intact mycorrhizal mycelia, colonisation of wood ash patches by one 'ash fungus' was good whereas colonisation by

  8. Role of environmental heterogeneity in structuring the macrobenthic community in a tropical sandy beach, west coast of India

    Sivadas, S.; Ingole, B.S.; Ganesan, P.; Sautya, S.; Nanajkar, M.

    In most ecosystems, community structure emerges as a result of the complex interaction between biotic and environmental variables. Sandy beaches connected to adjacent ecosystem like estuaries/creeks provide an opportunity to understand the role...

  9. Impact of predation by Ostracion immaculatus (Pisces: Ostraciidae) on the macrofouling community structure in Kanayama Bay, Kii Peninsula (Japan)

    Raveendran, T.V.; Harada, E.

    using predator inclusion as well as exclusion treatment confirmed that predation by this fish had significant impact on the structure of fouling community. The importance of predation was manifested mainly through the influence of fish on ascidians...

  10. [Spatial heterogeneity of community structure of Picea crassifolia forest in Qilian Mountains, China].

    Zhao, Wei-jun; Liu, Xian-de; Jing, Wen-mao; Xu, Li-heng; Niu, Yun; Qi, Peng; Zhao, Yong-hong

    2015-09-01

    We selected the grid of 5 m x 5 m in a dynamic monitoring plot (340 m x 300 m) as the sampling unites and chose 5 structural characteristics (density, average crown breadth, coverage, conspicuousness and average height) to study the spatial heterogeneity of community structure of Picea crassifolia forest in Dayekou Basin of Qilian Mountains by the fractal geometry and geostatistics methods. The results showed that the order of spatial variation in these characteristics was: density > average crown breadth > conspicuousness > coverage > average height, with the variation coefficient ranging from 43.7% to 79.6%. Moran's I index indicated that the structural variables had different degrees of spatial autocorrelation, and the order of autocorrelation was density > average height> coverage > average crown breadth > conspicuousness, with the range of -0.047-0.382. The exponential semivariation model well fitted the spatial variability in different structural features, and the range was 24.6-68.1 m. The variables displayed moderate spatial autocorrelation except for coverage, while the other variables had strong spatial autocorrelation, and the fractal dimension of the variables was close to 2, indicating a low spatial dependence among variables. The variables presented a superposing characteristic of zonal and patchy structures except for density and coverage, while the other variables presented strong patchiness property. Density and coverage had a certain spatial dependence on average crown breadth, conspicuousness and average height. Density and coverage for the spatial heterogeneity of community structural of P. crassifolia forests were 10 m and 0.5 hm2, respectively. PMID:26785538

  11. Variations in community structure and diversity associated with methane-rich sediments offshore southwestern Taiwan

    Lin, L.; Lin, J.; Wu, L.; Wang, P.

    2012-12-01

    Subseafloor sediments have been estimated to harbor more than 50% of the global prokaryotic cells. Such a large quantity of biomass has been considered to play an important role in regulating the elemental cycling between hydrosphere, atmosphere, and geosphere. On the basis of pore water geochemistry and molecular results, numerous studies have demonstrated that sulfate reduction, anaerobic methanotrophy, and methanogenesis appear to be the essential metabolic pathways controlling the organic mineralization and methane cycling in sediments of continental margins. As the extent of microbial community varies from site to site, spatial variations in community structures directly or indirectly catalyzing these metabolic pathways remain to be elucidated. This study aims to uncover community structures along a sediment core collected offshore southwestern Taiwan where the convergence between the Eurasian and Philippine Sea Plates leads to the rapid accumulation of sediments eroded from onshore mountainous regions. The samples were obtained at a 50-cm interval from a gravity core which penetrated to 5 m below seafloor. Crude DNA was extracted and the V4-V6 and V4-V5 regions of 16S rRNA genes in bacteria and archaea were amplified using the barcoded primers, respectively. The amplicons were pooled for sequencing on a Roche GS Junior platform. A total of more than 130,000 bacterial and archaeal reads each were obtained after the processing of raw data for quality check, and chimera, barcode and primer removals. The output reads were clustered into different OTU on the basis of 97% similarity and taxonomically categorized against the Silva database. Despite a significant proportion of sequences whose taxonomical assignments remain to be resolved, sequences affiliated with Firmicutes, Proteobacteria and Chloroflexi within Bacteria, and Thermoplasmata, MBG-B, ANME-1, and MCG within Archaea outnumber the other lineages. The proportions of major OTUs exhibit different trends of

  12. Small copepods structuring mesozooplankton community dynamics in a tropical estuary-coastal system

    Rakhesh, M.; Raman, A. V.; Ganesh, T.; Chandramohan, P.; Dehairs, F.

    2013-07-01

    It is important to know the ultimate role of small copepods in structuring mesozooplankton community pattern and diversity on an estuary-coastal gradient. Here multivariate analyses were used to elucidate this in the Godavari estuary, on the east coast of India. During May 2002, corresponding to the spring intermonsoon, mesozooplankton were sampled from 4 GPS fixed stations in the estuarine reaches of River Godavari and 19 in the coastal waters where Godavari enters the Bay of Bengal. There were 91 mesozooplankton taxa represented by 23 divergent groups. Copepods were by far the most prominent in terms of species richness, numerical abundance, and widespread distribution followed by appendicularians. Small copepods of families Paracalanidae, Acartiidae, Oithonidae, Corycaeidae, Oncaeidae, and Euterpinidae dominated. There were differing regional mesozooplankton/copepod communities, that segregated the estuary-coastal sites into different biotic assemblages: Group-I representing the estuary proper, Group-II estuary mouth and near shore, Group-III the intermediate coastal stations and Group-IV the coastal-offshore waters. Alpha (SRp, H', J', Δ*) and beta diversity (MVDISP, β, β-dissimilarity) measures varied noticeably across these assemblages/areas. The significant correlation of small copepod abundance with total mesozooplankton abundance and biomass (mgDM.m-3) in the estuarine (r: 0.40) and coastal (r: 0.46-0.83) waters together with a regression analysis of diversity measures have revealed the importance of small copepods in the overall mesozooplankton/copepod community structure. There were 'characterizing' and 'discriminating' species, responsible for the observed assemblage patterns. Mesozooplankton/copepod community structure and the size-spectra observed during this study indicate an estuarine-coastal gradient in plankton tropho-dynamics that may shift between a microbial dominated system inside the estuary and mixotrophy in the coastal waters. The

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

    Xi Li; Miaomiao Zhang; Feng Liu(Central China Normal University); Yong Li; Yang He; Shunan Zhang; Jinshui Wu

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different...

