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Sample records for archaeal community structure

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

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

    2013-11-01

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

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

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    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

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

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    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.

  4. Bacterial and archaeal community structures in the Arctic deep-sea sediment

    Institute of Scientific and Technical Information of China (English)

    LI Yan; LIU Qun; LI Chaolun; DONG Yi; ZHANG Wenyan; ZHANG Wuchang; XIAO Tian

    2015-01-01

    Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its rela-tionship with environmental factors, we applied Roche 454 sequencing of 16S rDNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities’ richness, compositions and structures as well as tax-onomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups;while the archaeal community is domi-nated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). This study describes the microbial diversity in the Arctic deep marine sediment (>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.

  5. Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters

    NARCIS (Netherlands)

    Cabrol, L.; Urra, J.; Rosenkranz, F.; Kroff, P.A.; Plugge, C.M.; Lesty, Y.; Chamy, R.

    2015-01-01

    The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale mu

  6. Forest strata drive spatial structure of bacterial and archaeal communities and microbial methane cycling in neotropical bromeliad wetlands

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    Martinson, Guntars; Brandt, Franziska; Conrad, Ralf

    2016-04-01

    , and their constrained environmental characteristics shape the spatial structure of archaeal and bacterial communities and microbial methane cycling in neotropical bromeliad wetlands.

  7. Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

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    Nathan eBasiliko

    2013-07-01

    Full Text Available Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide and methane production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between mined and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and methane or carbon dioxide production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought

  8. Environmental shaping of sponge associated archaeal communities.

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    Aline S Turque

    Full Text Available BACKGROUND: Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum. CONCLUSION/SIGNIFICANCE: The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition

  9. Archaeal community structures in the solfataric acidic hot springs with different temperatures and elemental compositions.

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    Satoh, Tomoko; Watanabe, Keiko; Yamamoto, Hideo; Yamamoto, Shuichi; Kurosawa, Norio

    2013-01-01

    Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L(-1), (2) Pond-B: 66°C and 2248 mg L(-1), (3) Pond-C: 88°C and 198 mg L(-1), and (4) Pond-D: 67°C and 340 mg L(-1). In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.

  10. Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs.

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    Fischer, Martin A; Güllert, Simon; Neulinger, Sven C; Streit, Wolfgang R; Schmitz, Ruth A

    2016-01-01

    The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis

  11. Archaeal community structure in leachate and solid waste is correlated to methane generation and volume reduction during biodegradation of municipal solid waste.

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    Fei, Xunchang; Zekkos, Dimitrios; Raskin, Lutgarde

    2015-02-01

    Duplicate carefully-characterized municipal solid waste (MSW) specimens were reconstituted with waste constituents obtained from a MSW landfill and biodegraded in large-scale landfill simulators for about a year. Repeatability and relationships between changes in physical, chemical, and microbial characteristics taking place during the biodegradation process were evaluated. Parameters such as rate of change of soluble chemical oxygen demand in the leachate (rsCOD), rate of methane generation (rCH4), rate of specimen volume reduction (rVt), DNA concentration in the leachate, and archaeal community structures in the leachate and solid waste were monitored during operation. The DNA concentration in the leachate was correlated to rCH4 and rVt. The rCH4 was related to rsCOD and rVt when waste biodegradation was intensive. The structures of archaeal communities in the leachate and solid waste of both simulators were very similar and Methanobacteriaceae were the dominant archaeal family throughout the testing period. Monitoring the chemical and microbial characteristics of the leachate was informative of the biodegradation process and volume reduction in the simulators, suggesting that leachate monitoring could be informative of the extent of biodegradation in a full-scale landfill.

  12. Combined monitoring of changes in delta13CH4 and archaeal community structure during mesophilic methanization of municipal solid waste.

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    Qu, Xian; Mazéas, Laurent; Vavilin, Vasily A; Epissard, Jonathan; Lemunier, Mélanie; Mouchel, Jean-Marie; He, Pin-jing; Bouchez, Théodore

    2009-05-01

    Reconstituted municipal solid waste (MSW) with varying contents of putrescible and cellulosic waste was incubated anaerobically under mesophilic conditions. Standard physicochemical parameters were monitored, together with stable isotopic signatures of produced CH(4) and CO(2). delta(13)C values for CH(4) indicated a change of methanogenic metabolism with time. CH(4) was predominantly produced from H(2)/CO(2) at the beginning of the incubations. This period was associated with important shifts in archaeal communities monitored by automated ribosomal intergenic spacer analysis (ARISA) and FISH of oligonucleotidic probes targeting specifically 16S rRNA gene of various methanogenic groups. The onset of the active methane generation phase was characterized by an increase of CH(4)delta(13)C, indicating a progressive shift toward an aceticlastic metabolism. When the methane production levelled off, a decrease in the isotopic signature was observed toward values characteristics of hydrogenotrophic metabolism. ARISA profiles were, however, found to be stable from the beginning of the active methane generation phase until the end of the experiment. FISH observation indicated that members of the family Methanosarcinaceae were predominant in the archaeal community during this period, suggesting that these methanogens might exhibit a high metabolic versatility during methanization of waste.

