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Sample records for actinobacterial community structure

  1. 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.

  2. Land use intensity controls actinobacterial community structure

    NARCIS (Netherlands)

    Hill, Patrick; Krištůfek, Václav; Dijkhuizen, Lubbert; Boddy, Christopher; Kroetsch, David; Elsas, Jan Dirk van

    2011-01-01

    Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicom

  3. 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.

  4. 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.

  5. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Hiras, Jennifer; Wu, Yu-Wei; Deng, Kai; Nicora, Carrie D.; Aldrich, Joshua T.; Frey, Dario; Kolinko, Sebastian; Robinson, Errol W.; Jacobs, Jon M.; Adams, Paul D.; Northen, Trent R.; Simmons, Blake A.; Singer, Steven W.

    2016-08-23

    ABSTRACT

    Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the cellulose chain. During cultivation of thermophilic cellulolytic microbial communities, substantial differences were observed in the crystalline cellulose saccharification activities of supernatants recovered from divergent lineages. Comparative community proteomics identified a set of cellulases from a population closely related to actinobacteriumThermobispora bisporathat were highly abundant in the most active consortium. Among the cellulases fromT. bispora, the abundance of a GH family 12 (GH12) protein correlated most closely with the changes in crystalline cellulose hydrolysis activity. This result was surprising since GH12 proteins have been predominantly characterized as enzymes active on soluble polysaccharide substrates. Heterologous expression and biochemical characterization of the suite ofT. bisporahydrolytic cellulases confirmed that the GH12 protein possessed the highest activity on multiple crystalline cellulose substrates and demonstrated that it hydrolyzes cellulose chains by a predominantly random mechanism. This work suggests that the role of GH12 proteins in crystalline cellulose hydrolysis by cellulolytic microbes should be reconsidered.

    IMPORTANCECellulose is the most abundant organic polymer on earth, and its enzymatic hydrolysis is a key reaction in the global carbon cycle and the conversion of plant biomass to biofuels. The glycoside hydrolases that depolymerize crystalline cellulose have been primarily characterized from isolates. In this study, we demonstrate that adapting microbial consortia from compost to grow on crystalline cellulose

  6. Actinobacterial melanins: current status and perspective for the future.

    Science.gov (United States)

    Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

    2013-10-01

    Melanins are enigmatic pigments that are produced by a wide variety of microorganisms including several species of bacteria and fungi. Melanins are biological macromolecules with multiple important functions, yet their structures are not well understood. Melanins are frequently used in medicine, pharmacology, and cosmetics preparations. Melanins also have great application potential in agriculture industry. They have several biological functions including photoprotection, thermoregulation, action as free radical sinks, cation chelators, and antibiotics. Plants and insects incorporate melanins as cell wall and cuticle strengtheners, respectively. Actinobacteria are the most economically as well as biotechnologically valuable prokaryotes. However, the melanin properties are, in general, poorly understood. In this review an evaluation is made on the present state of research on actinobacterial melanins and its perspectives. The highlights include the production and biotechnological applications of melanins in agriculture, food, cosmetic and medicinal fields. With increasing advancement in science and technology, there would be greater demands in the future for melanins produced by actinobacteria from various sources.

  7. A guide to successful bioprospecting: informed by actinobacterial systematics.

    Science.gov (United States)

    Goodfellow, Michael; Fiedler, Hans-Peter

    2010-08-01

    New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening 'old friends' leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.

  8. 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

  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. Discovering network structure beyond communities.

    Science.gov (United States)

    Nishikawa, Takashi; Motter, Adilson E

    2011-01-01

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

  13. Discovering Network Structure Beyond Communities

    CERN Document Server

    Nishikawa, Takashi; 10.1038/srep00151

    2011-01-01

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

  14. 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.

  15. Significant Scales in Community Structure

    CERN Document Server

    Traag, V A; Van Dooren, P

    2013-01-01

    Many complex networks show signs of modular structure, uncovered by community detection. Although many methods succeed in revealing various partitions, it remains difficult to detect at what scale some partition is significant. This problem shows foremost in multi-resolution methods. We here introduce an efficient method for scanning for resolutions in one such method. Additionally, we introduce the notion of "significance" of a partition, based on subgraph probabilities. Significance is independent of the exact method used, so could also be applied in other methods, and can be interpreted as the gain in encoding a graph by making use of a partition. Using significance, we can determine "good" resolution parameters, which we demonstrate on benchmark networks. Moreover, optimizing significance itself also shows excellent performance. We demonstrate our method on voting data from the European Parliament. Our analysis suggests the European Parliament has become increasingly ideologically divided and that nationa...

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

    Science.gov (United States)

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

    2016-01-01

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

  17. 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.

  18. 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...

  19. Social significance of community structure: Statistical view

    CERN Document Server

    Li, Hui-Jia

    2015-01-01

    Community structure analysis is a powerful tool for social networks, which can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of community structure partitioned is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a novel framework analyzing the significance of social community specially. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of nodes and their corresponding leaders. Then, using log-likelihood sco...

  20. Matching Community Structure Across Online Social Networks

    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...

  1. Social significance of community structure: statistical view.

    Science.gov (United States)

    Li, Hui-Jia; Daniels, Jasmine J

    2015-01-01

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

  2. Social significance of community structure: Statistical view

    Science.gov (United States)

    Li, Hui-Jia; Daniels, Jasmine J.

    2015-01-01

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

  3. Matching Community Structure Across Online Social Networks

    OpenAIRE

    Lin LI; Campbell, W. M.

    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 detecti...

  4. Understanding Microbial Communities: Function, Structure and Dynamics

    Science.gov (United States)

    2015-02-11

    microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014

  5. The cell aggregating propensity of probiotic actinobacterial isolates: isolation and characterization of the aggregation inducing peptide pheromone.

    Science.gov (United States)

    Muthu Selvam, Ramu; Vinothini, Gopal; Palliyarai Thaiyammal, Sethuramalingam; Latha, Selvanathan; Chinnathambi, Arunachalam; Dhanasekaran, Dharumadurai; Padmanabhan, Parasuraman; Ali Alharbi, Sulaiman; Archunan, Govindaraju

    2016-01-01

    The auto-aggregating ability of a probiotic is a prerequisite for colonization and protection of the gastrointestinal tract, whereas co-aggregation provides a close interaction with pathogenic bacteria. Peptide pheromone mediated signaling has been studied in several systems. However, it has not yet been explored in prokaryotes, especially actinobacteria. Hence, in the present study, the diffusible aggregation promoting factor was purified from the culture supernatant of a potent actinobacterial probiont and characterized using 20 different actinobacterial cultures isolated from the gut region of chicken and goat. The results showed that the pheromone-like compound induces the aggregation propensity of treated isolates. The factor was found to be a heat stable, acidic pH resistant, low molecular weight peptide which enhances the biofilm forming ability of other actinobacterial isolates. The aggregation promoting factor represents a bacterial sex factor (pheromone) and its characterization confirms its usage in the probiotic formulation.

  6. 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.

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

    Science.gov (United States)

    Nimaichand, Salam; Devi, Asem Mipeshwaree; Tamreihao, K; Ningthoujam, Debananda S; Li, Wen-Jun

    2015-01-01

    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.

  8. 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.

  9. Discovering Network Structure Beyond Communities

    OpenAIRE

    Nishikawa, Takashi; Adilson E Motter

    2011-01-01

    To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes chara...

  10. 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

  11. 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.

  12. Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

    Science.gov (United States)

    Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2015-04-01

    Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg, with increments in fungal and

  13. 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.

  14. Shifting Niches for Community Structure Detection

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  15. 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......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 determinants of community structure. In this study, we first examined the relative importance of environmental gradients, microclimate, and food resources in driving spatial variation in the structure of detrital communities in forests of the southeastern USA. Then, in order to assess whether the determinants...... for the effect of climatic variation along the elevational gradient, food resource addition and microclimate alteration influenced the richness and abundance of some taxa. However, the effect of food resource addition and microclimate alteration on the richness and abundance of arthropods did not vary...

  16. 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.

  17. School, Community Leadership, and Election Structure

    Science.gov (United States)

    Allen, Ann

    2008-01-01

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

  18. Information transfer in community structured multiplex networks

    Directory of Open Access Journals (Sweden)

    Albert eSolé Ribalta

    2015-08-01

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

  19. 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...

  20. Stochastic blockmodels and community structure in networks

    CERN Document Server

    Karrer, Brian

    2010-01-01

    Stochastic blockmodels have been proposed as a tool for detecting community structure in networks as well as for generating synthetic networks for use as benchmarks. Most blockmodels, however, ignore variation in vertex degree, making them unsuitable for applications to real-world networks, which typically display broad degree distributions that can significantly distort the results. Here we demonstrate how the generalization of blockmodels to incorporate this missing element leads to an improved objective function for community detection in complex networks. We also propose a heuristic algorithm for community detection using this objective function or its non-degree-corrected counterpart and show that the degree-corrected version dramatically outperforms the uncorrected one in both real-world and synthetic networks.

  1. 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.

  2. 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.

  3. A cheating limit for structured communities

    Energy Technology Data Exchange (ETDEWEB)

    Perelson, Alan S [Los Alamos National Laboratory; Gerrish, Philip J [Los Alamos National Laboratory

    2008-01-01

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

  4. Collective prediction based on community structure

    Science.gov (United States)

    Jiang, Yasong; Li, Taisong; Zhang, Yan; Yan, Yonghong

    2017-01-01

    Collective prediction algorithms have been used to improve performances when network structures are involved in prediction tasks. The training dataset of such tasks often contain information of content, links and labels, while the testing dataset have only content and link information. Conventional collective prediction algorithms conduct predictions based on the content of a node and the information of its direct neighbors with a base classifier. However, the information of some direct neighbor nodes may be not consistent with the target one. In addition, the information of indirect neighbors can be helpful when that of direct neighbors is scant. In this paper, instead of using information of direct neighbors, we propose to apply community structures in networks to prediction tasks. A community detection method is aggregated into the collective prediction process to improve prediction performance. Experimental results show that the proposed algorithm outperforms a number of standard prediction algorithms specially under conditions that labeled training dataset are limited.

  5. 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.

  6. 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.

  7. Epidemic spreading on complex networks with community structures

    CERN Document Server

    Stegehuis, Clara; van Leeuwaarden, Johan S H

    2016-01-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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 ...

  12. 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…

  13. 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 ...

  14. Typology of State-Level Community College Governance Structures

    Science.gov (United States)

    Fletcher, Jeffrey A.; Friedel, Janice Nahra

    2017-01-01

    Despite having a well-documented history about community colleges across the United States, relatively few discussions have covered state-level governance structures. To understand the typology of state community college governance structures, it must first be recognized that community college governance is characterized as a complex web of…

  15. 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.

  16. 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.

  17. 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.

  18. Pinning controllability of complex networks with community structure.

    Science.gov (United States)

    Miao, Qingying; Tang, Yang; Kurths, Jürgen; Fang, Jian-an; Wong, W K

    2013-09-01

    In this paper, we study the controllability of networks with different numbers of communities and various strengths of community structure. By means of simulations, we show that the degree descending pinning scheme performs best among several considered pinning schemes under a small number of pinned nodes, while the degree ascending pinning scheme is becoming more powerful by increasing the number of pinned nodes. It is found that increasing the number of communities or reducing the strength of community structure is beneficial for the enhancement of the controllability. Moreover, it is revealed that the pinning scheme with evenly distributed pinned nodes among communities outperforms other kinds of considered pinning schemes.

  19. Influence of community structure on the synchronization of power network

    Science.gov (United States)

    Yang, Li-Xin; Jiang, Jun; Liu, Xiao-Jun

    2016-12-01

    This paper studies the synchronizability of power network with community structure. Second-order Kuramoto-like oscillators with dissimilar natural frequencies are used as a coarse-scale model for an electrical power network that contains generators and consumers. The impact of community structure on frequency synchronization of power network is investigated, focusing on the parameters such as community strength, community number and connection strategy between communities. Numerical simulations show that increasing the community strength above a certain critical threshold or adding new communities to the network will be beneficial for the synchronization. Of course, connecting high-degree nodes among communities will be a best strategy to enhance synchronization. Furthermore, it is observed that the synchronizability of the network is significantly influenced by adding new links with different characteristics.

  20. A new dynamic null model for phylogenetic community structure.

    Science.gov (United States)

    Pigot, Alex L; Etienne, Rampal S

    2015-02-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.

  1. Enhancing community detection by using local structural information

    Science.gov (United States)

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

    2016-03-01

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

  2. 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.

  3. 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…

  4. 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…

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

    NARCIS (Netherlands)

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

    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

  6. The structure and evolution of plankton communities

    Science.gov (United States)

    Longhurst, Alan R.

    New understanding of the circulation of ancient oceans is not yet matched by progress in our understanding of their pelagic ecology, though it was the planktonic ecosystems that generated our offshore oil and gas reserves. Can we assume that present-day models of ecosystem function are also valid for ancient seas? This question is addressed by a study of over 4000 plankton samples to derive a comprehensive, global description of zooplankton community structure in modern oceans: this shows that copepods form only 50% of the biomass of all plankton, ranging from 70% in polar to 35% in tropical seas. Comparable figures are derived from 14 other taxonomic categories of zooplankton. For trophic groupings, the data indicate globally: geletinous predators - 14%; gelatinous herbivores - 4%; raptorial predators - 33%; macrofiltering herbivores - 20%; macrofiltering omnivores - 25%; and detritivores - 3%. A simple, idealized model for the modern pelagic ecosystem is derived from these percentages which indicates that metazooplankton are not the most important consumers of pico- and nano-plankton production which itself probably constitutes 90% of primary production in warm oceans. This model is then compared with candidate life-forms available in Palaeozoic and Mesozoic oceans to determine to what extent it is also valid for ancient ecosystems: it is concluded that it is probably unnecessary to postulate models fundamentally differing from it in order to accommodate the life-forms, both protozoic and metazoic, known to have populated ancient seas. Remarkably few life-forms have existed which cannot be paralleled in the modern ocean, which contains remarkably few life-forms which cannot be paralleled in the Palaeozoic ocean. As a first assumption, then, it is reasonable to assume that energy pathways were similar in ancient oceans to those we study today.

  7. Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.).

    Science.gov (United States)

    van Overbeek, Leo; van Elsas, Jan Dirk

    2008-05-01

    The effects of genotype, plant growth and experimental factors (soil and year) on potato-associated bacterial communities were studied. Cultivars Achirana Inta, Désirée, Merkur and transgenic Désirée line DL12 (containing T4 lysozyme gene) were assessed in two field experiments. Cross-comparisons between both experiments were made using Désirée plants. Culture-dependent and -independent approaches were used to demonstrate effects on total bacterial, actinobacterial and Pseudomonas communities in bulk and rhizosphere soils and endospheres. PCR-denaturing gradient gel electrophoresis fingerprints prepared with group-specific primers were analyzed using multivariate analyses and revealed that bacterial communities in Achirana Inta plants differed most from those of Désirée and Merkur. No significant effects were found between Désirée and DL12 lines. Plant growth stage strongly affected different plant-associated communities in both experiments. To investigate the effect of plant-associated communities on plant health, 800 isolates from rhizospheres and endospheres at the flowering stage were tested for suppression of Ralstonia solanacearum biovar 2 and/or Rhizoctonia solani AG3. A group of isolates closely resembling Lysobacter sp. dominated in young plants. Its prevalence was affected by plant growth stage and experiment rather than by plant genotype. It was concluded that plant growth stage overwhelmed any effect of plant genotype on the bacterial communities associated with potato.

  8. 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.  

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Ratnavelu, Kuru

    2016-01-01

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

  12. 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.

  13. 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.

  14. 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.

  15. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

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

    2009-01-01

    composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...... an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along...... the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight...

  16. Faculty Scholarship at Community Colleges: Culture, Institutional Structures, and Socialization

    Science.gov (United States)

    Morest, Vanessa Smith

    2015-01-01

    This chapter looks at community college faculty engagement in scholarship. Community college faculty spend the majority of their time engaged in teaching, and therefore their scholarship typically focuses on strengthening curriculum and instruction. The paper identifies some of the structural and cultural challenges and supports to scholarship at…

  17. A new dynamic null model for phylogenetic community structure

    NARCIS (Netherlands)

    Pigot, Alex L; Etienne, Rampal S

    2015-01-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by

  18. Exploratory Visualization of Graphs Based on Community Structure

    Science.gov (United States)

    Liu, Yujie

    2013-01-01

    Communities, also called clusters or modules, are groups of nodes which probably share common properties and/or play similar roles within a graph. They widely exist in real networks such as biological, social, and information networks. Allowing users to interactively browse and explore the community structure, which is essential for understanding…

  19. Host niches and defensive extended phenotypes structure parasitoid wasp communities.

    Directory of Open Access Journals (Sweden)

    Richard Bailey

    2009-08-01

    Full Text Available Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies.Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the "Enemy Hypothesis," which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness, supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed. The combined explanatory power of structural and

  20. 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.

  1. Community detection for networks with unipartite and bipartite structure

    OpenAIRE

    Chang, Chang; Tang, Chao

    2013-01-01

    Finding community structures in networks is important in network science, technology, and applications. To date, most algorithms that aim to find community structures only focus either on unipartite or bipartite networks. A unipartite network consists of one set of nodes and a bipartite network consists of two nonoverlapping sets of nodes with only links joining the nodes in different sets. However, a third type of network exists, defined here as the mixture network. Just like a bipartite net...

  2. Patterns in marine microbial community structure

    OpenAIRE

    2012-01-01

    Programa en Oceanografía [EN] Understanding the distribution of the different picoplankton groups represents a central tenet of marine microbial ecology. Centering our study on the three major groups constituting the bulk picoplankton community (size 0.2-3 mm), we sought to analyze the distribution of autotrophic bacteria (Synechococcus and Prochlorococcus), photosynthetic Picoeukaryotes pPeuk, and heterotrophic bacteria. [ES] La comprensión de la distribución de los distint...

  3. Covariance, correlation matrix, and the multiscale community structure of networks.

    Science.gov (United States)

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

    2010-07-01

    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 paper, we consider detecting the multiscale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multiscale community structure through the translation and rotation transformations. It is proved that the covariance matrix is the unbiased version of the well-known modularity matrix. We then point out that the translation and rotation transformations fail to deal with the heterogeneous network, which is very common in nature and society. To address this problem, a correlation matrix is proposed through introducing the rescaling transformation into the covariance matrix. Extensive tests on real world and artificial networks demonstrate that the correlation matrix significantly outperforms the covariance matrix, identically the modularity matrix, as regards identifying the multiscale community structure of network. This work provides a novel perspective to the identification of community structure and thus various dimension reduction methods might be used for the identification of community structure. Through introducing the correlation matrix, we further conclude that the rescaling transformation is crucial to identify the multiscale community structure of network, as well as the translation and rotation transformations.

  4. Community structure in time-dependent, multiscale, and multiplex networks.

    Science.gov (United States)

    Mucha, Peter J; Richardson, Thomas; Macon, Kevin; Porter, Mason A; Onnela, Jukka-Pekka

    2010-05-14

    Network science is an interdisciplinary endeavor, with methods and applications drawn from across the natural, social, and information sciences. A prominent problem in network science is the algorithmic detection of tightly connected groups of nodes known as communities. We developed a generalized framework of network quality functions that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices. This framework allows studies of community structure in a general setting encompassing networks that evolve over time, have multiple types of links (multiplexity), and have multiple scales.

  5. 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.

  6. 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.

  7. Jellyfish modulate bacterial dynamic and community structure.

    Science.gov (United States)

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

    2012-01-01

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

  8. 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

  9. 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.

  10. Linking community size structure and ecosystem functioning using metabolic theory.

    Science.gov (United States)

    Yvon-Durocher, Gabriel; Allen, Andrew P

    2012-11-05

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change.

  11. Microbial community structure of a freshwater system receiving wastewater effluent.

    Science.gov (United States)

    Hladilek, Matthew D; Gaines, Karen F; Novak, James M; Collard, David A; Johnson, Daniel B; Canam, Thomas

    2016-11-01

    Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at 14 sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated effluent from the Charleston Wastewater Treatment Plant (Charleston, IL). Total bacterial DNA was isolated and 16S rRNA sequences were analyzed using a metagenomics platform. The community structure in planktonic bacterial communities was significantly correlated with dissolved oxygen concentration. Benthic bacterial communities were not correlated with water quality but did have a significant geographic structuring. A local restructuring effect was observed in both planktonic and benthic communities near the treated wastewater effluent, which was characterized by an increase in abundance of sphingobacteria. Sites further downstream from the wastewater facility appeared to be less influenced by the effluent. Overall, the present study demonstrated the utility of targeted high-throughput sequencing as a tool to assess the effects of treated wastewater effluent on a receiving water system, and highlighted the potential for this technology to be used for routine monitoring by wastewater facilities.