  14. An integrated individual, community, and structural intervention to reduce HIV/STI risks among female sex workers in China

    Kang, Dianmin; Tao, Xiaorun; Liao, Meizhen; Li, Jianzhuo; Zhang, Na; Zhu, Xiaoyan; Sun, Xiaoguang; Lin, Bin; Su, Shengli; Hao, Lianzheng; Jia, Yujiang

    2013-01-01

    Background We assessed the effectiveness of an integrated individual, community, and structural intervention to reduce risks of HIV and sexually transmitted infections (STIs) among female sex workers (FSWs). Methods The integration individual, community, and structural intervention was implemented from 2004 to 2009 in six counties of Shandong Province. Post-intervention cross-sectional surveys were conducted in six intervention counties and 10 control counties. Results Of 3326 female sex work...

  15. Effects of a nuclear power plant thermal discharge on habitat complexity and fish community structure in Ilha Grande Bay, Brazil

    Teixeira, Tatiana Pires; Neves, Leonardo Mitrano; Araújo, Francisco Gerson

    2009-01-01

    Abstract Fish communities and habitat structures were evaluated by underwater visual censuses a rocky location impacted by thermal discharge (I) and at two control locations, one in a Sargassum bed (C1) and the other in a rocky shore with higher structural complexity (C2). Habitat indicators and fish communities exhibited significant differences between the impacted and control locations, with the impacted one showing a significant decrease in fish species richness and diversity, a...

  16. Can stable isotope ratios provide for community-wide measures of trophic structure?

    Layman, Craig A; Arrington, D Albrey; Montaña, Carmen G; Post, David M

    2007-01-01

    Stable isotope ratios (typically of carbon and nitrogen) provide one representation of an organism's trophic niche and are widely used to examine aspects of food web structure. Yet stable isotopes have not been applied to quantitatively characterize community-wide aspects of trophic structure (i.e., at the level of an entire food web). We propose quantitative metrics that can be used to this end, drawing on similar approaches from ecomorphology research. For example, the convex hull area occupied by species in delta13C-delta15N niche space is a representation of the total extent of trophic diversity within a food web, whereas mean nearest neighbor distance among all species pairs is a measure of species packing within trophic niche space. To facilitate discussion of opportunities and limitations of the metrics, we provide empirical and conceptual examples drawn from Bahamian tidal creek food webs. These examples illustrate how this methodology can be used to quantify trophic diversity and trophic redundancy in food webs, as well as to link individual species to characteristics of the food web in which they are embedded. Building from extensive applications of stable isotope ratios by ecologists, the community-wide metrics may provide a new perspective on food web structure, function, and dynamics. PMID:17489452

  17. Microbial community structure of activated sludge in treatment plants with different wastewater compositions

    Nataliya M. Shchegolkova

    2016-02-01

    Full Text Available Activated sludge (AS plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc. and inductors of AS bulking and flocculation (Comamonadaceae, Flavobacteriaceae, etc., which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater, which was rich in organic matter. Here we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS flocculation and bulking (abundant in AS of slaughterhouse wastewater played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will help to optimize bioreactor performance and

  18. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.

    Shchegolkova, Nataliya M; Krasnov, George S; Belova, Anastasia A; Dmitriev, Alexey A; Kharitonov, Sergey L; Klimina, Kseniya M; Melnikova, Nataliya V; Kudryavtseva, Anna V

    2016-01-01

    Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs) responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc.), which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater. Additional load of bioreactors with influent rich in petroleum products and organic matter was associated with the increase of bacteria responsible for AS bulking and foaming. Here, we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS bulking and foaming (most abundant in AS of slaughterhouse wastewater) played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect) represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will

  19. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    Evie A Wieters

    Full Text Available We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10's km and local (10's m scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3-4 main 'groups' of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site to stabilize patterns of biomass variability and, in this manner, provide a buffer, or "insurance", against

  20. Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress

    Zhifeng Zhou; Yuanming Zheng; Jupei Shen; Limei Zhang; Yurong Liu; Jizheng He

    2012-01-01

    The responses of activities,abundances and community structures of soil denitrifiers to mercury(Hg)stress were investigated through a short-term incubation experiment.Four soil treatments with different concentrations of Hg(CK,Hg25,Hg50,and Hgl00,denoted as 0,25,50,and 100 mg Hg/kg dry soil,respectively)were incubated for 28 days.Soil denitrification enzyme activity(DEA)was measured at day 3,7 and 28.The abundances and community structures of two denitrification concerning genes,nirS(Cd1-nitrite reductase gene)and nosZ(nitrous oxide reductase gene),were analyzed using real-time PCR and denaturing gradient gel electrophoresis(DGGE).Results showed that soil DEA was significantly stimulated in the treatments of Hg25 and Hg50 compared with others at day 7.Meanwhile,no difference in the abundances of soil nirS and nosZ was found between Hg spiked treatments and CK,except the lower abundance of nirS(P < 0.05)in the Hg added treatments compared with that in the CK at day 28.The community structures of denitrifiers based on nirS gene presented obvious change at day 7 along with the Hg additions,however,no variation was found in all treatments based on the nosZ gene.The results indicated that Hg(Hg25 and Hg50)had a strongly short-term stimulation on soil DEA,and nirS gene is more sensitive than nosZ gene to Hg stress.

  1. Unravelling the community structure of the climate system by using lags and symbolic time-series analysis

    Tirabassi, Giulio; Masoller, Cristina

    2016-07-01

    Many natural systems can be represented by complex networks of dynamical units with modular structure in the form of communities of densely interconnected nodes. Unraveling this community structure from observed data requires the development of appropriate tools, particularly when the nodes are embedded in a regular space grid and the datasets are short and noisy. Here we propose two methods to identify communities, and validate them with the analysis of climate datasets recorded at a regular grid of geographical locations covering the Earth surface. By identifying mutual lags among time-series recorded at different grid points, and by applying symbolic time-series analysis, we are able to extract meaningful regional communities, which can be interpreted in terms of large-scale climate phenomena. The methods proposed here are valuable tools for the study of other systems represented by networks of dynamical units, allowing the identification of communities, through time-series analysis of the observed output signals.

