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Sample records for actinobacterial community structure

  1. Actinobacterial community dynamics in long term managed grasslands.

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  4. Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.

    Science.gov (United States)

    Hubin, Elizabeth A; Tabib-Salazar, Aline; Humphrey, Laurence J; Flack, Joshua E; Olinares, Paul Dominic B; Darst, Seth A; Campbell, Elizabeth A; Paget, Mark S

    2015-06-01

    Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential in Mycobacterium tuberculosis (Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that the Mtb RbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of the Mtb RbpA-SID in complex with domain 2 of the housekeeping σ-factor, σ(A). The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σ(A) as well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator.

  5. Structure of an Actinobacterial-Type [NiFe]-Hydrogenase Reveals Insight into O2-Tolerant H2 Oxidation.

    Science.gov (United States)

    Schäfer, Caspar; Bommer, Martin; Hennig, Sandra E; Jeoung, Jae-Hun; Dobbek, Holger; Lenz, Oliver

    2016-02-01

    A novel group of bacterial [NiFe]-hydrogenases is responsible for high-affinity H2 uptake from the troposphere, and is therefore thought to play an important role in the global H2 cycle. Here we present the first crystal structure at 2.85-Å resolution of such an actinobacterial-type hydrogenase (AH), which was isolated from the dihydrogen oxidizing bacterium, Ralstonia eutropha. The enzyme has a dimeric structure carrying two active [NiFe] sites that are interconnected by six [4Fe4S] clusters over a range of approximately 90 Å. Unlike most other [NiFe]-hydrogenases, the [4Fe4S] cluster proximal to the [NiFe] site is coordinated by three cysteines and one aspartate. Mutagenesis experiments revealed that this aspartate residue is related to the apparent O2 insensitivity of the AH. Our data provide first structural insight into specialized hydrogenases that are supposed to consume atmospheric H2 under challenging conditions, i.e. at high O2 concentration and wide temperature and pH ranges.

  6. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

    Science.gov (United States)

    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

  7. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions.

    Science.gov (United States)

    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

    Directory of Open Access Journals (Sweden)

    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. Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.

    Science.gov (United States)

    Valverde, Angel; Tuffin, Marla; Cowan, Don A

    2012-07-01

    Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  12. An evolving network model with community structure

    International Nuclear Information System (INIS)

    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

  13. Identifying Community Structures in Dynamic Networks

    CERN Document Server

    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.

  14. Enhancing community detection by local structural information

    CERN Document Server

    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.

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

    OpenAIRE

    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. Community Extraction in Multilayer Networks with Heterogeneous Community Structure

    CERN Document Server

    Wilson, James D; Bhamidi, Shankar; Nobel, Andrew B

    2016-01-01

    Multilayer networks are a useful way to capture and model multiple, binary relationships among a fixed group of objects. While community detection has proven to be a useful exploratory technique for the analysis of single-layer networks, the development of community detection methods for multilayer networks is still in its infancy. We propose and investigate a procedure, called Multilayer Extraction, that identifies densely connected vertex-layer sets in multilayer networks. Multilayer Extraction makes use of a significance based score that quantifies the connectivity of an observed vertex-layer set by comparison with a multilayer fixed degree random graph model. Unlike existing detection methods, Multilayer Extraction handles networks with heterogeneous layers where community structure may be different from layer to layer. The procedure is able to capture overlapping communities, and it identifies background vertex-layer pairs that do not belong to any community. We establish large-graph consistency of the v...

  17. Community structure in the phonological network

    Directory of Open Access Journals (Sweden)

    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.

  18. Using Community Structure for Complex Network Layout

    CERN Document Server

    Dürr, Oliver

    2012-01-01

    We present a new layout algorithm for complex networks that combines a multi-scale approach for community detection with a standard force-directed design. Since community detection is computationally cheap, we can exploit the multi-scale approach to generate network configurations with close-to-minimal energy very fast. As a further asset, we can use the knowledge of the community structure to facilitate the interpretation of large networks, for example the network defined by protein-protein interactions.

  19. Matching Community Structure Across Online Social Networks

    CERN Document Server

    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...

  20. Cultural, Transcriptomic, and Proteomic Analyses of Water-Stressed Cells of Actinobacterial Strains Isolated from Compost: Ecological Implications in the Fed-Batch Composting Process.

    Science.gov (United States)

    Narihiro, Takashi; Kanosue, Yuji; Hiraishi, Akira

    2016-06-25

    This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts. PMID:27246805

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Evaluating the effectiveness of marine actinobacterial extract and its mediated titanium dioxide nanoparticles in the degradation of azo dyes.

    Science.gov (United States)

    Priyaragini, S; Veena, S; Swetha, D; Karthik, L; Kumar, G; Bhaskara Rao, K V

    2014-04-01

    Aim of the present study was to synthesize titanium dioxide nanoparticles (TiO2 NPs) from marine actinobacteria and to develop an eco-friendly azo-dye degradation method. A total of five actinobacterial isolates were isolated from Chennai marine sediments, Tamilnadu, India and analyzed for the synthesis of TiO2 NPs using titanium hydroxide. Among these, the isolate PSV 3 showed positive results for the synthesis of TiO2 NPs, which was confirmed by UV analysis. Further characterization of the synthesized TiO2 NPs was done using XRD, AFM and FT-IR analysis. Actinobacterial crude extract and synthesized TiO2 NPs was found efficient in degrading azo dye such as Acid Red 79 (AR-79) and Acid Red 80 (AR-80). Degradation percentage was found to be 81% for AR-79, 83% for AR-80 using actinobacterial crude extract and 84% for AR-79, 85% for AR-80 using TiO2 NPs. Immobilized actinobacterial cells showed 88% for AR-79 and 81% for AR-80, dye degrading capacity. Degraded components were characterized by FT-IR and GC-MS analysis. The phytotoxicity test with 500 μg/mL of untreated dye showed remarkable phenotypic as well as cellular damage to Tagetes erecta plant. Comparatively no such damage was observed on plants by degraded dye components. In biotoxicity assay, treated dyes showed less toxic effect as compared to the untreated dyes.

  3. Hierarchical community structure in complex (social) networks

    CERN Document Server

    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.

  4. Centrality measures for networks with community structure

    Science.gov (United States)

    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.

  5. Impact of Community Structure on Cascades

    OpenAIRE

    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...

  6. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

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

    2009-01-01

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic co...... into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world....

  7. Finding Community Structures In Social Activity Data

    KAUST Repository

    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

  8. Shifting Niches for Community Structure Detection

    DEFF Research Database (Denmark)

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

    2013-01-01

    We present a new evolutionary algorithm for com- munity structure detection in both undirected and unweighted (sparse) graphs and fully connected weighted digraphs (complete networks). Previous investigations have found that, although evolutionary computation can identify community structure...... 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...... experimentally compare the new algorithm to the well-known algorithms of Pizzuti and Tasgin, and find that we outperform those algorithms for sparse graphs under some conditions, and drastically outperform them on complete networks under all tested conditions....

  9. Emergent Community Structure in Social Tagging Systems

    CERN Document Server

    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.

  10. Modelling community structure in freshwater ecosystems

    NARCIS (Netherlands)

    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. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.;

    2011-01-01

    Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation in the dete...

  12. Emergence of structured communities through evolutionary dynamics.

    Science.gov (United States)

    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

  13. Emergence of structured communities through evolutionary dynamics.

    Science.gov (United States)

    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.

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

    CERN Document Server

    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...

  15. Distance, dissimilarity index, and network community structure

    CERN Document Server

    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.

  16. Walk modularity and community structure in networks

    CERN Document Server

    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.

  17. Identifying community structure in complex networks

    Science.gov (United States)

    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.

  18. Taxonomies of networks from community structure

    Science.gov (United States)

    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.

  19. Characterisation of the first actinobacterial group isolated from a Mexican extremophile environment.

    Science.gov (United States)

    Quintana, Erika T; Badillo, Ricardo Flores; Maldonado, Luis A

    2013-07-01

    The "Cave of Crystals" (aka 'Naica') in Chihuahua Mexico is a natural unique subterranean ecosystem which mainly consists of crystals made of calcium sulfate. The main system of caves are found at a depth of 300 meters (m) below sea level with crystals that range in size from a few centimeters to 15 m. The crystals date from nearly 400,000 years old and are thought to be formed when the cave was fully covered by water. At present time, this place shows a nearly constant temperature of 55 °C over the year and a humidity of 100 % which makes this place incomparable and unbearable to animal and/or human life. In the present study, two actinobacterial groups were isolated from within this system of caves and subjected to a systematic study to establish their phylogenetic relationship to microorganisms belonging to this vast group of Gram positive bacteria. Phenotypic properties, chemotaxonomic and 16S rRNA gene sequencing show that the microorganisms are members of the family Pseudonocardiaceae and are most closely related to the genus Prauserella. The present study is the first to report the isolation and presence of Actinobacteria or any other microbial form of life in this exceptional place. Moreover, this unexpected biodiversity can also provide an insight of the antibiotic resistome present in the isolates reported in this study.

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

    Science.gov (United States)

    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. Community Structure in Congressional Cosponsorship Networks

    CERN Document Server

    Zhang, Yan; Traud, Amanda L; Porter, Mason A; Fowler, James H; Mucha, Peter J

    2007-01-01

    We study the United States Congress by constructing networks between Members of Congress based on the legislation that they cosponsor. Using the concept of modularity, we identify the community structure of Congressmen, as connected via sponsorship/cosponsorship of the same legislation, to investigate the collaborative communities of legislators in both chambers of Congress. This analysis yields an explicit and conceptually clear measure of political polarization, demonstrating a sharp increase in partisan polarization which preceded and then culminated in the 104th Congress (1995-1996), when Republicans took control of both chambers. Although polarization has since waned in the U.S. Senate, it remains at historically high levels in the House of Representatives.

  2. Immunization of networks with community structure

    International Nuclear Information System (INIS)

    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.

  3. Information transfer in community structured multiplex networks

    CERN Document Server

    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 ...

  4. Community structure in introductory physics course networks

    CERN Document Server

    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.

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

    Science.gov (United States)

    Chertoprud, M V

    2007-01-01

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

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

    Science.gov (United States)

    Crowe, Jessica

    2010-01-01

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

  7. Permanence and Community Structure in Complex Networks

    CERN Document Server

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

    Digital Repository Service at National Institute of Oceanography (India)

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

    Diatoms, which are early autotrophic colonisers, are an important constituent of the biofouling community in the marine environment. The effects of substratum and temporal variations on the fouling diatom community structure in a monsooninfluenced...

  9. Community Structure in Online Collegiate Social Networks

    Science.gov (United States)

    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.

  10. Bipartite Community Structure of eQTLs.

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Marcel Salathé

    2010-04-01

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

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

    Science.gov (United States)

    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.

  13. Feature Analysis and Modeling of the Network Community Structure

    Institute of Scientific and Technical Information of China (English)

    袁超; 柴毅; 魏善碧

    2012-01-01

    Community structure has an important influence on the structural and dynamic characteristics of the complex systems.So it has attracted a large number of researchers.However,due to its complexity,the mechanism of action of the community structure is still not clear to this day.In this paper,some features of the community structure have been discussed.And a constraint model of the community has been deduced.This model is effective to identify the communities.And especially,it is effective to identify the overlapping nodes between the communities.Then a community detection algorithm,which has linear time complexity,is proposed based on this constraint model,a proposed node similarity model and the Modularity Q.Through some experiments on a series of real-world and synthetic networks,the high performances of the algorithm and the constraint model have been illustrated.

  14. Growing networks of overlapping communities with internal structure.

    Science.gov (United States)

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

    2016-08-01

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

  15. Growing networks of overlapping communities with internal structure

    Science.gov (United States)

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

    2016-08-01

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

  16. Detect overlapping and hierarchical community structure in networks

    CERN Document Server

    Shen, Huawei; Cai, Kai; Hu, Mao-Bin

    2008-01-01

    Clustering and community structure is crucial for many network systems and the related dynamic processes. It has been shown that communities are usually overlapping and hierarchical. However, previous methods investigate these two properties of community structure separately. This paper propose an algorithm (EAGLE) to detect both the overlapping and hierarchical properties of complex community structure together. This algorithm deals with the set of maximal cliques and adopts an agglomerative framework. The quality function of modularity is extended to evaluate the goodness of a cover. The examples of application to real world networks give excellent results.

  17. A Social Network Model Exhibiting Tunable Overlapping Community Structure

    NARCIS (Netherlands)

    Liu, D.; Blenn, N.; Van Mieghem, P.F.A.

    2012-01-01

    Social networks, as well as many other real-world networks, exhibit overlapping community structure. In this paper, we present formulas which facilitate the computation for characterizing the overlapping community structure of networks. A hypergraph representation of networks with overlapping commun

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

    NARCIS (Netherlands)

    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

  19. Investigating Effects of Invasive Species on Plant Community Structure

    Science.gov (United States)

    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…

  20. Community Structural Instability, Anomie, Imitation and Adolescent Suicidal Behavior

    Science.gov (United States)

    Thorlindsson, Thorolfur; Bernburg, Jon Gunnar

    2009-01-01

    The current study examines the contextual effects of community structural characteristics, as well as the mediating role of key social mechanisms, on youth suicidal behavior in Iceland. We argue that the contextual influence of community structural instability on youth suicidal behavior should be mediated by weak attachment to social norms and…

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

    DEFF Research Database (Denmark)

    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....

  2. Community Structure Detection Algorithm Based on the Node Belonging Degree

    Directory of Open Access Journals (Sweden)

    Jian Li

    2013-07-01

    Full Text Available In this paper, we propose a novel algorithm to identify communities in complex networks based on the node belonging degree. First, we give the concept of the node belonging degree, and then determine whether a node belongs to a community or not according to the belonging degree of the node with respect to the community. The experiment results of three real-world networks: a network with three communities with 19 nodes, Zachary Karate Club and network of American college football teams show that the proposed algorithm has satisfactory community structure detection.  

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Jia Hou Chin

    Full Text Available 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.

  5. A stochastic model for detecting overlapping and hierarchical community structure.

    Directory of Open Access Journals (Sweden)

    Xiaochun Cao

    Full Text Available Community detection is a fundamental problem in the analysis of complex networks. Recently, many researchers have concentrated on the detection of overlapping communities, where a vertex may belong to more than one community. However, most current methods require the number (or the size of the communities as a priori information, which is usually unavailable in real-world networks. Thus, a practical algorithm should not only find the overlapping community structure, but also automatically determine the number of communities. Furthermore, it is preferable if this method is able to reveal the hierarchical structure of networks as well. In this work, we firstly propose a generative model that employs a nonnegative matrix factorization (NMF formulization with a l(2,1 norm regularization term, balanced by a resolution parameter. The NMF has the nature that provides overlapping community structure by assigning soft membership variables to each vertex; the l(2,1 regularization term is a technique of group sparsity which can automatically determine the number of communities by penalizing too many nonempty communities; and hence the resolution parameter enables us to explore the hierarchical structure of networks. Thereafter, we derive the multiplicative update rule to learn the model parameters, and offer the proof of its correctness. Finally, we test our approach on a variety of synthetic and real-world networks, and compare it with some state-of-the-art algorithms. The results validate the superior performance of our new method.