  13. Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

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    Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

    2016-09-29

    Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

  14. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

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    Navarro-Noya, Yendi E.; Valenzuela-Encinas, César; Sandoval-Yuriar, Alonso; Jiménez-Bueno, Norma G.; Marsch, Rodolfo

    2015-01-01

    In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH. PMID:26074731

  15. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

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    Yendi E. Navarro-Noya

    2015-01-01

    Full Text Available In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5, indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances clearly clustered the communities by pH.

  16. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil.

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    Navarro-Noya, Yendi E; Valenzuela-Encinas, César; Sandoval-Yuriar, Alonso; Jiménez-Bueno, Norma G; Marsch, Rodolfo; Dendooven, Luc

    2015-01-01

    In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

  17. Human settlement as driver of bacterial, but not of archaeal, ammonia oxidizers abundance and community structure in tropical stream sediments

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    Mariana De Paula Reis

    2015-08-01

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

  18. RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight

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    Bernd Wemheuer

    2012-01-01

    Full Text Available Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota and the Marine Group I (Thaumarchaeota were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.

  19. The biogeography of soil archaeal communities on the eastern Tibetan Plateau

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    Shi, Yu; Adams, Jonathan M.; Ni, Yingying; Yang, Teng; Jing, Xin; Chen, Litong; He, Jin-Sheng; Chu, Haiyan

    2016-12-01

    The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = ‑0.47, P community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.

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

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

    2016-01-01

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

  1. Structure and function of the archaeal exosome.

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    Evguenieva-Hackenberg, Elena; Hou, Linlin; Glaeser, Stefanie; Klug, Gabriele

    2014-01-01

    The RNA-degrading exosome in archaea is structurally very similar to the nine-subunit core of the essential eukaryotic exosome and to bacterial polynucleotide phosphorylase (PNPase). In contrast to the eukaryotic exosome, PNPase and the archaeal exosome exhibit metal ion-dependent, phosphorolytic activities and synthesize heteropolymeric RNA tails in addition to the exoribonucleolytic RNA degradation in 3' → 5' direction. The archaeal nine-subunit exosome consists of four orthologs of eukaryotic exosomal subunits: the RNase PH-domain-containing subunits Rrp41 and Rrp42 form a hexameric ring with three active sites, whereas the S1-domain-containing subunits Rrp4 and Csl4 form an RNA-binding trimeric cap on the top of the ring. In vivo, this cap contains Rrp4 and Csl4 in variable amounts. Rrp4 confers poly(A) specificity to the exosome, whereas Csl4 is involved in the interaction with the archaea-specific subunit of the complex, the homolog of the bacterial primase DnaG. The archaeal DnaG is a highly conserved protein and its gene is present in all sequenced archaeal genomes, although the exosome was lost in halophilic archaea and some methanogens. In exosome-containing archaea, DnaG is tightly associated with the exosome. It functions as an additional RNA-binding subunit with poly(A) specificity in the reconstituted exosome of Sulfolobus solfataricus and enhances the degradation of adenine-rich transcripts in vitro. Not only the RNA-binding cap but also the hexameric Rrp41-Rrp42 ring alone shows substrate selectivity and prefers purines over pyrimidines. This implies a coevolution of the exosome and its RNA substrates resulting in 3'-ends with different affinities to the exosome.

  2. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

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    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  3. Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants▿

    OpenAIRE

    Nettmann, E.; Bergmann, I.; Pramschüfer, S.; Mundt, K; Plogsties, V.; Herrmann, C.; Klocke, M.

    2010-01-01

    Knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic Archaea in the reactor samples. In addition, quantitative r...

  4. Crystal structure of an archaeal actin homolog.

    Science.gov (United States)

    Roeben, Annette; Kofler, Christine; Nagy, István; Nickell, Stephan; Hartl, F Ulrich; Bracher, Andreas

    2006-04-21

    Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.