  2. Complex Network Structure Patterns in Open Internet Communities for People with Diabetes

    Chomutare, Taridzo Fred

    2014-01-01

    The papers of this thesis are not available in Munin: 1. Chomutare T, Fernandez-Luque L, Årsand E, Hartvigsen G.: 'Features of mobile diabetes applications: Review of the literature and analysis of current applications against evidence-based guidelines', Journal of Medical Internet Research (2011), vol. 13(3);e65. Available at http://dx.doi.org/10.2196/jmir.1874 2. Chomutare T, Årsand E, Fernandez-Luque L, Lauritzen J, Hartvigsen G.: 'Inferring community structure in healthcare forums: ...

  3. Insect community structure and function in Upper Three Runs, Savannah River Site, South Carolina

    Morse, J.C.; English, W.R. [Clemson Univ., SC (United States). Dept. of Entomology; Looney, B.B. [Westinghouse Savannah River Co., Aiken, SC (United States)

    1993-07-08

    A project to document the insect species in the upper reaches of Upper Three Runs at the Savannah River site was recently completed. This research was supported by the US Department of Energy under the National Environmental Research Park Program. The work was performed by the Department of Entomology at Clemson University in clemson, SC, by John C. Morse (principal investigator), William R. English and their colleagues. The major output from this study was the dissertation of Dr. William R. English entitled ``Ecosystem Dynamics of a South Carolina Sandhills Stream.`` He investigated selected environmental resources and determined their dynamics and the dynamics of the aquatic invertebrate community structure in response to them.

  4. Structure and diversity of scleractinia coral communities along the west seashore of Xuwen County

    Feng You; Xiubao Li; Jiansheng Lian; Yuyang Zhang; Hui Huang; Jianhui Yang; Xinming Lei; Chenglong Zhang

    2011-01-01

    We surveyed the community structure, species diversity and distribution of scleractinia coral off the shore of Xuwen County, Guangdong Province from May to June of 2008. A total of 57 species of scleractinia coral were documented from 25 sampling stations. Fewer than 30 species of coral were observed at any one station. The average Shannon-Wiener index of scleractinia coral diversity was 1.79 and the average Pielou index was 0.42. The dominant coral species within the study site were Goniopor...

  5. Effect of canopy density on litter invertebrate community structure in pine forests

    Brygadyrenko Viktor V.

    2016-01-01

    We investigated the structure of the litter invertebrate community in 141 pine (Pinus sylvestris Linnaeus, 1753) forest sites with five variants of canopy density (30-44, 45-59, 60-74, 75-89 and 90-100%) in the steppe zone of Ukraine. The total number of litter macrofauna specimens collected at each site decreased from an average of 84/100 trap-days in the sparsest stands (30-40% density) to 4-39 specimens/100 trap-days in the forests with a denser canopy. The number of macrofauna species cau...

  6. Community facilitation of problem structuring and decision making processes: Experiences from the EU LEADER+ programme

    Vidal, Rene Victor Valqui

    2009-01-01

    This paper reports on the work carried out supporting a rural community in Denmark under the LEADER+ programme. This is a programme that supports development in particularly vulnerable rural regions of the European countries members of EU. It supports creative and innovative projects that can...... making processes related to the agreement on action plans. Learning to design, plan, manage and facilitate conferences and workshops have also being another central activity. The main purpose of these conferences and workshops was not only problem structuring and decision making in connection with...

  7. Microgastrinae (Hymenoptera: Braconidae) in the Forest State of Artikutza (Navarra: Spain): Diversity and Community Structure

    Pérez-Rodríguez, Jesica; Oltra-Moscardó, Teresa; Peris-Felipo, Francisco Javier; Jiménez-Peydró, Ricardo

    2013-01-01

    Microgastrinae is one of the largest subfamilies of the Braconidae with about 2,000 described species worldwide. These wasps are of enormous ecological interest due to their role in controlling the caterpillar populations. This study analyses diversity and community structure within the Microgastrinae in the Artikutza Forest, located in the Peñas de Aia Natural Park, western Pyrenees, Spain. The specimens were collected in two different habitats: mixed forest and beech forest. A total of 524 specimens, belonging to nine separate genera and 27 species were captured. Alpha, beta and gamma diversity were analyzed. Additionally, the relationship between Microgastrinae phenology and climatic conditions were studied. PMID:26462432

  8. Microgastrinae (Hymenoptera: Braconidae in the Forest State of Artikutza (Navarra: Spain: Diversity and Community Structure

    Francisco Javier Peris-Felipo

    2013-09-01

    Full Text Available Microgastrinae is one of the largest subfamilies of the Braconidae with about 2,000 described species worldwide. These wasps are of enormous ecological interest due to their role in controlling the caterpillar populations. This study analyses diversity and community structure within the Microgastrinae in the Artikutza Forest, located in the Peñas de Aia Natural Park, western Pyrenees, Spain. The specimens were collected in two different habitats: mixed forest and beech forest. A total of 524 specimens, belonging to nine separate genera and 27 species were captured. Alpha, beta and gamma diversity were analyzed. Additionally, the relationship between Microgastrinae phenology and climatic conditions were studied.

  9. The structure and dynamics of a rhinolophid bat community of Latium (Central Italy) (Chiroptera)

    Pierangelo Crucitti; Marco Andreini; Roberto Morelli; Giovanni Rotella

    1998-01-01

    Abstract The present paper summarizes the results of 3 years of observation made at six month intervals for six months at a time (18 field surveys) in a man-made cave in Northern Latium (Central Italy) from April 1992 to April 1995. Its aim is to analyze the main structural and dynamic features of a bat community which hibernates at the shelter. Rhinolophus ferrumequinum and especially Rhinolophus euryale are the most abu...