  6. Community structure in traffic zones based on travel demand

    Science.gov (United States)

    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.

  7. Virality Prediction and Community Structure in Social Networks

    Science.gov (United States)

    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.

  8. Modeling community structure and topics in dynamic text networks

    CERN Document Server

    Henry, Teague; Chai, Christine; Owens-Oas, Derek

    2016-01-01

    The last decade has seen great progress in both dynamic network modeling and topic modeling. This paper draws upon both areas to create a Bayesian method that allows topic discovery to inform the latent network model and the network structure to facilitate topic identification. We apply this method to the 467 top political blogs of 2012. Our results find complex community structure within this set of blogs, where community membership depends strongly upon the set of topics in which the blogger is interested.

  9. Community detection using global and local structural information

    Indian Academy of Sciences (India)

    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.

  10. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    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

  11. Measuring robustness of community structure in complex networks

    CERN Document Server

    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.

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Science.gov (United States)

    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

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

    CERN Document Server

    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.

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

    CERN Document Server

    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...

  16. Community structures and role detection in music networks

    Science.gov (United States)

    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.

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

    CERN Document Server

    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...

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

    Directory of Open Access Journals (Sweden)

    Michaela Aschan

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

  19. Structure of an Anuran community in a Mediterranean area

    OpenAIRE

    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...

  20. Experimental sulfate amendment alters peatland bacterial community structure.

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2006-04-01

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

  2. Structural diversity of forest communities on Baihuashan Mountain,Beijing

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The structural diversity of forests on Baihuashan Mountain,Beijing,was surveyed by a plotless method combined with branch and leaf coverage estimation in the different layers.New structural indices were constructed,calculated and compared among different communities.On the basis of previous work,structural diversity of forest communities at the stand level was described by a vertical complexity index and a horizontal heterogeneity index.From a correlational analysis among the new indices and other commonly used biodiversity indices,we concluded that the new indices are closely related to a tree height inequality index and the Shannon-Wiener index of the tree and shrub layer,which indicated that the new indices were good at indicating structural diversity in the different forests on Baihuashan Mountain.The results show that,in natural forests,structural diversity of pioneer communities is much lower than in late successive communities.In plantations,structural diversity is determined by the stage of development and tree species.Tending would increase horizontal heterogeneity and decrease vertical complexity.

  3. Quantum Probabilistic Structures in Competing Lizard Communities

    CERN Document Server

    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...

  4. Community structure changes of macrobenthos in the South Yellow Sea

    Institute of Scientific and Technical Information of China (English)

    ZHANG Junlong; XU Fengshan; LIU Ruiyu

    2012-01-01

    The ecological environment in the Yellow Sea has changed greatly from the 1950s to 1990s and this has had significant impact on marine organisms.In this study,data on soft-sediment macrobenthos occurring in depths from 25 m to 81 m in the South Yellow Sea were used to compare changes in community structure.The agglomerative classification (CLUSTER) and multidimensional scaling (MDS) methods were applied.Five communities were recognized by cluster analysis:1.The Yellow Sea Cold Water Mass community dominated by cold water species,which changed slightly in species composition since the 1950s; 2.The mixed community with the coexistence of cold water species and warm water species,as had been reported previously; 3.The polychaete-dominated eurythermal community in which the composition changed considerably as some dominant species disappeared or decreased; 4.The Changjiang (Yangtze) River Estuarine community,with some typical estuarine species; 5.The community affected by the Yellow Sea Warm Current.The greatest change occurred in the coastal area,which indicated that the change may be caused by human activities.Macrobenthos in the central region remained almost unchanged,particularly the cold water species shielded by the Yellow Sea Cold Water Mass.The depth,temperature and median grain size of sediments were important factors affecting the distributions of macrobenthos in the South Yellow Sea.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone.

    Science.gov (United States)

    Tang, Hui; Shi, Xunxun; Wang, Xiaofei; Hao, Huanhuan; Zhang, Xiu-Min; Zhang, Li-Ping

    2016-01-01

    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°C 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. PMID:27047461

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

    Science.gov (United States)

    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

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

    NARCIS (Netherlands)

    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

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

    Science.gov (United States)

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

    2005-05-01

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

  10. Relating methanogen community structure and anaerobic digester function.

    Science.gov (United States)

    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

  11. The corporate elite community structure of global capitalism

    NARCIS (Netherlands)

    E.M. Heemskerk; F.W. Takes

    2015-01-01

    A key debate on the merits and consequences of globalisation asks to what extent we have moved to a multipolar global political economy. Here we investigate this issue through the properties and topologies of corporate elite networks and ask: what is the community structure of the global corporate e

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

    Science.gov (United States)

    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…

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  16. A framework for solving ill-structured community problems

    Science.gov (United States)

    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.

  17. Changes in soil bacterial community structure with increasing disturbance frequency.

    Science.gov (United States)

    Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

    2013-07-01

    Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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...

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

    CERN Document Server

    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...

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

    Science.gov (United States)

    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.

  2. Systems modeling approaches for microbial community studies: From metagenomics to inference of the community structure

    Directory of Open Access Journals (Sweden)

    Mark eHanemaaijer

    2015-03-01

    Full Text Available Microbial communities play important roles in health, industrial applications and earth's ecosystems. With current molecular techniques we can characterize these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the genetic properties and the dynamic couplings between individual microorganisms give rise to their dynamic activities. Neither do they give insight into what we call `the community state', that is the fluxes and concentrations of nutrients within the community. This knowledge is a prerequisite for rational control and intervention in microbial communities. Therefore, the inference of the community structure from experimental data is a major current challenge. We will argue that this inference problem requires mathematical models that can integrate heterogeneous experimental data with existing knowledge. We propose that two types of models are needed. Firstly, mathematical models that integrate existing genomic, physiological, and physicochemical information with metagenomics data so as to maximize information content and predictive power. This can be achieved with the use of constraint-based genome-scale stoichiometric modeling of community metabolism which is ideally suited for this purpose. Next, we propose a simpler coarse-grained model, which is tailored to solve the inference problem from the experimental data. This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators. The simpler inference models are, in our opinion, key to understanding microbial ecosystems, yet until now, have received remarkably little attention. This has led to the situation where the modeling of microbial communities, using only genome-scale models is currently more a computational, theoretical exercise than a method useful to the experimentalist.

  3. Trophic and individual efficiencies of size-structured communities

    DEFF Research Database (Denmark)

    Andersen, Ken Haste; Beyer, Jan; Lundberg, P.

    2009-01-01

    Individual and trophic efficiencies of size-structured communities are derived from mechanistically based principles at the individual level. The derivations are relevant for communities with a size-based trophic structure, i.e. where trophic level is strongly correlated with individual size...... as in many aquatic systems. The derivations are used to link Lindeman's trophic theory and trophic theory based on average individuals with explicit individual-level size spectrum theory. The trophic efficiency based on the transfer of mass between trophic levels through predator-prey interactions...... is demonstrated to be valid only when somatic growth can be ignored. Taking somatic growth into account yields an average individual growth efficiency that is smaller than the trophic efficiency....

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

    CERN Document Server

    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...

  5. Comparison and validation of community structures in complex networks

    Science.gov (United States)

    Gustafsson, Mika; Hörnquist, Michael; Lombardi, Anna

    2006-07-01

    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 believed to be 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 features and drawbacks. Further, we compare different partitions by applying some graph-theoretic concepts of distance, which indicate that one of the quality measures of the degree of modularity corresponds quite well with the distance from the true partition. Finally, we introduce a way to validate the partitionings with respect to external data when the nodes are classified but the network structure is unknown. This is here possible since we know everything of the computer generated networks, as well as the historical answer to how the karate club and the football teams are partitioned in reality. The partitioning of the gene network is validated by use of the Gene Ontology database, where we show that a community in general corresponds to a biological process.

  6. Phytoplankton community structure and its succession in Dianshan Lake

    OpenAIRE

    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...

  7. Resource variation and the structure of British bird communities

    OpenAIRE

    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...

  8. Comparison and validation of community structures in complex networks

    CERN Document Server

    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...

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

    Science.gov (United States)

    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

  10. Bacterial community structure in aquifers corresponds to stratigraphy

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  12. Microbial community structure in the rhizosphere of rice plants

    Directory of Open Access Journals (Sweden)

    Björn eBreidenbach

    2016-01-01

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

  13. Competition for space and the structure of ecological communities

    CERN Document Server

    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...

  14. Improved community structure detection using a modified fine tuning strategy

    CERN Document Server

    Sun, Yudong; Josic, Kresimir; Bassler, Kevin E

    2009-01-01

    The community structure of a complex network can be determined by finding the partitioning of its nodes that maximizes modularity. Many of the proposed algorithms for doing this work by recursively bisecting the network. We show that this unduely constrains their results, leading to a bias in the size of the communities they find and limiting their effectivness. To solve this problem, we propose adding a step to the existing algorithms that does not increase the order of their computational complexity. We show that, if this step is combined with a commonly used method, the identified constraint and resulting bias are removed, and its ability to find the optimal partitioning is improved. The effectiveness of this combined algorithm is also demonstrated by using it on real-world example networks. For a number of these examples, it achieves the best results of any known algorithm.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kardol, Paul [ORNL; Reynolds, W. Nicholas [University of Tennessee, Knoxville (UTK); Norby, Richard J [ORNL; Classen, Aimee T [University of Tennessee, Knoxville (UTK)

    2011-01-01

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

  16. Distributional shifts in size structure of phytoplankton community

    Science.gov (United States)

    Waga, H.; Hirawake, T.; Fujiwara, A.; Nishino, S.; Kikuchi, T.; Suzuki, K.; Takao, S.

    2015-12-01

    Increased understanding on how marine species shift their distribution is required for effective conservation of fishery resources under climate change. Previous studies have often predicted distributional shifts of fish using satellite derived sea surface temperature (SST). However, SST may not fully represent the changes in species distribution through food web structure and as such this remains an open issue due to lack of ecological perspective on energy transfer process in the earlier studies. One of the most important factors in ecosystem is composition of phytoplankton community, and its size structure determines energy flow efficiency from base to higher trophic levels. To elucidate spatiotemporal variation in phytoplankton size structure, chlorophyll-a size distribution (CSD) algorithm was developed using spectral variance of phytoplankton absorption coefficient through principal component analysis. Slope of CSD (CSD slope) indicates size structure of phytoplankton community where, strong and weak magnitudes of CSD slope indicate smaller and larger phytoplankton structure, respectively. Shifts in CSD slope and SST were derived as the ratio of temporal trend over the 12-year period (2003-2014) to 2-dimensional spatial gradient and the resulting global median velocity of CSD slope and SST were 0.361 and 0.733 km year-1, respectively. In addition, the velocity of CSD slope monotonically increases with increasing latitude, while relatively complex latitudinal pattern for SST emerged. Moreover, angle of shifts suggest that species are required to shift their distribution toward not limited to simple pole-ward migration, and some regions exhibit opposite direction between the velocity of CSD slope and SST. These findings further imply that combined phytoplankton size structure and SST may contribute for more accurate prediction of species distribution shifts relative to existing studies which only considering variations in thermal niches.

  17. The Evolution of Community Structure in a Coauthorship Network

    Directory of Open Access Journals (Sweden)

    William Mcdowell

    2011-12-01

    Full Text Available Mechanisms such as triadic closure and preferential attachment drive the evolution of social networks. Many models use these mechanisms to predict future links, and they generate realistic networks with scale-free degree distributions. These social networks also have community structure, or sets of vertices which are more connected to each other than the rest of the network. To study the evolution of research groups of scientists in a coauthorship network, we use a timeheterarchy representation to extend the mechanisms driving the evolution of the network to the level of this community structure. Specifically, we examine changes in the structure of groups in terms of mechanisms analogous to triadic closure and preferential attachment, and as a result, we find that the network evolves in the same way at the group-level and the individual-level. In addition, we find that interactions at the group-level might affect interactions at the individual-level in that members of a single group are more likely to strengthen their relationships than members of separate groups.

  18. Interlinking backscatter, grain size and benthic community structure

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  20. Analysis of community structure in networks of correlated data

    Energy Technology Data Exchange (ETDEWEB)

    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).

  1. Trophic structure and community stability in an overfished ecosystem

    KAUST Repository

    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.

  2. Comparison of adult mosquito community structure on various habitats

    Institute of Scientific and Technical Information of China (English)

    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).

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  5. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    Science.gov (United States)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (Pconservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  6. Perspectives on the Gender-Integrated Gay Community: Its Formal Structure and Social Functions

    Science.gov (United States)

    Fein, Sara Beck; Nuehring, Elane M.

    1975-01-01

    A gender-integrated homosexual community is described. Male and female members are compared as to participation in the community's formal organizational structure as well as in relation to several functions of that community. The integrated community differed in a number of dimensions from exclusively male and exclusively female homosexual…

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

    CERN Document Server

    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...

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

    OpenAIRE

    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...

  9. Network community structure alterations in adult schizophrenia: identification and localization of alterations.

    Science.gov (United States)

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

    A growing body of literature suggests functional connectivity alterations in schizophrenia. While findings have been mixed, evidence points towards a complex pattern of hyper-connectivity and hypo-connectivity. This altered connectivity can be represented and analyzed using the mathematical frameworks provided by graph and information theory to represent functional connectivity data as graphs comprised of nodes and edges linking the nodes. One analytic technique in this framework is the determination and analysis of network community structure, which is the grouping of nodes into linked communities or modules. This data-driven technique finds a best-fit structure such that nodes in a given community have greater connectivity with nodes in their community than with nodes in other communities. These community structure representations have been found to recapitulate known neural-systems in healthy individuals, have been used to identify novel functional systems, and have identified and localized community structure alterations in a childhood onset schizophrenia cohort. In the present study, we sought to determine whether community structure alterations were present in an adult onset schizophrenia cohort while stringently controlling for sources of imaging artifacts. Group level average graphs in healthy controls and individuals with schizophrenia exhibited visually similar network community structures and high amounts of normalized mutual information (NMI). However, testing of individual subject community structures identified small but significant alterations in community structure with alterations being driven by changes in node community membership in the somatosensory, auditory, default mode, salience, and subcortical networks.

  10. Community structure and composition of the Cambrian Chengjiang biota

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Science.gov (United States)

    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.

  12. Generalized method for finding community structures in networks

    CERN Document Server

    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...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  15. Measuring and Modeling Bipartite Graphs with Community Structure

    CERN Document Server

    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.

  16. Effect of power plant emissions on plant community structure

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    CERN Document Server

    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.