  5. Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells

    KAUST Repository

    Siegert, Michael

    2015-07-06

    © 2015 American Chemical Society. Methane is the primary end product from cathodic current in microbial electrolysis cells (MECs) in the absence of methanogenic inhibitors, but little is known about the archaeal communities that develop in these systems. MECs containing cathodes made from different materials (carbon brushes, or plain graphite blocks or blocks coated with carbon black and platinum, stainless steel, nickel, ferrihydrite, magnetite, iron sulfide, or molybdenum disulfide) were inoculated with anaerobic digester sludge and acclimated at a set potential of -600 mV (versus a standard hydrogen electrode). The archaeal communities on all cathodes, except those coated with platinum, were predominated by Methanobacterium (median 97% of archaea). Cathodes with platinum contained mainly archaea most similar to Methanobrevibacter. Neither of these methanogens were abundant (<0.1% of archaea) in the inoculum, and therefore their high abundance on the cathode resulted from selective enrichment. In contrast, bacterial communities on the cathode were more diverse, containing primarily δ-Proteobacteria (41% of bacteria). The lack of a consistent bacterial genus on the cathodes indicated that there was no similarly selective enrichment of bacteria on the cathode. These results suggest that the genus Methanobacterium was primarily responsible for methane production in MECs when cathodes lack efficient catalysts for hydrogen gas evolution. (Figure Presented).

  6. Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants.

    Science.gov (United States)

    Nettmann, E; Bergmann, I; Pramschüfer, S; Mundt, K; Plogsties, V; Herrmann, C; Klocke, M

    2010-04-01

    Knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic Archaea in the reactor samples. In addition, quantitative real-time PCR (Q-PCR) was used to support and complete the FISH analysis. Five of the six biogas reactors were dominated by hydrogenotrophic Methanomicrobiales. The average values were between 60 to 63% of archaeal cell counts (FISH) and 61 to 99% of archaeal 16S rRNA gene copies (Q-PCR). Within this order, Methanoculleus was found to be the predominant genus as determined by amplified rRNA gene restriction analysis. The aceticlastic family Methanosaetaceae was determined to be the dominant methanogenic group in only one biogas reactor, with average values for Q-PCR and FISH between 64% and 72%. Additionally, in three biogas reactors hitherto uncharacterized but potentially methanogenic species were detected. They showed closest accordance with nucleotide sequences of the hitherto unclassified CA-11 (85%) and ARC-I (98%) clusters. These results point to hydrogenotrophic methanogenesis as a predominant pathway for methane synthesis in five of the six analyzed biogas plants. In addition, a correlation between the absence of Methanosaetaceae in the biogas reactors and high concentrations of total ammonia (sum of NH(3) and NH(4)(+)) was observed.

  7. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M. [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  8. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    Science.gov (United States)

    Frade, Pedro R; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.

  9. 长期定位施肥对石灰性紫色水稻土古菌群落结构的影响%Effect of long-term fertilization on archaeal community structure in calcareous purplish paddy soil

    Institute of Scientific and Technical Information of China (English)

    辜运富; 张小平; 涂仕华; Kristina Lindstr(o)m

    2011-01-01

    为了认识长期施肥对石灰性紫色水稻土培肥和肥力演化的作用,结合变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)和限制性酶切片段长度多态性(RFLP)技术,研究了稻麦轮作下农家肥(M)、氮肥+农家肥(NM)、氮磷肥+农家肥(NPM)、氮磷钾肥+农家肥(NPKM)、无肥(CK)、氮肥(N)、氮磷肥(NP)、氮磷钾肥(NPK)等不同施肥制度对石灰性紫色水稻土古菌群落结构的影响.研究结果表明,长期定位施肥明显影响土壤中的古菌组成.在长期施用氮肥+农家肥、氮磷肥和氮磷钾肥+农家肥处理的土壤中,古菌多样性指数低于农家肥、氮磷肥+农家肥、无肥、氮肥和氮磷钾肥处理.在DGGE图谱的基础上,分别选择种植水稻和小麦的氮磷钾肥处理土壤样品,对古菌克隆子的16S rDNA序列进行了系统发育分析,发现水稻七古菌与各种土壤及水体环境的古菌极其相似.对DGGE图谱的聚类分析发现,不管是种植水稻还是小麦,8种施肥处理的古菌都聚在3个群里.种植水稻时,M和NPK处理下的土壤古菌聚成第一个群,NP处理下的聚成第二个群,另外5种施肥处理(NPKM,NM,Ck,N和NPM)聚成第三个群.种植小麦时,NPKM和M处理下的土壤古菌聚成一个群,NP处理下的聚成第二个群,N、NPK、NM、NPM和CK处理下的聚成第三个群.聚类分析结果显示,作物类型会影响土壤古菌群落结构.%To better understand the role that fertilization systems play in soil fertility buildup and evolution,we employed denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) to determine the influence of different fertilization treatments on archaeal community structure in calcareous purplish paddy soil under rice/wheat rotations. The eight fertilization treatments were as follows:manure only (M), nitrogen plus manure (NM), nitrogen and phosphorus plus manure (NPM), nitrogen,phosphorus and potassium plus