  10. Host genetics is associated with the gut microbial community membership rather than the structure.

    Zhao, Peihua; Irwin, David M; Dong, Dong

    2016-04-26

    The issue of what factors shape the gut microbiota has been studied for years. However, questions on the contribution of host genetics to the colonizing process of the gut microbiota and to the extent that host genetics affect the gut microbiota have not yet been clearly answered. Most recently published reports have concluded that host genetics make a smaller contribution than other factors, such as diet, in determining the gut microbiota. Here we have exploited the increasing amount of fecal 16S rRNA gene sequencing data that are becoming available to conduct an analysis to assess the influence of host genetics on the diversity of the gut microbiota. By re-analyzing data obtained from over 5000 stool samples, representing individuals living on five continents and ranging in age from 3 days to 87 years, we found that the strength of the various factors affecting the membership or structure of the gut microbiota are quite different, which leads us to a hypothesis that the presence or absence of taxa is largely controlled by host genetics, whereas non-genetic factors regulate the abundance of each taxon. This hypothesis is supported by the finding that the genome similarity positively correlates with the similarity of community membership. Finally, we showed that only severe perturbations are able to alter the gut microbial community membership. In summary, our work provides new insights into understanding the complexities of the gut microbial community and how it responds to changes imposed on it. PMID:27033168

  11. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    Bougouffa, Salim

    2013-03-29

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

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

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

    2012-04-01

    Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  13. Zooplankton community structure in the Yellow Sea and East China Sea in autumn

    Hongju Chen

    2015-12-01

    Full Text Available Abstract Study on zooplankton spatial distribution is essential for understanding food web dynamics in marine ecosystems and fishery management. Here we elucidated the composition and distribution of large mesozooplankton on the continental shelf of the Yellow Sea and East China Sea, and explored the zooplankton community structure in these water masses. Sixty vertical hauls (bottom or 200 m in deep water to surface using a ring net (diameter 0.8 m, 505-μm mesh were exploited in November 2007. The biogeographic patterns of zooplankton communities were investigated using multivariate analysis methods; copepod biodiversity was analyzed using univariate indices. Copepods and protozoans were dominate in the communities. Based on the species composition, we divided the study areas into six station groups. Significant differences in zooplankton assemblages were detected between the Yellow Sea and East China Sea. Species richness was higher in East China Sea groups than those in Yellow Sea, whereas taxonomic distinctness was higher in Yellow Sea than in East China Sea. There was a clear relationship between the species composition and water mass group.

  14. Mosquito community structure in phytotelmata from a South American temperate wetland.

    Albicócco, Andrea Paola; Carbajo, Aníbal Eduardo; Vezzani, Darío

    2011-12-01

    Phytotelmata, or plant-held waters, are considered to be good model systems for the study of community ecology. The fauna of these natural container habitats, particularly the mosquitoes, have been extensively investigated in tropical regions, but there is little known about them in temperate South America. We assessed the structure of immature mosquito communities in leaf axils, tree holes, and bamboo stumps from a temperate wetland of Argentina. A total of 4,330 immature mosquitoes were collected among the 2,606 phytotelmata inspected. Leaf axils of eight plant species and tree holes were larval habitats for nine mosquito species belonging to the genus Culex, Wyeomyia, Isostomyia, and Toxorhynchites. The mosquito communities showed richness ranging from one to four species. Marked differences were detected in the plant specificity for the species collected. Some of them were exclusively found in one plant species (Isostomyia paranensis in Scirpus giganteus), whereas others were collected in up to five plant species but belonging to the same phytotelm class, the leaf axils. Those from tree holes are well-known dwellers of artificial containers and ground water habitats, such as Culex pipiens. Our results support the idea of low mosquito richness in phytotelmata from temperate regions in comparison with tropical areas, but the observed specificity patterns echo the findings of tropical forests. PMID:22129416

  15. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    Wei Hui

    2012-04-01

    Full Text Available Abstract Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera wood-chips and mown lawn grass clippings (85:15 in dry-weight and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  16. Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

    CHEN Yu-Qing; REN Guan-Ju; AN Shu-Qing; SUN Qing-Ye; LIU Chang-Hong; SHUANG Jing-Lei

    2008-01-01

    Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable otassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P < 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P < 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.

  17. Preliminary study of the mite community structure in different black truffle producing soils

    Mikel Queralt

    2014-08-01

    Full Text Available Aims of the study: The goals of this paper are to provide preliminary data on the composition of the mite community in truffle-producing soils (both wild and plantations; and to elucidate those species which may interact with the black truffle life cycle.Area of study: The study was carried out in two black truffle productive zones in Navarra (Spain, in four different plantations and five wild production areas.Material and Methods: Fauna was extracted using Berlese Tullgren funnels. Animals were separated into taxonomic groups, and mites were identified. To analyse the composition and community structure of the different habitats, parameters such as abundance, species richness, and Shanon Weiner diversity index (H’ were calculated.Main results: A total of 305 mites were recognized, belonging to 58 species representing the three major taxonomic groups (Oribatida, Prostigmata, Mesostigmata.Research highlights: The results show a possible trend towards wild areas having greater diversity and species richness than plantations. Furthermore, community analysis shows differences in species compositions among different study areas, and oribatid mites always exhibit the highest relative abundance and species richness.Keywords: Acari; Tuber melanosporum; Oribatida; Mesostigmata; Prostigmata; truffle orchards. 

  18. [Macrobenthic community structure of intertidal zone of Rushan Bay in spring].

    Ji, Ying-lu; Zhao, Ning; Wang, Zhen-zhong; Ji, Xiang-xing; Yang, Chuan-ping; Yu, Zi-shan

    2015-02-01

    Quantitative study on macrobenthos was carried out in 8 transects along intertidal zone of Rushan Bay in May, 2011. In total, 116 macrobenthic species were identified, among which 58 were polychaetes, 15 were mollusks, 27 were crustaceans, 3 were echinoderms and 13 were other groups. The average abundance and biomass of macrobenthos were 872.6 ind · m(-2) and 9.37 g · M(-2), respectively. By IRI index, Mediomastus sp., Helice sheni, Nemertinea and Neanthes sp. were ranked as the top 4 dominant species in the study area. Average Margalef's species richness diversity (d), Shannon diversity (H) and Pielou's evenness index (J) of macrobenthos were 2.119, 2.384 and 0.608, respectively, indicating slight pollution in the study area. Based on 30% similarity level, 8 transects could be grouped into 3 different communities. Compared with other intertidal zones in similar latitude, macrobenthos of Rushan Bay intertidal zone were characterized by higher species number, smaller body size and higher abundance. Besides the macrobenthic community structure and diversities, more exhaustive studies were needed to reveal the possible influence of shellfish culture on intertidal macrobenthic community. PMID:26094480