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

    OpenAIRE

    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 ...

  19. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

    Science.gov (United States)

    de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

    2016-01-01

    The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  20. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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)....

  4. Community structure of zooplankton in the main entrance of Bahia Magdalena, Mexico during 1996

    OpenAIRE

    Gómez Gutiérrez, Jaime; Palomares García, José Ricardo; Hernández Trujillo, Sergio; Carballido Carranza, Azucena

    2001-01-01

    The zooplankton community structure, including copepods, euphausiids, chaetognaths, and decapod larvae, was monitored during six circadian cycles using Bongo net (500 *m mesh net) samples from Bahía Magdalena, on the southwest coast of Baja California, México. Samples were obtained during three oceanographic surveys (March, July, and December 1996) to describe the changes in the zooplankton community structure throughout the main mouth of Bahía Magdalena. The zooplankton community structure s...

  5. Community structure discovery method based on the Gaussian kernel similarity matrix

    Science.gov (United States)

    Guo, Chonghui; Zhao, Haipeng

    2012-03-01

    Community structure discovery in complex networks is a popular issue, and overlapping community structure discovery in academic research has become one of the hot spots. Based on the Gaussian kernel similarity matrix and spectral bisection, this paper proposes a new community structure discovery method. First, by adjusting the Gaussian kernel parameter to change the scale of similarity, we can find the corresponding non-overlapping community structure when the value of the modularity is the largest relatively. Second, the changes of the Gaussian kernel parameter would lead to the unstable nodes jumping off, so with a slight change in method of non-overlapping community discovery, we can find the overlapping community nodes. Finally, synthetic data, karate club and political books datasets are used to test the proposed method, comparing with some other community discovery methods, to demonstrate the feasibility and effectiveness of this method.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    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

  8. Microbial Community Structure of Casing Soil During Mushroom Growth

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Microbial community structure in the rhizosphere of rice plants

    OpenAIRE

    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...

  11. Microbial Community Structure in the Rhizosphere of Rice Plants

    OpenAIRE

    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...

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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…

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

    NARCIS (Netherlands)

    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

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

    NARCIS (Netherlands)

    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

  16. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.;

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across t...

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

    Science.gov (United States)

    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…

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

    Directory of Open Access Journals (Sweden)

    Jana S Petermann

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  20. Supraglacial bacterial community structures vary across the Greenland ice sheet.

    Science.gov (United States)

    Cameron, Karen A; Stibal, Marek; Zarsky, Jakub D; Gözdereliler, Erkin; Schostag, Morten; Jacobsen, Carsten S

    2016-02-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community dissimilarities (2.3% of total variability calculated). The majority of dissimilarities found between cryoconite 16S rRNA gene amplicons from DNA and RNA was calculated to be the result of changes in three taxa, Pseudanabaenaceae, Sphingobacteriaceae and WPS-2, which together contributed towards 80.8 ± 12.6% of dissimilarities between samples. Bacterial communities across the GrIS are spatially variable active communities that are likely influenced by localized biological inputs and physicochemical conditions.

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

    DEFF Research Database (Denmark)

    Lessard, Jean-Philippe; Borregaard, Michael Krabbe; Fordyce, James A.;

    2012-01-01

    of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution......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 the definition of the source pool influences interpretations of patterns of community structure. We use...

  2. Light structures phototroph, bacterial and fungal communities at the soil surface.

    Directory of Open Access Journals (Sweden)

    Lawrence O Davies

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

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

    Digital Repository Service at National Institute of Oceanography (India)

    Raveendran, T.V.; Harada, E.

    was generally observed on the subsurface panels. Significant depth wise variation in abundance seems to be the result of predation, competition and the effect of residents on recruits. Succession in the community was divided into three stages by dendrogram...

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

    Data.gov (United States)

    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...

  5. Assembly and phylogenetic structure of Neotropical palm communities

    DEFF Research Database (Denmark)

    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...

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

    OpenAIRE

    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 ...

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  11. Structure and function of fish communities in the southern Lake Michigan basin with emphasis on restoration of native fish communities

    Science.gov (United States)

    Simon, Thomas P.; Stewart, Paul M.

    1999-01-01

    The southern Lake Michigan basin in northwest Indiana possesses a variety of aquatic habitats including riverine, palustrine, and lacustrine systems. The watershed draining this area is a remnant of glacial Lake Chicago and supports fish communities that are typically low in species richness. Composition of the presettlement Lake Michigan fish community near the Indiana Dunes has been difficult to reconstruct. Existing data indicate that the number of native species in the Lake Michigan watershed, including nearshore Lake Michigan, has declined by 22% since the onset of European settlement. Few remnants of natural fish communities exist, and those occur principally in the ponds of Miller Woods, the Grand Calumet Lagoons, and the Little Calumet River. These communities have maintained a relatively diverse assemblage of fishes despite large-scale anthropogenic disturbances in the area, including channelization, massive river redirection, fragmentation, habitat alteration, exotic species invasions, and the introduction of toxic chemicals. Data that we collected from 1985 to 1996 suggested that the Grand Calumet River has the highest proportion of exotic fish species of any inland wetland in northwest Indiana. Along the Lake Michigan shoreline, another group of exotics (e.g., round goby, alewife, and sea lamprey) have affected the structure of native fish communities, thereby altering lake ecosystem function. Stocking programs contribute to the impairment of native communities. Nonindigenous species have restructured the function of Lake Michigan tributaries, causing disruptions in trophic dynamics, guild structure, and species diversity. Several fish communities have been reduced or eliminated by the alteration and destruction of spawning and nursery areas. Degradation of habitats has caused an increase in numbers and populations of species able to tolerate and flourish when confronted with hydrologic alteration. Fish communities found on public lands in northwest

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

    Science.gov (United States)

    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

  13. The reconstruction of complex networks with community structure

    Science.gov (United States)

    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.

  14. Metastable Chimera States in Community-Structured Oscillator Networks

    CERN Document Server

    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.

  15. The structure of small mammal communities in some alpine habitats

    Directory of Open Access Journals (Sweden)

    Roberta Locatelli

    1998-12-01

    Full Text Available Abstract We studied the composition of several small mammal communities living in different mountain and forest habitats of the central eastern Italian Alps. The small mammals were then grouped together, by cluster analysis, according to similarities in species and density. From the 22 stations investigated, five groups emerged, each one having also distinct environmental characteristics. We observed that spruce forest communities are grouped separately from those of mixed forests (larch and Swiss stone pine. We must stress the considerable difference existing between the small mammal communities living in different kinds of coniferous forests. The larch and Swiss stone pine forest seem to be able to support a greater density of small mammals, which includes in particular the bank vole (Clethrionomys glareolus.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Indian Academy of Sciences (India)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    OpenAIRE

    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...

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

    OpenAIRE

    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...

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

    NARCIS (Netherlands)

    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

  2. Nematode community structure along a Mediterranean shelf-slope gradient

    NARCIS (Netherlands)

    Soetaert, K.E.R.; Vincx, M.; Heip, C.H.R.

    1995-01-01

    Nematode assemblages along a Mediterranean depth transect (160- 1220 m) and vertically in the sediment were investigated. The station at the edge of the continental shelf (160 m) was distinctly different from those situated on the continental slope (280-1220 m). On the slope, nematode communities in

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

    Institute of Scientific and Technical Information of China (English)

    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.

  4. Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

    NARCIS (Netherlands)

    Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

    2006-01-01

    Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled fro

  5. Impacts of Information Subsidies and Community Structure on Local Press Coverage of Environmental Contamination.

    Science.gov (United States)

    Griffin, Robert J.; Dunwoody, Sharon

    1995-01-01

    Finds that a press kit sent by an environmental group to midwestern newspapers influenced them to delegate local staff to cover the story. Indicates that the press's function to report or raise issues concerning industrial toxic releases and related health risks is tempered by community structure and particularly by community reliance on…

  6. Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

    Science.gov (United States)

    Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

    2013-10-01

    A key goal in comparative metagenomics is to identify microbial group(s) which are responsible for conferring specific characteristics to a given environment. These characteristics are the result of the inter-microbial interactions between the resident microbial groups. We present a new GUI-based comparative metagenomic analysis application called Community-Analyzer which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed microbial communities (in terms of their taxonomic composition), but also provides insights into the inherent inter-microbial interactions occurring therein. Notably, this layout algorithm also enables grouping of the metagenomes based on the probable inter-microbial interaction patterns rather than simply comparing abundance values of various taxonomic groups. In addition, the tool implements several interactive GUI-based functionalities that enable users to perform standard comparative analyses across microbiomes. For academic and non-profit users, the Community-Analyzer is currently available for download from: http://metagenomics.atc.tcs.com/Community_Analyzer/.

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

    Science.gov (United States)

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

    2007-06-01

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

  8. [Colonization and community structural features of AM fungi in urban ecosystem: a review].

    Science.gov (United States)

    Shi, Li-jun; Diao, Zhi-kai; Liu, Run-jin

    2011-07-01

    Arbuscular mycorrhizal (AM) fungi, an important component of soil microbes, are of significance in maintaining the sustainable development of urban ecosystem. This paper summarized the characteristics of the colonization and community structure of AM fungi in urban ecosystems, and discussed the effects of urban ecological factors, e.g., human activities, vegetation re-establishment and maintenance, and urban soil status, on the colonization and community structure. It was considered that the researches on the community structure and function of AM fungi in urban ecosystems, such as the effects and mechanisms of the key urban ecological factors (e.g., water resource shortage and heat island effect) on the alternation of AM fungal community structure should be strengthened in the future.

  9. Covariance, correlation matrix and the multi-scale community structure of networks

    OpenAIRE

    Shen, Hua-Wei; Cheng, Xue-Qi; Fang, Bin-Xing

    2010-01-01

    Empirical studies show that real world networks often exhibit multiple scales of topological descriptions. However, it is still an open problem how to identify the intrinsic multiple scales of networks. In this article, we consider detecting the multi-scale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multi-scale community structure through the translation and rotation transf...

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

    OpenAIRE

    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...

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

    OpenAIRE

    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...

  12. Variability in a Community-Structured SIS Epidemiological Model.

    Science.gov (United States)

    Hiebeler, David E; Rier, Rachel M; Audibert, Josh; LeClair, Phillip J; Webber, Anna

    2015-04-01

    We study an SIS epidemiological model of a population partitioned into groups referred to as communities, households, or patches. The system is studied using stochastic spatial simulations, as well as a system of ordinary differential equations describing moments of the distribution of infectious individuals. The ODE model explicitly includes the population size, as well as the variability in infection levels among communities and the variability among stochastic realizations of the process. Results are compared with an earlier moment-based model which assumed infinite population size and no variance among realizations of the process. We find that although the amount of localized (as opposed to global) contact in the model has little effect on the equilibrium infection level, it does affect both the timing and magnitude of both types of variability in infection level.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  14. Mapping scientific literature. Structuring scientific communities through scientometrics

    OpenAIRE

    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 ...

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

    OpenAIRE

    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...

  16. Microbial community structure affects marine dissolved organic matter composition

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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

  19. [Insect community structure and its stability in a Zanthoxylum bungeanum garden with different planting pattern].

    Science.gov (United States)

    Zhang, Xiao-Ming; Li, Qiang; Chen, Guo-Hua; Yang, Jie; Gao, Xin; Song, Jia-Xiong

    2009-08-01

    An investigation was made on the insect community composition and structure in a Zanthoxylum bungeanum garden with corn-soybean - Z. bungeanum intercropping, soybean - Z. bungeanum intercropping, corn - Z. bungeanum intercropping, and only Z. bungeanum planting in Zhaotong City of Yunnan Province, and the community character index and principal component analysis were used to study the characters and stability of the insect community. A total of 326 insect species were recorded. In intercropped plots, the abundance, diversity, and evenness index of insect community were higher while the dominance index was lower, compared with those in monocultured Z. bungeanum plot. The diversity index of insect community decreased in the order of corn-soybean- Z. bungeanum intercropping > soybean - Z. bungeanum intercropping > corn - Z. bungeanum intercropping > only Z. bungeanum planting, and the insect community in corn-soybean - Z. bungeanum intercropping plot was relatively stable. PMID:19947222

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

    Science.gov (United States)

    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

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

    Institute of Scientific and Technical Information of China (English)

    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.

  2. Structure and seasonality in a Malaysian mudflat community

    Science.gov (United States)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  4. Optimal Control Strategy for Traffic Driven Epidemic Spreading Based on Community Structure

    Directory of Open Access Journals (Sweden)

    Fei Shao

    2013-01-01

    Full Text Available It is shown that community structure has a great impact on traffic transportation and epidemic spreading. The density of infected nodes and the epidemic threshold have been proven to have significant relationship with the node betweenness in traffic driven epidemic spreading method. In this paper, considering the impact of community structure on traffic driven epidemic spreading, an effective and novel strategy to control epidemic spreading in scale-free networks is proposed. Theoretical analysis shows that the new control strategy will obviously increase the ratio between the first and the second moments of the node betweenness distribution in scale-free networks. It is also found that the more accurate the community is identified, the stronger community structure the network has and the more efficient the control strategy is. Simulations on both computer-generated and real-world networks have confirmed the theoretical results.

  5. On the relationship between the structural and socioacademic communities of an interdisciplinary coauthorship network

    CERN Document Server

    Rodriguez, Marko A

    2008-01-01

    This article presents a study that compares detected structural communities in a coauthorship network to the socioacademic characteristics of the scholars that compose the network. The coauthorship network was created from the bibliographic record of an overt interdisciplinary research group focused on sensor networks and wireless communication. The popular leading eigenvector community detection algorithm was employed to assign a structural community to each scholar in the network. Socioacademic characteristics were gathered from the scholars and include such information as their academic department, academic affiliation, country of origin, and academic position. A Pearson's $\\chi^2$ test, with a simulated Monte Carlo, revealed that structural communities best represent groupings of individuals working in the same academic department and at the same institution. A generalization of this result indicates that, contrary to the common conception of a multi-institutional interdisciplinary research group, collabo...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  10. Bioluminescence to reveal structure and interaction of coastal planktonic communities

    Science.gov (United States)

    Moline, Mark A.; Blackwell, Shelley M.; Case, James F.; Haddock, Steven H. D.; Herren, Christen M.; Orrico, Cristina M.; Terrill, Eric

    2009-02-01

    Ecosystem function will in large part be determined by functional groups present in biological communities. The simplest distinction with respect to functional groups of an ecosystem is the differentiation between primary and secondary producers. A challenge thus far has been to examine these groups simultaneously with sufficient temporal and spatial resolution for observations to be relevant to the scales of change in coastal oceans. This study takes advantage of general differences in the bioluminescence flash kinetics between planktonic dinoflagellates and zooplankton to measure relative abundances of the two groups within the same-time space volume. This novel approach for distinguishing these general classifications using a single sensor is validated using fluorescence data and exclusion experiments. The approach is then applied to data collected from an autonomous underwater vehicle surveying >500 km in Monterey Bay and San Luis Obispo Bay, CA during the summers of 2002-2004. The approach also reveals that identifying trophic interaction between the two planktonic communities may also be possible.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  13. Microbial activity and bacterial community structure during degradation of microcystins

    DEFF Research Database (Denmark)

    Christoffersen, K.; Lyck, Susanne; Winding, A.