  10. Drivers of archaeal ammonia-oxidizing communities in soil

    Directory of Open Access Journals (Sweden)

    Kateryna eZhalnina

    2012-06-01

    Full Text Available Soil ammonia-oxidizing archaea (AOA are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. AOA may cause nitrogen loss from soils, and the nitrate produced by AOA can lead to ground and surface water contamination, water eutrophication, and soil subsidence. The ammonia-oxidizing archaea discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.

  11. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.

    Science.gov (United States)

    Hugoni, Mylène; Taib, Najwa; Debroas, Didier; Domaizon, Isabelle; Jouan Dufournel, Isabelle; Bronner, Gisèle; Salter, Ian; Agogué, Hélène; Mary, Isabelle; Galand, Pierre E

    2013-04-01

    Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.

  12. Effect of soil properties and hydrology on Archaeal community composition in three temperate grasslands on peat

    DEFF Research Database (Denmark)

    Görres, Carolyn-Monika; Conrad, Ralf; Petersen, Søren O

    2013-01-01

    Grasslands established on drained peat soils are regarded as negligible methane (CH4) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark....... We used terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and clone libraries to characterize the soils' archaeal community composition to gain a better understanding of relationships between peat properties and land use, respectively, and CH4 dynamics. Samples were taken...... at three different depths and at four different seasons. Archaeal community composition varied considerably between the three peatlands and, to a certain degree, also with peat depth, but seemed to be quite stable at individual sampling depths throughout the year. Archaeal community composition was mainly...

  13. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

    Science.gov (United States)

    Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

  14. Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods.

    Science.gov (United States)

    Li, Ping; Jiang, Dawei; Li, Bing; Dai, Xinyue; Wang, Yanhong; Jiang, Zhou; Wang, Yanxin

    2014-12-01

    A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. 12 bacterial and 18 archaeal DGGE bands and 26-136 species-level OTUs were detected for all the samples. 299 bacterial and 283 archaeal 16S rRNA gene clones for two typical samples were identified by phylogenetic analysis. Most of the results from these different methods were consistent with the dominant bacterial populations. But the proportions of the microbial populations were mostly different and the bacterial communities in most of these samples from pyrosequencing were both more abundant and more diverse than those from the traditional methods. Even after quality filtering, pyrosequencing revealed some populations including Alishewanella, Sulfuricurvum, Arthrobacter, Sporosarcina and Algoriphagus which were not detected with traditional techniques. The most dominant bacterial populations in these samples identified as some arsenic, iron, nitrogen and sulfur reducing and oxidizing related populations including Acinetobacter, Pseudomonas, Flavobacterium, Brevundimonas, Massilia, Planococcus, and Aquabacterium and archaeal communities Nitrosophaera and Methanosaeta. Acinetobacter and Pseudomonas were distinctly abundant in most of these samples. Methanogens were found as the dominant archeal population with three methods. From the results of traditional methods, the dominant archaeal populations apparently changed from phylum Thaumarchaeota to Euryarchaeota with the arsenic concentrations increasing. But this structure dynamic change was not revealed with pyrosequencing. Our results imply that an integrated approach combining the traditional methods and next generation sequencing approaches to characterize the microbial communities in high arsenic groundwater is recommended.

  15. Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater.

    Science.gov (United States)

    Lee, Changsoo; Kim, Jaai; Shin, Seung Gu; Hwang, Seokhwan

    2008-09-01

    Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas-like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts.