  19. Effect of long-term drainage of peatland on whole-profile microbial community structure

    Mpamah, Promise; Taipale, Sami; Rissanen, Antti; Biasi, Christina; Nykänen, Hannu

    2015-04-01

    Peatlands are crucial global carbon stores largely due to prevailing hydrological regime leading to higher rate of carbon input than loss. Like other changes in environmental conditions, alteration in peatland water table, which causes increased aeration in the upper layer, does not only cause a shift in this exchange rates, but leads to changes in plant species cover, litter quality as well as the niches of microbes, by affecting their functions and activities. Effects of changes in peatland hydrology are therefore complex, and play a key role in peat carbon cycles. Changed peat hydrology may especially affect the inter-play between methanogens and methanotrophs which are important members of the microbial community taking part in anaerobic/aerobic peatland carbon cycles. We provide more information on the effect of long-term (more than 33 years) changes in hydrology on the whole-peat-profile microbes, from top to bottom. We studied drained and adjacent non-drained peatlands in Lakkasuo mire complex and Lammi area of Finland, which differed in vegetation cover and management history. We focused majorly on the phospholipid fatty acids (PLFA) analysis as an indicator of the overall microbial community structure, but also used DNA analysis to mainly compare the methane oxidizing bacteria (MOB) of the different peatland types with different vegetation. Our PLFA results showed that peat mire complexes are more similar in their microbial community, within location and profiles than between locations irrespective of hydrological changes and types or vegetation covers. PLFA and DNA analysis also showed that MOB species belonging to type II were more dominant than those of type I in both locations studied. Our study also showed that long-term draining of peatlands does not change the biomass of soil microbial communities, but alters their structural or relative composition. The effect of long-term peatland drainage is mostly located at the surface. Depth gradient effects

  20. Concentration of petroleum-hydrocarbon contamination shapes fungal endophytic community structure in plant roots

    Guillaume eBourdel

    2016-05-01

    Full Text Available Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous patterns of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of

  1. The effects of climate variability on the structure of the phytoplankton community in Tumaco Bay, Colombia

    Honkala, Ingrid Garcia-Hansen

    2009-12-01

    Spatiotemporal variability in the diatom and dinoflagellate community structure and chlorophyll a (chl a) concentrations in Tumaco Bay during the 1993--2005 period was related clearly to seasonal and interannual variability in environmental conditions due to the migration of the Inter-tropical Convergence Zone (ITCZ) and the influence of El Nino Southern Oscillation (ENSO) events. A total of 134 species of diatoms that belong to 57 genera, and 78 species of dinoflagellates that belong to 25 genera were identified during the survey. The diatom community was the dominant group in the waters of the bay, being the most abundant with the greatest number of species observed. The most important species was the centric diatom Skeletonema costatum (Cleve 1878). It was found that the migration of the ITCZ on the region caused a strong annual cycle. With the migration of the ITCZ to the south, Northeasterly Trade Winds dominated the area from about December to April producing oceanic and coastal upwelling. Colder sea surface temperatures (SST), the rising of the thermocline and halocline to the surface, increased nutrients and abundant rainfall were detected. This time of the year was described as the rainy season (RS)/cold phase. Opposite conditions were observed the rest of the year, defined as the dry season (DS)/warm phase. Southeasterly Trade Winds dominated at this time of the year due to the migration of the ITCZ back to the north. This seasonal cycle was affected by interannual variability due to ENSO. Five El Nino and four La Nina events were identified. In general, La Nina episodes were characterized by a shallow thermocline, cold SST, higher salinities, and the highest concentrations of nutrients. Opposite characteristics were observed during El Nino events. However, during the highest precipitations observed in every El Nino event, nutrient concentrations increased significantly. Important environmental correlates of community structure were identified using

  2. The Effect of Nitrogen Deposition on Plant Performance and Community Structure: Is It Life Stage Specific?

    Tulloss, Elise M; Cadenasso, Mary L

    2016-01-01

    Nitrogen (N) deposition is a key global change factor that is increasing and affecting the structure and function of many ecosystems. To determine the influence of N deposition on specific systems, however, it is crucial to understand the temporal and spatial patterns of deposition as well as the response to that deposition. Response of the receiving plant communities may depend on the life stage-specific performance of individual species. We focus on the California oak savanna because N deposition to this system is complex-characterized by hotspots on the landscape and seasonal pulses. In a greenhouse experiment, we investigated the relative influence of N deposition on plant performance during early growth, peak biomass, and senescent life stages across different soil types, light, and community compositions. To represent the community we used three grass species-a native, naturalized exotic, and invasive exotic. At early growth and peak biomass stages performance was measured as height, and shoot and root biomass, and at the senescent stage as seed production. Simulated N deposition 1) increased shoot biomass and height of the native and, even more so, the naturalized exotic during early growth, 2) positively affected root biomass in all species during peak biomass, and 3) had no influence on seed production at the senescent stage. Alone, N deposition was not a strong driver of plant performance; however, small differences in performance among species in response to N deposition could affect community composition in future years. In particular, if there is a pulse of N deposition during the early growth stage, the naturalized exotic may have a competitive advantage that could result in its spread. Including spatial and temporal heterogeneity in a complex, manipulative experiment provides a clearer picture of not only where N management efforts should be targeted on the landscape, but also when. PMID:27253718

  3. Community structure of microorganisms associated with reddish-brown iron-rich snow.

    Kojima, Hisaya; Fukuhara, Haruo; Fukui, Manabu

    2009-09-01

    Reddish-brown colored snow, containing spherical brown particles, has been observed in several mires in Japan. In order to characterize this remarkable phenomenon, the microbial community and chemical species in snow were analyzed. A core sample of snow which had a colored region was investigated and it revealed vertical shifts in physicochemical characteristics and the microbial community structure. The abundance of particles peaked within the colored layer, and correlated with the amount of reducible Fe(III). The interstitial water of the colored layer was enriched with Fe(II), and characterized by reduced concentration of dissolved methane. The bacterial community in the colored region was characterized by higher relative abundance of iron-reducing bacteria and methanotrophs. Aggregates of the brown particles were found as precipitates in snow melt pools, and were subjected to cloning analyses targeting several different genes. The majority of bacterial 16S rRNA gene clones belonged to the class Betaproteobacteria or the phylum Bacteroidetes. No snow algae were detected in the eukaryotic small subunit rRNA gene clone library. As a possible carbon source to sustain the community in the snow, involvements of carbon dioxide and methane were investigated by analyzing the genes involved in their assimilation. In the analyses of genes for ribulose-1,5-biphosphate carboxylase/oxygenase, clones related to sulfur oxidizers were obtained. The analysis of particulate methane monooxygenase genes indicated dominance of Methylobacter species. These results emphasized the uniqueness of this phenomenon, and iron reducers of the genus Geobacter are suggested to be the key organisms that could be investigated in order to understand the mechanism of this phenomenon. PMID:19560891