    2002-01-01

    experiment to evaluate the effects of organic lysates on bacterial proliferation in the absence of microcystin. An exponential decline of the dissolved toxins was observed in all cases with toxins present, and the degradation rates ranged between 0.5 and 1.0 d(-1). No lag phases were observed but slow...... including microcystins, and this resulted in a net accumulation of bacterial cells. The heterotrophic nanoflagellates responded quickly to the bacterial growth and probably consumed a considerable amount of the bacteria. The microbial activities returned to initial values within 5 to 6 d as the toxins....... It was hypothesised that the bacterial community from a lake with frequent occurrence of toxic cyanobacteria can degrade microcystin along with other organic compounds. The initial dissolved microcystin concentrations ranged between 10 and 136 mug 1(-1) (microcystin-LR equivalents) in the laboratory experiment, using...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  16. Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities.

    Directory of Open Access Journals (Sweden)

    Sylvie Estrela

    Full Text Available Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships, and species spatial organization (structural relationships are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource is traded for detoxification (service and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition, and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  18. Forest age influences oak insect herbivore community structure, richness, and density.

    Science.gov (United States)

    Jeffries, June M; Marquis, Robert J; Forkner, Rebecca E

    2006-06-01

    Plant succession is one of many factors that may affect the composition and structure of herbivorous insect communities. However, few studies have examined the effect of forest age on the diversity and abundance of insect communities. If forest age influences insect diversity, then the schedule of timber harvest rotation may have consequent effects on biodiversity. The insect herbivore community on Quercus alba (white oak) in the Missouri Ozarks was sampled in a chronoseries, from recently harvested (2 yr) to old-growth (approximately 313 yr) forests. A total of nine sites and 39 stands within those sites were sampled in May and August 2003. Unique communities of plants and insects were found in the oldest forests (122-313 yr). Density and species richness of herbivores were positively correlated with increasing forest age in August but not in May. August insect density was negatively correlated with heat load index; in addition, insect density and richness increased over the chronoseries, but not on the sunniest slopes. Forest structural diversity (number of size classes) was positively correlated with forest age, but woody plant species richness was not. In sum, richness, density, and community structure of white oak insect herbivores are influenced by variation in forest age, forest structure, relative abundance of plant species, and abiotic conditions. These results suggest that time between harvests of large, long-lived, tree species such as white oak should be longer than current practice in order to maintain insect community diversity. PMID:16826990

  19. Habitat structure alters top-down control in litter communities.

    Science.gov (United States)

    Kalinkat, Gregor; Brose, Ulrich; Rall, Björn Christian

    2013-07-01

    The question whether top-down or bottom-up forces dominate trophic relationships, energy flow, and abundances within food webs has fuelled much ecological research with particular focus on soil litter ecosystems. Because litter simultaneously provides habitat structure and a basal resource, disentangling direct trophic and indirect non-trophic effects on different trophic levels remains challenging. Here, we focussed on short-term per capita interaction strengths of generalist predators (centipedes) on their microbi-detritivore prey (springtails) and addressed how the habitat structuring effects of the leaf litter modifies this interaction. We performed a series of laboratory functional response experiments where four levels of habitat structure were constructed by adding different amounts of leaf litter to the experimental arenas. We found that increased leaf litter reduced the consumption rate of the predator. We interpreted this as a dilution effect of the augmented habitat size provided by the increasing leaf litter surface available to the species. Dilution of the prey population decreased encounter rates, whereas the capture success was not affected. Interestingly, our results imply that top-down control by centipedes decreased with increasing resource supply for the microbi-detritivore prey (i.e. the leaf litter that simultaneously provides habitat structure). Therefore, effective top-down control of predators on microbi-detritvore populations seems unlikely in litter-rich ecosystems due to the non-trophic, habitat-structuring effect of the basal litter resource. PMID:23188055

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

    CERN Document Server

    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...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    Binzer, Thomas; Sand-Jensen, Kaj

    2002-01-01

    studies. To evaluate the regulation of aquatic community production, we measured the photosynthetic production of thallus parts and entire communities of Fucus serratus (L.) of different density and spatial structure exposed to varying photon flux density and dissolved CO2 concentration. Photosynthetic...... production in relation to photon flux density differed considerably between entire communities and individual thallus parts. No light saturation occurred in the communities, and all photosynthetic variables such as light compensation point, efficiency of light utilisation at low light and maximum production......Determination of photosynthetic production in plant communities is essential for evaluating plant growth rates and carbon fluxes in ecosystems, but it cannot easily be derived from the photosynthetic response of individual leaves or thalli, which has been the focus of virtually all previous aquatic...

  5. Finding Community Structure in Networks Using a Shortest-Path-Based k-Means Algorithm

    Institute of Scientific and Technical Information of China (English)

    Jinglu GAO

    2013-01-01

    We consider the problem of detecting the community structure in a complex network,groups of nodes with a higher-than-average density of edges connecting them.In this paper we use the simulated annealing strategy to maximize the modularity,which has been indicated as a robust benefit function,associating with a shortest-path-based k-means iterative procedure for network partition.The proposed algorithm can not only find the communities,but also identify the nodes which occupy central positions under the metric of the shortest path within the communities to which they belong.The optimal number of communities can be automatically determined without any prior knowledge about the network structure.The applications to both artificial and real-world networks demonstrate the effectiveness of our algorithm.

  6. Locating Elementary Teachers' Professional Communities in a Structured Collaboration Environment

    Science.gov (United States)

    Chu, Szu Yang

    2016-01-01

    As teacher collaboration becomes an increasingly common goal in school organization, teachers' experiences and perspectives in a Structured Collaboration Environment remain under-examined. This qualitative case study explored how teachers participated in collaborative work, the outcomes of collaboration, and supports and obstacles to productive…

  7. School Structures: Transforming Urban Complex Schools into Better Learning Communities

    Science.gov (United States)

    Haimendorf, Max; Kestner, Jacob

    2008-01-01

    This article, which forms part of the policy booklet "Lessons from the Front" written by participants and Ambassadors of the Teach First scheme, argues that educational outcomes are often adversely affected by the size and structure of many urban complex schools. Rather than multiplying the efforts of teachers, too often the organisational model…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  12. Effect of tropical rainfall in structuring the macrobenthic community of Mandovi estuary, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Gaonkar, U.V.; Sivadasa, S.K.; Ingole, B.S.

    of the annual monsoon also influenced the macrofaunal community of Mandovi estuary. The macrofaunal community structure is determined by a number of factors such as salinity, temperature, food availability, recruitment and hydrographic conditions (Henning..., the planktonic recruiting larvae are ensured of abundant food. Further, the water turbulence during the monsoon helps in the wide dispersal of both, larvae and the adults of the sedentary benthic species (Dobbs & Vozarik, 1983; Hernández-Arana et al., 2003...

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

    OpenAIRE

    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...

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

    OpenAIRE

    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'...

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

    Science.gov (United States)

    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.

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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...

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

    OpenAIRE

    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 ...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Science.gov (United States)

    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.

  3. Genetics-based interactions among plants, pathogens, and herbivores define arthropod community structure.

    Science.gov (United States)

    Busby, Posy E; Lamit, Louis J; Keith, Arthur R; Newcombe, George; Gehring, Catherine A; Whitham, Thomas G; Dirzo, Rodolfo

    2015-07-01

    Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens' indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens' indirect effects on arthropod communities and insect herbivory. First, due in part to the pathogens' differential impacts on leaf biomass among the two Populus species and the hybrids, the pathogen most strongly impacted arthropod community composition, richness, and abundance on the pathogen-susceptible tree species. Second, we found similar patterns comparing pathogen-susceptible and pathogen-resistant genotypes within species. Third, within a plant species, pathogens caused a fivefold greater reduction in herbivory on insect-herbivore-susceptible plant genotypes than on herbivore-resistant genotypes, demonstrating that the pathogen-herbivore interaction is genotype dependent. We conclude that interactions among plants, pathogens, and herbivores can structure multitrophic communities, supporting the interacting foundation species hypothesis. Because these interactions are genetically based, evolutionary changes in genetic resistance could result in ecological changes in associated communities, which may in turn feed back to affect plant fitness.

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

    Science.gov (United States)

    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.

  5. Friendship Concept and Community Network Structure among Elementary School and University Students

    Science.gov (United States)

    Hernández-Hernández, Ana María; Viga-de Alva, Dolores; Huerta-Quintanilla, Rodrigo; Canto-Lugo, Efrain; Laviada-Molina, Hugo; Molina-Segui, Fernanda

    2016-01-01

    We use complex network theory to study the differences between the friendship concepts in elementary school and university students. Four friendship networks were identified from surveys. Three of these networks are from elementary schools; two are located in the rural area of Yucatán and the other is in the urban area of Mérida, Yucatán. We analyzed the structure and the communities of these friendship networks and found significant differences among those at the elementary schools compared with those at the university. In elementary schools, the students make friends mainly in the same classroom, but there are also links among different classrooms because of the presence of siblings and relatives in the schools. These kinds of links (sibling-friend or relative-friend) are called, in this work, “mixed links”. The classification of the communities is based on their similarity with the classroom composition. If the community is composed principally of students in different classrooms, the community is classified as heterogeneous. These kinds of communities appear in the elementary school friendship networks mainly because of the presence of relatives and siblings. Once the links between siblings and relatives are removed, the communities resembled the classroom composition. On the other hand, the university students are more selective in choosing friends and therefore, even when they have friends in the same classroom, those communities are quite different to the classroom composition. Also, in the university network, we found heterogeneous communities even when the presence of sibling and relatives is negligible. These differences made up a topological structure quite different at different academic levels. We also found differences in the network characteristics. Once these differences are understood, the topological structure of the friendship network and the communities shaped in an elementary school could be predicted if we know the total number of

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment.

    Science.gov (United States)

    Mitchell, E A D; Gilbert, D; Buttler, A; Amblard, C; Grosvernier, P; Gobat, J M

    2003-08-01

    Little is known about the structure of microbial communities in Sphagnum peatlands, and the potential effects of the increasing atmospheric CO2 concentration on these communities are not known. We analyzed the structure of microbial communities in five Sphagnum-dominated peatlands across Europe and their response to CO2 enrichment using miniFACE systems. After three growing seasons, Sphagnum samples were analyzed for heterotrophic bacteria, cyanobacteria, microalgae, heterotrophic flagellates, ciliates, testate amoebae, fungi, nematodes, and rotifers. Heterotrophic organisms dominated the microbial communities and together represented 78% to 97% of the total microbial biomass. Testate amoebae dominated the protozoan biomass. A canonical correspondence analysis revealed a significant correlation between the microbial community data and four environmental variables (Na+, DOC, water table depth, and DIN), reflecting continentality, hydrology, and nitrogen deposition gradients. Carbon dioxide enrichment modified the structure of microbial communities, but total microbial biomass was unaffected. The biomass of heterotrophic bacteria increased by 48%, and the biomass of testate amoebae decreased by 13%. These results contrast with the absence of overall effect on methane production or on the vegetation, but are in line with an increased below-ground vascular plant biomass at the same sites. We interpret the increase in bacterial biomass as a response to a CO2-induced enhancement of Sphagnum exudation. The causes for the decrease of testate amoebae are unclear but could indicate a top-down rather than a bottom-up control on their density.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  12. Microbial Community Structure of Subglacial Lake Whillans, West Antarctica

    Science.gov (United States)

    Achberger, Amanda M.; Christner, Brent C.; Michaud, Alexander B.; Priscu, John C.; Skidmore, Mark L.; Vick-Majors, Trista J.; Adkins, W.

    2016-01-01

    Subglacial Lake Whillans (SLW) is located beneath ∼800 m of ice on the Whillans Ice Stream in West Antarctica and was sampled in January of 2013, providing the first opportunity to directly examine water and sediments from an Antarctic subglacial lake. To minimize the introduction of surface contaminants to SLW during its exploration, an access borehole was created using a microbiologically clean hot water drill designed to reduce the number and viability of microorganisms in the drilling water. Analysis of 16S rRNA genes (rDNA) amplified from samples of the drilling and borehole water allowed an evaluation of the efficacy of this approach and enabled a confident assessment of the SLW ecosystem inhabitants. Based on an analysis of 16S rDNA and rRNA (i.e., reverse-transcribed rRNA molecules) data, the SLW community was found to be bacterially dominated and compositionally distinct from the assemblages identified in the drill system. The abundance of bacteria (e.g., Candidatus Nitrotoga, Sideroxydans, Thiobacillus, and Albidiferax) and archaea (Candidatus Nitrosoarchaeum) related to chemolithoautotrophs was consistent with the oxidation of reduced iron, sulfur, and nitrogen compounds having important roles as pathways for primary production in this permanently dark ecosystem. Further, the prevalence of Methylobacter in surficial lake sediments combined with the detection of methanogenic taxa in the deepest sediment horizons analyzed (34–36 cm) supported the hypothesis that methane cycling occurs beneath the West Antarctic Ice Sheet. Large ratios of rRNA to rDNA were observed for several operational taxonomic units abundant in the water column and sediments (e.g., Albidiferax, Methylobacter, Candidatus Nitrotoga, Sideroxydans, and Smithella), suggesting a potentially active role for these taxa in the SLW ecosystem. Our findings are consistent with chemosynthetic microorganisms serving as the ecological foundation in this dark subsurface environment, providing new

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    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...

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

    Science.gov (United States)

    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

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

    KAUST Repository

    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.

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

    CERN Document Server

    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 ...