  12. 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.

  13. 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.)

  14. 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.

  15. Observing and modelling phytoplankton community structure in the North Sea

    Science.gov (United States)

    Ford, David A.; van der Molen, Johan; Hyder, Kieran; Bacon, John; Barciela, Rosa; Creach, Veronique; McEwan, Robert; Ruardij, Piet; Forster, Rodney

    2017-03-01

    Phytoplankton form the base of the marine food chain, and knowledge of phytoplankton community structure is fundamental when assessing marine biodiversity. Policy makers and other users require information on marine biodiversity and other aspects of the marine environment for the North Sea, a highly productive European shelf sea. This information must come from a combination of observations and models, but currently the coastal ocean is greatly under-sampled for phytoplankton data, and outputs of phytoplankton community structure from models are therefore not yet frequently validated. This study presents a novel set of in situ observations of phytoplankton community structure for the North Sea using accessory pigment analysis. The observations allow a good understanding of the patterns of surface phytoplankton biomass and community structure in the North Sea for the observed months of August 2010 and 2011. Two physical-biogeochemical ocean models, the biogeochemical components of which are different variants of the widely used European Regional Seas Ecosystem Model (ERSEM), were then validated against these and other observations. Both models were a good match for sea surface temperature observations, and a reasonable match for remotely sensed ocean colour observations. However, the two models displayed very different phytoplankton community structures, with one better matching the in situ observations than the other. Nonetheless, both models shared some similarities with the observations in terms of spatial features and inter-annual variability. An initial comparison of the formulations and parameterizations of the two models suggests that diversity between the parameter settings of model phytoplankton functional types, along with formulations which promote a greater sensitivity to changes in light and nutrients, is key to capturing the observed phytoplankton community structure. These findings will help inform future model development, which should be coupled

  16. 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...

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

    DEFF Research Database (Denmark)

    Olsen, Martin

    2009-01-01

      We prove that the problem of deciding whether a Nash stable   partition exists in an Additively Separable Hedonic Game is   NP-complete. We also show that the problem of deciding whether a   non trivial Nash stable partition exists in an   Additively Separable Hedonic Game with   non......-negative and 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....

  18. 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.

  19. Bootstrap Percolation on Complex Networks with Community Structure

    CERN Document Server

    Chong, Wu; Rui, Zhang; Liujun, Chen; Jiawei, Chen; Xiaobin, Li; Yanqing, Hu

    2014-01-01

    Real complex networks usually involve community structure. How innovation and new products spread on social networks which have internal structure is a practically interesting and fundamental question. In this paper we study the bootstrap percolation on a single network with community structure, in which we initiate the bootstrap process by activating different fraction of nodes in each community. A previously inactive node transfers to active one if it detects at least $k$ active neighbors. The fraction of active nodes in community $i$ in the final state $S_i$ and its giant component size $S_{gci}$ are theoretically obtained as functions of the initial fractions of active nodes $f_i$. We show that such functions undergo multiple discontinuous transitions; The discontinuous jump of $S_i$ or $S_{gci}$ in one community may trigger a simultaneous jump of that in the other, which leads to multiple discontinuous transitions for the total fraction of active nodes $S$ and its associated giant component size $S_{gc}$...

  20. 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.

  1. 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

  2. Impacts of chemical gradients on microbial community structure

    DEFF Research Database (Denmark)

    Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E

    2017-01-01

    Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox ...... Journal advance online publication, 17 January 2017; doi:10.1038/ismej.2016.175....

  3. 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

  4. 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.

  5. Oceanographic structure drives the assembly processes of microbial eukaryotic communities.

    Science.gov (United States)

    Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

    2015-03-17

    Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance-decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community.

  6. Correlations between community structure and link formation in complex networks.

    Directory of Open Access Journals (Sweden)

    Zhen Liu

    Full Text Available BACKGROUND: Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. METHODOLOGY/PRINCIPAL FINDINGS: Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. CONCLUSIONS/SIGNIFICANCE: Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction.

  7. 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.

  8. A seed-expanding method based on random walks for community detection in networks with ambiguous community structures

    Science.gov (United States)

    Su, Yansen; Wang, Bangju; Zhang, Xingyi

    2017-02-01

    Community detection has received a great deal of attention, since it could help to reveal the useful information hidden in complex networks. Although most previous modularity-based and local modularity-based community detection algorithms could detect strong communities, they may fail to exactly detect several weak communities. In this work, we define a network with clear or ambiguous community structures based on the types of its communities. A seed-expanding method based on random walks is proposed to detect communities for networks, especially for the networks with ambiguous community structures. We identify local maximum degree nodes, and detect seed communities in a network. Then, the probability of a node belonging to each community is calculated based on the total probability model and random walks, and each community is expanded by repeatedly adding the node which is most likely to belong to it. Finally, we use the community optimization method to ensure that each node is in a community. Experimental results on both computer-generated and real-world networks demonstrate that the quality of the communities detected by the proposed algorithm is superior to the- state-of-the-art algorithms in the networks with ambiguous community structures.

  9. 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...

  10. Microbial community structure of Arctic seawater as revealed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    LI Yang; WANG Zhen; LIN Xuezheng

    2016-01-01

    This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95%and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.

  11. Community structure and population genetics of Eastern Mediterranean polychaetes

    Directory of Open Access Journals (Sweden)

    Giorgos eChatzigeorgiou

    2014-10-01

    Full Text Available Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1776 during two successive years at two locations in northern Crete (Aegean Sea and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community.

  12. 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.

  13. 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...

  14. Dynamical evolution of the community structure of complex earthquake network

    CERN Document Server

    Abe, Sumiyoshi

    2012-01-01

    Earthquake network is known to be complex in the sense that it is scale-free, small-world, hierarchically organized and assortatively mixed. Here, the time evolution of earthquake networks is analyzed around main shocks in the context of the community structure. It is found that the maximum of the modularity measure quantifying existence of communities exhibits a peculiar behavior: its maximum value stays at a large value before a main shock, suddenly drops to a small values at the main shock, and then increases to relax to a large value again relatively slowly. In this way, a main shock is characterized in the language of theory of complex networks. The result is also interpreted in terms of the clustering structure of the earthquake network.

  15. 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.

  16. 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...

  17. 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.

  18. 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.

  19. Elucidation of haem-binding sites in the actinobacterial protein HbpS

    NARCIS (Netherlands)

    Torda, Andrew E; Groves, Matthew R; Wedderhoff, Ina; Ortiz de Orué Lucana, Darío

    2013-01-01

    The extracellular haem-binding protein from Streptomyces reticuli (HbpS) has been shown to be involved in redox sensing and to bind haem. However, the residues involved in haem coordination are unknown. Structural alignments to distantly related haem-binding proteins from Mycobacterium tuberculosis

  20. 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.

  1. Variation of ant community structure on Ficus benguetensis

    Directory of Open Access Journals (Sweden)

    Shang-Yang Lin

    2016-03-01

    Full Text Available Although ants are commonly found on Ficus trees, information remains lacking on the pattern and diversity of the ant community visiting these trees. We hypothesize that dynamic changes in the availability and types of food can affect the composition as well as abundance of ant communities occurring on fig trees. To investigate the impact of resource availability, diversity, and variability on the ant community structure, we surveyed and recorded the fig phenology and ant abundance on 17 trees (11 male and six female trees of Ficus benguetensis in New Taipei City in northern Taiwan from 2011 to 2013. A total of 13 ant species were found on these fig trees, with 6 species more abundant than the others. The composition and relative abundance of the ant species occurring on F. benguetensis trees showed significant variations associated with tree sex, fig abundance, fig developmental phase, as well as temperature. A degree of dietary niche partitioning was also observed. We suggest that sexual differentiation in fig phenology plays a major role in controlling the availability and variance in food resources for ants, thereby shaping the complex ant communities foraging on F. benguetensis.

  2. 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...

  3. A local immunization strategy for networks with overlapping community structure

    Science.gov (United States)

    Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

    2017-02-01

    Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

  4. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    Science.gov (United States)

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  5. Functional and spatial structure of the urbotechnozem mesopedobiont community

    Directory of Open Access Journals (Sweden)

    O. N. Kunah

    2016-09-01

    Full Text Available The results of studying the spatial structure of soil mesofauna of an urbanotechnozem by OMI- and RLQ-analysis are presented. The research was conducted on 5 June 2012 in the Botanic Garden of Oles Gonchar University (previously – territory of the Park Y. Gagarin, Dnipropetrovsk. The studied plot is situated on the slope of the Krasnopostachekaya balka (48°25'57.43" N, 35°2'16.52" E. The plot consists of 15 transects directed in a perpendicular manner in relation to the talweg. Each transect is made of seven sample points. The distance between points is 2 m. The coordinates of the lower left point were taken as (0; 0. The plot consisted of artificial grassland with a single tree. The vegetation was composed of grassland and steppe, of a mega-mesotrophic, xeromesophilic character. At each point the mesopedobionts were studied (data presented as L-table; temperature, electrical conductivity and soil penetration resistance, and grass height were measured (data presented as R-table. The soil-zoological test area was 25×25 cm. The mesopedobiont community was represented by 28 species and with total abundance 70.1 ind./m2. The following groups were dominant in the ecological structure of the soil animal community; saprohages, pratants, mesotrophocoenomorphs and the endogeic group. The measured edaphic characteristics were shown to play an important role in structurization of the ecological niche of the mesopedobiont community. The usage of morphological or physiological features of animals for the assessment of degree of specific distinctions is applicable for homogeneous taxonomic or ecological groups possessing comparable characteristics which also can be interpreted ecologically. The soil mesofauna is characterized by high taxonomic and ecological diversity of forms,which are difficult to compare by morphological or physiological criteria. The ecological value of characteristics in different groups will be not identical, and the basis for

  6. 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.

  7. The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

    Science.gov (United States)

    Oliveira, Micael

    The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

  8. 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.

  9. [Effects of colistin sulfate residue on soil microbial community structure].

    Science.gov (United States)

    Ma, Yi; Peng, Jin-Ju; Chen, Jin-Jun; Fan, Ting-Li; Sun, Yong-Xue

    2014-06-01

    By using fumigation extraction and phospholipid fatty acid (PLFA) methods, the change of characteristics of soil microbial community structure caused by residue of colistin sulfate (CS) was studied. The results showed that the CS (w(cs) > or = 5 mg x kg(-1)) had a significant effect on the microbial biomass carbon (MBC) and it was dose-dependent where MBC decreased with the increase of CS concentration in soil. The MBC in soil decreased by 52. 1% when the CS concentration reached 50 mg x kg(-1). The total PLFA of soil in each CS treatment was significantly decreased during the sampling period compared with the control group and showed a dose-dependent relationship. The soil microbial community structure and diversity in the low CS group (w(cs) = 0.5 mg x kg(-1)) were not significantly different from the control group on 7th and 49th day. However, they were significantly different on 21st and 35th day especially in the high CS group (w(cs) = 50 mg x kg(-1)). It was concluded that CS could change the structure of soil microorganisms and varied with time which might be caused by the chemical conversion and degradation of CS in soil.

  10. 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.

  11. 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).

  12. Experimental warming effects on the bacterial community structure and diversity

    Science.gov (United States)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  13. 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…

  14. Maps of random walks on complex networks reveal community structure.

    Science.gov (United States)

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  15. 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.

  16. 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.

  17. [Community structure of planktonic rotifers in the Pearl River Delta].

    Science.gov (United States)

    Gao, Yuan; Li, Xin-Hui; Lai, Zi-Ni; Yu, Jing; Wang, Chao; Zeng, Yan-Yi; Liu, Qian-Fu; Yang, Wan-Ling

    2014-07-01

    Four ecological investigations were carried out on planktonic rotifers in Pearl River Delta in 2012. The community structure, including spatial and temporal patterns of species composition, dominant species, biomass and biodiversity, was investigated. The correlation between the community structure of rotifers and the environmental factors was discussed. Moreover, the aggregation structures of rotifers were analyzed. A total of 53 rotifer species were found. Dominant species changed markedly with season and space. Polyarthra trigla had higher dominance. In terms of seasonal changes, the density and biomass were higher in dry season than in wet season, while the biodiversity and evenness indices were vice versa. The biomass and biodiversity of rotifers showed highly significant differences among seasons. In terms of spatial distribution, the average density and the average biomass showed an increase from the southwest to the northeast. The highest density and biomass were recorded in Shiqiao. The biodiversity and evenness indices had an opposite spatial distribution, with the highest values being recorded in Qingqi. The rotifer density was significantly different among the investigated sites, while the biomass and biodiversity were not significantly different. Correlation analysis demonstrated a highly significant positive correlation between rotifer density and biomass, as well as between biodiversity and evenness indices, and a highly negative correlation between biodiversity and biomass. The biodiversity and evenness indices both decreased markedly with the increase of biomass. Principal component analysis indicated that the rotifer density was closely correlated with environment factors, such as water temperature, pH, dissolved oxy- gen, chlorophyll a content, total phosphorus, and total nitrogen, in different seasons. Aggregation analysis based on rotifer density revealed five aggregation structures in the investigated sites, indicating significant differences

  18. 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...

  19. 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.

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

    Science.gov (United States)

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

    2013-06-01

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

  1. Phytoplankton community structure in the VAHINE mesocosm experiment

    Science.gov (United States)

    Leblanc, Karine; Cornet, Véronique; Caffin, Mathieu; Rodier, Martine; Desnues, Anne; Berthelot, Hugo; Turk-Kubo, Kendra; Heliou, Jules

    2016-09-01

    The VAHINE mesocosm experiment was designed to trigger a diazotroph bloom and to follow the subsequent transfer of diazotroph-derived nitrogen (DDN) in the rest of the food web. Three mesocosms (50 m3) located inside the Nouméa lagoon (New Caledonia, southwestern Pacific) were enriched with dissolved inorganic phosphorus (DIP) in order to promote N2 fixation in these low-nutrient, low-chlorophyll (LNLC) waters. Initially, the diazotrophic community was dominated by diatom diazotroph associations (DDAs), mainly by Rhizosolenia/Richelia intracellularis, and by Trichodesmium, which fueled enough DDN to sustain the growth of other diverse diatom species and Synechococcus populations that were well adapted to limiting DIP levels. After DIP fertilization (1 µM) on day 4, an initial lag time of 10 days was necessary for the mesocosm ecosystems to start building up biomass. However, changes in community structure were already observed during this first period, with a significant drop of both Synechococcus and diatom populations, while Prochlorococcus benefited from DIP addition. At the end of this first period, corresponding to when most added DIP was consumed, the diazotroph community changed drastically and became dominated by Cyanothece-like (UCYN-C) populations, which were accompanied by a monospecific bloom of the diatom Cylindrotheca closterium. During the second period, biomass increased sharply together with primary production and N2-fixation fluxes near tripled. Diatom populations, as well as Synechococcus and nanophytoeukaryotes, showed a re-increase towards the end of the experiment, showing efficient transfer of DDN to non-diazotrophic phytoplankton.

  2. 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.

  3. The effect of bacteria on diatom community structure - The 'antibiotics' approach

    Digital Repository Service at National Institute of Oceanography (India)

    DeCosta, P.M.; Anil, A.C.

    . The bacterial community preferred the ‘tolerance’ strategy over ‘resistance’ in response to treatment with penicillin; these changes in bacterial dynamics were probably linked to concurrent changes in diatom community structure. The observations with penicillin...

  4. 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...

  5. Community structure of ectomycorrhizal fungi in Swedish boreal forests

    Energy Technology Data Exchange (ETDEWEB)

    Jonsson, Lena [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Forest Mycology and Pathology

    1998-12-31

    The main aim of this work has been to elucidate the species composition and community structure of ectomycorrhizal fungi associated with mature trees and naturally regenerated seedlings in natural boreal forests in Sweden. Further, the effects of disturbances, such as wildfire and nitrogen inputs, were studied. Sporocarp surveys, morphological stratification and DNA-based analyses of mycorrhizas were used to describe the mycorrhizal fungal communities. In addition, a reference database useful for identifying individual mycorrhizas was developed based on analyses of sporocarp tissue. Overall, the species richness of ectomycorrhizal fungi was at least 30 to 40 times higher than that of their host trees. Naturally regenerated seedlings were colonized by the ectomycorrhizal fungal species present in the mycelial network of the old trees, indicating that the species composition will remain about the same provided that the host does not disappear. Wildfire, disturbing the fungal continuum, caused a shift in the frequencies of ectomycorrhizal fungi rather than a change in species composition. Nitrogen addition did not have any detectable effect on the abundance or species richness of mycorrhizas, but led to a decrease in sporocarp production. In all the studies, there was little resemblance between the species composition of sporocarps and that of mycorrhizas. The ITS-RFLP reference database was very useful in identifying single mycorrhizas, and proved to be a powerful tool for species identification of unknown mycorrhizas 76 refs, 2 figs, 2 tabs

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  10. Pregnancy and birth in an indigenous Huichol community: from structural violence to structural policy responses.

    Science.gov (United States)

    Gamlin, Jennie B; Hawkes, Sarah J

    2015-01-01

    Mexico's indigenous regions are characterised by socio-economic marginalisation and poor health outcomes and the Maternal Mortality Rate in indigenous communities continues to be around six times higher than the national rate. Using as a case study the Huichol community of North-Western Mexico we will discuss how institutional health and welfare programmes which aim to address accepted risk factors for maternal health are undermined by a series of structural barriers which put indigenous women especially in harm's way. Semi-structured interviews and observational data were gathered between 2009 and 2011 in highland communities and on coastal tobacco plantations to where a large number of this ethnic group migrate. Many Huichol women birth alone, and to facilitate this process they maintain a low nutritional intake to reduce their infant's growth and seek spiritual guidance during pregnancy from a shaman. These practices are reinforced by feelings of shame and humiliation encountered when using institutional health provision. These are some of the structural barriers to care that need to be addressed. Effective interventions could include addressing the training of health professionals, focusing on educational inequalities and the structural determinants of poverty whilst designing locally specific programmes that encourage acceptance of available health care.

  11. 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.

  12. Nematode community structure in the vicinity of a metallurgical factory.

    Science.gov (United States)

    Salamún, Peter; Renčo, Marek; Miklisová, Dana; Hanzelová, Vladimíra

    2011-12-01

    Soil nematode communities (taxa composition, trophic structure, ecological indices) in the area of metallurgical factory (Oravské ferozliatinárske závody) in Široká, Northern Slovakia were investigated in 2009. The factory belongs to main sources of emissions originated by ferroalloy production in this region. Four sites (meadows) were selected in a downwind direction from the factory: site A was located 0.85 km far from the factory, and the other sites were maintained in approximately 2-km intervals from each other. Chemical analysis of soil samples showed low concentrations of heavy metals (As, Cd, Cr, Cu, Ni, Pb and Zn), with all values being under Slovak limit concentrations of heavy metals in soils. Only the Cd content in the soil sample from site A slightly exceeded the allowable threshold, but it was decreasing with the distance from the factory, similarly as remaining metals except Cr, with slightly increasing trend of concentration. Within 64 identified nematode genera, the Helicotylenchus, Paratylenchus, Pratylenchus, Acrobeloides, Cephalobus and Rhabditis were most common and eudominant. This was clearly reflected on the trophic structure of nematode communities, where plant feeding nematodes and bacteriovorous prevailed. Significant negative correlation (P < 0.05) was observed between the abundance of bacteriovores and the concentration of Cu in the soil. On the other hand, fungivores showed significant correlation with Ni and Cr (P < 0.05) as well as predators with Cd, Pb and Zn contents in the soil (P < 0.01). The highly significant correlation (P < 0.05; P < 0.01) was found between As, Cd, Ni, Pb and Zn and Maturity Index 2-5. A negative relationship was detected between Maturity Index and the concentration of Cr in the soil (P < 0.01). On the other hand, Cu was in positive correlation with MI values. The MI, reflecting the degree of disturbances and changes in the structure and function of the soil ecosystem, was found

  13. The actinobacterial signature protein ParJ (SCO1662) regulates ParA polymerization and affects chromosome segregation and cell division during Streptomyces sporulation.