  4. Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

    Daniel J Mayor

    Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

  5. The Impact of Host Rock Geochemistry on Bacterial Community Structure in Oligotrophic Cave Environments.

    Hazel A. Barton

    2007-07-01

    Full Text Available Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX. Our results suggest that on the chemically complex Yates Formation (sF88, the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1, despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88 reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.

  6. Black-tailed prairie dogs and the structure of avian communities on the shortgrass plains.

    Smith, Gregory A; Lomolino, Mark V

    2004-03-01

    We tested the hypothesis that black-tailed prairie dogs (Cynomys ludovicianus) influence avian community structure on the shortgrass prairie. We surveyed 36 prairie dog towns and 36 paired sites without prairie dogs during summer and fall of 1997, 1998, and 1999 in the Oklahoma Panhandle. Our surveys totaled 9,040 individual observations for 73 avian species. Significantly distinct avian communities were present on prairie dog towns when compared to sites within four different macrohabitats of the surrounding landscape: open rangeland, scrub/sandsage (Artemisia filifolia) habitats, Conservation Reserve Program (CRP) plots, and fallow crop fields. Relative densities of all bird species combined was higher on prairie dog towns versus paired sites in summer and fall. Mean species richness of birds was significantly higher on prairie dog towns than paired sites during summer, but there were no significant differences in fall. Open rangeland had the highest mean species richness in fall. Assemblages of avian communities differed significantly between prairie dog towns and the four macrohabitat types during summer. Burrowing owls (Athene cunicularia), killdeer (Charadrius vociferous), horned larks (Eremophila alpestris), and meadowlarks (Sturnella spp.) were positively and significantly associated with prairie dog towns during summer, while horned larks and ferruginous hawks (Buteo regalis) were significantly associated with prairie dog towns during fall. Even in their current remnant state, black-tailed prairie dogs continue to play a significant role in the assembly of ecological communities across the Great Plains. Conservation of prairie dogs goes well beyond a single species, and is an important strategy for the preservation of the prairie ecosystem as a whole. PMID:14685848

  7. Earthworm-mycorrhiza interactions can affect the diversity, structure and functioning of establishing model grassland communities.

    Johann G Zaller

    demonstrates that belowground-aboveground linkages involving earthworms and AMF are important mediators of the diversity, structure and functioning of plant communities.

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

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

    2016-01-01

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

  9. Plant community structure regulates responses of prairie soil respiration to decadal experimental warming.

    Xu, Xia; Shi, Zheng; Li, Dejun; Zhou, Xuhui; Sherry, Rebecca A; Luo, Yiqi

    2015-10-01

    Soil respiration is recognized to be influenced by temperature, moisture, and ecosystem production. However, little is known about how plant community structure regulates responses of soil respiration to climate change. Here, we used a 13-year field warming experiment to explore the mechanisms underlying plant community regulation on feedbacks of soil respiration to climate change in a tallgrass prairie in Oklahoma, USA. Infrared heaters were used to elevate temperature about 2 °C since November 1999. Annual clipping was used to mimic hay harvest. Our results showed that experimental warming significantly increased soil respiration approximately from 10% in the first 7 years (2000-2006) to 30% in the next 6 years (2007-2012). The two-stage warming stimulation of soil respiration was closely related to warming-induced increases in ecosystem production over the years. Moreover, we found that across the 13 years, warming-induced increases in soil respiration were positively affected by the proportion of aboveground net primary production (ANPP) contributed by C3 forbs. Functional composition of the plant community regulated warming-induced increases in soil respiration through the quantity and quality of organic matter inputs to soil and the amount of photosynthetic carbon (C) allocated belowground. Clipping, the interaction of clipping with warming, and warming-induced changes in soil temperature and moisture all had little effect on soil respiration over the years (all P > 0.05). Our results suggest that climate warming may drive an increase in soil respiration through altering composition of plant communities in grassland ecosystems. PMID:25846478

  10. Effect of cow slurry amendment on atrazine dissipation and bacterial community structure in an agricultural Andisol.

    Briceño, G; Jorquera, M A; Demanet, R; Mora, M L; Durán, N; Palma, G

    2010-06-15

    Atrazine is a commonly used herbicide for maize production in Chile, but it has recently been shown to be ineffective in soils that receive applications of cow slurries generated from the dairy industry. This effect may be caused either by the sorption of the pesticide to organic matter or more rapid degradation in slurry-amended soils. The objectives of this study were to evaluate the effects of cow slurry on atrazine dissipation, the formation of atrazine metabolites and the modification of bacterial community in Andisol. The cow slurry was applied at doses of 100,000-300,000 Lha(-1). After 4 weeks, atrazine was applied to the slurry-amended soils at concentrations of 1-3 mg kg(-1). The amounts of atrazine and its metabolites were determined by high performance liquid chromatography (HPLC). The soil microbial community was monitored by measurement of CO(2) evolution and changes in bacterial community using PCR-DGGE of 16S rRNA genes. The results show that cow slurry applications had no effect on atrazine dissipation, which had a half-life of 15-19 days. The atrazine metabolites were detected after 20 days and were significantly higher in soils amended with the slurry at both 20 and 40 days after application of the herbicide. Respiration rates were elevated after 10 days in all soils with atrazine addition. Both the atrazine and slurry amendments altered the bacterial community structures, indicated by the appearance of specific bands in the DGGE gels after 10 days. Cloning and sequencing of the 16S rRNA genes from the DGGE gels showed that the bands represented various genera of beta-proteobacteria that appeared in response to atrazine. According to our results, further field studies are required to explain the lower effectiveness of atrazine in weed control. These studies may include the effect of dissolved organic carbon on the atrazine mobility. PMID:20388570

  11. [Effects of Organic and Inorganic Slow-Release Compound Fertilizer on Different Soils Microbial Community Structure].