  18. Subsidies to predators, apparent competition and the phylogenetic structure of prey communities.

    Science.gov (United States)

    Helmus, Matthew R; Mercado-Silva, Norman; Vander Zanden, M Jake

    2013-11-01

    Ecosystems are fragmented by natural and anthropogenic processes that affect organism movement and ecosystem dynamics. When a fragmentation restricts predator but not prey movement, then the prey produced on one side of an ecosystem edge can subsidize predators on the other side. When prey flux is high, predator density on the receiving side increases above that possible by in situ prey productivity, and when low, the formerly subsidized predators can impose strong top-down control of in situ prey--in situ prey experience apparent competition from the subsidy. If predators feed on some evolutionary clades of in situ prey over others, then subsidy-derived apparent competition will induce phylogenetic structure in prey composition. Dams fragment the serial nature of river ecosystems by prohibiting movement of organisms and restricting flowing water. In the river tailwater just below a large central Mexican dam, fish density was high and fish gorged on reservoir-derived zooplankton. When the dam was closed, water flow and the zooplankton subsidy ceased, densely packed pools of fish formed, fish switched to feed on in situ prey, and the tailwater macroinvertebrate community was phylogenetic structured. We derived expectations of structure from trait-based community assembly models based on macroinvertebrate body size, tolerance to anthropogenic disturbance, and fish-diet selectivity. The diet-selectivity model best fit the observed tailwater phylogenetic structure. Thus, apparent competition from subsidies phylogenetically structures prey communities, and serial variation in phylogenetic community structure can be indicative of fragmentation in formerly continuous ecosystems.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  20. Nematode Community Structure along the Continental Slope off the Kenyan Coast, Western Indian Ocean

    Science.gov (United States)

    Muthumbi, Agnes W.; Vanreusel, Ann; Duineveld, Gerard; Soetaert, Karline; Vincx, Magda

    2004-05-01

    Metazoan meiofauna and in particular nematode densities, diversity, community structure were studied in relation to water depth (20 m, 50 m, 500 m, 1000 m and 2000 m) along four bathymetric transects in the Western Indian Ocean off the Kenyan coast. Nematode densities ranged between 276-944 ind./10 cm2, which is comparable to values from other oligotrophic areas in the world. Densities was correlated with oxygen concentrations in the overlying water, since they were lowest at mid-depth (500-1000 m) coinciding with the minimum oxygen level. Nematode community structure (at genus level) resembles communities found in temperate slope regions, which are also characterized by a low productivity. The community structure showed correlations with sediment composition, water depth and oxygen levels in the overlying water. Sediment composition was mainly important at the shelf where nematodes separated into a silty sediment-dwelling community with high abundances of Daptonema, Dorylaimopsis, Terschellingia and Halalaimus, and a sandy sediment-dwelling community characterised by high abundances of Microlaimus and Halalaimus. The genera Monhystera, Acantholaimus, Sabatieria, Molgolaimus and Halalaimus dominated the slope communities. The characteristic deep-sea taxa, the monhysterids and Acantholaimus increased in relative abundance with increasing depth, to become dominant at the lower slope (2000 m). The upper (500 m) and mid-slope (1000 m), which coincided with the lowest oxygen concentrations, were colonised by Sabatieria, a genus that is known to inhabit suboxic sediments. Diversity at the level of the genera showed an unimodal trend along the sampled gradient, with highest values at mid-depth (500 m). Although the oxygen minimum at mid depths is much less pronounced than in adjacent areas, the results of this study suggest an impact on the present communities.

  1. Detecting the community structure in complex networks based on quantum mechanics

    Science.gov (United States)

    Niu, Yan Qing; Hu, Bao Qing; Zhang, Wen; Wang, Min

    2008-10-01

    In this paper, we develop a novel method to detect the community structure in complex networks. This approach is based on the combination of kernel-based clustering using quantum mechanics, the spectral clustering technique and the concept of the Bayesian information criterion. We test the proposed algorithm on Zachary’s karate club network and the world of American college football. Experimental results indicate that our algorithm is efficient and effective at finding both the optimal number of clusters, and the best clustering of community structures.

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

    Science.gov (United States)

    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

  3. Molecular tools for investigating ANME community structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  4. Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient

    Science.gov (United States)

    Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

    2016-01-01

    Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells

  5. Community investment in wind farms: funding structure effects in wind energy infrastructure development.

    Science.gov (United States)

    Beery, Joshua A; Day, Jennifer E

    2015-03-01

    Wind energy development is an increasingly popular form of renewable energy infrastructure in rural areas. Communities generally perceive socioeconomic benefits accrue and that community funding structures are preferable to corporate structures, yet lack supporting quantitative data to inform energy policy. This study uses the Everpower wind development, to be located in Midwestern Ohio, as a hypothetical modeling environment to identify and examine socioeconomic impact trends arising from corporate, community and diversified funding structures. Analysis of five National Renewable Energy Laboratory Jobs and Economic Development Impact models incorporating local economic data and review of relevant literature were conducted. The findings suggest that community and diversified funding structures exhibit 40-100% higher socioeconomic impact levels than corporate structures. Prioritization of funding sources and retention of federal tax incentives were identified as key elements. The incorporation of local shares was found to mitigate the negative effects of foreign private equity, local debt financing increased economic output and opportunities for private equity investment were identified. The results provide the groundwork for energy policies focused to maximize socioeconomic impacts while creating opportunities for inclusive economic participation and improved social acceptance levels fundamental to the deployment of renewable energy technology. PMID:25621885

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  15. Influence of different fertilizer types of zucchini (Cucurbita pepo) on the structure of nematode communities.

    Science.gov (United States)

    Haytova, D; Bileva, T

    2011-01-01

    Increasing efficiency of production of vegetable crops is directly related to search for appropriate solution to increase their productivity. Organic amendments have been used for centuries to improve soil fertility and crop yield. Our study suggests that organic amendments can also be used as nematicidal agents. The survey was conducted on Experimental field of Department Horticulture at Agricultural University of Plovdiv, Bulgaria in 2009 on nematode infested sites. Combination with two types of fertilizers was used to investigate their effects on the community of soil nematodes. Characterization and comparative analysis among treatments of soil nematode community structure based on different ecological measures such as total nematode abundance, number of genera, trophic diversity and etc., was made. Changes in the composition and structure of nematode community as result of different fertilizer types were assessed.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  19. Impacts of feeding strategy on microbial community structure diversity in vertical flow constructed wetlands

    Science.gov (United States)

    Jia, W. L.; Zhang, J.; Wang, Q.

    2016-08-01

    The impacts of feeding strategy (intermittently or continuously) on contaminant removal performance and microbial community structure in vertical flow constructed wetlands (VFCWs) were evaluated. The results showed that intermittent feeding strategy improved the removal of COD, TP and ammonium in VFCWs, although TN removal was weakened correspondingly The bacterial diversity decreased with the increase of substratum depth in all CWs. The intermittent feeding favored the growth of microorganisms due to the enhancement of oxygen content in the substratum. The feeding strategy had little impact on the microbial community in the surface substratum. However, in the bottom substratum, the impacts were of great significance. The microbial community structure similarity between the CWs with different feeding strategies was low.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  4. Linking microbial community structure and microbial processes: An empirical and conceptual overview

    Science.gov (United States)

    Bier, R.L.; Bernhardt, E.S.;; Boot, C.M.; Graham, E.B.;; Hall, E.K.; Lennon, J.T.; Nemergut, D.R.; Osborne, B.B.; Ruiz-Gonzalez, C.; Schimel, J.P.; Waldrop, Mark P.; Wallenstein, M.D.

    2015-01-01

    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.

  5. Historical changes in the structure and functioning of the benthic community in the lagoon of Venice

    Science.gov (United States)

    Pranovi, Fabio; Da Ponte, Filippo; Torricelli, Patrizia

    2008-03-01

    One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore-detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.

  6. An evaluation of the influence of environment and biogeography on community structure: the case of Holarctic mammals

    DEFF Research Database (Denmark)

    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......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...... climates differ in ecological structure irrespective of their biogeographical location. On the other hand, the structures of Nearctic and Palearctic communities from regions of similar climate radically differ in some features. Thus, although present climatic conditions influence community structure...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Microbial community structure of three traditional zambian fermented products: mabisi, chibwantu and munkoyo.

    Directory of Open Access Journals (Sweden)

    Sijmen E Schoustra

    Full Text Available Around the world, raw materials are converted into fermented food products through microbial and enzymatic activity. Products are typically produced using a process known as batch culture, where small volumes of an old culture are used to initiate a fresh culture. Repeated over many years, and provided samples are not shared among producers, batch culture techniques allow for the natural evolution of independent microbial ecosystems. While these products form an important part of the diets of many people because of their nutritional, organoleptic and food safety properties, for many traditional African fermented products the microbial communities responsible for fermentation are largely unknown. Here we describe the microbial composition of three traditional fermented non-alcoholic beverages that are widely consumed across Zambia: the milk based product Mabisi and the cereal based products Munkoyo and Chibwantu. Using culture and non-culture based techniques, we found that six to eight lactic acid bacteria predominate in all products. We then used this data to investigate in more detail the factors affecting community structure. We found that products made from similar raw materials do not harbor microbial communities that are more similar to each other than those made from different raw materials. We also found that samples from the same product taken at the same location were as different from each other in terms of microbial community structure and composition, as those from geographically very distant locations. These results suggest that microbial community structure in these products is neither a simple consequence of the raw materials used, nor the particular suite of microbes available in the environment but that anthropogenic variables (e.g., competition among sellers or organoleptic preferences by different tribes are important in shaping the microbial community structures.

  11. Microbial community structure of three traditional zambian fermented products: mabisi, chibwantu and munkoyo.

    Science.gov (United States)

    Schoustra, Sijmen E; Kasase, Chitundu; Toarta, Cristian; Kassen, Rees; Poulain, Alexandre J

    2013-01-01

    Around the world, raw materials are converted into fermented food products through microbial and enzymatic activity. Products are typically produced using a process known as batch culture, where small volumes of an old culture are used to initiate a fresh culture. Repeated over many years, and provided samples are not shared among producers, batch culture techniques allow for the natural evolution of independent microbial ecosystems. While these products form an important part of the diets of many people because of their nutritional, organoleptic and food safety properties, for many traditional African fermented products the microbial communities responsible for fermentation are largely unknown. Here we describe the microbial composition of three traditional fermented non-alcoholic beverages that are widely consumed across Zambia: the milk based product Mabisi and the cereal based products Munkoyo and Chibwantu. Using culture and non-culture based techniques, we found that six to eight lactic acid bacteria predominate in all products. We then used this data to investigate in more detail the factors affecting community structure. We found that products made from similar raw materials do not harbor microbial communities that are more similar to each other than those made from different raw materials. We also found that samples from the same product taken at the same location were as different from each other in terms of microbial community structure and composition, as those from geographically very distant locations. These results suggest that microbial community structure in these products is neither a simple consequence of the raw materials used, nor the particular suite of microbes available in the environment but that anthropogenic variables (e.g., competition among sellers or organoleptic preferences by different tribes) are important in shaping the microbial community structures.

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

    DEFF Research Database (Denmark)

    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...

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

    OpenAIRE

    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 ...

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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;...

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

    NARCIS (Netherlands)

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

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and

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

    DEFF Research Database (Denmark)

    Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær;

    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...

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

    Institute of Scientific and Technical Information of China (English)

    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.

  19. The community structure of a tropical intertidal mudflat under human exploitation

    NARCIS (Netherlands)

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

    2002-01-01

    The impact of human exploitation on the community structure of intertidal mudflats was investigated in an exploited and unexploited control area at Inhaca Island, Mozambique. An increase in the species richness in the exploited area, as expected by the intermediate disturbance hypothesis, was not co

  20. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rdna sequences

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Holtgrewe-Stukenbrock, Eva

    2004-01-01

    Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with plant roots and are found in most ecosystems. In this study the community structure of AMF in a clade of the genus Glomus was examined in undisturbed costal grassland using LSU rDNA sequences amplified from roots of Hieracium pi...

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

    NARCIS (Netherlands)

    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

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

    NARCIS (Netherlands)

    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

  3. Ecosystem engineering effects of Aster tripolium and Salicornia procumbens saltmarsh on macrofaunal community structure

    NARCIS (Netherlands)

    Van der Wal, D.; Herman, P.M.J.

    2012-01-01

    This paper examines how perennial Aster tripolium and annual Salicornia procumbens salt marshes alter the biomass, density, taxon diversity, and community structure of benthic macrofauna, and also examines the role of elevation, sediment grain size, plant cover, and marsh age. Core samples were coll

  4. EFFECTS OF VALLISNERIA AMERICANA (L.) ON COMMUNITY STRUCTURE AND ECOSYSTEM FUNCTION IN LAKE MESOCOSMS

    Science.gov (United States)

    Submerged aquatic vegetation is known as a key structural component and regulator in ecosystems. In this mesocosm study, we examine community- and system-level responses to the presence of Valisneria americana (L), a deep-rooted macrophyte, Phytoplankton, bacteria and filamentous...

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

    Science.gov (United States)

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

    2016-08-01

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

  6. Zooplankton standing stock, community structure and diversity in the northern Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Goswami, S.C.; Srivastava, Y.

    The effects of large scale oil spill, which occurred during the Gulf War in 1991 on zooplankton standing stock, community structure and diversity in the northern Arabian Sea were studied. Surface (1-0 m) and vertical zooplankton hauls (200-0 m, 250...

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Huiwen; ZHOU; Qixing; ZHANG; Qianru; ZHANG; Chengg

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  9. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  10. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2015-07-01

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

  13. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    OpenAIRE

    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). ...

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    International Nuclear Information System (INIS)

    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.)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  7. [Influence of Submerged Plants on Microbial Community Structure in Sediment of Hongze Lake].

    Science.gov (United States)

    Zhang, Ding-yu; Zhang, Ting-xi; Dong, Dan-ping; Li, De-fang; Wang, Guo-xiang

    2016-05-15

    Phospholipid fatty acids (PLFAs) method was applied to analyze the influence of submerged plants on sediment microbial community structure, in order to investigate the changes of sediment microbial community structure for different kinds of the submerged plants in different growth periods. Particularly, Potamogeton crispus L., Potamogeton pectinatus L and the mixed group were chosen as the typical submerged plants in Hongze Lake for investigation in this paper. The results indicated that the change of total PLFAs in different periods was significant, on the contrary, the PLFA change for different groups in the same period was insignificant. The values of G⁺ PLFA/G⁻ PLFA in the submerged plant group were also highly related to the different growth periods, which demonstrated that the root function of the submerged plant had a severe impact on the microbial community in sediment. Furthermore, some environmental factors, such as Temperature, pH, TOC and DO, were correlated to characteristic phospholipid of PLFAs in sediment, which means the environmental factors could also affect the microbial community structure.

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

    Directory of Open Access Journals (Sweden)

    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.

  9. [Preliminary study on the changes of bacterial community structure in Qingcaosha Reservoir during water storage period].

    Science.gov (United States)

    Peng, Qing; Xie, Bing; Yuan, Qi; Huang, Zhi-Ting; Cui, Lu-Lu; Wang, Wen-Ting

    2012-10-01

    In order to investigate the changes in water quality and the bacterial community structure in Qingcaosha Reservoir during water storage and supply period, the microorganisms in water body were studied by microbial culture counting and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DEEG) technique. Results showed that the water quality had been improved significantly and the nitrogen and phosphorus concentrations significantly reduced after the Yangtze River water flowed into the reservoir. The number of culturable microorganisms in the influent and the reservoir changed with the seasons, and there were more microorganisms in the influent than these in the reservoir during spring and summer, and fewer in autumn and winter, and the precipitation of suspended microorganisms in the water caused the increase of organic matter content in the sediment. PCR-DGGE results showed that bacterial community structure in the reservoir changed with the seasons, and the microbial community diversity was the highest in summer and the lowest in autumn. The cluster analysis showed that the similarity of microbial community structure of water and sediment samples was 62% , which might be due to the contribution of the precipitation of the suspended microorganisms. The dominant microbial species in water had high similarity with alpha, beta-Proteobacteria, Flavobacterium, Rheinheimera, Prochlorococcus, Synechococcus and Marine metagenome, indicating that Qingcaosha Reservoir faced the risk of algae bloom and seawater intrusion. The results provide the fundamental understanding on reservoir operation and can be used as reference for future studies.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  12. [Vertical structure of bacterial communities in peats of the Yakhroma River floodplain].