    Science.gov (United States)

    Ditkowski, Bartosz; Troć, Paulina; Ginda, Katarzyna; Donczew, Magdalena; Chater, Keith F; Zakrzewska-Czerwińska, Jolanta; Jakimowicz, Dagmara

    2010-12-01

    Bacterial chromosome segregation usually involves cytoskeletal ParA proteins, ATPases which can form dynamic filaments. In aerial hyphae of the mycelial bacterium Streptomyces coelicolor, ParA filaments extend over tens of microns and are responsible for segregation of dozens of chromosomes. We have identified a novel interaction partner of S. coelicolor ParA, ParJ. ParJ negatively regulates ParA polymerization in vitro and is important for efficient chromosome segregation in sporulating aerial hyphae. ParJ-EGFP formed foci along aerial hyphae even in the absence of ParA. ParJ, which is encoded by sco1662, turned out to be one of the five actinobacterial signature proteins, and another of the five is a ParJ paralogue. We hypothesize that polar growth, which is characteristic not only of streptomycetes, but even of simple Actinobacteria, may be interlinked with ParA polymer assembly and its specific regulation by ParJ.

  14. 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.

  15. Scalably Revealing the Dynamics of Soft Community Structure in Complex Networks

    Institute of Scientific and Technical Information of China (English)

    LI Huijia; LI Huiying

    2016-01-01

    Revealing the dynamics of community structure is of great concern for scientists from many fields.Specifically,how to quantify the dynamic details of soft community structure is a very interesting topic.In this paper,the authors propose a novel framework to study the scalable dynamic behavior of the soft community structure.First,the authors model the Potts dynamics to detect community structure using a "soft" Markov process.Then the soft stability of in a multiscale view is proposed to naturally uncover the local uniform behavior of spin values across multiple hierarchical levels.Finally,a new partition index is developed to detect fuzzy communities based on the stability and the dynamical information.Experiments on the both synthetically generated and real-world networks verify that the framework can be used to uncover hierarchical community structures effectively and efficiently.

  16. Detecting community structure in complex networks using an interaction optimization process

    Science.gov (United States)

    Kim, Paul; Kim, Sangwook

    2017-01-01

    Most complex networks contain community structures. Detecting these community structures is important for understanding and controlling the networks. Most community detection methods use network topology and edge density to identify optimal communities; however, these methods have a high computational complexity and are sensitive to network forms and types. To address these problems, in this paper, we propose an algorithm that uses an interaction optimization process to detect community structures in complex networks. This algorithm efficiently searches the candidates of optimal communities by optimizing the interactions of the members within each community based on the concept of greedy optimization. During this process, each candidate is evaluated using an interaction-based community model. This model quickly and accurately measures the difference between the quantity and quality of intra- and inter-community interactions. We test our algorithm on several benchmark networks with known community structures that include diverse communities detected by other methods. Additionally, after applying our algorithm to several real-world complex networks, we compare our algorithm with other methods. We find that the structure quality and coverage results achieved by our algorithm surpass those of the other methods.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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…

  2. 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...

  3. 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…

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. 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...

  9. 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...

  10. Polychaete community structure of Indian west coast shelf, Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Joydas, T.V.; Jayalakshmy, K.V.; Damodaran, R.

    ; version 5) with the polychaete species abundance matrix. One way ANOSIM (analysis of similarity) was carried out to test differ- ences found in the communities (square- root transformed data) between different depth habitats 14 . For the convenience...

  11. 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.

  12. 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

  13. Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

    Science.gov (United States)

    Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

    2012-07-01

    Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

  14. Environmental factors shaping the abundance and distribution of laccase-encoding bacterial community with potential phenolic oxidase capacity during composting.

    Science.gov (United States)

    Lu, Lunhui; Zeng, Guangming; Fan, Changzheng; Guo, Jinsong; Zhang, Jiachao; Chen, Ming; Wu, Haipeng; Yuan, Yujie; He, Xiaoxiao; He, Yan

    2015-11-01

    Increasing molecular evidence points to a wide occurrence of laccase-like multicopper oxidase (LMCO)-encoding genes in bacteria. Most researches mainly focused on the bacterial LMCO diversity, whereas the processes and the environmental factors responsible for structuring bacterial LMCO communities remain relatively unknown in a composting system. Six gene libraries were constructed from samples in representative stages during composting. A total of 185 sequences obtained from sample DNA extracts were classified to 59 operational taxonomic units (OTUs) based on 10 % cutoff. The distribution profile of bacterial LMCO genes showed that proteobacterial- and actinobacterial-associated species were the dominant communities during composting. Pearson correlation analysis indicated that the pile temperature and water-soluble carbon (WSC) content were significantly positively correlated with bacterial LMCO gene OTU numbers, Chao1 and Shannon index, whereas the humic acid (HA)-like carbon content had the most significant effect on the distribution of the bacterial LMCO genes during composting by redundancy analysis. These findings will improve the understanding of the mutual relationship between environmental factors and bacterial LMCO community compositions in composting.

  15. 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.

  16. 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.

  17. 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.

  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. The Structure and Distribution of Benthic Communities on a Shallow Seamount (Cobb Seamount, Northeast Pacific Ocean)

    Science.gov (United States)

    Curtis, Janelle M. R.; Clarke, M. Elizabeth

    2016-01-01

    Partially owing to their isolation and remote distribution, research on seamounts is still in its infancy, with few comprehensive datasets and empirical evidence supporting or refuting prevailing ecological paradigms. As anthropogenic activity in the high seas increases, so does the need for better understanding of seamount ecosystems and factors that influence the distribution of sensitive benthic communities. This study used quantitative community analyses to detail the structure, diversity, and distribution of benthic mega-epifauna communities on Cobb Seamount, a shallow seamount in the Northeast Pacific Ocean. Underwater vehicles were used to visually survey the benthos and seafloor in ~1600 images (~5 m2 in size) between 34 and 1154 m depth. The analyses of 74 taxa from 11 phyla resulted in the identification of nine communities. Each community was typified by taxa considered to provide biological structure and/or be a primary producer. The majority of the community-defining taxa were either cold-water corals, sponges, or algae. Communities were generally distributed as bands encircling the seamount, and depth was consistently shown to be the strongest environmental proxy of the community-structuring processes. The remaining variability in community structure was partially explained by substrate type, rugosity, and slope. The study used environmental metrics, derived from ship-based multibeam bathymetry, to model the distribution of communities on the seamount. This model was successfully applied to map the distribution of communities on a 220 km2 region of Cobb Seamount. The results of the study support the paradigms that seamounts are diversity 'hotspots', that the majority of seamount communities are at risk to disturbance from bottom fishing, and that seamounts are refugia for biota, while refuting the idea that seamounts have high endemism. PMID:27792782

  20. Trophic structure of the fouling community in Odessa Bay (Black Sea

    Directory of Open Access Journals (Sweden)

    A. Y. Varigin

    2016-06-01

    Full Text Available The trophic structure of the coastal fouling community of Odessa Bay (Black Sea, which was composed of 10 species of macrophytes, 57 invertebrate species and 4 species of fish, was determined. The basic trophic relationship between organisms composing the community is shown. A minimization of interspecific trophic competition within the community is noted. The main sources of food material entering the fouling community were determined. We show that a significant proportion of food in the form of detritus, dissolved organic matter and small planktonic organisms enters the community from the water column. Filtration and pumping activity of sestonophage-organisms, particularly mussels, helps to attract food material to the community. Primary producers of the community are macrophytes and microphytes, which develop on account of their photosynthetic activity and ensure the provision of food to herbivores. The trophic group of detritophages consumes different fractions of the detritus which accumulates in the byssus threads of bivalve molluscs. In this context, mussel druses act as sediment traps, collecting detritus. Numerous polyphages, which are essentially omnivores and do not usually lack food material, were noted in the community. A small group of carnivorous invertebrates, whose representatives actively attack small animals, was identified. The abundance of these species in the community was about 1%, and their biomass less than 0.6%. Fish living in macrophyte weeds are the consumers in the community. We determined that the highest relative abundance (over 36% in the fouling community was reached by sestonophages and polyphages. We found that the undisputed leader in the relative biomass (over 97% in the fouling community ofOdessaBaywas the sestonophages (mainly composed of mussels. We determined that the trophic structure index of the community was 0.94, which confirms the significant dominance in biomass of bivalves over other species in

  1. Teaching Interpersonal Skills to Psychiatric Outpatients: Using Structured Learning Therapy in a Community-Based Setting

    Science.gov (United States)

    Sprafkin, Robert P.; And Others

    1978-01-01

    The Structured Learning Therapy (SLT), a type of treatment used to assist psychiatric patients to learn skills they need for effective and satisfying living in the community, is described in this article. A description of the community-based treatment facility in which SLT may be utilized and the results of the evaluation studies are also…

  2. 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.

  3. 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...... with community development but also the transfer of facilitation skills and appropriate methods to the community....

  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. Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters

    NARCIS (Netherlands)

    Regueiro, L.; Veiga, P.; Figueroa, M.; Alonso-Gutierrez, J.; Stams, A.J.M.; Lema, J.M.; Carballa, M.

    2012-01-01

    High activity levels and balanced anaerobic microbial communities are necessary to attain proper anaerobic digestion performance. Therefore, this work was focused on the kinetic performance and the microbial community structure of six full-scale anaerobic digesters and one lab-scale co-digester. Hyd

  6. 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…

  7. Post fumigation recovery of soil microbial community structure

    Science.gov (United States)

    Soil fumigants have been extensively used to control target soil-borne pathogens and weeds for the past few decades. It is known that the fumigants with broad biocidal activity can affect both target and non-target soil organisms, but the recovery of soil microbial communities are unknown until rece...

  8. 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

  9. Characterization and exploitation of community structure in cover song networks

    CERN Document Server

    Serrà, Joan; Herrera, Perfecto; Serra, Xavier

    2011-01-01

    The use of community detection algorithms is explored within the framework of cover song identification, i.e. the automatic detection of different audio renditions of the same underlying musical piece. Until now, this task has been posed as a typical query-by-example task, where one submits a query song and the system retrieves a list of possible matches ranked by their similarity to the query. In this work, we propose a new approach which uses song communities to provide more relevant answers to a given query. Starting from the output of a state-of-the-art system, songs are embedded in a complex weighted network whose links represent similarity (related musical content). Communities inside the network are then recognized as groups of covers and this information is used to enhance the results of the system. In particular, we show that this approach increases both the coherence and the accuracy of the system. Furthermore, we provide insight into the internal organization of individual cover song communities, s...

  10. The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples.

    Science.gov (United States)

    Maukonen, Johanna; Simões, Catarina; Saarela, Maria

    2012-03-01

    Recently several human health-related microbiota studies have had partly contradictory results. As some differences may be explained by methodologies applied, we evaluated how different storage conditions and commonly used DNA-extraction kits affect bacterial composition, diversity, and numbers of human fecal microbiota. According to our results, the DNA-extraction did not affect the diversity, composition, or quantity of Bacteroides spp., whereas after a week's storage at -20 °C, the numbers of Bacteroides spp. were 1.6-2.5 log units lower (P DNA-extraction as detected with qPCR, regardless of storage. Furthermore, the bacterial composition of Erec-group differed significantly after different DNA-extractions; after enzymatic DNA-extraction, the most prevalent genera detected were Roseburia (39% of clones) and Coprococcus (10%), whereas after mechanical DNA-extraction, the most prevalent genera were Blautia (30%), Coprococcus (13%), and Dorea (10%). According to our results, rigorous mechanical lysis enables detection of higher bacterial numbers and diversity from human fecal samples. As it was shown that the results of clostridial and actinobacterial populations are highly dependent on the DNA-extraction methods applied, the use of different DNA-extraction protocols may explain the contradictory results previously obtained.

  11. 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/.

  12. [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.

  13. Organizational Structures and Perceived Cultures of Community-Charter School in Ohio.

    Science.gov (United States)

    Fox, Jeannie L.

    2002-01-01

    Challenges the assumption that bureaucracy is bad for charter schools. Examines perceived autonomy, governance structures, leadership, and perceived culture of community-charter schools in Ohio. (Contains 15 references.) (PKP)

  14. Subtidal micro and meiobenthic community structure in the Gulf of Kachchh

    Digital Repository Service at National Institute of Oceanography (India)

    Ingole, B.S.; Goltekar, R.

    Community structure of the micro- and meiobenthos of subtidal sediment from the Gulf of Kachchh were investigated during April 2002 (premonsoon season). Sediment samples were collected from 23 stations representing the entire Gulf area. A total...

  15. 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.

  16. Structure and function of a benthic invertebrate stream community as influenced by beaver (Castor canadensis).

    Science.gov (United States)

    McDowell, Donald M; Naiman, Robert J

    1986-03-01

    Beaver (Castor canadensis) affect the benthic invertebrate community of small woodland streams in Quebec through habitat modifications. Their activities influence community structure through the replacement of lotic taxa by lentic forms and community function by increasing the absolute importance of collectors and predators while decreasing the relative importance of shredders and scrapers in impounded sites. At our study site during the 1983 ice-free season, standing stocks of coarse particulate organic matter (>1 mm) were 2-5 times greater (Podonates, Tubificidae, and filtering pelycopods. Our results suggest that current paradigms applied to lotic ecosystems need to be reevaluated to incorporate the influence of beaver upon invertebrate communities.

  17. The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure

    OpenAIRE

    Louati, H.; Ben Said, O.; A. Soltani; Got, P; Mahmoudi, E.; Cravo-Laureau, C.; Duran, R.; Aissa, P.; Pringault, Olivier

    2013-01-01

    Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30...

  18. 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.

  19. Disturbance drives phylogenetic community structure in coastal dune vegetation

    DEFF Research Database (Denmark)

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

    2012-01-01

    sorting to be the dominant determinant in this metacommunity system, with soil moisture, pH, and fertility requirement patterns explaining ≥77% of the compositional gradients, while geographic factors accounted for ≤2%. Partial Mantel tests confirmed this finding, with 31.6% of the variation in species......It has long been thought that environmental factors determine plant community assembly, but it is now increasingly argued that geographic spatial processes such as dispersal may also matter. Notably, the metacommunity framework considers local communities to be linked by dispersal and different...... by the local environment and broader-scale geographic spatial processes for local plant species composition using a data set of 3924 plots from coastal dunes across a large region (Denmark). We used ordination to identify the main gradients in species composition, and Linear Mixed-Effects modelling (LME...

  20. 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.

  1. Modeling Risk Perception in Networks with Community Structure

    CERN Document Server

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

    2012-01-01

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

  2. 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

  3. 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.

  4. 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.

    -chemical and biological properties. Of these, physical variability, driven primarily by external forces is fundamental. Wind- and weather-driven events cause physical changes and disruptions. These events lead to variability in temperature, irradiance, precipitation, run... in the microphyto- benthic community of this study area (Mitabavkar & Anil, 2002). They frequently resuspend into the surface waters through physical processes such as waves, tides and currents (de Jonge, 1995; de Jonge & van Beusekom, 1995) and thereby influence...

  5. Using a two-phase evolutionary framework to select multiple network spreaders based on community structure

    Science.gov (United States)

    Fu, Yu-Hsiang; Huang, Chung-Yuan; Sun, Chuen-Tsai

    2016-11-01

    Using network community structures to identify multiple influential spreaders is an appropriate method for analyzing the dissemination of information, ideas and infectious diseases. For example, data on spreaders selected from groups of customers who make similar purchases may be used to advertise products and to optimize limited resource allocation. Other examples include community detection approaches aimed at identifying structures and groups in social or complex networks. However, determining the number of communities in a network remains a challenge. In this paper we describe our proposal for a two-phase evolutionary framework (TPEF) for determining community numbers and maximizing community modularity. Lancichinetti-Fortunato-Radicchi benchmark networks were used to test our proposed method and to analyze execution time, community structure quality, convergence, and the network spreading effect. Results indicate that our proposed TPEF generates satisfactory levels of community quality and convergence. They also suggest a need for an index, mechanism or sampling technique to determine whether a community detection approach should be used for selecting multiple network spreaders.

  6. Genetic variation in plant morphology contributes to the species-level structure of grassland communities.

    Science.gov (United States)

    Whitlock, Raj; Grime, J Phil; Burke, Terry

    2010-05-01

    It is becoming apparent that genetic diversity can influence the species diversity and structure of ecological communities. Here, we investigated the intraspecific trait variation responsible for this relationship. We grew 10 genotypes of the sedge Carex caryophyllea, as monocultures, under standardized conditions and measured traits related to morphology, growth, and life history. The same genotypes had been prominent in determining the structure of multispecies experimental communities, equivalent in species diversity, in which the genetic diversity of the constituent plant species had been varied in parallel. The trait measurements revealed substantial phenotypic variation among Carex genotypes, related predominantly to differences in physical size and to the spatial deployment of above- and belowground tissue. Genotypes successful in experimental communities were larger in size and tended to adopt a "guerrilla" clonal growth strategy. In general, multivariate trait summaries of genotype size (and to a lesser extent, variation along a linear discriminant axis) predicted genotype and species abundance in experimental communities. However, one genotype exhibited a large disparity in this respect. The performance of this genotype lay closer to prediction when it was growing with a highly competitive grass genotype. The strength of the relationship between genotype size and performance within communities decreased with decreasing community genetic diversity. These results indicate that intraspecific trait measurements are useful for predicting and understanding community structure. They also imply that competitive interactions between the genotypes of different species play an increased role in determining phenotype in genetically impoverished communities.

  7. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

    Science.gov (United States)

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-08-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska.

  8. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

    Science.gov (United States)

    Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Lange, Anja; Westendorf, Astrid M.; Seifert, Marc; Küppers, Ralf

    2017-01-01

    The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities. PMID:28114391

  9. [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.

  10. The impacts of triclosan on anaerobic community structures, function, and antimicrobial resistance.

    Science.gov (United States)

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

    2014-07-01

    Triclosan is a widespread antimicrobial agent that accumulates in anaerobic digesters used to treat the residual solids generated at municipal wastewater treatment plants; there is very little information, however, about how triclosan impacts microbial communities in anaerobic digesters. We investigated how triclosan impacts the community structure, function and antimicrobial resistance genes in lab-scale anaerobic digesters. Previously exposed (to triclosan) communities were amended with 5, 50, and 500 mg/kg of triclosan, corresponding to the median, 95th percentile, and 4-fold higher than maximum triclosan concentration that has been detected in U.S. biosolids. Triclosan amendment caused all of the Bacteria and Archaea communities to structurally diverge from that of the control cultures (based on ARISA). At the end of the experiment, all triclosan-amended Archaea communities had diverged from the control communities, regardless of the triclosan concentration added. In contrast, over time the Bacteria communities that were amended with lower concentrations of triclosan (5 mg/kg and 50 mg/kg) initially diverged and then reconverged with the control community structure. Methane production at 500 mg/kg was nearly half the methane production in control cultures. At 50 mg/kg, a large variability in methane production was observed, suggesting that 50 mg/kg may be a tipping point where function begins to fail in some communities. When previously unexposed communities were exposed to 500 mg triclosan/kg, function was maintained, but the abundance of a gene encoding for triclosan resistance (mexB) increased. This research suggests that triclosan could inhibit methane production in anaerobic digesters if concentrations were to increase and may also select for resistant Bacteria. In both cases, microbial community composition and exposure history alter the influence of triclosan.

  11. 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.

  12. 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.

  13. 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...

  14. The type of carbohydrates specifically selects microbial community structures and fermentation patterns.

    Science.gov (United States)

    Chatellard, Lucile; Trably, Eric; Carrère, Hélène

    2016-12-01

    The impact on dark fermentation of seven carbohydrates as model substrates of lignocellulosic fractions (glucose, cellobiose, microcrystalline cellulose, arabinose, xylose, xylan and wheat straw) was investigated. Metabolic patterns and bacterial communities were characterized at the end of batch tests inoculated with manure digestate. It was found that hydrogen production was linked to the sugar type (pentose or hexose) and the degree of polymerisation. Hexoses produced less hydrogen, with a specific selection of lactate-producing bacterial community structures. Maximal hydrogen production was five times higher on pentose-based substrates, with specific bacterial community structures producing acetate and butyrate as main metabolites. Low hydrogen amounts accumulated from complex sugars (cellulose, xylan and wheat straw). A relatively high proportion of the reads was affiliated to Ruminococcaceae suggesting an efficient hydrolytic activity. Knowing that the bacterial community structure is very specific to a particular substrate offers new possibilities to design more efficient H2-producing biological systems.

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    T. A. S. V. Paes

    Full Text Available Abstract 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.

  18. 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.

  19. Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter

    Science.gov (United States)

    Findlay, S.E.G.; Sinsabaugh, R. L.; Sobczak, W.V.; Hoostal, M.