    Wang, Fei; Yuan, Ting; Gu, Shou-kuan; Wang, Zheng-yin

    2015-04-01

    As a new style fertilizer, slow-control release fertilizer had been an important subject in recent years, but few researches were about soil microbial community structure diversity. Phospholipid fatty acid method was used to determined the microbial community structure diversity of acid soil and slight alkaline soil applied with slow-release compound fertilizer (SRF), chemical fertilizer (CF) and common compound fertilizer (CCF) at the 10th, 30th, 60th and 90th day under the constant temperature incubation condition. Results indicated that various bacteria (i. e 13:0, i14:0,14:0, i15:0, a15:0, i16:0, 16:12OH, 16:1w5c,16:0, i17:0, a17:0, cy17:0, 17:02OH, i18:0, 18:0 and cy19:0w8c), two actinomycetes (10Me17:0 and 10Me18:0) and only one fungus (18:1 w9c) were detected in two soils after applying slow-release compound fertilizer and other fertilizers during the whole incubation period. SRF could significantly increase the fungi PLFA content by 8.3% and 6.8% at the early stage (the 10th day and 30th day) compared with CF, as well as significantly increase by 22.7% and 17.1% at the late stage (the 60th day and 90th day) compared with CCF in acid soil. SRF significantly increased bacteria, fungi and gram positive bacteria compared with CF and CCF in incubation period (except at the 30th day) in slight alkaline soil. SRF could significantly improve the ratio of normal saturated fatty acid and monounsaturated fatty acid at the 30th day and 90th days in acid soil compared with no fertilizer (CK), CF and CCF, while as to slight alkaline soil, SRF was significantly greater than that of CK, CF and CCF only at the 60th day. SRF could significantly decrease the ratio of iso PLFA and anteiso PLFA in acid soil (in 30-90 days) and slight alkaline soil (in 10-60 days). For two soils PLFA varieties, contents and ratios of microbial community, slow-release compound fertilizer increased soil microbial PLFA varieties and contents, and decreased the influence to microbial survival

  12. The importance of different spatial scales in determining structural and functional characteristics of deep-sea infauna communities

    J. Ingels

    2013-07-01

    Full Text Available The urge to understand spatial distributions of species and communities and their causative processes has continuously instigated the development and testing of conceptual models in spatial ecology. For the deep sea, there is evidence that structural and functional characteristics of benthic communities are regulated by a multitude of biotic and environmental processes that act in concert on different spatial scales, but the spatial patterns are poorly understood compared to those for terrestrial ecosystems. Deep-sea studies generally focus on very limited scale ranges, thereby impairing our understanding of which spatial scales and associated processes are most important in driving structural and functional diversity of communities. Here, we used an extensive integrated dataset of free-living nematodes from deep-sea sediments to unravel the importance of different spatial scales in determining benthic infauna communities. Multiple-factor multivariate permutational analyses were performed on different sets of community descriptors (structure, structural and functional diversity, standing stock. The different spatial scales investigated cover two margins in the northeast Atlantic, several submarine canyons/channel/slope areas, a bathymetrical range of 700–4300 m, different sampling locations at each station, and vertical sediment profiles. The results indicated that the most important spatial scale for structural and functional diversity and standing stock variability is the smallest one; infauna communities changed substantially more with differences between sediment depth layers than with differences associated to larger geographical or bathymetrical scales. Community structure differences were greatest between stations at both margins. Important regulating ecosystem processes and the scale on which they occur are discussed. The results imply that, if we are to improve our understanding of ecosystem patterns of deep-sea infauna and the

  13. Enhanced detectability of community structure in multilayer networks through layer aggregation

    Taylor, Dane; Stanley, Natalie; Mucha, Peter J

    2015-01-01

    Community detection is a central pursuit for understanding the structure and function of biological, social and technological networks, and it is important to understand the fundamental limitations on detectability. Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different--but potentially related--types of interactions. Using random matrix theory for stochastic block models, we analyze detectability limitations for multilayer networks and find that by aggregating together similar layers, it is possible to identify structure that is undetectable in a single layer. We explore this phenomenon for several aggregation methods including summation of the layers' adjacency matrices, for which detectability limit vanishes with increasing number of layers, L, decaying as O(L^{-1/2}). Interestingly, we find a similar scaling behavior when the summation is thresholded at an optimal value, supporting the common--but not well understood--practice of thresh...

  14. Structuring oil and gas joint ventures with aboriginal communities: conference papers conference

    The Insight Conference featured twelve articles on the following topics: 1 - researching and understanding your legal partners; II - an aboriginal game plan - a plan for success; III - legal and management issues relating to aboriginal ventures; IV - tax status of reserve-based aboriginal people and businesses under the Indian Act; v - first nations as exempt bodies under the Income Tax Act; V I - innovative options for structuring oil and gas leases and exploration permits on aboriginal lands; VII - joint venture and partnership arrangements; V III - the impact of taxation on aboriginal ventures; I X - bankruptcy and insolvency issues for on-reserve businesses; X - financing options for oil and gas ventures with first nations; XI - Syncrude's commitment to aboriginal development; and X II - structuring oil and gas ventures with aboriginal communities. Articles abstracted/indexed separately include: I, II, V I (2), V III, X, XI, and X II

  15. Species composition and community structure of subtropical forest stands in western himalayan foothills of kashmir

    Lesser Himalayan subtropical forests have unique species composition due to diverse climatic and topographic factors which create numerous microhabitats. Phytosociological characteristics, structural attributes and biological spectrum of plant communities in the forests of Himalayan foothills in Kashmir were analyzed. A total of 65 species belonging to 26 plant families were recorded constituting 6 plant communities. Average value of diversity recorded for the communities was 2.44; species richness 4.01; whereas evenness was found to be 0.48. The species data indicated random distribution of species with a hump shaped diversity pattern directly correlated with increasing altitude. Themeda anathera was the dominant species with an importance value percentage of 14.7 percentage followed by Pinus roxburghii (9.6 percentage), Mallotus philippenensis (5.2 percentage), Malvastrum coromandelianum (5.1 percentage), Acacia modesta (5 percentage), Olea ferruginea (3.8 percentage) and Oxalis corniculata (3.2 percentage). Vegetation was dominated by Therophytes (30 percentage) and megaphanerophytes (23.3) with dominant leaf spectrum as leptophylls (31.6 percentage). Thirty seven percent plants had medicinal values followed by 31 percentage having fodder values where as 12 percentage used as fuel. Principal component analyses and cluster analyses revealed the association of dominant species with specific sites due to prevailing environmental conditions. The distribution of species in ordination diagrams indicated a continuous change in species composition along the altitudinal gradient. Key stone tree species were subject to immense tree felling resulting in deteriorating changes in forest structure. Visual indicators showed over grazing at all the studied sites evident from the dominance of unpalatable species. Local forest stands demand immediate attention of policy makers as well as forest management so that local diversity and floristic richness could be conserved and