    Science.gov (United States)

    Dobrovol'skaia, T G; Golovchenko, A V; Pozdniakov, A I

    2007-01-01

    The abundance and taxonomic structure of soil bacterial communities have been studied in different geomorphological parts of the Yakhroma floodplain. It has been found that the numbers of bacteria reach a peak in calcareous peat soil under forest near the floodplain terrace, decreasing to a minimum in soddy alluvial soil near the riverbed. All soils are characterized by the presence of different ecological-trophic bacterial groups capable of peat destruction. Seasonal dynamics of the structure of bacterial communities and, in some soil types, its spatial dynamics accounted for by changes in the botanical structure of peat across its profile have been revealed. All peat soils in the floodplain have high contents of organic matter and neutral pH and, therefore, are favorable biotopes for the development of saprotrophic bacteria. This, in turn, largely accounts for high productivity and stability of this agroecosystem as a whole. PMID:18038631

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

    Science.gov (United States)

    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

  14. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

    Directory of Open Access Journals (Sweden)

    Salamon Peter

    2005-03-01

    Full Text Available Abstract Background Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses. PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. Results PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. Conclusion PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    International Nuclear Information System (INIS)

    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

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

    Directory of Open Access Journals (Sweden)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Veronica; Lopes, Isabel [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rocha-Santos, Teresa [ISEIT/Viseu, Instituto Piaget, Estrada do Alto do Gaio, Galifonge, 3515-776 Lordosa, Viseu (Portugal); Santos, Ana L. [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rasteiro, Graca M.; Antunes, Filipe [CIEPQPF, Department of Chemical Engineering, Faculty of Science and Technology, Polo II, University of Coimbra, 3030-290 Coimbra (Portugal); Goncalves, Fernando; Soares, Amadeu M.V.M.; Cunha, Angela; Almeida, Adelaide [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Gomes, Newton N.C.M., E-mail: gomesncm@ua.pt [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Pereira, Ruth [Department of Biology, Faculty of Science, University of Porto, Rua do Campo Alegre 4169-007 Porto (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal)

    2012-05-01

    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 (TiO{sub 2}), titanium silicon oxide (TiSiO{sub 4}), 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, TiO{sub 2}, CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: Black-Right-Pointing-Pointer Organic and inorganic nanomaterials on soil microbial community. Black-Right-Pointing-Pointer Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. Black-Right-Pointing-Pointer All the organic nanomaterials, TiO{sub 2} and gold nanorods significantly affected the structural diversity.

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

    CERN Document Server

    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 ...

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

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

    2012-02-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that 'Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in 'Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of 'Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the 'Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the 'Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by 'Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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

  10. Fish community structure and distribution in a macro-tidal inshore habitat in the Irish Sea

    Science.gov (United States)

    Jovanovic, Boris; Longmore, Craig; O'Leary, Áine; Mariani, Stefano

    2007-10-01

    Estuaries, lagoons and mudflat habitats represent a crucial biodiversity component in coastal waters and may act as vital nurseries and shelters for the juvenile stages of many commercial fish species. A study of the spatial distribution of inshore fish fauna around the shallow coastal habitats of North Bull Island (Dublin Bay, Ireland) was carried out during summer and autumn of 2005, in order to characterise the fish community present therein. Four stations were examined, situated along a putative environmental gradient, between the mudflat and the open sea shore. Stations were surveyed at both high and low tide and sampling was repeated weekly for eight weeks, spanning over four spring and four neap tidal events. A total of 17 fish species were caught, belonging to 13 families. The community was largely dominated by the lesser sandeel ( Ammodytes tobianus) and the common goby ( Pomatoschistus microps). Ordination techniques were used to generate hypotheses as to the general patterns in the fish community; Shannon-Wiener index was employed to estimate spatial, temporal and tidal trends in diversity; and analysis of variance (ANOVA) was employed to test for the influence of time of the year, habitat, tidal phase and tidal state on the spatial distribution of fishes. Results reveal that time of the year and habitat variation across the environmental gradient are the major factors in determining fish community structure. The influence of tidal dynamics seem to have a lesser impact on the overall community, but can significantly and variably affect the distribution of individual species.

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Science.gov (United States)

    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

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

    Institute of Scientific and Technical Information of China (English)

    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.

  14. A multi-decade time series of kelp forest community structure at San Nicolas Island, California

    Science.gov (United States)

    Lafferty, Kevin D.; Kenner, Michael C.; Estes, James A.; Tinker, M. Tim; Bodkin, James L.; Cowen, Robert K.; Harrold, Christopher; Novak, Mark; Rassweiler, Andrew; Reed, Daniel C.

    2013-01-01

    San Nicolas Island is surrounded by broad areas of shallow subtidal habitat, characterized by dynamic kelp forest communities that undergo dramatic and abrupt shifts in community composition. Although these reefs are fished, the physical isolation of the island means that they receive less impact from human activities than most reefs in Southern California, making San Nicolas an ideal place to evaluate alternative theories about the dynamics of these communities. Here we present monitoring data from seven sampling stations surrounding the island, including data on fish, invertebrate, and algal abundance. These data are unusual among subtidal monitoring data sets in that they combine relatively frequent sampling (twice per year) with an exceptionally long time series (since 1980). Other outstanding qualities of the data set are the high taxonomic resolution captured and the monitoring of permanent quadrats and swaths where the history of the community structure at specific locations has been recorded through time. Finally, the data span a period that includes two of the strongest ENSO events on record, a major shift in the Pacific decadal oscillation, and the reintroduction of sea otters to the island in 1987 after at least 150 years of absence. These events provide opportunities to evaluate the effects of bottom-up forcing, top-down control, and physical disturbance on shallow rocky reef communities.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands.

    Science.gov (United States)

    Hartmann, Martin; Lee, Sangwon; Hallam, Steven J; Mohn, William W

    2009-12-01

    Disturbances caused by timber harvesting have critical long-term effects on the forest soil microbiota and alter fundamental ecosystem services provided by these communities. This study assessed the effects of organic matter removal and soil compaction on microbial community structures in different soil horizons 13 years after timber harvesting at the long-term soil productivity site at Skulow Lake, British Columbia. A harvested stand was compared with an unmanaged forest stand. Ribosomal intergenic spacer profiles of bacteria, archaea and eukarya indicated significantly different community structures in the upper three soil horizons of the two stands, with differences decreasing with depth. Large-scale sequencing of the ribosomal intergenic spacers coupled to small-subunit ribosomal RNA genes allowed taxonomic identification of major microbial phylotypes affected by harvesting or varying among soil horizons. Actinobacteria and Gemmatimonadetes were the predominant phylotypes in the bacterial profiles, with the relative abundance of these groups highest in the unmanaged stand, particularly in the deeper soil horizons. Predominant eukaryal phylotypes were mainly assigned to known mycorrhizal and saprotrophic species of Basidiomycetes and Ascomycetes. Harvesting affected Basidiomycetes to a minor degree but had stronger effects on some Ascomycetes. Archaeal profiles had low diversity with only a few predominant crenarchaeal phylotypes whose abundance appeared to increase with depth. Detection of these effects 13 years after harvesting may indicate a long-term change in processes mediated by the microbial community with important consequences for forest productivity. These effects warrant more comprehensive investigation of the effects of harvesting on the structure of forest soil microbial communities and the functional consequences. PMID:19659501

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

    Science.gov (United States)

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

    2014-10-01

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

  18. Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system.

    Science.gov (United States)

    Anderson, Rika E; Beltrán, Mónica Torres; Hallam, Steven J; Baross, John A

    2013-02-01

    Physical and chemical gradients are dominant factors in shaping hydrothermal vent microbial ecology, where archaeal and bacterial habitats encompass a range between hot, reduced hydrothermal fluid and cold, oxidized seawater. To determine the impact of these fluid gradients on microbial communities inhabiting these systems, we surveyed bacterial and archaeal community structure among and between hydrothermal plumes, diffuse flow fluids, and background seawater in several hydrothermal vent sites on the Juan de Fuca Ridge using 16S rRNA gene diversity screening (clone libraries and terminal restriction length polymorphisms) and quantitative polymerase chain reaction methods. Community structure was similar between hydrothermal plumes and background seawater, where a number of taxa usually associated with low-oxygen zones were observed, whereas high-temperature diffuse fluids exhibited a distinct phylogenetic profile. SUP05 and Arctic96BD-19 sulfur-oxidizing bacteria were prevalent in all three mixing regimes where they exhibited overlapping but not identical abundance patterns. Taken together, these results indicate conserved patterns of redox-driven niche partitioning between hydrothermal mixing regimes and microbial communities associated with sinking particles and oxygen-deficient waters. Moreover, the prevalence of SUP05 and Arctic96BD-19 in plume and diffuse flow fluids indicates a more cosmopolitan role for these groups in the ecology and biogeochemistry of the dark ocean.

  19. Influence of microbial community structure of seed sludge on the properties of aerobic nitrifying granules.

    Science.gov (United States)

    Song, Zhiwei; Li, Ting; Wang, Qiuxu; Pan, Yu; Li, Lixin

    2015-09-01

    In order to evaluate the influence of microbial community structure of seed sludge on the properties of aerobic nitrifying granules, these granules were cultivated with different seed sludge, and the variation of microbial community and dominant bacterial groups that impact the nitrogen removal efficiency of the aerobic nitrifying granules were analyzed and identified using 16s rDNA sequence and denaturing gradient gel electrophoresis (DGGE) profiles. The results presented here demonstrated that the influence of the community structure of seed sludge on the properties of aerobic nitrifying granules was remarkable, and the granules cultivated by activated sludge from a beer wastewater treatment plant showed better performance, with a stable sludge volume index (SVI) value of 20mL/g, high extracellular polymeric substance (EPS) content of 183.3mg/L, high NH4(+)-N removal rate of 89.42% and abundant microbial population with 10 dominant bacterial groups. This indicated that activated sludge with abundant communities is suitable for use as seed sludge in culturing aerobic nitrifying granules. PMID:26354703

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  4. Influence of toxic cyanobacteria on community structure and microcystin accumulation of freshwater molluscs

    International Nuclear Information System (INIS)

    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

  5. Effect of slow-release urea on soil nematode community structure in a Chinese soybean field

    Institute of Scientific and Technical Information of China (English)

    Xuekun HOU; Ruichang ZHAI

    2009-01-01

    The effect of slow-release urea on soil nematode community structure was investigated in a soybean field in northeast China.Three treatments,no urea (CK),conventional urea (U) and slow-release urea (SRU),were arranged in a completely random design.The results show that the abundance of total nematodes was significantly higher in SRU than in CK and U.Significant differences in the abundance of bacterivores with colonizer-persister (cp) values 2-3,fungivores with cp 2 and herbivores with cp 3 were found among different treatments.Forty-one genera were identified,of which Acrobeloides,Aphelenchus and Heterodera were dominant.Soil nematode guilds and genera exhibited different responses to slow-release urea.The most trophic groups and genera had greater abundances in SRU than in CK and U.Slow-release urea had a positive effect on soil nematode community structure.

  6. The effect of salinity levels on the structure of zooplankton communities

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    International Nuclear Information System (INIS)

    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)

  9. Alternative Stable States in Size-Structured Communities : Patterns, Processes, and Mechanisms

    OpenAIRE

    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; ...

  10. Urban Ecological Stewardship: Understanding the Structure, Function and Network of Community-based Urban Land Management

    OpenAIRE

    Lindsay K. Campbell; Erika S. Svendsen

    2008-01-01

    Urban environmental stewardship activities are on the rise in cities throughout the Northeast. Groups participating in stewardship activities range in age, size, and geography and represent an increasingly complex and dynamic arrangement of civil society, government and business sectors. To better understand the structure, function and network of these community-based urban land managers, an assessment was conducted in 2004 by the research subcommittee of the Urban Ecology Collaborative. The ...

  11. Effects of grassland conversion and tillage intensities on soil microbial biomass, residues and community structure

    OpenAIRE

    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...

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

    OpenAIRE

    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...

  13. Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations▿†

    OpenAIRE

    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. Structure of a toothed cetacean community around a tropical island (Mayotte, Mozambique Channel)

    OpenAIRE

    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...

  15. Quantifying heterogeneous responses of fish community size structure using novel combined statistical techniques.

    Science.gov (United States)

    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

  16. Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management

    OpenAIRE

    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...

  17. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Energy Technology Data Exchange (ETDEWEB)

    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)

  18. Species diversity and community structure in trap-nesting bees in Southern Brazil

    OpenAIRE

    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...

  19. Change in Phylogenetic Community Structure during Succession of Traditionally Managed Tropical Rainforest in Southwest China

    OpenAIRE

    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...

  20. Statistical test for detecting community structure in real-valued edge-weighted graphs

    CERN Document Server

    Tokuda, Tomoki

    2016-01-01

    We propose a novel method to test the existence of community structure of undirected real-valued edge-weighted graph. The method is based on Wigner semicircular law on the asymptotic behavior of the random distribution for eigenvalues of a real symmetric matrix. We provide a theoretical foundation for this method and report on its performance in synthetic and real data, suggesting that our method outperforms other state-of-the-art methods.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

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

    2011-10-01

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

  3. Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

    Science.gov (United States)

    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.

  4. Macrozoobenthic community structure in two Portuguese estuaries: Relationship with organic enrichment and nutrient gradients

    Science.gov (United States)

    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.

  5. Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.

    Science.gov (United States)

    Jorquera, Milko A; Maruyama, Fumito; Ogram, Andrew V; Navarrete, Oscar U; Lagos, Lorena M; Inostroza, Nitza G; Acuña, Jacquelinne J; Rilling, Joaquín I; de La Luz Mora, María

    2016-10-01

    Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments. PMID:27406732

  6. Improved chalcopyrite bioleaching by Acidithiobacillus sp. via direct step-wise regulation of microbial community structure.

    Science.gov (United States)

    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.

  7. Improved chalcopyrite bioleaching by Acidithiobacillus sp. via direct step-wise regulation of microbial community structure.

    Science.gov (United States)

    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

  8. Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China.

    Science.gov (United States)

    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

  9. Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China.

    Directory of Open Access Journals (Sweden)

    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.

  10. Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8.

    Directory of Open Access Journals (Sweden)

    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.

  11. Diversity and network structure of invertebrate communities associated to Heliconia species in natural and human disturbed tropical rain forests

    OpenAIRE

    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...