    2003-01-01

    Hyporheic sediment bacterial communities were exposed to dissolved organic matter (DOM) from a variety of sources to assess the interdependence of bacterial metabolism and community composition. Experiments ranged from small-scale core perfusions with defined compounds (glucose, bovine serum albumin) to mesocosms receiving natural leaf leachate or water from different streams. Response variables included bacterial production, oxygen consumption, extracellular enzyme activity, and community similarity as manifest by changes in banding patterns of randomly amplified polymorphic DNA (RAPD). All DOM manipulations generated responses in at least one metabolic variable. Additions of both labile and recalcitrant materials increased either oxygen consumption, production, or both depending on background DOM. Enzyme activities were affected by both types of carbon addition with largest effects from the labile mixture. Cluster analysis of RAPD data showed strong divergence of communities exposed to labile versus recalcitrant DOM. Additions of leaf leachate to mesocosms representing hyporheic flow-paths caused increases in oxygen consumption and some enzyme activities with weaker effects on production. Community structure yeas strongly affected; samples from the leachate-amended mesocosms clustered separately from the control samples. In mesocosms receiving water from streams ranging in DOC (0.5-4.5 mg L-1), there were significant differences in bacterial growth, oxygen consumption, and enzyme activities. RAPD analysis showed strongest clustering of samples by stream type with more subtle effects of position along the flowpaths. Responses in community metabolism were always accompanied by shifts in community composition, suggesting carbon supply affects both functional and structural attributes of hyporheic bacterial communities.

  20. 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.

  1. Traveling salesman problems with PageRank Distance on complex networks reveal community structure

    Science.gov (United States)

    Jiang, Zhongzhou; Liu, Jing; Wang, Shuai

    2016-12-01

    In this paper, we propose a new algorithm for community detection problems (CDPs) based on traveling salesman problems (TSPs), labeled as TSP-CDA. Since TSPs need to find a tour with minimum cost, cities close to each other are usually clustered in the tour. This inspired us to model CDPs as TSPs by taking each vertex as a city. Then, in the final tour, the vertices in the same community tend to cluster together, and the community structure can be obtained by cutting the tour into a couple of paths. There are two challenges. The first is to define a suitable distance between each pair of vertices which can reflect the probability that they belong to the same community. The second is to design a suitable strategy to cut the final tour into paths which can form communities. In TSP-CDA, we deal with these two challenges by defining a PageRank Distance and an automatic threshold-based cutting strategy. The PageRank Distance is designed with the intrinsic properties of CDPs in mind, and can be calculated efficiently. In the experiments, benchmark networks with 1000-10,000 nodes and varying structures are used to test the performance of TSP-CDA. A comparison is also made between TSP-CDA and two well-established community detection algorithms. The results show that TSP-CDA can find accurate community structure efficiently and outperforms the two existing algorithms.

  2. Relationship between phenol degradation efficiency and microbial community structure in an anaerobic SBR.

    Science.gov (United States)

    Rosenkranz, F; Cabrol, L; Carballa, M; Donoso-Bravo, A; Cruz, L; Ruiz-Filippi, G; Chamy, R; Lema, J M

    2013-11-01

    Phenol is a common wastewater contaminant from various industrial processes, including petrochemical refineries and chemical compounds production. Due to its toxicity to microbial activity, it can affect the efficiency of biological wastewater treatment processes. In this study, the efficiency of an Anaerobic Sequencing Batch Reactor (ASBR) fed with increasing phenol concentrations (from 120 to 1200 mg L(-1)) was assessed and the relationship between phenol degradation capacity and the microbial community structure was evaluated. Up to a feeding concentration of 800 mg L(-1), the initial degradation rate steadily increased with phenol concentration (up to 180 mg L(-1) d(-1)) and the elimination capacity remained relatively constant around 27 mg phenol removed∙gVSS(-1) d(-1). Operation at higher concentrations (1200 mg L(-1)) resulted in a still efficient but slower process: the elimination capacity and the initial degradation rate decreased to, respectively, 11 mg phenol removed∙gVSS(-1) d(-1) and 154 mg L(-1) d(-1). As revealed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, the increase of phenol concentration induced level-dependent structural modifications of the community composition which suggest an adaptation process. The increase of phenol concentration from 120 to 800 mg L(-1) had little effect on the community structure, while it involved drastic structural changes when increasing from 800 to 1200 mg L(-1), including a strong community structure shift, suggesting the specialization of the community through the emergence and selection of most adapted phylotypes. The thresholds of structural and functional disturbances were similar, suggesting the correlation of degradation performance and community structure. The Canonical Correspondence Analysis (CCA) confirmed that the ASBR functional performance was essentially driven by specific community traits. Under the highest feeding concentration, the most abundant ribotype probably involved in

  3. 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.

  4. Violence, omissions and structures faced by LGBTI community individuals

    Directory of Open Access Journals (Sweden)

    Manuel Fernando Quinche Ramírez

    2016-07-01

    text works on the issue of legislative and conventional omissions, and identifies some of the traditional domain structures, those that impede the recognition and protection of this community’s rights.

  5. Communities, modules and large-scale structure in networks

    Science.gov (United States)

    Newman, M. E. J.

    2012-01-01

    Networks, also called graphs by mathematicians, provide a useful abstraction of the structure of many complex systems, ranging from social systems and computer networks to biological networks and the state spaces of physical systems. In the past decade there have been significant advances in experiments to determine the topological structure of networked systems, but there remain substantial challenges in extracting scientific understanding from the large quantities of data produced by the experiments. A variety of basic measures and metrics are available that can tell us about small-scale structure in networks, such as correlations, connections and recurrent patterns, but it is considerably more difficult to quantify structure on medium and large scales, to understand the `big picture'. Important progress has been made, however, within the past few years, a selection of which is reviewed here.

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

    Directory of Open Access Journals (Sweden)

    Benjamin J Gosney

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

  7. 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.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    Degradation of realistic microcystin concentrations in lake water with indigenous bacteria was studied in laboratory and field experiments following inoculation with lysed toxic algal material containing microcystin primarily from Microcystis sp. or purified commercial microcystin-LR to microcosms...... initial degradation rates occurred in 2 out of 7 cases, Microcystin was almost eliminated from the water after around 8 d. Results from concomitant measurements of bacterial abundance and net production showed an elevated bacterial activity within 1 to 2 d after the inoculation with algal lysates...... experiments were analysed by polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE) of 16S rDNA, which showed that the indigenous bacterial community responded quickly to the addition of lysates. Our study confirms that bacteria can efficiently degrade microcystins in natural waters...

  9. Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

    Science.gov (United States)

    Urbach, Ena; Vergin, Kevin L.; Morse, Ariel

    2001-01-01

    The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

  10. 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.

  11. Diatom community structure on commercially available ship hull coatings.

    Science.gov (United States)

    Zargiel, Kelli A; Coogan, Jeffrey S; Swain, Geoffrey W

    2011-10-01

    Diatoms are primary colonizers of both antifouling and fouling-release ship hull coatings. There are few published studies which report on diatom community development on modern ship hull coatings. This study reports diatom communities on eight commercial marine ship hull coatings exposed at three static immersion sites along the east coast of Florida, viz. Daytona, Sebastian, and Miami. The coatings tested were three ablative copper systems (Ameron ABC-3, International BRA-640, and Hempel Olympic 76600), two copper-free biocidal systems (E-Paint SN-1, Sherwin Williams HMF), and three fouling-release (FR) systems (International Intersleek 700, International Intersleek 900, and Hempel Hempasil). One hundred and twenty-seven species comprising 44 genera were identified, including some of the more commonly known foulers, viz. Achnanthes, Amphora, Cocconeis, Entomoneis, Licmophora, Melosira, Navicula, Nitzschia, Synedra, and Toxarium. A significant difference was seen among sites, with the more estuarine site, Sebastian, having lower overall diatom abundance and higher diversity than Daytona and Miami. Copper coatings were primarily fouled by Amphora delicatissima and Entomoneis pseudoduplex. Copper-free coatings were fouled by Cyclophora tenuis, A. delicatissima, Achnanthes manifera, and Amphora bigibba. FR surfaces were typified by C. tenuis, and several species of Amphora. The presence of C. tenuis is new to the biofouling literature, but as new coatings are developed, this diatom may be one of many that prove to be problematic for static immersion. Results show coatings can be significantly influenced by geographical area, highlighting the need to test ship hull coatings in locations similar to where they will be utilized.

  12. 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.

  13. 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.

  14. Dynamic community detection based on network structural perturbation and topological similarity

    Science.gov (United States)

    Wang, Peizhuo; Gao, Lin; Ma, Xiaoke

    2017-01-01

    Community detection in dynamic networks has been extensively studied since it sheds light on the structure-function relation of the overall complex systems. Recently, it has been demonstrated that the structural perturbation in static networks is excellent in characterizing the topology. In order to investigate the perturbation structural theory in dynamic networks, we extend the theory by considering the dynamic variation information between networks of consecutive time. Then a novel similarity is proposed by combing structural perturbation and topological features. Finally, we present an evolutionary clustering algorithm to detect dynamic communities under the temporal smoothness framework. Experimental results on both artificial and real dynamic networks demonstrate that the proposed similarity is promising in dynamic community detection since it improves the clustering accuracy compared with state-of-the-art methods, indicating the superiority of the presented similarity measure.

  15. 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...

  16. 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.

  17. 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.

  18. A Novel Top-k Strategy for Influence Maximization in Complex Networks with Community Structure.

    Directory of Open Access Journals (Sweden)

    Jia-Lin He

    Full Text Available In complex networks, it is of great theoretical and practical significance to identify a set of critical spreaders which help to control the spreading process. Some classic methods are proposed to identify multiple spreaders. However, they sometimes have limitations for the networks with community structure because many chosen spreaders may be clustered in a community. In this paper, we suggest a novel method to identify multiple spreaders from communities in a balanced way. The network is first divided into a great many super nodes and then k spreaders are selected from these super nodes. Experimental results on real and synthetic networks with community structure show that our method outperforms the classic methods for degree centrality, k-core and ClusterRank in most cases.

  19. Temporal change in biological community structure in the Fountain Creek basin, Colorado, 2001-2008

    Science.gov (United States)

    Zuellig, Robert E.; Bruce, James F.; Stogner, Robert W.

    2010-01-01

    In 2001, the U.S. Geological Survey, in cooperation with Colorado Springs City Engineering, began a study to better understand the relations between environmental characteristics and biological communities in the Fountain Creek basin in order to aide water-resource management and guide future monitoring activities. To accomplish this task, environmental (streamflow, habitat, and water chemistry) and biological (fish and macroinvertebrate) data were collected annually at 24 sites over a 6- or 8-year period (fish, 2003 to 2008; macroinvertebrates, 2001 to 2008). For this report, these data were first analyzed to determine the presence of temporal change in macroinvertebrate and fish community structure among years using nonparametric multivariate statistics. Where temporal change in the biological communities was found, these data were further analyzed using additional nonparametric multivariate techniques to determine which subset of selected streamflow, habitat, or water-chemistry variables best described site-specific changes in community structure relative to a gradient of urbanization. This study identified significant directional patterns of temporal change in macroinvertebrate and fish community structure at 15 of 24 sites in the Fountain Creek basin. At four of these sites, changes in environmental variables were significantly correlated with the concurrent temporal change identified in macroinvertebrate and fish community structure (Monument Creek above Woodmen Road at Colorado Springs, Colo.; Monument Creek at Bijou Street at Colorado Springs, Colo.; Bear Creek near Colorado Springs, Colo.; Fountain Creek at Security, Colo.). Combinations of environmental variables describing directional temporal change in the biota appeared to be site specific as no single variable dominated the results; however, substrate composition variables (percent substrate composition composed of sand, gravel, or cobble) collectively were present in 80 percent of the environmental

  20. Soil resources and topography shape local tree community structure in tropical forests.

    Science.gov (United States)

    Baldeck, Claire A; Harms, Kyle E; Yavitt, Joseph B; John, Robert; Turner, Benjamin L; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J; Chuyong, George B; Kenfack, David; Thomas, Duncan W; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N Nur; Dalling, James W

    2013-02-22

    Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24-50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9-34% and 5-29%, respectively), and all environmental variables together explain 13-39% of compositional variation within a plot. A large fraction of variation (19-37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe.

  1. 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…

  2. 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…

  3. 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…

  4. 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.

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

    OpenAIRE

    Shelton, Jenna L.; Akob, Denise M.; Jennifer C McIntosh; Noah Fierer; 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, a...

  6. Abundance, richness and structure of soil fungal communities across an European transect

    OpenAIRE

    Buee, Marc; Tisserant, Emilie; Hannula, S. E.; Fauchery, Laure; Plassart, Pierre; Stone, D; R. Creamer; W. Boer; van Veen, J.A.; Martin, Francis; and al, ..

    2014-01-01

    In contrast with plants and animals, biogeographical patterns of fungal assemblages have been little explored. Consequently, the factors driving the diversity and the composition of these communities are poorly understood. The EcoFINDERS project aimed at (i) characterizing the soil fungal diversity according to soil types, land uses and climate, and (ii) determining environmental variables explaining the fungal richness and community structure. Highthroughput sequencing of the ITS2 region was...

  7. Bacterial Community Structure and Biochemical Changes Associated With Composting of Lignocellulosic Oil Palm Empty Fruit Bunch

    OpenAIRE

    Mohd Huzairi Mohd Zainudin; Mohd Ali Hassan,; Umi Kalsom Md Shah; Norhani Abdullah; Mitsunori Tokura; Hisashi Yasueda; Yoshihito Shirai; Kenji Sakai; Azhari Samsu Baharuddin

    2013-01-01

    Bacterial community structure and biochemical changes during the composting of lignocellulosic oil palm empty bunch (EFB) and palm oil mill effluent (POME) anaerobic sludge were studied by examining the succession of the bacterial community and its association with changes in lignocellulosic components by denaturing gradient gel electrophoresis (DGGE) and the 16S rRNA gene clone library. During composting, a major reduction in cellulose after 10 days from 50% to 19% and the carbon content fro...

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

    Science.gov (United States)

    Silva, Pedro Giovâni da; Hernández, Malva Isabel Medina

    2015-01-01

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

  9. A Java program for non-parametric statistic comparison of community structure

    Directory of Open Access Journals (Sweden)

    WenJun Zhang

    2011-09-01

    Full Text Available The Java algorithm to statistically compare structure difference of two communities was presented in this study. Euclidean distance, Manhattan distance, Pearson correlation, Point correlation, quadratic correlation and Jaccard coefficient were included in the algorithm. The algorithm was used to compare rice arthropod communities in Pearl River Delta, China, and the results showed that the family composition of arthropods for Guangzhou, Zhongshan, Zhuhai, and Dongguan are not significantly different.

  10. 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.

  11. 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.

    2015-01-01

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

  12. Mechanisms shaping size structure and functional diversity of phytoplankton communities in the ocean

    Science.gov (United States)

    Acevedo-Trejos, Esteban; Brandt, Gunnar; Bruggeman, Jorn; Merico, Agostino

    2015-03-01

    The factors regulating phytoplankton community composition play a crucial role in structuring aquatic food webs. However, consensus is still lacking about the mechanisms underlying the observed biogeographical differences in cell size composition of phytoplankton communities. Here we use a trait-based model to disentangle these mechanisms in two contrasting regions of the Atlantic Ocean. In our model, the phytoplankton community can self-assemble based on a trade-off emerging from relationships between cell size and (1) nutrient uptake, (2) zooplankton grazing, and (3) phytoplankton sinking. Grazing `pushes' the community towards larger cell sizes, whereas nutrient uptake and sinking `pull' the community towards smaller cell sizes. We find that the stable environmental conditions of the tropics strongly balance these forces leading to persistently small cell sizes and reduced size diversity. In contrast, the seasonality of the temperate region causes the community to regularly reorganize via shifts in species composition and to exhibit, on average, bigger cell sizes and higher size diversity than in the tropics. Our results raise the importance of environmental variability as a key structuring mechanism of plankton communities in the ocean and call for a reassessment of the current understanding of phytoplankton diversity patterns across latitudinal gradients.

  13. 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

  14. Chitin amendment raises the suppressiveness of soil towards plant pathogens and modulates the actinobacterial and oxalobacteriaceal communities in an experimental agricultural field

    NARCIS (Netherlands)

    Cretoiu, M.S.; Korthals, G.W.; Visser, J.H.M.; Elsas, van J.D.

    2013-01-01

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

  15. Structuring Community Care using Multi-Agent Systems

    Science.gov (United States)

    Beer, Martin D.

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

  16. Geographic variation in plant community structure of salt marshes: species, functional and phylogenetic perspectives.

    Science.gov (United States)

    Guo, Hongyu; Chamberlain, Scott A; Elhaik, Eran; Jalli, Inder; Lynes, Alana-Rose; Marczak, Laurie; Sabath, Niv; Vargas, Amy; Więski, Kazimierz; Zelig, Emily M; Pennings, Steven C

    2015-01-01

    In general, community similarity is thought to decay with distance; however, this view may be complicated by the relative roles of different ecological processes at different geographical scales, and by the compositional perspective (e.g. species, functional group and phylogenetic lineage) used. Coastal salt marshes are widely distributed worldwide, but no studies have explicitly examined variation in salt marsh plant community composition across geographical scales, and from species, functional and phylogenetic perspectives. Based on studies in other ecosystems, we hypothesized that, in coastal salt marshes, community turnover would be more rapid at local versus larger geographical scales; and that community turnover patterns would diverge among compositional perspectives, with a greater distance decay at the species level than at the functional or phylogenetic levels. We tested these hypotheses in salt marshes of two regions: The southern Atlantic and Gulf Coasts of the United States. We examined the characteristics of plant community composition at each salt marsh site, how community similarity decayed with distance within individual salt marshes versus among sites in each region, and how community similarity differed among regions, using species, functional and phylogenetic perspectives. We found that results from the three compositional perspectives generally showed similar patterns: there was strong variation in community composition within individual salt marsh sites across elevation; in contrast, community similarity decayed with distance four to five orders of magnitude more slowly across sites within each region. Overall, community dissimilarity of salt marshes was lowest on the southern Atlantic Coast, intermediate on the Gulf Coast, and highest between the two regions. Our results indicated that local gradients are relatively more important than regional processes in structuring coastal salt marsh communities. Our results also suggested that in

  17. Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures

    Science.gov (United States)

    Wang, Hui; Wang, Bin; Dong, Wenwen; Hu, Xiaoke

    2016-10-01

    Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution.

  18. 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.

  19. 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.

  20. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  2. 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.

  3. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

    Science.gov (United States)

    He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

    2012-02-01

    One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

  4. 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

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

    Directory of Open Access Journals (Sweden)

    Amanda M Achberger

    2016-09-01

    Full Text Available Subglacial Lake Whillans (SLW, located beneath ~800 m of ice on the Whillans Ice Stream in West Antarctica 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 Nitrosoarcheaum 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 provided evidence for methane cycling beneath the West Antarctic Ice Sheet. Large ratios of rRNA to rDNA were observed for several OTUs 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 organic matter that sustains a

  6. 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.

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

    Science.gov (United States)

    Ma, Lili; Zhang, Zhanli; Li, Meng

    2016-07-01

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

  8. 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.

  9. 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 ...

  10. 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.

  11. 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.

  12. The relationship between community structural characteristics, the context of crack use, and HIV risk behaviors in San Salvador, El Salvador.

    Science.gov (United States)

    Dickson-Gomez, Julia; McAuliffe, Timothy; Rivas de Mendoza, Lorena; Glasman, Laura; Gaborit, Mauricio

    2012-02-01

    This paper explores community structural factors in different low-income communities in the San Salvador, El Salvador, that account for differences in the social context in which crack is used and HIV risk behaviors among crack users. Results suggest that both more distal (type of low-income community, level of violent crime, and poverty) and proximate structural factors (type of site where drugs are used, and whether drugs are used within or outside of community of residence) influence HIV risk behaviors among drug users. Additionally, our results suggest that community structural factors influence the historical and geographic variation in drug use sites.

  13. Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps.