  16. Bryophyte species richness on retention aspens recovers in time but community structure does not.

    Anna Oldén

    Full Text Available Green-tree retention is a forest management method in which some living trees are left on a logged area. The aim is to offer 'lifeboats' to support species immediately after logging and to provide microhabitats during and after forest re-establishment. Several studies have shown immediate decline in bryophyte diversity after retention logging and thus questioned the effectiveness of this method, but longer term studies are lacking. Here we studied the epiphytic bryophytes on European aspen (Populus tremula L. retention trees along a 30-year chronosequence. We compared the bryophyte flora of 102 'retention aspens' on 14 differently aged retention sites with 102 'conservation aspens' on 14 differently aged conservation sites. We used a Bayesian community-level modelling approach to estimate the changes in bryophyte species richness, abundance (area covered and community structure during 30 years after logging. Using the fitted model, we estimated that two years after logging both species richness and abundance of bryophytes declined, but during the following 20-30 years both recovered to the level of conservation aspens. However, logging-induced changes in bryophyte community structure did not fully recover over the same time period. Liverwort species showed some or low potential to benefit from lifeboating and high potential to re-colonise as time since logging increases. Most moss species responded similarly, but two cushion-forming mosses benefited from the logging disturbance while several weft- or mat-forming mosses declined and did not re-colonise in 20-30 years. We conclude that retention trees do not function as equally effective lifeboats for all bryophyte species but are successful in providing suitable habitats for many species in the long-term. To be most effective, retention cuts should be located adjacent to conservation sites, which may function as sources of re-colonisation and support the populations of species that require old

  17. Diversity and structure of Chironomidae communities in relation to water quality differences in the Swartkops River

    Odume, O. N.; Muller, W. J.

    The Swartkops River is an important freshwater ecosystem in South Africa. But owing to its location, it suffers varying degrees of human induced impacts which include industrial and domestic effluent discharges, deforestation as well as agricultural land use which have negatively impacted on the water quality. Diversity and community composition of aquatic insects are frequently used to assess environmental water quality status. Chironomids occupy extremely varied biotopes. Their extraordinary ecological range and environmental sensitivity make them particularly useful for assessing and interpreting changes in water quality of aquatic ecosystems. The community structure of chironomid larvae was investigated at four sites in the Swartkops River and effects of different chemical and physical variables on their distribution were explored. Chironomid larvae were collected using the South African Scoring System version 5 (SASS5) protocol. A total of 26 taxa from four sampling sites in the Swartkops River were identified. Margalef’s species richness index, equitability, Shannon and Simpson diversity indices were highest at site 1 (reference site). The downstream sites contained 6-20 taxa compared to the 25 taxa at site 1. Site 1 was characterised by the subfamilies Orthocladiinae, Tanypodinae and the tribe Tanytarsini while the impacted sites were characterised by Orthocladiinae and Chironomini. Chironomus spp., Dirotendipes sp., Kiefferulus sp. and Tanypus sp. seemed to be tolerant to pollution, occurring in high abundance at sites 2, 3 and 4. In contrast, Polypedilum sp., Tanytarsus sp., Orthocladius sp., Cricotopus spp. and Ablabesmyia sp. appeared to be more sensitive taxa, being less common at the impacted sites (sites 2, 3 and 4). Five days biochemical oxygen demand, dissolved oxygen, electrical conductivity, orthophosphate-phosphorus and total inorganic nitrogen were among the important variables that determine the observed chironomid community structure

  18. Impact of heterogeneous activity and community structure on the evolutionary success of cooperators in social networks

    Wu, Zhi-Xi; Rong, Zhihai; Yang, Han-Xin

    2015-01-01

    Recent empirical studies suggest that heavy-tailed distributions of human activities are universal in real social dynamics [L. Muchnik, S. Pei, L. C. Parra, S. D. S. Reis, J. S. Andrade Jr., S. Havlin, and H. A. Makse, Sci. Rep. 3, 1783 (2013), 10.1038/srep01783]. On the other hand, community structure is ubiquitous in biological and social networks [M. E. J. Newman, Nat. Phys. 8, 25 (2012), 10.1038/nphys2162]. Motivated by these facts, we here consider the evolutionary prisoner's dilemma game taking place on top of a real social network to investigate how the community structure and the heterogeneity in activity of individuals affect the evolution of cooperation. In particular, we account for a variation of the birth-death process (which can also be regarded as a proportional imitation rule from a social point of view) for the strategy updating under both weak and strong selection (meaning the payoffs harvested from games contribute either slightly or heavily to the individuals' performance). By implementing comparative studies, where the players are selected either randomly or in terms of their actual activities to play games with their immediate neighbors, we figure out that heterogeneous activity benefits the emergence of collective cooperation in a harsh environment (the action for cooperation is costly) under strong selection, whereas it impairs the formation of altruism under weak selection. Moreover, we find that the abundance of communities in the social network can evidently foster the formation of cooperation under strong selection, in contrast to the games evolving on randomized counterparts. Our results are therefore helpful for us to better understand the evolution of cooperation in real social systems.

  19. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

    William P Inskeep

    Full Text Available The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site was obtained for five high-temperature (>65 degrees C chemotrophic microbial communities sampled from geothermal springs (or pools in Yellowstone National Park (YNP that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3 Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in

  20. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

    Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y.; Luo, J.; Carley, J.; Ginder-Vogel, M.; Gentry, T.J.; Gu, B.; Watson, D.; Jardine, P.M.; Marsh, T.L.; Tiedje, J.M.; Hazen, T.C.; Criddle, C.S.; Zhou, J.

    2010-02-15

    A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.