  12. Patterns of the benthic community structure in coral reefs of the north western Caribbean

    OpenAIRE

    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...

  13. Community facilitation of problem structuring and decision making processes: Experiences from the EU LEADER+ programme

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    2009-01-01

    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...... contribute to long-term and sustainable development in these regions. The main tasks have been the organisation and facilitation of conferences and workshops to structure the problematic situation of identifying and designing innovative projects for the development of the community and to support decision...

  14. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Directory of Open Access Journals (Sweden)

    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.

  15. Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea ice.

    Science.gov (United States)

    Eddie, Brian; Juhl, Andrew; Krembs, Christopher; Baysinger, Charles; Neuer, Susanne

    2010-03-01

    Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice.

  16. Mangrove community in an abandoned brick kiln: A structural and association analysis

    Directory of Open Access Journals (Sweden)

    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.

  17. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Science.gov (United States)

    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

  18. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers.

    Directory of Open Access Journals (Sweden)

    Kelly L Cobaugh

    Full Text Available The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death. Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a periods of increased activity during decomposition are associated with particular taxa; and b human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem, respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance and Firmicutes (increased from 1.0 to 29.0%, with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%. Once decay rates slowed (10 - 23 d postmortem, respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9% and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional

  19. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots.

    Science.gov (United States)

    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

  20. Structure and spatial patterns of macrobenthic community in Tai Lake, a large shallow lake, China

    Science.gov (United States)

    Di Li,; Erickson, Richard A.; Song Tang,; Xuwen Li,; Zhichun Niu,; Xia Wang,; Hongling Liu,; Hongxia Yu,

    2016-01-01

    Tai Lake (Chinese: Taihu), the third-largest freshwater lake in China, suffers from harmful cyanobacteria blooms that are caused by economic development and population growth near the lake. Several studies have focused on phytoplankton in Tai Lake after a drinking water crisis in 2007; however, these studies primarily focused on microcystin bioaccumulation and toxicity to individual species without examining the effects of microcystin on macrobenthic community diversity. In this study, we conducted a survey of the lake to examine the effects of microcystine and other pollutants on marcobenthic community diversity. A totally of forty-nine species of macroinvertebrates were found in Tai Lake. Limnodrilus hoffmeisteri and Corbicula fluminea were the most abundant species. Cluster-analysis and one-way analysis of similarity (ANOSIM) identified three significantly different macrobenthic communities among the sample sites. More specifically, sites in the eastern bays, where aquatic macrophytes were abundant, had the highest diversity of macrobenthic communities, which were dominated by Bellamya aeruginosa, Bellamya purificata, L. hoffmeisteri, and Alocinma longicornis. Sites in Zhushan Bay contained relatively diverse communities, mainly composed of L. hoffmeisteri, C. fluminea, L. claparederanus, R. sinicus, and Cythura sp. Sites in the western region, Meiliang Bay and Wuli Bay had the lowest diversity, mainly composed ofL. hoffmeisteri, C. fluminea, Branchiura sowerbyi, and Rhyacodrilus sinicus. In addition, the relationships between macrobenthic metrics (Shannon–Wiener, Margalef, and Pielou) and environmental variables showed that community structure and spatial patterns of macrobenthos in Tai Lake were significantly influenced by chemical oxygen demand (CODCr), biochemical oxygen demand (BOD5), lead (Pb), and microcystin-LR (L for leucine and R for arginine). Our findings provide critical information that could help managers and policymakers

  1. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

    Science.gov (United States)

    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

  2. Comparative study of fermentation and methanogen community structure in the digestive tract of goats and rabbits.

    Science.gov (United States)

    Abecia, L; Fondevila, M; Rodríguez-Romero, N; Martínez, G; Yáñez-Ruiz, D R

    2013-05-01

    Methane is the most important anthropogenic contribution to climate change after carbon dioxide and represents a loss of feed energy for the animal, mainly for herbivorous species. However, our knowledge about the ecology of Archaea, the microbial group responsible for methane synthesis in the gut, is very poor. Moreover, it is well known that hindgut fermentation differs from rumen fermentation. The composition of archaeal communities in fermentation compartments of goats and rabbits were investigated using DGGE to generate fingerprints of archaeal 16S rRNA gene. Ruminal contents and faeces from five Murciano-Granadina goats and caecal contents of five commercial White New Zealand rabbits were compared. Diversity profile of methanogenic archaea was carried out by PCR-DGGE. Quantification of methanogenic archaea and the abundance relative to bacteria was determined by real-time PCR. Methanogenic archaeal species were relatively constant across species. Dendrogram from DGGE of the methanogen community showed one cluster for goat samples with two sub-clusters by type of sample (ruminal and faeces). In a second cluster, samples from rabbit were grouped. No differences were found either in richness or Shannon index as diversity indexes. Although the primer sets used was developed to investigate rumen methanogenic archaeal community, primers specificity did not affect the assessment of rabbit methanogen community structure. Rumen content showed the highest number or methanogenic archaea (log₁₀ 9.36), followed by faeces (log₁₀ 8.52) and showing rabbit caecum the lower values (log₁₀ 5.52). DGGE profile showed that pre-gastric and hindgut fermenters hold a very different methanogen community. Rabbits hold a microbial community of similar complexity than that in ruminants but less abundant, which agrees with the type of fermentation profile.

  3. Structure of parasite component communities of didelphid marsupials: insights from a comparative study.

    Science.gov (United States)

    Jiménez, F Agustín; Catzeflis, François; Gardner, Scott L

    2011-10-01

    chance, in the structuring of parasite communities in marsupials. PMID:21506798

  4. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots

    Science.gov (United States)

    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

  5. Structure of parasite component communities of didelphid marsupials: insights from a comparative study.

    Science.gov (United States)

    Jiménez, F Agustín; Catzeflis, François; Gardner, Scott L

    2011-10-01

    chance, in the structuring of parasite communities in marsupials.

  6. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

    Science.gov (United States)

    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

  7. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots.

    Science.gov (United States)

    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

  8. [Sabina przewalskii community structure in the upper reaches of Minjiang River].

    Science.gov (United States)

    Chen, Wennian; Wu, Ning; Luo, Peng

    2005-02-01

    In this paper, the physiognomy and the structure of Sabina przewalskii community were studied by sample plot method. The results showed that in the life spectrum of the community, hemicryptophyte was dominated, but therophytes also occurred frequently, which presented some features of temperate vegetation. The vertical structure of the community was quite simple, consisting of tree layer, shrub layer and herb layer, and there were no interstratum plants and ground layer. Sabina przewalskii was the only species in the tree layer. In fruticose stratum, the important value of Spiraea alpina was 153.3, ranking the first; while in herb layer, the important value of Carex caespifosa ranked the first, amounting to 36.8. Among the three plot groups on different slopes, spiny-shrubs such as Berberis wilsonae and Caragana erinacea grown on small slope were more than those on bigger slope, so did unpalatable grasses such as Pedicularis axillaries and Artemisia tauguticat, which mainly owed to retrogressive succession caused by frequently grazing. The age and height structures of Sabina przewalskii population indicated a declining trend, and the community would develop retrogressively if disturbances (e.g., grazing) could not be reduced. The disturbance caused by livestock was more obvious in the plot group on small slope than on bigger slope, and livestock mainly destroyed seedlings and small trees, which made tree population be impossible to regenerate. The coverage of upper layers had a notable impact on the lower layers, and there wasn't any correlation between coverage and diversity index (Shannon-Wiener Index) in each layer. PMID:15852907

  9. Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands.

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  11. Hemosporid (Apicomplexa, Hematozoea, Hemosporida) community structure off pattern in wintering wild turkeys.

    Science.gov (United States)

    Fedynich, A M; Rhodes, O E

    1995-07-01

    The hemosporid community of 76 wild turkeys (Meleagris gallopavo silvestris) from South Carolina (USA) was examined using thin blood smears collected during January and February 1994. High prevalences and low abundances of hemosporids characterized this community. Leucocytozoon smithi and Haemoproteus meleagridis occurred in 100% and 54% of the turkeys, respectively; a Plasmodium sp. was found in one bird. Prevalence of H. meleagridis was significantly higher in juvenile turkeys than adults, but prevalences did not differ significantly among four trap sites or by host sex. Mean (+/- SE) intensities of L. smithi, H. meleagridis, and Plasmodium sp. were 3.4 +/- 0.4, 1.8 +/- 0.3, and 3.0 per 10,000 erythrocytes, respectively. Abundances of L. smithi, H. meleagridis, and Plasmodium sp. were 3.4 +/- 0.9 +/- 0.2, and < 0.1 +/- < 0.1 per 10,000 erythrocytes, respectively. Juvenile turkeys had higher rank abundance values of L. smithi than adults, whereas no differences were found among trap sites or between sexes. No differences in rank abundances of H. meleagridis were found among trap sites, host age, or host sex variables. Collectively, both common hemosporid species varied by host age, reflecting higher abundances in juvenile turkeys. patterns of hemosporid prevalence appeared similar to patterns found in subtropical regions. Based on our data, we recommend using prevalence and abundance data to analyze the structure and pattern of hemosporid communities at the component community level.

  12. Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

    International Nuclear Information System (INIS)

    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.

  13. Plant growth and soil microbial community structure of legumes and grasses grown in monoculture or mixture

    Institute of Scientific and Technical Information of China (English)

    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.

  14. Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Community Structure of a Bank-Firm Credit Network in Japan

    Science.gov (United States)

    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.

  16. Community structure of shallow rocky shore fish in a tropical bay of the southwestern Atlantic

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  18. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Community Structure and Survival of Tertiary Relict Thuja sutchuenensis (Cupressaceae) in the Subtropical Daba Mountains, Southwestern China

    OpenAIRE

    Tang, Cindy Q.; Yongchuan Yang; Masahiko Ohsawa; Arata Momohara; Si-Rong Yi; Kevin Robertson; Kun Song; Shi-Qiang Zhang; Long-Yuan He

    2015-01-01

    A rare coniferous Tertiary relict tree species, Thuja sutchuenensis Franch, has survived in the Daba Mountains of southwestern China. It was almost eliminated by logging during the past century. We measured size and age structures and interpreted regeneration dynamics of stands of the species in a variety of topographic contexts and community associations. Forest communities containing T. sutchuenensis were of three types: (1) the Thuja community dominated by T. sutchuenensis, growing on clif...

  20. SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF SUCKING LICE IN YUNNAN, CHINA

    Institute of Scientific and Technical Information of China (English)

    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.

  1. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil

    Science.gov (United States)

    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

  2. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Science.gov (United States)

    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.

  3. Dynamic changes in microbial activity and community structure during biodegradation of petroleum compounds: A laboratory experiment

    Institute of Scientific and Technical Information of China (English)

    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.

  4. Soil enzymatic activities and microbial community structure with different application rates of Cd and Pb

    Institute of Scientific and Technical Information of China (English)

    KHAN Sardar; CAO Qing; HESHAM Abd El-Latif; XIA Yue; HE Ji-zheng

    2007-01-01

    This study focused on the changes of soil microbial diversity and potential inhibitory effects of heavy metals on soil enzymatic activities at different application rates of Cd and Pb. The soil used for experiments was collected from Beijing and classified as endoaquepts. Pots containing 500 g of the soil with different Cd or/and Pb application rates were incubated for a period of 0, 2, 9, 12 weeks in a glasshouse and the soil samples were analyzed for individual enzymes, including catalase, alkaline phosphatase and dehydrogenase, and the changes of microbial community structure. Results showed that heavy metals slightly inhibited the enzymatic activities in all the samples spiked with heavy metals. The extent of inhibition increased significantly with increasing level of heavy metals, and varied with the incubation periods. The soil bacterial community structure, as determined by polymerase chain reaction-denaturing gradient gel electrophoresis techniques, was different in the contaminated samples as compared to the control. The highest community change was observed in the samples amended with high level of Cd. Positive correlations were observed among the three enzymatic activities, but negative correlations were found between the amounts of the heavy metals and the enzymatic activities.

  5. Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.

    Science.gov (United States)

    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

  6. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Science.gov (United States)

    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

  7. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    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.

  8. Habitat heterogeneity determines climate impact on zooplankton community structure and dynamics.

    Directory of Open Access Journals (Sweden)

    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.

  9. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes).

    Science.gov (United States)

    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

  10. Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

    Directory of Open Access Journals (Sweden)

    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.

  11. Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil

    Directory of Open Access Journals (Sweden)

    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.

  12. Change and recovery of coastal mesozooplankton community structure during the Deepwater Horizon oil spill

    Science.gov (United States)

    Carassou, L.; Hernandez, F. J.; Graham, W. M.

    2014-12-01

    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.

  13. Change and recovery of coastal mesozooplankton community structure during the Deepwater Horizon oil spill

    International Nuclear Information System (INIS)

    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)

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

    Science.gov (United States)

    Sheik, Cody S; Stevenson, Emily I; Den Uyl, Paul A; Arendt, Carli A; Aciego, Sarah M; Dick, Gregory J

    2015-01-01

    Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier's terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  15. Ecological assessment of an intermitent Mediterranean river using community structure and function: evaluating the role of different organism groups

    OpenAIRE

    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...

  16. Structured Communities, Science Instruction Development, and the Use of Blogging in a Pre-Service Elementary Teacher Education Program

    Science.gov (United States)

    Wall, Steven C.; Anderson, Janice; Justice, Julie

    2014-01-01

    This study evaluates the use of blogging and what it reveals about the development of science teaching ability in pre-service elementary education majors. The investigation occurs in a structured community and takes into consideration interactions among community members as they reflect on their own experiences and respond to the blogs of other…

  17. EFFECTS OF COVER CROPPING AND PLASTICULTURE ON SOIL AND RHIZOSPHERE MICROBIAL COMMUNITY STRUCTURE IN TOMATO PRODUCTION SYSTEMS

    Science.gov (United States)

    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...

  18. Complex networks from experimental horizontal oil–water flows: Community structure detection versus flow pattern discrimination

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

    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

  20. Differential response of high-elevation planktonic bacterial community structure and metabolism to experimental nutrient enrichment.

    Directory of Open Access Journals (Sweden)

    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

  1. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Structure of dung beetle communities in an altitudinal gradient of neotropical dry forest.

    Science.gov (United States)

    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

  3. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington: Community Structural Responses to Seasonal Cycling

    Directory of Open Access Journals (Sweden)

    Stephen R Lindemann

    2013-11-01

    Full Text Available 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 and disassembles each fall and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO42- 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 sequencing 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.

  4. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta.

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  6. Benthic Ammonia Oxidizers Differ in Community Structure and Biogeochemical Potential Across a Riverine Delta

    Directory of Open Access Journals (Sweden)

    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.

  7. Bacterial community structure and nitrogen transformation in hyporheic zones of arid-land streams

    Science.gov (United States)

    Zeglin, L. H.; Crenshaw, C. L.; Dahm, C. N.; Takacs-Vesbach, C.