    Directory of Open Access Journals (Sweden)

    Jarrod J Scott

    Full Text Available BACKGROUND: Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies. METHODOLOGY/PRINCIPAL FINDINGS: Using microbial membrane lipid analysis and a variety of community metrics, we assessed and compared the microbiota of fungus gardens and refuse dumps from both laboratory-maintained and field-collected colonies. We found that gardens contained a diverse and consistent community of microbes, dominated by Gram-negative bacteria, particularly gamma-Proteobacteria and Bacteroidetes. These findings were consistent across lab and field gardens, as well as host ant taxa. In contrast, dumps were enriched for Gram-positive and anaerobic bacteria. Broad-scale clustering analyses revealed that community relatedness between samples reflected system component (gardens/dumps rather than colony source (lab/field. At finer scales samples clustered according to colony source. CONCLUSIONS/SIGNIFICANCE: Here we report the first comparative analysis of the microbiota from leaf-cutter ant colonies. Our work reveals the presence of two distinct communities: one in the fungus garden and the other in the refuse dump. Though we find some effect of colony source on community structure, our data indicate the presence of consistently associated microbes within gardens and dumps. Substrate composition and system component appear to be the most important factor in structuring the microbial communities

  14. Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

    Science.gov (United States)

    2004-09-01

    Du, Y., et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron...C.A., Newell, S.Y., and Paerl, H.W. (1995) The role References of standing dead Spartina alternfflora and benthic microal- gae in salt marsh food webs ...q Ja 1,4 1 S., fn.i.to) 47. 145-1 156 (19r . lntiutoide Geologia’ Mineria , Universidad Nactonalde Jujuy, Avenida Bolwiva . V~a. C 3. j kLmnnnaommntal

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  18. 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

  19. Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

    Directory of Open Access Journals (Sweden)

    Jenna L Shelton

    2016-09-01

    Full Text Available 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, and that

  20. 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

  1. 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

  2. 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

  3. Helminth community composition, structure, and pattern in six dove species (Columbiformes: Columbidae) of South Texas.

    Science.gov (United States)

    Smith, Autumn J; Fedynich, Alan M

    2012-02-01

    The helminth community composition and structure of 6 species of columbids residing in south Texas are reported and compared herein. Sixty individuals of the following species, rock pigeons (Columba livia [RP]), mourning doves (Zenaida macroura [MD]), Eurasian collared-doves (Streptopelia decaocto [ECD]), white-winged doves (Zenaida asiatica [WWD]), and common ground doves (Columbina passerina [CGD]), and 48 Inca doves (Columbina inca [ID]) were collected during the summer of 2006 and examined for helminths. Twelve helminth species were found (9 nematodes and 3 cestodes), representing 486 individuals. Nematodes numerically dominated the component community in all host species. Overall, helminth prevalence was similar among host sex within all dove species. However, prevalence of Skrjabinia bonini and Hymenolepis sp. in RPs was significantly different among host age groups (P = 0.01, P = 0.0002, respectively). Likewise, prevalence of Killigrewia delafondi was higher (P = 0.0001) in adult WWDs. Based on percent similarity and Jaccard's coefficient of community indices, helminth component communities were dissimilar, and the number of shared helminth species varied among host species. Data from this study suggest that the environment surrounding preferred host habitat and foraging strategies of each host species is the driving force behind helminth component communities. This study emphasizes the importance of examining co-occurring hosts at both local and regional scales to elucidate helminth community structure and patterns.

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

    Science.gov (United States)

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

    2014-12-01

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

  5. Coal mining activities change plant community structure due to air pollution and soil degradation.

    Science.gov (United States)

    Pandey, Bhanu; Agrawal, Madhoolika; Singh, Siddharth

    2014-10-01

    The aim of this study was to investigate the effects of coal mining activities on the community structures of woody and herbaceous plants. The response of individual plants of community to defilement caused by coal mining was also assessed. Air monitoring, soil physico-chemical and phytosociological analyses were carried around Jharia coalfield (JCF) and Raniganj coalfield. The importance value index of sensitive species minified and those of tolerant species enhanced with increasing pollution load and altered soil quality around coal mining areas. Although the species richness of woody and herbaceous plants decreased with higher pollution load, a large number of species acclimatized to the stress caused by the coal mining activities. Woody plant community at JCF was more affected by coal mining than herbaceous community. Canonical correspondence analysis revealed that structure of herbaceous community was mainly driven by soil total organic carbon, soil nitrogen, whereas woody layer community was influenced by sulphur dioxide in ambient air, soil sulphate and soil phosphorus. The changes in species diversity observed at mining areas indicated an increase in the proportion of resistant herbs and grasses showing a tendency towards a definite selection strategy of ecosystem in response to air pollution and altered soil characteristics.

  6. Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities

    DEFF Research Database (Denmark)

    Zhang, Lai; Andersen, Ken Haste; Dieckmann, Ulf

    2015-01-01

    -structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze...... the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken...

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

    Science.gov (United States)

    Beery, Joshua A; Day, Jennifer E

    2015-03-03

    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.

  8. 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.

  9. Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany.

    Science.gov (United States)

    Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E; Ellerbrock, Ruth; Bruelheide, Helge; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

    2015-01-01

    Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.

  10. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

    Science.gov (United States)

    Delgado-Balbuena, Laura; Bello-López, Juan M; Navarro-Noya, Yendi E; Rodríguez-Valentín, Analine; Luna-Guido, Marco L; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  11. 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.

  12. [Spacial structure of epiphytic yeast communities on fruits of Sorbus aucuparia L].

    Science.gov (United States)

    Maksimova, I A; Iurkov, A M; Chernov, I Iu

    2009-01-01

    The subject of this research is epiphytic yeast communities that form on the surface of Sorbus aucuparia. The object is to make quantitative assessment of the yeast communities' differentiation of the same but distant substratum. Results of the factor variance nidicolous analysis demonstrated that with increase in distances, there are increases in the variation of total number and relative abundance of the dominant yeast communities. The average similarity between groups of single fruits (Sorensen's Quotient of Similarity) regularly decreased with distance. The results demonstrate that the number and structure of separate yeast groups depend not only on ecological factors but also on proximity to other communities. Such aggregation in the distribution of the microorganisms' species caused by migration and colonial resettlement should be taken into account when analyzing their diversity in natural habitats.

  13. 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.

  14. An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Pfiffner, Susan M.; Brandt, Craig C.; Kostka, Joel E.; Palumbo, Anthony V.

    2005-08-11

    Our current research represents a joint effort between Oak Ridge National Laboratory (ORNL), Florida State University (FSU), and the University of Tennessee. ORNL will serve as the lead institution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliverables. This project was initiated in November, 2004, in the Integrative Studies Element of the NABIR program. The overall goal of our project is to provide an improved understanding of the relationships between microbial community structure, geochemistry, and metal reduction rates. The research seeks to address the following questions: Is the metabolic diversity of the in situ microbial community sufficiently large and redundant that bioimmobilization of uranium will occur regardless of the type of electron donor added to the system? Are their donor specific effects that lead to enrichment of specific community members that then impose limits on the functional capabilities of the system? Will addition of humics change rates of uranium reduction without changing community structure? Can resource-ratio theory be used to understand changes in uranium reduction rates and community structure with respect to changing C:P ratios?

  15. [Effects of wheat root exudates on cucumber growth and soil fungal community structure].

    Science.gov (United States)

    Wu, Feng-Zhi; Li, Min; Cao, Peng; Ma, Ya-Fei; Wang, Li-Li

    2014-10-01

    With wheat as the donor plant and cucumber as the receptor plant, this study investigated the effects of root exudates from wheat cultivars with different allelopathic potentials (positive or negative) and companion cropping with wheat on soil fungal community structure by PCR-DGGE method and cucumber growth. Results showed that the wheat root exudates with positive allelopathic potential increased height and stem diameter of cucumber seedlings significantly, compared to the control seedlings (W) after 6 days and 12 days treatment, respectively. Also, wheat root exudates with both positive and negative allelopathic potential increased the seedling height of cucumber significantly after 18 days treatment. The wheat root exudates with different allelopathic potentials decreased the band number, Shannon and evenness indices of soil fungal community significantly in cucumber seedling rhizosphere, and those in the soil with the control seedlings (W) were also significantly higher than that in the control soil without seedlings (Wn) after 6 days treatment. The band number, Shannon and evenness indices in all the treatments were significantly higher than those in the control soil without seedlings (Wn) after 18 days treatment. Companion cropping with negative allelopathic potential wheat decreased the Shannon and evenness indices of soil fungi community significantly in the cucumber seedling rhizosphere, suggesting the wheat root exudates and companion cropping with wheat changed soil fungal community structure in the cucumber seedling rhizosphere. The results of DGGE map and the principal component analysis showed that companion cropping with wheat cultivars with different allelopathic potentials changed soil fungal community structure in cucumber seedling rhizosphere.

  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. Community Structures of Arbuscular Mycorrhizal Fungi in Soils and Plant Roots Inhabiting Abandoned Mines of Korea

    Science.gov (United States)

    Park, Hyeok; Lee, Eun-Hwa; Ka, Kang-Hyeon

    2016-01-01

    In this study, we collected rhizosphere soils and root samples from a post-mining area and a natural forest area in Jecheon, Korea. We extracted spores of arbuscular mycorrhizal fungi (AMF) from rhizospheres, and then examined the sequences of 18S rDNA genes of the AMF from the collected roots of plants. We compared the AMF communities in the post-mining area and the natural forest area by sequence analysis of the AMF spores from soils and of the AMF clones from roots. Consequently, we confirmed that the structure of AMF communities varied between the post-mining area and the natural forest area and showed significant relationship with heavy metal contents in soils. These results suggest that heavy metal contamination by mining activity significantly affects the AMF community structure. PMID:28154485

  18. 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.

  19. Separating natural and contaminant related gradients in estuarine macrobenthic community structure

    Energy Technology Data Exchange (ETDEWEB)

    Rakocinski, C.; Heard, R.; Walker, W. [Gulf Coast Research Lab., Ocean Springs, MS (United States); Brown, S.; Gaston, G. [Univ. of Mississippi, University, MS (United States). Biology Dept.; Summers, J.K. [Environmental Protection Agency, Gulf Breeze, FL (United States)

    1995-12-31

    Using whole-community macrobenthic responses to assess pollution impacts in estuaries presents a difficult challenge due to dynamic natural conditions that may impose their own physical limitations on the biota. For example, the recognition of bioindicator taxa becomes confounded when correlations exist between gradients in natural environmental variables, such as salinity, and gradients in contaminants, such as trace metals. The authors used partial Canonical Correspondence Analysis (CCA) to separate natural and contaminant related gradients in macrobenthic community structure across 319 EMAP sites dispersed throughout the northern Gulf of Mexico. Residual variation in macrobenthic community structure was examined with respect to gradients in contaminant levels to identify responses by positive and negative bioindicator taxa. Gradients in concentrations of trace metals do not coincide completely with those in other chemical contaminants, and responses by characteristic bioindicator taxa reveal information regarding effects of specific contaminants. Several indigenous taxa serve as good negative bioindicators, whereas other opportunistic taxa serve as positive bioindicators of estuarine contamination.

  20. 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.

  1. 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.

  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. 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.

  4. 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.

  5. An Analysis of the Effects of Program Structure and Content on Outcomes of Community Leadership Education Programs

    Science.gov (United States)

    Apaliyah, Godwin Tayese

    2011-01-01

    This study examined community leadership education programs employed in rural communities and organizations of several states to empower both local leaders and residents. In particular, the study investigated the relationships between community leadership education program design and structure (contact hours and content) and six outcome indices of…

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Invertebrate grazing during the regenerative phase affects the ultimate structure of macrophyte communities

    NARCIS (Netherlands)

    Elger, A.F.; Willby, N.; Cabello-Martinez, M.

    2009-01-01

    1. Although the biomass of freshwater macrophytes consumed by invertebrate herbivores (excluding crayfish) is usually low, there is growing evidence that invertebrates do exert a structuring effect on macrophyte communities. To explain this, we postulated that the effect of invertebrates may be conc

  11. Assessment of the effects of genetically modified potatoes on structure and functioning of soil fungal communities

    NARCIS (Netherlands)

    Hannula, Emilia

    2012-01-01

    This thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter composition, and compares the observed differences between the GM- and its parental variety in the context o

  12. 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...

  13. 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...

  14. 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.

  15. 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...

  16. 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

  17. Community structure of filamentous, sheath-building sulfur bacteria, Thioploca spp, off the coast of Chile

    DEFF Research Database (Denmark)

    Schulz, HN; Jørgensen, BB; Fossing, HA

    1996-01-01

    The filamentous sulfur bacteria Thioploca spp, produce dense bacterial mats in the shelf area off the coast of Chile and Peru. The mat consists of common sheaths, shared by many filaments, that reach 5 to 10 cm dean into the sediment, The structure of the Thioploca communities off the Bay...

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

    NARCIS (Netherlands)

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

    2013-01-01

    Increasing evidence shows that spatial interactions between sedentary organisms can structure communities and promote landscape complexity in many ecosystems. Here we tested the hypothesis that reef-forming mussels (Mytilus edulis L.), a dominant intertidal ecosystem engineer in the Wadden Sea, prom

  19. 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.

  20. Structure and function of methanotrophic communities in a landfill-cover soil.

    Science.gov (United States)

    Henneberger, Ruth; Lüke, Claudia; Mosberger, Lona; Schroth, Martin H

    2012-07-01

    In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P structure are driving factors in CH(4) oxidation at this landfill.

  1. Effect of preservation method on the assessment of bacterial community structure in soil and water samples.

    Science.gov (United States)

    Tatangelo, Valeria; Franzetti, Andrea; Gandolfi, Isabella; Bestetti, Giuseppina; Ambrosini, Roberto

    2014-07-01

    The methods used in sample preservation may affect the description of the microbial community structure by DNA-based techniques. This study aims at evaluating the effect of different storage conditions, including freezing, adding two liquid-based preservatives or simply storing samples with no preservative, on the structure of the microbial communities in aliquots of organic-rich soil and water samples as revealed by a terminal restriction fragment length polymorphisms. The results showed that the number of terminal restriction fragments (TRFs) detected in soil aliquots stored with LifeGuard(™) solution was significantly lower than that of samples analyzed immediately after sampling. Moreover, cluster and PCA analyses showed that soil aliquots stored using LifeGuard(™) clustered separately from those stored with the other methods. Conversely, soil and water aliquots stored with DMSO-EDTA-salt solution did not show either significant reduction in the number of TRFs or any change in the structure of the microbial community. Finally, the number of TRFs and the structure of microbial communities from soil aliquots stored with no preservative did not differ from those of aliquots analyzed immediately after sampling. Preservation methods should therefore be accurately evaluated before collecting samples that have to be stored for long time before DNA extraction.

  2. Engaging and sustaining adolescents in community-based participatory research: structuring a youth-friendly community-based participatory research environment.

    Science.gov (United States)

    LoIacono Merves, Marni; Rodgers, Caryn R R; Silver, Ellen Johnson; Sclafane, Jamie Heather; Bauman, Laurie J

    2015-01-01

    Community-Based Participatory Research partnerships typically do not include adolescents as full community partners. However, partnering with adolescents can enhance the success and sustainability of adolescent health interventions. We partnered with adolescents to address health disparities in a low-income urban community. In partnering with youth, it is important to consider their developmental stage and needs to better engage and sustain their involvement. We also learned the value of a Youth Development framework and intentionally structuring a youth-friendly Community-Based Participatory Research environment. Finally, we will raise some ethical responsibilities to consider when working with youth partners.

  3. 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

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

    Science.gov (United States)

    Webb, A. E.

    2012-12-01

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

  5. Dominant predators mediate the impact of habitat size on trophic structure in bromeliad invertebrate communities.

    Science.gov (United States)

    Petermann, Jana S; Farjalla, Vinicius F; Jocque, Merlijn; Kratina, Pavel; MacDonald, A Andrew M; Marino, Nicholas A C; De Omena, Paula M; Piccoli, Gustavo C O; Richardson, Barbara A; Richardson, Michael J; Romero, Gustavo Q; Videla, Martin; Srivastava, Diane S

    2015-02-01

    Local habitat size has been shown to influence colonization and extinction processes of species in patchy environments. However, species differ in body size, mobility, and trophic level, and may not respond in the same way to habitat size. Thus far, we have a limited understanding of how habitat size influences the structure of multitrophic communities and to what extent the effects may be generalizable over a broad geographic range. Here, we used water-filled bromeliads of different sizes as a natural model system to examine the effects of habitat size on the trophic structure of their inhabiting invertebrate communities. We collected composition and biomass data from 651 bromeliad communities from eight sites across Central and South America differing in environmental conditions, species pools, and the presence of large-bodied odonate predators. We found that trophic structure in the communities changed dramatically with changes in habitat (bromeliad) size. Detritivore : resource ratios showed a consistent negative relationship with habitat size across sites. In contrast, changes in predator: detritivore (prey) ratios depended on the presence of odonates as dominant predators in the regional pool. At sites without odonates, predator: detritivore biomass ratios decreased with increasing habitat size. At sites with odonates, we found odonates to be more frequently present in large than in small bromeliads, and predator: detritivore biomass ratios increased with increasing habitat size to the point where some trophic pyramids became inverted. Our results show that the distribution of biomass amongst food-web levels depends strongly on habitat size, largely irrespective of geographic differences in environmental conditions or detritivore species compositions. However, the presence of large-bodied predators in the regional species pool may fundamentally alter this relationship between habitat size and trophic structure. We conclude that taking into account the

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

    Science.gov (United States)

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

    2015-10-01

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

  7. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    OpenAIRE

    Lee, Charles K.; Craig W. Herbold; Polson, Shawn W.; K Eric Wommack; Williamson, Shannon J.; McDonald, Ian R.; S. Craig Cary

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure est...

  8. 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

  9. Imidacloprid induces changes in the structure, genetic diversity and catabolic activity of soil microbial communities.

    Science.gov (United States)

    Cycoń, Mariusz; Markowicz, Anna; Borymski, Sławomir; Wójcik, Marcin; Piotrowska-Seget, Zofia

    2013-12-15

    This is the first report describing the effect of imidacloprid applied at field rate (FR, 1 mg/kg of soil) and 10 times the FR (10*FR, 10 mg/kg of soil) on the structural, genetic and physiological diversity of soil bacterial community as determined by the phospholipid fatty acid (PLFA), the denaturing gradient gel electrophoresis (DGGE), and the community level physiological profile (CLPP) approaches. PLFA profiles showed that imidacloprid significantly shifted the microbial community structure and decreased the biomass of the total, bacterial and fungal PLFAs, however, this effect was transient at the FR dosage. The alterations in DGGE patterns caused by imidacloprid application, confirmed considerable changes in the overall richness and diversity of dominant bacteria. Although, as a result of imidacloprid application, the metabolic activity of microbial communities was generally lower, the richness and functional biodiversity of the soil microbial community were not negatively affected. In general, the analysis of the variance indicated that the measured parameters were significantly affected by treatment and the incubation time, however, the incubation time effect explained most of the observed variance. Imidacloprid degradation and the appearance of some new bands in DGGE profiles suggest the evolution of bacteria capable of degrading imidacloprid among indigenous microflora.

  10. Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure.

    Science.gov (United States)

    Rodríguez-Echeverría, Susana; Teixeira, Helena; Correia, Marta; Timóteo, Sérgio; Heleno, Ruben; Öpik, Maarja; Moora, Mari

    2017-01-01

    Understanding the distribution and diversity of arbuscular mycorrhizal fungi (AMF) and the rules that govern AMF assemblages has been hampered by a lack of data from natural ecosystems. In addition, the current knowledge on AMF diversity is biased towards temperate ecosystems, whereas little is known about other habitats such as dry tropical ecosystems. We explored the diversity and structure of AMF communities in grasslands, savannas, dry forests and miombo in a protected area under dry tropical climate (Gorongosa National Park, Mozambique) using 454 pyrosequencing. In total, 147 AMF virtual taxa (VT) were detected, including 22 VT new to science. We found a high turnover of AMF with ˂ 12% of VT present in all vegetation types. Forested areas supported more diverse AMF communities than savannas and grassland. Miombo woodlands had the highest AMF richness, number of novel VT, and number of exclusive and indicator taxa. Our data reveal a sharp differentiation of AMF communities between forested areas and periodically flooded savannas and grasslands. This marked ecological structure of AMF communities provides the first comprehensive landscape-scale evidence that, at the background of globally low endemism of AMF, local communities are shaped by regional processes including environmental filtering by edaphic properties and natural disturbance.

  11. 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.

  12. 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.

  13. Herpetofaunal community structure and habitat associations in Gunung Ciremai National Park, West Java, Indonesia

    Directory of Open Access Journals (Sweden)

    AWAL RIYANTO

    2011-01-01

    Full Text Available Riyanto A (2011 Herpetofaunal community structure and habitat associations in Gunung Ciremai National Park, West Java, Indonesia. Biodiversitas 12: 38-44. Community structure and habitat associations of amphibians and reptiles on both rainy and dry seasons of six habitat types of three sites in Gunung Ciremai National Park, West Java were investigated in March and October 2008. The data of herpetofauna was obtained by opportunistic searches. Herpetofaunal diversity for each habitat was determined by using Shannon Wiener index, the species abundance per unit area was calculated by using Margalef’s index, and the homogeneity of distribution of species in relation to other species in a sampled per unit area was evaluated using Evenness index. The similarity in herpetofauna communities among habitat types was determined using Sorensen’s coefficient, meanwhile the Jaccard’s index was used to estimate similarities in habitat utilization. Thus, both of community similarities and habitat utilization displayed in cluster dendrogram. A total of 46 amphibian and reptile taxa were recorded, comprising 16 anurans, 22 lizards and 8 snakes. Of the total taxa, four anurans are endemic and an unusual specimens probably new in sciences referred to the genus Cyrtodactylus and Eutropis. There were differed in sequential of biological indices among habitat types but not much different in their values. The result of cluster analysis showed different patterns on the community similarity among habitat type and habitat utilization during rainy and dry seasons.

  14. 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.

  15. 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.

  16. 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.

  17. Nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and the productivity and structure of prairie grassland communities.

    Science.gov (United States)

    Bauer, Jonathan T; Kleczewski, Nathan M; Bever, James D; Clay, Keith; Reynolds, Heather L

    2012-12-01

    Due to their complementary roles in meeting plant nutritional needs, arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (N(2)-fixers) may have synergistic effects on plant communities. Using greenhouse microcosms, we tested the effects of AMF, N(2)-fixers (symbiotic: rhizobia, and associative: Azospirillum brasilense), and their potential interactions on the productivity, diversity, and species composition of diverse tallgrass prairie communities and on the productivity of Panicum virgatum in monoculture. Our results demonstrate the importance of AMF and N(2)-fixers as drivers of plant community structure and function. In the communities, we found a positive effect of AMF on diversity and productivity, but a negative effect of N(2)-fixers on productivity. Both AMF and N(2)-fixers affected relative abundances of species. AMF shifted the communities from dominance by Elymus canadensis to Sorghastrum nutans, and seven other species increased in abundance with AMF, accounting for the increased diversity. N(2)-fixers led to increases in Astragalus canadensis and Desmanthus illinoense, two legumes that likely benefited from the presence of the appropriate rhizobia symbionts. Sorghastrum nutans declined 44 % in the presence of N(2)-fixers, with the most likely explanation being increased competition from legumes. Panicum monocultures were more productive with AMF, but showed no response to N(2)-fixers, although inference was constrained by low Azospirillum treatment effectivity. We did not find interactions between AMF and N(2)-fixers in communities or Panicum monocultures, indicating that short-term effects of these microbial functional groups are additive.

  18. Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest.

    Science.gov (United States)

    Sun, Hui; Terhonen, Eeva; Kovalchuk, Andriy; Tuovila, Hanna; Chen, Hongxin; Oghenekaro, Abbot O; Heinonsalo, Jussi; Kohler, Annegret; Kasanen, Risto; Vasander, Harri; Asiegbu, Fred O

    2016-05-01

    Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (Pstructure (Psoil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

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

    Science.gov (United States)

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

    2014-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Jichen Wang

    2016-08-01

    Full Text Available Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer 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 organic fertilizer (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 organic fertilizer application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR versus sequence analysis, yet poor correlations were found for the Alpha- and Beta- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil

  1. Bacterial Community Structure and Dynamics During Corn-Based Bioethanol Fermentation.

    Science.gov (United States)

    Li, Qing; Heist, E Patrick; Moe, Luke A

    2016-02-01

    Corn-based fuel ethanol facilities mix enzymatically treated, gelatinized corn starch with water to generate a "mash" that is used as the substrate in large-scale (∼500,000 gallon) yeast-based fermentations. In contrast to other food and beverage fermentations (e.g., cheese, wine), bioethanol production is presumed to be optimal when bacteria are absent from the fermentation-thus maximizing conversion of glucose to ethanol-yet the facilities are not sterilized. Culture-based analysis has suggested that lactic acid bacteria occupy this niche and, under certain circumstances, can outcompete the dedicated fermentation yeast for nutrients. Here, we use 16S rRNA gene amplicon sequencing to probe bacterial community structure during bioethanol fermentation. Nineteen total batches from five corn-based fuel ethanol fermentation facilities were analyzed. From each batch, five samples were taken. This includes the contents of the yeast propagation tank at inoculation, three samples taken at intervals during the fermentation, and a sample taken at the end of fermentation. Bacterial community structure was compared with time, between facility, between fermentor, between batches from the same fermentor, and against environmental variables within each fermentation. Communities were dominated by members of the Firmicutes and Proteobacteria phyla, with lactic acid bacteria dominating the communities in two of the five facilities. In the other facilities, Proteobacteria (largely members of the Pseudomonas and Escherichia-Shigella genera) outcompete the lactic acid bacteria. In most cases, the yeast propagation tank inoculum imparted a rich bacterial community, but the batches vary regarding whether this inoculum was the primary driver of the fermentation community structure.

  2. 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

  3. Relating Microbial Community Structure to a Dominant Environmental Variable in a Complex Environment; An Example from a Chromium Contaminated Site

    Energy Technology Data Exchange (ETDEWEB)

    Palumbo, Anthony Vito [ORNL; Schryver, Jack C [ORNL; Pfiffner, Susan M. [University of Tennessee, Knoxville (UTK); Marsh, Terence [Michigan State University, East Lansing; Brandt, Craig C [ORNL

    2008-01-01

    In a complex environment, it can be difficult to assess the degree to which a continuous variable influences microbial community structure. We propose a method that involves using the community data to "predict" the value of the presumed dominant variable. The assumption is that in order to "predict" the variable the community composition must be sensitive to or affected by the variable in question. The concentration range over which the prediction is accurate should thus provide information on the concentrations that influence community structure. We explored this approach using T-RLFP data on at a site polluted by tannery wastes. We were able to use the microbial community structure measures to predict Cr concentration over a surprisingly wide range of concentration. Although, it appears from this work that this approach can give useful information about the relationships between microbial community structure and specific environmental conditions much further testing is required.

  4. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status.

    Science.gov (United States)

    Yang, C H; Crowley, D E

    2000-01-01

    Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.

  5. Disturbance frequency and community structure in a twenty-five year intervention study

    Science.gov (United States)

    Trexler, J.C.; Loftus, W.F.; Perry, S.

    2005-01-01

    Models of community regulation commonly incorporate gradients of disturbance inversely related to the role of biotic interactions in regulating intermediate trophic levels. Higher trophic-level organisms are predicted to be more strongly limited by intermediate levels of disturbance than are the organisms they consume. We used a manipulation of the frequency of hydrological disturbance in an intervention analysis to examine its effects on small-fish communities in the Everglades, USA. From 1978 to 2002, we monitored fishes at one long-hydroperiod (average 350 days) and at one short-hydroperiod (average 259 days; monitoring started here in 1985) site. At a third site, managers intervened in 1985 to diminish the frequency and duration of marsh drying. By the late 1990s, the successional dynamics of density and relative abundance at the intervention site converged on those of the long-hydroperiod site. Community change was manifested over 3 to 5 years following a dry-down if a site remained inundated; the number of days since the most recent drying event and length of the preceding dry period were useful for predicting population dynamics. Community dissimilarity was positively correlated with the time since last dry. Community dynamics resulted from change in the relative abundance of three groups of species linked by life-history responses to drought. Drought frequency and intensity covaried in response to hydrological manipulation at the landscape scale; community-level successional dynamics converged on a relatively small range of species compositions when drought return-time extended beyond 4 years. The density of small fishes increased with diminution of drought frequency, consistent with disturbance-limited community structure; less-frequent drying than experienced in this study (i.e., longer return times) yields predator-dominated regulation of small-fish communities in some parts of the Everglades. ?? Springer-Verlag 2005.

  6. [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.

  7. 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.

  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. [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.

  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. [Community structure characteristics of phytoplankton and related affecting factors in Hengshan Reservoir, Zhejiang, China].

    Science.gov (United States)

    Yang, Liang-Jie; Yu, Peng-Fei; Zhu, Jun-Quan; Xu, Zhen; Lü, Guang-Han; Jin, Chun-Hua

    2014-02-01

    In order to reveal the community structure characteristics of phytoplankton and the relationships with environmental factors in Hengshan Reservoir, the phytoplankton species composition, abundance, biomass and 12 environmental factors at 4 sampling sites were analyzed from March 2011 to February 2012. A total of 246 phytoplankton species were identified, which belong to 78 genera and 7 phyla. The dominant species were Melosira varians, M. granulate, Cyclotella meneghiniana, Asterianella formosa, Synedra acus, Achnanthes exigua, Ankistrodesmus falcatus, Oscillatoria lacustris, Cryptomonas erosa, Chroomonas acuta, Phormidium tenue and Microcystis aeruginosa, etc. Seasonal variations of species were obvious. The annual abundance and biomass of the phytoplankton were 0.51 x 10(5)-14.22 x 10(5) ind x L(-1) and 0.07-1.27 mg x L(-1), respectively. The values of the Margelef index, Pielou index and Shannon index of the phytoplankton community were 1.10-3.33, 0.26-0.81 and 0.51-2.38, respectively. The phytoplankton community structure was of Bacillariophyta-Cryptophyta type in spring and winter, of Chlorophyta-Cyanophyta type in summer, and of Bacillariophyta type in autumn. Canonical correlation analysis (CCA) showed that temperature, transparency, chemical oxygen demand and pH had the closest relationships with the phytoplankton community structure in the reservoir. Water quality evaluation showed that Hengshan Reservoir was in a secondary pollution with a meso-trophic level.

  12. 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.

  13. The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

    Science.gov (United States)

    Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

    2007-01-01

    The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

  14. 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

  15. 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.

  16. Influence of grazing and fire frequency on small-scale plant community structure and resource variability in native tallgrass prairie

    NARCIS (Netherlands)

    Veen, G. F. (Ciska); Blair, John M.; Smith, Melinda D.; Collins, Scott L.

    2008-01-01

    In grasslands worldwide, grazing by ungulates and periodic fires are important forces affecting resource availability and plant community structure. It is not clear, however, whether changes in community structure are the direct effects of the disturbance (i.e. fire and grazing) or are mediated indi

  17. 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.

  18. 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.

  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. 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 ...

  2. 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

  3. Tropical Estuarine Macrobenthic Communities Are Structured by Turnover Rather than Nestedness.

    Science.gov (United States)

    Medeiros, Carlinda Raílly; Hepp, Luiz Ubiratan; Patrício, Joana; Molozzi, Joseline

    2016-01-01

    Turnover (i.e., species substitution) and nestedness (i.e., subsets of species from more diverse locations), the two main mechanisms used to explain the beta diversity of biological communities, have different implications for biodiversity conservation. To better understand how these mechanisms contribute to beta diversity, we tested the following hypotheses: (i) greater dissimilarity in community composition occurs between estuarine zones than other hierarchical level studied; (ii) beta diversity in these communities develops by turnover in estuaries with a lower degree of anthropogenic impact, but by nestedness in estuaries with a greater degree of anthropogenic impact; and (iii) the structuring mechanism is independent of season. We studied two tropical estuaries (dry and wet seasons) that vary in terms of land-use of the drainage basins. Subtidal benthic macroinvertebrates were sampled along the estuarine gradient in each of the two estuaries. The additive partitioning approach to species diversity was used to determine the hierarchical scale with the greatest dissimilarity in community composition. General beta diversity was measured using the Sorensen dissimilarity index, partitioning the turnover and nestedness components. The greatest dissimilarity in the composition of the communities occurred between the zones along the estuarine gradient in both seasons (dry = 58.6%; wet = 46.3%). In the estuary with a lower degree of anthropogenic influence, benthic macroinvertebrate diversity was generated by turnover regardless of the season. In the estuary with a greater degree of anthropogenic impact, beta diversity was structured by turnover during the dry season and a combination of both mechanisms during the wet season. We conclude that turnover is the principal mechanism responsible for beta diversity in benthic macroinvertebrate communities in tropical estuaries.

  4. 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

  5. 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.

  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. Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion.

    Science.gov (United States)

    Stiborova, Hana; Wolfram, Jan; Demnerova, Katerina; Macek, Tomas; Uhlik, Ondrej

    2015-11-01

    Stabilized sewage sludge is applied to agricultural fields and farmland due to its high organic matter content. The aim of this study was to investigate the effects of two types of sludge stabilization, mesophilic anaerobic digestion (MAD) and thermophilic anaerobic digestion (TAD), on bacterial communities in sludge, including the presence of pathogenic microorganisms. Bacterial community structure and phylogenetic diversity were analyzed in four sewage sludge samples from the Czech Republic. Analysis of 16S ribosomal RNA (rRNA) genes showed that investigated sludge samples harbor diverse bacterial populations with only a few taxa present across all samples. Bacterial diversity was higher in sludge samples after MAD versus TAD treatment, and communities in MAD-treated sludge shared the highest genetic similarities. In all samples, the bacterial community was dominated by reads affiliated with Proteobacteria. The sludge after TAD treatment had considerably higher number of reads of thermotolerant/thermophilic taxa, such as the phyla Deinococcus-Thermus and Thermotogae or the genus Coprothermobacter. Only one operational taxonomic unit (OTU), which clustered with Rhodanobacter, was detected in all communities at a relative abundance >1 %. All of the communities were screened for the presence of 16S rRNA gene sequences of pathogenic bacteria using a database of 122 pathogenic species and ≥98 % identity threshold. The abundance of such sequences ranged between 0.23 and 1.57 % of the total community, with lower numbers present after the TAD treatment, indicating its higher hygienization efficiency. Sequences clustering with nontuberculous mycobacteria were present in all samples. Other detected sequences of pathogenic bacteria included Streptomyces somaliensis, Acinetobacter calcoaceticus, Alcaligenes faecalis, Gordonia spp., Legionella anisa, Bordetella bronchiseptica, Enterobacter aerogenes, Brucella melitensis, and Staphylococcus aureus.

  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.

  10. 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.

  11. 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.

  12. Ecological Effects of Biochar on the Structure and Function of Stream Benthic Communities.

    Science.gov (United States)

    Clements, William H; Stahl, Ralph G; Landis, Richard C

    2015-12-15

    The introduction of biochar, activated carbon, and other carbonaceous materials to aquatic ecosystems significantly reduces the toxicity and bioavailability of contaminants. However, previous studies have shown that these materials can have negative effects on aquatic organisms. We conducted field and mesocosm experiments to test the hypothesis that biochar altered the structure and function of stream benthic communities. After 30 d in the field, colonization by stoneflies (Plecoptera) was significantly lower in trays containing biochar compared to the results from the controls. In stream mesocosms, biochar increased macroinvertebrate drift and significantly reduced community metabolism. However, most measures of community composition showed little variation among biochar treatments, and significant responses were limited to a single stonefly species (Capnia confusa). When benthic communities were simultaneously exposed to biochar and Cu, effects were primarily associated with metal exposure. Because it is unlikely that biochar treatments would be employed in uncontaminated areas, these moderately negative effects should be considered within the context of the positive benefits associated with reduced contaminant bioavailability and toxicity. Additional research is necessary to improve our understanding of the mechanisms responsible for biochar effects on benthic communities and to identify the optimal application rates and size fractions that will maximize contaminant sorption but minimize potential negative effects.

  13. 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 fungi were influenced by each other.

  14. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  16. 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.

  17. Microbial community structure and activity in arsenic-, chromium- and copper-contaminated soils.

    Science.gov (United States)

    Turpeinen, Riina; Kairesalo, Timo; Häggblom, Max M

    2004-01-01

    Microbial community structure, potential microbial activity and As resistance were affected by arsenic (As), chromium (Cr) and copper (Cu) contamination in soils of abandoned wood impregnating plants. Contaminated soils differed in the concentrations of soil acid-soluble and total water-soluble As, Cr and Cu, and in the concentration of bioavailable As analyzed with a bacterial sensor. Phospholipid fatty acid (PLFA) and 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) profiles indicated that exposure to high metal contamination or subsequent effects of this exposure permanently changed microbial community structure. The total number of colony forming units (CFU) was not affected by metal contamination and the As(V)-resistant bacterial ratio to total heterotrophic plate counts was high (0.5-1.1) and relatively independent of the concentration of As. In contrast, the proportion of As(III)-resistant bacteria was dependent on the concentration of As in the soils and a significant positive relationship was found between the bioavailability of As and the proportion of As(III)-resistant bacteria. Dominant As-resistant isolates from contaminated soils were identified by their fatty acid methyl ester (FAME) profiles as Acinetobacter, Edwardsiella, Enterobacter, Pseudomonas, Salmonella and Serratia species. No differences were noted in glucose mineralization among contaminated and control soil samples within sites. Based on [(14)C]glucose mineralization the community was able to compensate for the reduced diversity. According to t-RFLP results, this was not due to a reversion towards the unexposed community, but mainly due to the appearance of new dominating species. This study, combining complementary culture-dependent and -independent methods, suggests that microbes are able to respond to soil metal contamination and maintain metabolic activity apparently through changes in microbial community structure and selection for resistance.

  18. Effects of transgenic fructan-producing potatoes on the community structure of rhizosphere and phyllosphere bacteria.

    Science.gov (United States)

    Becker, Regina; Behrendt, Undine; Hommel, Bernd; Kropf, Siegfried; Ulrich, Andreas

    2008-11-01

    The rhizosphere and phyllosphere microbial communities of transgenic potatoes producing fructan were studied in comparison with isogenic controls and conventional varieties in a field release experiment over a period of 3 years. Population densities and 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analysis of the rhizosphere bacterial community only displayed the influence of annual and seasonal effects and the influence of field heterogeneity. In contrast, the T-RFLP analysis of the phyllosphere bacteria revealed in two of the 3 years significant differences in the community structure between the transgenic lines producing inulin and the other variants. This effect was studied in more detail through the analysis of bacterial isolates and a 16S rRNA gene clone library obtained from a transgenic line and the control. Both methods revealed a lower genetic diversity in the transgenic line and changes in the abundance of several bacterial groups. The isolates of the transgenic line were dominated by Bacilli, whereas most of the control isolates represented Actinobacteria. The clones were dominated by Proteobacteria, with main differences between both variants in Deltaproteobacteria, Bacilli and Bacteroidetes. However, all in all, the impact of the transgenic lines did not exceed the natural variability of the phyllosphere community structure on potato plants.

  19. 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.

  20. Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens)

    Science.gov (United States)

    Zhou, Zhenming; Fang, Lei; Meng, Qingxiang; Li, Shengli; Chai, Shatuo; Liu, Shujie; Schonewille, Jan Thomas

    2017-01-01

    The aim of this study was to determine the microbial community composition in the rumen of yaks under different feeding regimes. Microbial communities were assessed by sequencing bacterial and archaeal 16S ribosomal RNA gene fragments obtained from yaks (Bos grunniens) from Qinghai-Tibetan Plateau, China. Samples were obtained from 14 animals allocated to either pasture grazing (Graze), a grazing and supplementary feeding regime (GSF), or an indoor feeding regime (Feed). The predominant bacterial phyla across feeding regimes were Bacteroidetes (51.06%) and Firmicutes (32.73%). At genus level, 25 genera were shared across all samples. The relative abundance of Prevotella in the graze and GSF regime group were significantly higher than that in the feed regime group. Meanwhile, the relative abundance of Ruminococcus was lower in the graze group than the feed and GSF regime groups. The most abundant archaeal phylum was Euryarchaeota, which accounted for 99.67% of the sequences. Ten genera were detected across feeding regimes, seven genera were shared by all samples, and the most abundant was genus Methanobrevibacter (91.60%). The relative abundance of the most detected genera were similar across feeding regime groups. Our results suggest that the ruminal bacterial community structure differs across yak feeding regimes while the archaeal community structures are largely similar. PMID:28223980

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Mingxu Zhao

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

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

    Science.gov (United States)

    Zhao, Mingxu; Geekiyanage, Nalaka; Xu, Jianchu; Khin, Myo Myo; Nurdiana, Dian Ridwan; Paudel, Ekananda; Harrison, Rhett Daniel

    2015-01-01

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

  4. Bacterial Community Structure and Biochemical Changes Associated With Composting of Lignocellulosic Oil Palm Empty Fruit Bunch

    Directory of Open Access Journals (Sweden)

    Mohd Huzairi Mohd Zainudin

    2013-11-01

    Full Text Available Bacterial community structure and biochemical changes during the composting of lignocellulosic oil palm empty bunch (EFB and palm oil mill effluent (POME anaerobic sludge were studied by examining the succession of the bacterial community and its association with changes in lignocellulosic components by denaturing gradient gel electrophoresis (DGGE and the 16S rRNA gene clone library. During composting, a major reduction in cellulose after 10 days from 50% to 19% and the carbon content from 44% to 27% towards the end of the 40-day composting period were observed. The C/N ratio also decreased. A drastic change in the bacterial community structure and diversity throughout the composting process was clearly observed using PCR-DGGE banding patterns. The bacterial community drastically shifted between the thermophilic and maturing stages. 16s rRNA clones belonging to the genera Bacillus, Exiguobacterium, Desemzia, and Planococcus were the dominant groups throughout composting. The species closely related to Solibacillus silvestris were found to be major contributors to changes in the lignocellulosic component. Clones identified as Thermobacillus xylanilyticus, Brachybacterium faecium, Cellulosimicrobium cellulans, Cellulomonas sp., and Thermobifida fusca, which are known to be lignocellulosic-degrading bacteria, were also detected and are believed to support the lignocellulose degradation.