    2007-12-01

    Hyporheic zones of desert streams can be areas of high biological activity and consequent nutrient transformation, particularly where land use change increases nutrient concentrations in a stream. Does hyporheic bacterial community composition vary, and does this biotic heterogeneity covary with water and nutrient supply? Bromide (Br-) and 15N-NO3- was injected for 24 hr in six streams (three "natural" reference streams, three streams in agricultural/urbanized catchments) in New Mexico and Arizona, USA. Four transects of 3 to 4 wells were placed along a longitudinal gradient within the study reach, and from these hyporheic water and gas samples were collected during and after each experiment. Gas samples were analyzed for O2, 15N2O, and 15N2. Hyporheic water samples were analyzed for major cations and anions, DOC, 15NO3- and 15NH4+. Bacterial diversity of hyporheic water was assessed using Denaturing Gradient Gel Electrophoresis (DGGE). There was high spatial and temporal variability in hyporheic bacterial community structure, connection with surface water and nutrient concentrations both within and among streams. For example, mean subsurface DGGE band richness per stream ranged from 9 to 21, and surface water comprised between 0 to 100 percent of hyporheic water in each well. There were strong differences in bacterial richness between streams (ANOVA, p nutrient concentration. 15NH4+ levels were higher in modified stream than reference stream subsurface waters, suggesting dissimilatory nitrate reduction to ammonium (DNRA) may be an important process in these hyporheic sediments. Our results to date suggest that though hyporheic microbial community structure is highly heterogeneous, this biological variability may be due to different factors than variability in stream nitrogen cycling function. Further work will identify dominant sequences within these bacterial communities and investigate within-stream heterogeneity.

  8. Structure and phylogenetic diversity of post-fire ectomycorrhizal communities of maritime pine.

    Science.gov (United States)

    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

  9. [Impact of Mikania micrantha invasion on soil meso- and micro-invertebrate community structure].

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  11. Local and regional effects on community structure of dung beetles in a mainland-island scenario.

    Directory of Open Access Journals (Sweden)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  13. Mineralization Of PAHs In Coal-Tar Impacted Aquifer Sediments And Associated Microbial Community Structure Investigated With FISH

    Science.gov (United States)

    The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detect...

  14. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

    DEFF Research Database (Denmark)

    Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.;

    2014-01-01

    Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction frag...

  15. Variations in community structure and diversity associated with methane-rich sediments offshore southwestern Taiwan

    Science.gov (United States)

    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

  16. Small copepods structuring mesozooplankton community dynamics in a tropical estuary-coastal system

    Science.gov (United States)

    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

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

    OpenAIRE

    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...

  18. Can stable isotope ratios provide for community-wide measures of trophic structure?

    Science.gov (United States)

    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

  19. Microbial community structure of activated sludge in treatment plants with different wastewater compositions

    Directory of Open Access Journals (Sweden)

    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

  20. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.

    Science.gov (United States)

    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

  1. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    Directory of Open Access Journals (Sweden)

    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

  2. Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress

    Institute of Scientific and Technical Information of China (English)

    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.

  3. Structure and diversity of scleractinia coral communities along the west seashore of Xuwen County

    OpenAIRE

    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...

  4. Ocean plankton. Determinants of community structure in the global plankton interactome.

    Science.gov (United States)

    Lima-Mendez, Gipsi; Faust, Karoline; Henry, Nicolas; Decelle, Johan; Colin, Sébastien; Carcillo, Fabrizio; Chaffron, Samuel; Ignacio-Espinosa, J Cesar; Roux, Simon; Vincent, Flora; Bittner, Lucie; Darzi, Youssef; Wang, Jun; Audic, Stéphane; Berline, Léo; Bontempi, Gianluca; Cabello, Ana M; Coppola, Laurent; Cornejo-Castillo, Francisco M; d'Ovidio, Francesco; De Meester, Luc; Ferrera, Isabel; Garet-Delmas, Marie-José; Guidi, Lionel; Lara, Elena; Pesant, Stéphane; Royo-Llonch, Marta; Salazar, Guillem; Sánchez, Pablo; Sebastian, Marta; Souffreau, Caroline; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Gorsky, Gabriel; Not, Fabrice; Ogata, Hiroyuki; Speich, Sabrina; Stemmann, Lars; Weissenbach, Jean; Wincker, Patrick; Acinas, Silvia G; Sunagawa, Shinichi; Bork, Peer; Sullivan, Matthew B; Karsenti, Eric; Bowler, Chris; de Vargas, Colomban; Raes, Jeroen

    2015-05-22

    Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

  5. Insect community structure and function in Upper Three Runs, Savannah River Site, South Carolina

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    OpenAIRE

    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...

  7. Effect of canopy density on litter invertebrate community structure in pine forests

    OpenAIRE

    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...

  8. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

    Science.gov (United States)

    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

  9. Unravelling the community structure of the climate system by using lags and symbolic time-series analysis

    Science.gov (United States)

    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.

  10. Preliminary study of the mite community structure in different black truffle producing soils

    Directory of Open Access Journals (Sweden)

    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. 

  11. Microbial community structure and performance of an anaerobic reactor digesting cassava pulp and pig manure.

    Science.gov (United States)

    Panichnumsin, P; Ahring, B; Nopharatana, A; Chaiprasert, P

    2012-01-01

    Microbial community dynamics in response to changes in substrate types (i.e. pig manure (PM), cassava pulp (CP) and mixtures of PM and CP) were investigated in an anaerobic continuously stirred tank reactor (CSTR). Molecular identification of bacterial and archaeal domains were performed, using a 16S rDNA clone library with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) screening and phylogenetic analysis. Analysis of bacterial clone libraries revealed that the differences in the community structure corresponded to the substrate types. However, the Bacteroidetes were the most abundant group in all substrates, followed by the Clostridia. With pure PM, the dominant bacterial groups were Bacteroidales, Clostridia and Paludibacter. With a co-substrate, at CP to PM (CP:PM) ratio of 50:50, the sequences analysis revealed the greatest diversity of bacterial communities at class level, and the sequences affiliated with Cytophaga sp. became an exclusive predominant. With CP alone, Bacteroides sp. was the dominant species and this reactor had the lowest diversity of bacteria. Archaea observed in the CSTR fed with all substrate types were Methanosaeta sp., Methanosaeta concilii and Methanospirillum hungatei. Among the Archaea, Methanosaeta sp. was the exclusive predominant. The relative distribution of Archaea also changed regarding to the substrate types.

  12. Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

    Energy Technology Data Exchange (ETDEWEB)

    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. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    Directory of Open Access Journals (Sweden)

    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.

  14. [Macrobenthic community structure of intertidal zone of Rushan Bay in spring].

    Science.gov (United States)

    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

  15. Differences in coprophilous beetle communities structure in Sierra de Minas (Uruguay): a mosaic landscape.

    Science.gov (United States)

    González-Vainer, Patricia; Morelli, E; Defeo, O

    2012-10-01

    Coprophilous beetles represent an abundant and rich group with critical importance in the functioning of terrestrial ecosystems. Most coprophagous beetles have a stenotopic distribution in relation to vegetation types. Because of this, they are usually very sensitive to environmental changes and are considered well suited as bioindicator organisms. The aim of this study was to analyze variations in coprophilous beetle assemblages in natural and anthropogenic habitats. Coprophilous beetle communities were sampled monthly for 1 year using pitfall traps baited with cow dung, in native xeric upland forests, 15-years-old plantations of Pinus elliottii and pastures in Sierra de Minas, Lavalleja, Uruguay. A total of 7,436 beetles were caught and identified to species or morphospecies level. The most abundant families were Aphodiidae, Scarabaeidae, and Staphylinidae. Differences in species richness, abundance, Shannon index, evenness, and dominance were detected between habitats. Abundances of most frequent families were significantly higher in both kinds of forests. Species richness and diversity of Aphodiidae and Staphylinidae were higher in forests, while Scarabaeidae showed the highest richness and diversity in pine plantations. Species composition significantly differed between habitats. Uroxys terminalis Waterhouse and Ataenius perforatus Harold typified the assemblages in native forests and pine plantations and also discriminated both communities because of their differential pattern of abundance between habitats. Typifying species in pastures were Onthophagus hirculus, Ateuchus robustus (Harold), and Ataenius platensis Blanchard. Habitat type had a strong effect on the coprophilous beetle community structure and composition. PMID:23950086

  16. pH dominates variation in tropical soil archaeal diversity and community structure.

    Science.gov (United States)

    Tripathi, Binu M; Kim, Mincheol; Lai-Hoe, Ang; Shukor, Nor A A; Rahim, Raha A; Go, Rusea; Adams, Jonathan M

    2013-11-01

    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.

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

    Science.gov (United States)

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

    2014-02-01

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

  18. Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

    Institute of Scientific and Technical Information of China (English)

    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.

  19. Zooplankton community structure in the Yellow Sea and East China Sea in autumn

    Directory of Open Access Journals (Sweden)

    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.

  20. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    KAUST Repository

    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.

  1. Effect of trichloroethylene and tetrachloroethylene on methane oxidation and community structure of methanotrophic consortium.

    Science.gov (United States)

    Choi, Sun-Ah; Lee, Eun-Hee; Cho, Kyung-Suk

    2013-01-01

    The methane oxidation rate and community structure of a methanotrophic consortium were analyzed to determine the effects of trichloroethylene (TCE) and tetrachloroethylene (PCE) on methane oxidation. The maximum methane oxidation rate (Vmax ) of the consortium was 326.8 μmol·g-dry biomass(-1)·h(-1), and it had a half-saturation constant (Km ) of 143.8 μM. The addition of TCE or PCE resulted in decreased methane oxidation rates, which were decreased from 101.73 to 5.47-24.64 μmol·g-dry biomass(-1)·h(-1) with an increase in the TCE-to-methane ratio, and to 61.95-67.43 μmol·g-dry biomass(-1)·h(-1) with an increase in the PCE-to-methane ratio. TCE and PCE were non-competitive inhibitors for methane oxidation, and their inhibition constants (Ki ) were 33.4 and 132.0 μM, respectively. When the methanotrophic community was analyzed based on pmoA using quantitative real-time PCR (qRT-PCR), the pmoA gene copy numbers were shown to decrease from 7.3 ± 0.7 × 10(8) to 2.1-5.0 × 10(7) pmoA gene copy number · g-dry biomass(-1) with an increase in the TCE-to-methane ratio and to 2.5-7.0 × 10(7) pmoA gene copy number · g-dry biomass(-1) with an increase in the PCE-to-methane ratio. Community analysis by microarray demonstrated that Methylocystis (type II methanotrophs) were the most abundant in the methanotrophic community composition in the presence of TCE. These results suggest that toxic effects caused by TCE and PCE change not only methane oxidation rates but also the community structure of the methanotrophic consortium.

  2. Effect of long-term drainage of peatland on whole-profile microbial community structure

    Science.gov (United States)

    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

  3. Concentration of petroleum-hydrocarbon contamination shapes fungal endophytic community structure in plant roots

    Directory of Open Access Journals (Sweden)

    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

  4. The effects of climate variability on the structure of the phytoplankton community in Tumaco Bay, Colombia

    Science.gov (United States)

    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

  5. Community structure of microorganisms associated with reddish-brown iron-rich snow.

    Science.gov (United States)

    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

  6. The Effect of Nitrogen Deposition on Plant Performance and Community Structure: Is It Life Stage Specific?

    Science.gov (United States)

    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

  7. The Impact of Host Rock Geochemistry on Bacterial Community Structure in Oligotrophic Cave Environments.

    Directory of Open Access Journals (Sweden)

    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.

  8. Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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).

  10. Earthworm-Mycorrhiza Interactions Can Affect the Diversity, Structure and Functioning of Establishing Model Grassland Communities

    Science.gov (United States)

    Zaller, Johann G.; Heigl, Florian; Grabmaier, Andrea; Lichtenegger, Claudia; Piller, Katja; Allabashi, Roza; Frank, Thomas; Drapela, Thomas

    2011-01-01

    belowground-aboveground linkages involving earthworms and AMF are important mediators of the diversity, structure and functioning of plant communities. PMID:22216236

  11. Earthworm-mycorrhiza interactions can affect the diversity, structure and functioning of establishing model grassland communities.

    Directory of Open Access Journals (Sweden)

    Johann G Zaller

    demonstrates that belowground-aboveground linkages involving earthworms and AMF are important mediators of the diversity, structure and functioning of plant communities.

  12. Plant community structure regulates responses of prairie soil respiration to decadal experimental warming.

    Science.gov (United States)

    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

  13. Enhanced detectability of community structure in multilayer networks through layer aggregation

    CERN Document Server

    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. Effect of biodiesel addition on microbial community structure in a simulated fuel storage system.

    Science.gov (United States)

    Restrepo-Flórez, Juan-Manuel; Bassi, Amarjeet; Rehmann, Lars; Thompson, Michael R

    2013-11-01

    Understanding changes in microbial structure due to biodiesel storage is important both for protecting integrity of storage systems and fuel quality management. In this work a simulated storage system was used to study the effect of biodiesel (0%, 25%, 50%, 75% and 100%) on a microbial population, which was followed by community level physiological profiling (CLPP), 16s rDNA analysis and plating in selective media. Results proved that structure and functionality were affected by biodiesel. CLPP showed at least three populations: one corresponding to diesel, one to biodiesel and one to blends of diesel and biodiesel. Analysis of 16s rDNA revealed that microbial composition was different for populations growing in diesel and biodiesel. Genera identified are known for degradation of hydrocarbons and emulsifier production. Maximum growth was obtained in biodiesel; however, microbial counts in standard media were lower for this samples. Acidification of culture media was observed at high biodiesel concentration.

  15. [Effects of Organic and Inorganic Slow-Release Compound Fertilizer on Different Soils Microbial Community Structure].

    Science.gov (United States)

    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

  16. A phylogenetic approach to octocoral community structure in the deep Gulf of Mexico

    Science.gov (United States)

    Quattrini, Andrea M.; Etnoyer, Peter J.; Doughty, Cheryl; English, Lisa; Falco, Rosalia; Remon, Natasha; Rittinghouse, Matthew; Cordes, Erik E.

    2014-01-01

    Deep-sea communities are becoming increasingly vulnerable to anthropogenic disturbances, as fishing, hydrocarbon exploration and extraction, and mining activities extend into deeper water. Negative impacts from such activities were recently documented in the Gulf of Mexico (GoM), where the Deepwater Horizon oil spill caused substantial damage to a deep-water octocoral community. Although a faunal checklist and numerous museum records are currently available for the entire GoM, local-scale diversity and assemblage structure of octocoral communities remains unknown, particularly in deep water. On a series of recent cruises (2008-2011) using remotely operated vehicles, 435 octocorals were collected from 33 deep-water sites (250-2500 m) in the northern GoM. To elucidate species boundaries, the extended mitochondrial barcode (COI+igr1+msh) was successfully