  5. 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.

  6. [Analysis of microbial community structure in lactic acid fermentation from kitchen waste].

    Science.gov (United States)

    Liu, Jian-Guo; Wang, Qun-Hui; Wang, Shuang; Sun, Xiao-Hong; Qiu, Tian-Lei; Li, Huan

    2012-09-01

    In this study, PCR-DGGE was used to analyze the microbial community structure in lactic acid fermentation from kitchen waste. The results showed that with Lactobacillus amylophilus inoculation, both the microbial diversity and lactic acid production in the open fermentation system were higher than those in the sterilized fermentation system. These results indicated that the microbial diversity and the lactic acid production have great correlation in the kitchen waste fermentation system. Through analyzing the sequence of some DNA bands excised from the DGGE gel, it showed that in addition to the inoculation of Lactobacillus amylophilus there were some indigenous lactic acid bacteria, such as Lactobacillus sp., Lactobacillus casei, Lactobacillus plantarum and indigenous hydrolytic bacteria, such as Pseudomonas sp.. These indigenous bacteria can help to promote lactic acid production. PCR-DGGE is feasible for analyzing the dynamic changes of microbial community structure in kitchen waste with complicated composition.

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gerard, Claudia [ECOBIO, Universite de Rennes 1, CNRS, Avenue du General Leclerc, 35042 Rennes (France)], E-mail: claudia.gerard@univ-rennes1.fr; Poullain, Virginie [Department of Biological Sciences, University of Idaho, Moscow, ID 83844 (United States); Lance, Emilie [ECOBIO, Universite de Rennes 1, CNRS, Avenue du General Leclerc, 35042 Rennes (France); Acou, Anthony [ERT 52, Universite de Rennes 1, CNRS, Avenue du General Leclerc, 35042 Rennes (France); Brient, Luc; Carpentier, Alexandre [ECOBIO, Universite de Rennes 1, CNRS, Avenue du General Leclerc, 35042 Rennes (France)

    2009-02-15

    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.

  9. 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.

  10. Marine chemical ecology: chemical signals and cues structure marine populations, communities, and ecosystems.

    Science.gov (United States)

    Hay, Mark E

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  11. Habitat structure, trophic structure and ecosystem function: interactive effects in a bromeliad-insect community.

    Science.gov (United States)

    Srivastava, Diane S

    2006-09-01

    Although previous studies have shown that ecosystem functions are affected by either trophic structure or habitat structure, there has been little consideration of their combined effects. Such interactions may be particularly important in systems where habitat and trophic structure covary. I use the aquatic insects in bromeliads to examine the combined effects of trophic structure and habitat structure on a key ecosystem function: detrital processing. In Costa Rican bromeliads, trophic structure naturally covaries with both habitat complexity and habitat size, precluding any observational analysis of interactions between factors. I therefore designed mesocosms that allowed each factor to be manipulated separately. Increases in mesocosm complexity reduced predator (damselfly larva) efficiency, resulting in high detritivore abundances, indirectly increasing detrital processing rates. However, increased complexity also directly reduced the per capita foraging efficiency of the detritivores. Over short time periods, these trends effectively cancelled each other out in terms of detrital processing. Over longer time periods, more complex patterns emerged. Increases in mesocosm size also reduced both predator efficiency and detritivore efficiency, leading to no net effect on detrital processing. In many systems, ecosystem functions may be impacted by strong interactions between trophic structure and habitat structure, cautioning against examining either effect in isolation.

  12. Structural guarantees for the state aid field. The community's last best hope against national arbitrariness

    OpenAIRE

    Ericsson, Angelica

    2011-01-01

    In line with current tendencies of ‘new modes of governance’, this essay introduces judicial tools, which strike a balance between the respect for national autonomy in individual assessments and the effective implementation of Community law. The balance is struck through the demands of structural guarantees; administrative safeguards, which weed out arbitrary national decision-making. These administrative safeguards are particularly needed in areas where the Member States of the EU have been ...

  13. 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)

  14. 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.

  15. EFFECTS OF LAND USE TRANFORMATION ON MIRCOARTHROPOD COMMUNITY STRUCTURE IN MEDITERRANEAN AREA

    OpenAIRE

    Santorufo, Lucia

    2013-01-01

    Human activities frequently lead to the conversion of natural habitats into human mediated ones. Land use transformation is an important form of global pressure as affects biodiversity, and gradually causes soil functionality loss. Therefore, soil biodiversity loss may cause significant alteration of regulatory services of terrestrial ecosystems. The analysis of taxonomical and functional structure of microarthropod communities is revealing to be an useful tool to understand changes in soil f...

  16. 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 ...

  17. Assessing mariculture water quality with the structural and functional characteristics of a ciliate community

    Institute of Scientific and Technical Information of China (English)

    LI Jiqiu; XU Henglong; LIN Xiaofeng; AL-RASHEID Khaled A.S.

    2011-01-01

    Ciliated protozoa play important roles in micro-ecosystems, especially in marine biotopes. However, few studies have been carried out on the periphytic, or aufwuch, forms in mariculture waters so far. In this study, we sampled periphytic ciliate communities in two closed mariculture ponds (ponds CP1 and CP2) and a natural seawater reservoir (pond RP) using a glass slide method to evaluate their colonizing processes and general ecological features, as well as their application as water quality indicators. We analyzed species compositions, structural parameters (species number, richness, diversity, evenness, abundance and dBP) and functional parameters (G, Seq, and T90%). Pond RP was characterized by higher levels of structural parameters (except for abundance and dBp) and more equal proportion of the major taxonomic groups. The values of 5eq were significantly higher in pond RP and similar in both pond CP1 and CP2. It was also demonstrated that environmental factors, including NO2-H, NO3-H, NH3-H, soluble reactive phosphate, temperature and pH, were the first principal factors affecting the communities. Among them, temperature and chemical factors were all significantly and negatively correlated with species number (P<0.01), richness (P<0.01), diversity (P<0.01), and positive correlated with abundance (P<0.01). Opposite correlations between pH and structural parameters were observed. This study showed that there were significant differences in species composition, structural parameters and functional parameters of the periphytic ciliate communities among the ponds, which were in agreement with the water quality. Results of this study confirmed the periphytic ciliate communities to be useful bioindicators of water quality in intensive mariculture waters.

  18. Influence of phosphorus availability on the community structure and physiology of cultured biofilms.

    Science.gov (United States)

    Li, Shuangshuang; Wang, Chun; Qin, Hongjie; Li, Yinxia; Zheng, Jiaoli; Peng, Chengrong; Li, Dunhai

    2016-04-01

    Biofilms have important effects on nutrient cycling in aquatic ecosystems. However, publications about the community structure and functions under laboratory conditions are rare. This study focused on the developmental and physiological properties of cultured biofilms under various phosphorus concentrations performed in a closely controlled continuous flow incubator. The results showed that the biomass (Chl a) and photosynthesis of algae were inhibited under P-limitation conditions, while the phosphatase activity and P assimilation rate were promoted. The algal community structure of biofilms was more likely related to the colonization stage than with the phosphorus availability. Cyanobacteria were more competitive than other algae in biofilms, particularly when cultured under low P levels. A dominance shift occurred from non-filamentous algae in the early stage to filamentous algae in the mid and late stages under P concentrations of 0.01, 0.1 and 0.6 mg/L. However, the total N content, dry weight biomass and bacterial community structure of biofilms were unaffected by phosphorus availability. This may be attributed to the low respiration rate, high accumulation of extracellular polymeric substances and high alkaline phosphatase activity in biofilms when phosphorus availability was low. The bacterial community structure differed over time, while there was little difference between the four treatments, which indicated that it was mainly affected by the colonization stage of the biofilms rather than the phosphorus availability. Altogether, these results suggested that the development of biofilms was influenced by the phosphorus availability and/or the colonization stage and hence determined the role that biofilms play in the overlying water.

  19. Distribution and community structure of butterflyfishes (Pisces: Chaetodontidae) in southern Mozambique.

    OpenAIRE

    2005-01-01

    Even though Mozambique has the greatest reported diversity of butterflyfishes (24 species) of the continental states of the Western Indian Ocean region, aspects of the ecology and distribution of this group in Mozambique are poorly documented. The distribution, diversity and community structure of butterflyfishes were studied on nine reefs in southern Mozambique using the point count method. Nineteen species from four genera were identified. Three with generalist feeding habits (i.e. Chaetodo...

  20. Bacterial community structure and functional potential in the northeastern Chukchi Sea

    Science.gov (United States)

    McFarlin, Kelly M.; Questel, Jennifer M.; Hopcroft, Russell R.; Leigh, Mary Beth

    2017-03-01

    We performed a molecular microbial ecological analysis in the northeastern Chukchi Sea in order to characterize bacterial community structure and genetic potential for biogeochemical cycling and oil biodegradation in a region targeted for oil and gas exploration (Burger lease area). Samples were collected from the surface, middle (20 m), and bottom (2-3 m above seafloor) of the water column during the open-water season of August and September 2012 at 17 different locations. We determined bacterial community structure with 16S rRNA genes sequencing and detected functional genes, including an array of oil biodegradation and biogeochemical cycling (carbon, nitrogen and phosphorus cycling) genes, using the GeoChip 5.0 microarray, and then correlated molecular data to contextual physical and biogeochemical factors. Bacterial community structure differed significantly by depth (surface water vs. bottom water) and between sampling dates (August vs. September). While the relative abundance of major functional gene categories did not differ with depth, the abundance of individual functional genes for carbon cycling, nitrogen cycling, organic contaminant remediation, phosphorus cycling, sulfur cycling, virulence, and viruses differed between surface and bottom seawater samples. Aerobic oil degradation genes and taxa known to include oil-degrading bacteria were found at all three depths. These findings support previous observations that two different water masses contribute to a stratified water column in the summer open-water season of the Burger lease area, but indicate that potential function is fairly similar with depth despite differences in temperature, water chemistry, bacterial community structure, and individual functional gene alleles.

  1. Microbial community structure of methane-fermentation liquid of swine slurry

    OpenAIRE

    佐伯, 雄一; 園田, 亮一; 城, 惣吉; 矢野, 翼; 赤木, 功; 山本, 昭洋; 杉本, 安寛

    2013-01-01

    Domestic animal excrement is known as biomass resources for soil improvement material and manure, and methane fermentation process is known as a remarkable method other than composting as the animal waste management. In our previous study, the existence of pathogenic microbes was not identified about methane-fermentation liquid from a methane fermentation biogas plant in University of Miyazaki. In this study, bacterial community structures of eubacteria and archaebacteria were investigated fo...

  2. Marine fish community structure and habitat associations on the Canadian Beaufort shelf and slope

    Science.gov (United States)

    Majewski, Andrew R.; Atchison, Sheila; MacPhee, Shannon; Eert, Jane; Niemi, Andrea; Michel, Christine; Reist, James D.

    2017-03-01

    Marine fishes in the Canadian Beaufort Sea have complex interactions with habitats and prey, and occupy a pivotal position in the food web by transferring energy between lower- and upper-trophic levels, and also within and among habitats (e.g., benthic-pelagic coupling). The distributions, habitat associations, and community structure of most Beaufort Sea marine fishes, however, are unknown thus precluding effective regulatory management of emerging offshore industries in the region (e.g., hydrocarbon development, shipping, and fisheries). Between 2012 and 2014, Fisheries and Oceans Canada conducted the first baseline survey of offshore marine fishes, their habitats, and ecological relationships in the Canadian Beaufort Sea. Benthic trawling was conducted at 45 stations spanning 18-1001 m depths across shelf and slope habitats. Physical oceanographic variables (depth, salinity, temperature, oxygen), biological variables (benthic chlorophyll and integrated water-column chlorophyll) and sediment composition (grain size) were assessed as potential explanatory variables for fish community structure using a non-parametric statistical approach. Selected stations were re-sampled in 2013 and 2014 for a preliminary assessment of inter-annual variability in the fish community. Four distinct fish assemblages were delineated on the Canadian Beaufort Shelf and slope: 1) Nearshore-shelf: 50 and ≤200 m depths, 3) Upper-slope: ≥200 and ≤500 m depths, and 4) Lower-slope: ≥500 m depths. Depth was the environmental variable that best explained fish community structure, and each species assemblage was spatially associated with distinct aspects of the vertical water mass profile. Significant differences in the fish community from east to west were not detected, and the species composition of the assemblages on the Canadian Beaufort Shelf have not changed substantially over the past decade. This community analysis provides a framework for testing hypotheses regarding the trophic

  3. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

    Science.gov (United States)

    Fang, Hua; Lian, Jianjun; Wang, Huifang; Cai, Lin; Yu, Yunlong

    2015-04-09

    Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils.

  4. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.

    Science.gov (United States)

    Kennedy, Nabla; Brodie, Eoin; Connolly, John; Clipson, Nicholas

    2004-10-01

    A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.

  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.

  6. Nitrogen forms influence microcystin concentration and composition via changes in cyanobacterial community structure.

    Directory of Open Access Journals (Sweden)

    Marie-Eve Monchamp

    Full Text Available The eutrophication of freshwaters is a global health concern as lakes with excess nutrients are often subject to toxic cyanobacterial blooms. Although phosphorus is considered the main element regulating cyanobacterial biomass, nitrogen (N concentration and more specifically the availability of different N forms may influence the overall toxicity of blooms. In this study of three eutrophic lakes prone to cyanobacterial blooms, we examined the effects of nitrogen species and concentrations and other environmental factors in influencing cyanobacterial community structure, microcystin (MC concentrations and MC congener composition. The identification of specific MC congeners was of particular interest as they vary widely in toxicity. Different nitrogen forms appeared to influence cyanobacterial community structure leading to corresponding effects on MC concentrations and composition. Total MC concentrations across the lakes were largely explained by a combination of abiotic factors: dissolved organic nitrogen, water temperature and ammonium, but Microcystis spp. biomass was overall the best predictor of MC concentrations. Environmental factors did not appear to affect MC congener composition directly but there were significant associations between specific MC congeners and particular species. Based on redundancy analyses (RDA, the relative biomass of Microcystis aeruginosa was associated with MC-RR, M. wesenbergii with MC-LA and Aphanizomenon flos-aquae with MC-YR. The latter two species are not generally considered capable of MC production. Total nitrogen, water temperature, ammonium and dissolved organic nitrogen influenced the cyanobacterial community structure, which in turn resulted in differences in the dominant MC congener and the overall toxicity.

  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.

  8. The role of macrobiota in structuring microbial communities along rocky shores.

    Science.gov (United States)

    Pfister, Catherine A; Gilbert, Jack A; Gibbons, Sean M

    2014-01-01

    Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  9. The role of macrobiota in structuring microbial communities along rocky shores

    Directory of Open Access Journals (Sweden)

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

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

    Science.gov (United States)

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

    2014-03-01

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

  11. 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.

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

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    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.

  13. Influence of plankton community structure on the sinking velocity of marine aggregates

    Science.gov (United States)

    Bach, L. T.; Boxhammer, T.; Larsen, A.; Hildebrandt, N.; Schulz, K. G.; Riebesell, U.

    2016-08-01

    About 50 Gt of carbon is fixed photosynthetically by surface ocean phytoplankton communities every year. Part of this organic matter is reprocessed within the plankton community to form aggregates which eventually sink and export carbon into the deep ocean. The fraction of organic matter leaving the surface ocean is partly dependent on aggregate sinking velocity which accelerates with increasing aggregate size and density, where the latter is controlled by ballast load and aggregate porosity. In May 2011, we moored nine 25 m deep mesocosms in a Norwegian fjord to assess on a daily basis how plankton community structure affects material properties and sinking velocities of aggregates (Ø 80-400 µm) collected in the mesocosms' sediment traps. We noted that sinking velocity was not necessarily accelerated by opal ballast during diatom blooms, which could be due to relatively high porosity of these rather fresh aggregates. Furthermore, estimated aggregate porosity (Pestimated) decreased as the picoautotroph (0.2-2 µm) fraction of the phytoplankton biomass increased. Thus, picoautotroph-dominated communities may be indicative for food webs promoting a high degree of aggregate repackaging with potential for accelerated sinking. Blooms of the coccolithophore Emiliania huxleyi revealed that cell concentrations of 1500 cells/mL accelerate sinking by about 35-40%, which we estimate (by one-dimensional modeling) to elevate organic matter transfer efficiency through the mesopelagic from 14 to 24%. Our results indicate that sinking velocities are influenced by the complex interplay between the availability of ballast minerals and aggregate packaging; both of which are controlled by plankton community structure.

  14. Biodiversity and community structure of deep-sea foraminifera around New Zealand

    Science.gov (United States)

    Buzas, Martin A.; Hayek, Lee-Ann C.; Hayward, B. W.; Grenfell, Hugh R.; Sabaa, Ashwaq T.

    2007-09-01

    The biodiversity and community structure of benthic foraminifera were estimated from 217 stations distributed in four geographic regions (north, south, east, west) around New Zealand. An analytical method accumulating sample values of species richness (S), the information function (H) and evenness (E) with increasing number of individuals (N) called SHE analysis was used to establish 16 foraminiferal communities and their community structure at shelf (0-200 m), bathyal (200-2000 m) and abyssal (>2000m) depths. A decrease in S, H and E occurs from north to south and this latitudinal gradient extends to abyssal depths. An increase in S and H with depth occurs in the northern and southern areas. For lnS, H and lnE against lnN, regression lines on values obtained from SHE analysis at shelf, bathyal and abyssal depths all diverge in the southern area. Each of the other areas exhibits crossing of regression lines so that establishing the rank order of S, H or E with depth within an area requires consideration of N. For a log series pattern, H is a constant proportional to α, the parameter of the log series, and, based on the decomposition equation lnS=H+lnE, a regression of lnS against lnE yields a regression coefficient of -1 and an intercept of H. At depths of less than 1000 m, 2 of 8 communities have regression coefficient confidence intervals that include -1. At depths of greater than 1000 m, 7 of 8 communities intervals include -1. Thus, overall, the majority of cases, but especially those at depths greater than 1000 m, have a log series pattern.

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

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    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.

  16. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

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    C Ryan Penton

    Full Text Available Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

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

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    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

  18. 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.

  19. 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

  20. 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

  1. 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

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

    Science.gov (United States)

    Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

    2015-01-01

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

  3. Effects of marine reserves versus nursery habitat availability on structure of reef fish communities.

    Science.gov (United States)

    Nagelkerken, Ivan; Grol, Monique G G; Mumby, Peter J

    2012-01-01

    No-take marine fishery reserves sustain commercial stocks by acting as buffers against overexploitation and enhancing fishery catches in adjacent areas through spillover. Likewise, nursery habitats such as mangroves enhance populations of some species in adjacent habitats. However, there is lack of understanding of the magnitude of stock enhancement and the effects on community structure when both protection from fishing and access to nurseries concurrently act as drivers of fish population dynamics. In this study we test the separate as well as interactive effects of marine reserves and nursery habitat proximity on structure and abundance of coral reef fish communities. Reserves had no effect on fish community composition, while proximity to nursery habitat only had a significant effect on community structure of species that use mangroves or seagrass beds as nurseries. In terms of reef fish biomass, proximity to nursery habitat by far outweighed (biomass 249% higher than that in areas with no nursery access) the effects of protection from fishing in reserves (biomass 21% lower than non-reserve areas) for small nursery fish (≤ 25 cm total length). For large-bodied individuals of nursery species (>25 cm total length), an additive effect was present for these two factors, although fish benefited more from fishing protection (203% higher biomass) than from proximity to nurseries (139% higher). The magnitude of elevated biomass for small fish on coral reefs due to proximity to nurseries was such that nursery habitats seem able to overrule the usually positive effects on fish biomass by reef reserves. As a result, conservation of nursery habitats gains importance and more consideration should be given to the ecological processes that occur along nursery-reef boundaries that connect neighboring ecosystems.

  4. Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.

    Science.gov (United States)

    Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas

    2013-10-01

    The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites

  5. 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.

  6. Zonation and structuring factors of meiofauna communities in a tropical seagrass bed (Gazi Bay, Kenya)

    Science.gov (United States)

    De Troch, Marleen; Gurdebeke, Shirley; Fiers, Frank; Vincx, Magda

    2001-02-01

    This study deals with the relation between tropical meiofauna and environmental variables by comparing the 'benthic' (i.e. in the bare sediment adjacent to seagrass plants) and the 'epiphytic' (i.e. in samples including seagrass plants) meiofauna associated with five seagrass species from the high intertidal to the high subtidal zone in Gazi Bay (Kenya). Ordination and variance analysis revealed three distinct 'benthic' and two 'epiphytic' meiofauna assemblages. These assemblages corresponded entirely with those identified for the seagrass species: a high intertidal pioneer association ( Halophila ovalis/ Halodule wrightii), an intertidal climax assemblage ( Thalassia hemprichii) and a high subtidal pioneer association ( Halophila stipulacea/ Syringodium isoetifolium). These data support the hypothesis that meiofaunal communities correspond to the characteristic zonation of the seagrass vegetation in Gazi Bay. In beds of the pioneer seagrass species, the close relationship between sediment characteristics and both 'benthic' and 'epiphytic' meiofauna communities suggests that these pioneer communities were mainly driven by physical factors. The 'benthic' communities adjacent to the climax seagrass species T. hemprichii were more structured by biogenic factors, e.g. % TOM, chlorophyll a and c, fucoxanthin, habitat complexity and growth form of the seagrass species. For its associated 'epiphytic' meiofauna the latter conclusion was even more striking. These data corroborate the importance of physical factors in disturbed environments (intertidal zone, near pioneer seagrasses) and of biotic factors in more stable conditions (subtidal zone, near climax seagrasses).

  7. Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

    Directory of Open Access Journals (Sweden)

    Danyang Zheng

    2016-01-01

    Full Text Available In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

  8. 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.

  9. Shift of bacterial community structure in two Thai soil series affected by silver nanoparticles using ARISA.

    Science.gov (United States)

    Chunjaturas, Wariya; Ferguson, John A; Rattanapichai, Wutthida; Sadowsky, Michael J; Sajjaphan, Kannika

    2014-07-01

    In this study we examined the influence of silver nanoparticles (SNP) on the bacterial community and microbial processes in two soils from Thailand, a Ayutthaya (Ay) and Kamphaengsaen soil series (Ks). Results of this analysis revealed that SNP did not affect to pH, electrical conductivity, cation exchange capacity, and organic matter in both the Ay and Ks series. Automated ribosomal intergenic spacer analysis (ARISA) analysis profiles showed that bacterial community decreased with increasing SNP concentration. Pearson's correlation coefficient and multidimensional scaling analyses indicated that the effects of SNP on the bacterial community structure depended more on soil types than SNP application rates and incubation periods. Additionally, the results showed that SNP application rates affected on amount of CO2 emissions, while SNP application rates had no effect on N mineralization in both soil types. This study is the first investigation of the effects of SNP on bacterial community using ARISA analysis. Our results might be useful to evaluate the risk associated with the applications of SNP for consumer products and agricultural practices.

  10. Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets.

    Science.gov (United States)

    Jeyanathan, Jeyamalar; Kirs, Marek; Ronimus, Ron S; Hoskin, Simone O; Janssen, Peter H

    2011-05-01

    Development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on knowledge of the methanogens present. We investigated the composition of archaeal communities in the rumens of farmed sheep (Ovis aries), cattle (Bos taurus) and red deer (Cervus elaphus) using denaturing gradient gel electrophoresis (DGGE) to generate fingerprints of archaeal 16S rRNA genes. The total archaeal communities were relatively constant across species and diets, and were less variable and less diverse than bacterial communities. There were diet- and ruminant-species-based differences in archaeal community structure, but the same dominant archaea were present in all rumens. These were members of three coherent clades: species related to Methanobrevibacter ruminantium and Methanobrevibacter olleyae; species related to Methanobrevibacter gottschalkii, Methanobrevibacter thaueri and Methanobrevibacter millerae; and species of the genus Methanosphaera. Members of an archaeal group of unknown physiology, designated rumen cluster C (RCC), were also present. RCC-specific DGGE, clone library analysis and quantitative real-time PCR showed that their 16S rRNA gene sequences were very diverse and made up an average of 26.5% of the total archaea. RCC sequences were not readily detected in the DGGE patterns of total archaeal 16S rRNA genes because no single sequence type was abundant enough to form dominant bands.

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

    Science.gov (United States)

    Martins, Mónica; Faleiro, Maria Leonor; Chaves, Sandra; Tenreiro, Rogério; Santos, Erika; Costa, Maria Clara

    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(-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.

  12. 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.

  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. 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.

  15. A trait based dynamic energy budget approach to explore emergent microalgal community structure

    Science.gov (United States)

    Cheng, Y.; Bouskill, N.; Karaoz, U.; Geng, H.; Lane, T.; Pett-Ridge, J.; Mayali, X.; Brodie, E.

    2015-12-01

    Microalgae play important roles in the global carbon budget. Phytoplankton, including microalgae, are responsible for around 50% of global primary production, and also hold promise as a viable renewable biofuel source. Research has been underway for decades to realize the full potential of algal biofuels at the commercial scale, however, uni-algal ponds are typically threatened by collapse due to microalgal grazing and parasite invasions. Recently, it has been proposed that functionally diverse microalgal-bacterial communities can achieve high biomass and/or lipid yields, and are more stable (less susceptible to invasion) than a monoculture. Similar positive diversity-productivity relationships have been observed in a wide range of ecosystem studies, but the purposeful maintenance of a diverse microbiome is less common in managed systems. In our work, a trait based dynamic energy budget model was developed to explore emergent microalgal community structure under various environmental (e.g. light, temperature, nutrient availability) conditions. The complex algal community can be reduced into functional groups (guilds). Each guild (algae or bacteria) is characterized by distinct physiological traits (e.g. nutrient requirement, growth rate, substrate affinity, lipid production) constrained by biochemical trade-offs. These trait values are derived from literature and information encoded in genomic data. Metabolism of the algae and the bacterial species (symbiotic or non-symbiotic) are described within a dynamic energy budget framework. The model offers a mechanistic framework to predict the optimal microalgal community assemblage towards high productivity and resistance to invasion under prevailing environmental conditions.

  16. 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.

  17. Bandwidth turbulence control based on flow community structure in the Internet

    Science.gov (United States)

    Wu, Xiaoyu; Gu, Rentao; Ji, Yuefeng

    2016-10-01

    Bursty flows vary rapidly in short period of time, and cause fierce bandwidth turbulence in the Internet. In this letter, we model the flow bandwidth turbulence process by constructing a flow interaction network (FIN network), with nodes representing flows and edges denoting bandwidth interactions among them. To restrain the bandwidth turbulence in FIN networks, an immune control strategy based on flow community structure is proposed. Flows in community boundary positions are immunized to cut off the inter-community turbulence spreading. By applying this control strategy in the first- and the second-level flow communities separately, 97.2% flows can effectively avoid bandwidth variations by immunizing 21% flows, and the average bandwidth variation degree reaches near zero. To achieve a similar result, about 70%-90% immune flows are needed with targeted control strategy based on flow degrees and random control strategy. Moreover, simulation results showed that the control effect of the proposed strategy improves significantly if the immune flow number is relatively smaller in each control step.

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

    Science.gov (United States)

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

    2016-05-01

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

  19. Gut bacterial community structure (Porcellio scaber, Isopoda, Crustacea) as a measure of community level response to long-term and short-term metal pollution.

    Science.gov (United States)

    Lapanje, Ales; Rupnik, Maja; Drobne, Damjana

    2007-04-01

    Prokaryotes are of high importance in the assessment of environmental pollution effects. Due to fast responsiveness of bacterial communities to environmental physicochemical factors, it is difficult to compare results of bacterial community investigations on the temporal and spatial scale. To reduce the effects of variable physicochemical environmental conditions on bacterial microbiota when investigating the specific impact of contaminants on bacterial communities, we investigated the bacterial community in the gut of terrestrial isopods (Porcellio scaber, Isopoda, Crustacea) from clean and metal-polluted environments. Animals were collected from a chronically mercury-polluted site, a chronically multiple metal-(Cd, Pb, Zn) polluted site, and two reference sites. In addition, animals from an unpolluted site were laboratory exposed to 5 microg Hg/g food in order to compare the effect of acute and chronic Hg exposure. The bacterial gut microbiota was investigated by temporal temperature gradient gel electrophoresis (TTGE) and clone library construction based on polymerase chain reaction amplified 16S rRNA genes. The major bacterial representatives of the emptied gut microbiota in the animals from the chronically polluted environments seemed not affected when analyzed by TTGE. The detailed bacterial community structure investigated by 16S rRNA clone library construction, however, showed that the community from the Hg-polluted site also was affected severely (242.4 operational taxonomic units [OTU] in the polluted and 650.6 OTU in the unpolluted environment). When animals were acutely exposed to mercury, changes of bacterial community structures already were seen on TTGE profiles and no additional analysis was needed. We suggest the use of P. scaber gut bacterial community structure as a measure of effects caused by both long- and short-term exposure to pollution.

  20. Coral reef microbes : the influences of benthic primary producers, nutrient availability, and anthropogenic stressors on community structure and metabolism

    OpenAIRE

    Kelly, Linda Ellen Wegley

    2013-01-01

    Genomic studies of marine microbes have advanced our understanding of community ecology and the vast array of metabolisms microbes utilize for acquiring energy and nutrients in the ocean. The structure of microbial communities overlying coral reefs have been shown to reflect ecosystem health. For example, algal-dominated reefs are inhabited by more pathogen-like microbes. The objective of my PhD thesis was to use metagenomics to investigate the microbial communities associated with the coral ...

  1. Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

    Science.gov (United States)

    Malek, A J; Collie, J S; Taylor, D L

    2016-09-01

    A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. (Asynchronous availabilities of N and P regulate the activity and structure of the microbial decomposer community

    Directory of Open Access Journals (Sweden)

    Nicolas eFanin

    2016-01-01

    Full Text Available Nitrogen (N and phosphorus (P availability both control microbial decomposers and litter decomposition. However, these two key nutrients show distinct release patterns from decomposing litter and are unlikely available at the same time in most ecosystems. Little is known about how temporal differences in N and P availability affect decomposers and litter decomposition, which may be particularly critical for tropical rainforests growing on old and nutrient-impoverished soils. Here we used three chemically contrasted leaf litter substrates and cellulose paper as a widely accessible substrate containing no nutrients to test the effects of temporal differences in N and P availability in a microcosm experiment under fully controlled conditions. We measured substrate mass loss, microbial activity (by substrate induced respiration, SIR as well as microbial community structure (using phospholipid fatty acids, PLFAs in the litter and the underlying soil throughout the initial stages of decomposition. We generally found a stronger stimulation of substrate mass loss and microbial respiration, especially for cellulose, with simultaneous NP addition compared to a temporally separated N and P addition. However, litter types with a relatively high N to P availability responded more to initial P than N addition and vice versa. A third litter species showed no response to fertilization regardless of the sequence of addition, likely due to strong C limitation. Microbial community structure in the litter was strongly influenced by the fertilization sequence. In particular, the fungi to bacteria ratio increased following N addition alone, a shift that was reversed with complementary P addition. Opposite to the litter layer microorganisms, the soil microbial community structure was more strongly influenced by the identity of the decomposing substrate than by fertilization treatments, reinforcing the idea that C availability can strongly constrain decomposer

  10. 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.

  11. Spatial structure facilitates cooperation in a social dilemma: empirical evidence from a bacterial community.

    Directory of Open Access Journals (Sweden)

    Felix J H Hol

    Full Text Available Cooperative organisms are ubiquitous in nature, despite their vulnerability to exploitation by cheaters. Although numerous theoretical studies suggest that spatial structure is critical for cooperation to persist, the spatial ecology of microbial cooperation remains largely unexplored experimentally. By tracking the community dynamics of cooperating (rpoS wild-type and cheating (rpoS mutant Escherichia coli in well-mixed flasks and microfabricated habitats, we demonstrate that spatial structure stabilizes coexistence between wild-type and mutant and thus facilitates cooperator maintenance. We develop a method to interpret our experimental results in the context of game theory, and show that the game wild-type and mutant bacteria play in an unstructured environment changes markedly over time, and eventually obeys a prisoner's dilemma leading to cheater dominance. In contrast, when wild-type and mutant E. coli co-inhabit a spatially-structured habitat, cooperators and cheaters coexist at intermediate frequencies. Our findings show that even in microhabitats lacking patchiness or spatial heterogeneities in resource availability, surface growth allows cells to form multi-cellular aggregates, yielding a self-structured community in which cooperators persist.

  12. 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…

  13. Trophic structure and levels of selected metals in the zooplankton community of Thane-Bassein Creek, Bombay

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, V.R.; Krishnamurti, A.J.; Gajbhiye, S.N.

    Community structure of zooplankton at 4 locations, 2 in the coastal waters off Bombay and 2 in interior Thane-Bassein Creek System, Maharashtra, India were studied for a period of one year. Copepods as the major herbivore community contributed 76...

  14. Organic content influences sediment microbial fuel cell performance and community structure.

    Science.gov (United States)

    Zhao, Qing; Li, Ruying; Ji, Min; Ren, Zhiyong Jason

    2016-11-01

    This study constructed sediment microbial fuel cells (SMFCs) with different organic loadings without the amendment of external substrates, and it investigated how such variation affects electricity generation and microbial community structure. Results found sediment characteristics significantly influenced SMFC performance and appropriate organic content is important to maintain stable power outputs. SMFCs with loss of ignition (LOI) of 5% showed the most reliable performance in this study, while high organic content (LOI 10-16%) led to higher but very unstable voltage output because of biogas accumulation and worm activities. SMFCs with low organic content (1-3%) showed low power output. Different bacterial communities were found in SMFCs shown various power generation performance even those with similar organic contents. Thermodesulfovibrionaceae was found closely related to the system startup and Desulfobulbaceae showed great abundance in SMFCs with high power production.

  15. 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.

  16. Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

    Science.gov (United States)

    Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

    2014-11-01

    Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output.

  17. 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.

  18. 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.

  19. Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China.

    Science.gov (United States)

    Yun, Juanli; Ju, Yiwen; Deng, Yongcui; Zhang, Hongxun

    2014-08-01

    Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.

  20. 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.

  1. Alkyl polyglucoside compound influences freshwater plankton community structure in floating field mesocosms.

    Science.gov (United States)

    Riera, Steven F; Cohen, Risa A

    2016-10-01

    Synthetic surfactants in cleaners and detergents commonly contaminate freshwater systems, therefore use of low-toxicity alternatives is becoming increasingly important. Alkyl polyglucosides (APGs) derived from natural products are less toxic than synthetic surfactants, and degrade rapidly reducing chemical exposure time. However, single species toxicity tests showed APGs have toxic effects on aquatic primary producers and zooplankton, and that species demonstrate different sensitivities to APGs. Furthermore, species unaffected by APGs directly may be indirectly affected by removal of a food source or changes in predator densities, thereby changing plankton community structure. To determine the effects of APGs on plankton communities under environmental conditions, floating mesocosms were deployed in a shallow pond in southeast Georgia, USA and dosed with 0, 0.01, 2.5, 5, or 10 mg L(-1) APG. Zooplankton community composition and abundance, phytoplankton abundance (as chlorophyll a), and water column dissolved oxygen concentration were determined weekly for 1 month. Zooplankton abundance decreased primarily due to loss of copepods, and community composition shifted toward small-bodied cladocerans (Bosmina sp.), and chlorophyll a concentrations declined by up to 81 % following exposure to APG concentrations of 2.5 mg L(-1) or greater. Concentrations of dissolved oxygen never dropped below 5.70 mg L(-1), but the observed declines of ~2 mg L(-1) could become stressful during periods of high water temperatures. Nevertheless, the APG-induced shift from copepod to cladoceran dominated communities and decrease in autochthonous carbon availability has important implications for food availability and quality to higher trophic levels such as planktivorous fishes.

  2. 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

  3. The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities.

    Science.gov (United States)

    Clark, Graeme F; Stark, Jonathan S; Palmer, Anne S; Riddle, Martin J; Johnston, Emma L

    2017-01-01

    On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics.

  4. 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.

  5. The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction.

    Science.gov (United States)

    Yu, Zhengsheng; He, Zhili; Tao, Xuanyu; Zhou, Jizhong; Yang, Yunfeng; Zhao, Mengxin; Zhang, Xiaowei; Zheng, Zhe; Yuan, Tong; Liu, Pu; Chen, Yong; Nolan, Virgo; Li, Xiangkai

    2016-12-01

    The Lanzhou reach of the Yellow River, located at the upstream of Lanzhou, has been contaminated by heavy metals and polycyclic aromatic hydrocarbons over a long-time. We hypothesized that indigenous microbial communities would remediate those contaminants and some unique populations could play an important role in this process. In this study, we investigated the sediment microbial community structure and function from the Lanzhou reach. Sediment samples were collected from two nearby sites (site A and site B) in the Lanzhou reach along the Yellow River. Sediment geochemical property data showed that site A sediment samples contained significantly (p < 0.05) higher heavy metals than site B, such as chromium (Cr), manganese (Mn), and copper (Cu). Both site A and B samples were incubated with or without hexavalent chromium (Cr (VI)) for 30 days in the laboratory, and Cr (VI) reduction was only observed in site A sediment samples. After incubation, MiSeq sequencing of 16S rRNA gene amplicons revealed that the phylogenetic composition and structure of microbial communities changed in both samples, and especially Proteobacteria, as the most abundant phylum increased from 45.1 % to 68.2 % in site A, and 50.1 % to 71.3 % in site B, respectively. Some unique OTUs and populations affiliated with Geobacter, Clostridium, Desulfosporosinus and Desulfosporosinus might be involved in Cr (VI) reduction in site A. Furthermore, GeoChip 4.0 (a comprehensive functional gene array) data showed that genes involved in carbon and nitrogen cycling and metal resistance significantly (p < 0.05) increased in site A sediment samples. All the results indicated that indigenous sediment microbial communities might be able to remediate contaminants like Cr (VI), and this information provides possible strategies for future bioremediation of the Lanzhou reach.

  6. Effects of fungicides and biofungicides on population density and community structure of soil oribatid mites.

    Science.gov (United States)

    Al-Assiuty, Abdel-Naieem I M; Khalil, Mohamed A; Ismail, Abdel-Wahab A; van Straalen, Nico M; Ageba, Mohamed F

    2014-01-01

    To compare the side-effects of chemical versus biofungicides on non-target organisms in agricultural soil, a study of population structure, spatial distribution and fecundity of oribatid mites, a diverse and species-rich group of microarthropods indicative of decomposer activity in soil was done. Plots laid out in agricultural fields of a research station in Egypt, were cultivated with cucumber and treated with two chemical fungicides: Ridomil Plus 50% wp (active ingredients=metalaxyl and copper oxychloride) and Dithane M-45 (active ingredient=mancozeb), and two biofungicides: Plant Guard (containing the antagonistic fungus Trichoderma harzianum) and Polyversum (containing the fungi-parasitic oomycete Pythium oligandrum). All treatments were done using both low-volume and high-volume spraying techniques to check whether any effects were dependent on the method of application. Oribatid mite communities were assessed from soil core samples collected during the growing season. Total abundance of oribatids was not different across the plots, but some species decreased in number, while one species increased. Species diversity and community equitability decreased with the application of chemical and biofungicides especially when using high-volume spraying. In control plots most oribatid species showed a significant degree of aggregation, which tended to decrease under fungicide treatment. Ridomil Plus, Plant Guard and Polyversum had a negative effect on the gravid/ungravid ratio of some species. Egg number averaged over the whole adult population was not directly related to the application of chemical and biofungicides but it showed a species-specific relationship with population density. In general biofungicides had a smaller effect on population size and community structure of oribatid mite species than chemical fungicides. The results indicate that biofungicides may be the preferred option when aiming to prevent side-effects on sensitive groups among the species

  7. 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

  8. Impact of predation by Ostracion immaculatus (Pisces: Ostraciidae) on the macrofouling community structure in Kanayama Bay, Kii Peninsula (Japan)

    Digital Repository Service at National Institute of Oceanography (India)

    Raveendran, T.V.; Harada, E.

    An investigation on the impact of predation by Ostracion immaculatus on fouling community structure in Kanayama Bay, Kii Peninsula, Japan was undertaken from April 1994 to February 1995. Caging experiments with three size groups of O. immaculatus...

  9. 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...

  10. 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 s