  16. Response of Archaeal communities in beach sediments to spilled oil and bioremediation.

    Science.gov (United States)

    Röling, Wilfred F M; de Brito Couto, Ivana R; Swannell, Richard P J; Head, Ian M

    2004-05-01

    While the contribution of Bacteria to bioremediation of oil-contaminated shorelines is well established, the response of Archaea to spilled oil and bioremediation treatments is unknown. The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial. 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 days. In contrast, in oil-polluted microcosms a dramatic decrease in the ability to detect Archaea was observed, and it was not possible to amplify fragments of archaeal 16S rRNA genes from samples taken from microcosms treated with oil. This was the case irrespective of whether a bioremediation treatment (addition of inorganic nutrients) was applied. Since rapid oil biodegradation occurred in nutrient-treated microcosms, we concluded that Archaea are unlikely to play a role in oil degradation in beach ecosystems. A clear-cut relationship between the presence of oil and the absence of Archaea was not apparent in the field experiment. This may have been related to continuous inoculation of beach sediments in the field with Archaea from seawater or invertebrates and shows that the reestablishment of Archaea following bioremediation cannot be used as a determinant of ecosystem recovery following bioremediation. Comparative 16S rRNA sequence analysis showed that the majority of the Archaea detected (94%) belonged to a novel, distinct cluster of group II uncultured Euryarchaeota, which exhibited less than 87% identity to previously described sequences. A minor contribution of group I uncultured Crenarchaeota was observed.

  17. Effect of soil properties and hydrology on archaeal community composition in three temperate grasslands on peat.

    Science.gov (United States)

    Görres, Carolyn-Monika; Conrad, Ralf; Petersen, Søren O

    2013-08-01

    Grasslands established on drained peat soils are regarded as negligible methane (CH4 ) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark. We used terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and clone libraries to characterize the soils' archaeal community composition to gain a better understanding of relationships between peat properties and land use, respectively, and CH4 dynamics. Samples were taken at three different depths and at four different seasons. Archaeal community composition varied considerably between the three peatlands and, to a certain degree, also with peat depth, but seemed to be quite stable at individual sampling depths throughout the year. Archaeal community composition was mainly linked to soil pH. No methanogens were detected at one fen site with soil pH ranging from 3.2 to 4.4. The methanogenic community of the bog (soil pH 3.9-4.6) was dominated by hydrogenotrophs, whereas the second fen site (soil pH 5.0-5.3) comprised both aceticlastic and hydrogenotrophic methanogens. Overall, there seemed to be a significant coupling between peat type and archaeal community composition, with local hydrology modifying the strength of this coupling.

  18. Structure and cell biology of archaeal virus STIV.

    Science.gov (United States)

    Fu, Chi-yu; Johnson, Johnson E

    2012-04-01

    Recent investigations of archaeal viruses have revealed novel features of their structures and life cycles when compared to eukaryotic and bacterial viruses, yet there are structure-based unifying themes suggesting common ancestral relationships among dsDNA viruses in the three kingdoms of life. Sulfolobus solfataricus and the infecting virus Sulfolobus turreted icosahedral virus (STIV) is one of the well-established model systems to study archaeal virus replication and viral-host interactions. Reliable laboratory conditions to propagate STIV and available genetic tools allowed structural characterization of the virus and viral components that lead to the proposal of common capsid ancestry with PRD1 (bacteriophage), Adenovirus (eukaryotic virus) and PBCV (chlorellavirus). Microarray and proteomics approaches systematically analyzed viral replication and the corresponding host responses. Cellular cryo-electron tomography and thin-section EM studies uncovered the assembly and maturation pathway of STIV and revealed dramatic cellular ultra-structure changes upon infection. The viral-induced pyramid-like protrusions on cell surfaces represent a novel viral release mechanism and previously uncharacterized functions in viral replication.

  19. Spatiotemporal variability in archaeal communities of tropical coastal waters

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.

    (Woese 1987), have changed our perceptions on their bio- diversity, distribution and function in natural marine ecosys- tems. Meticulous and extensive analyses of ribosomal RNA gene sequences from environmental samples have revealed that archaea.... (2001) concluded that there are 1.3×1028 archaeal cells (of which ∼20 % are thaumarchaeotes) and 3.1×1028 bacterial cells in the world oceans. A combination of in-situ hybrid- ization and micro-autoradiography has shown that marine archaea are active...

  20. Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

    Science.gov (United States)

    Fan, Xianfang; Xing, Peng

    2016-01-01

    In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats. PMID:27708641

  1. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments.

    Science.gov (United States)

    Porat, Iris; Vishnivetskaya, Tatiana A; Mosher, Jennifer J; Brandt, Craig C; Yang, Zamin K; Brooks, Scott C; Liang, Liyuan; Drake, Meghan M; Podar, Mircea; Brown, Steven D; Palumbo, Anthony V

    2010-11-01

    Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.

  2. Drying effects on archaeal community composition and methanogenesis in bromeliad tanks.

    Science.gov (United States)

    Brandt, Franziska B; Martinson, Guntars O; Pommerenke, Bianca; Pump, Judith; Conrad, Ralf

    2015-02-01

    Tank bromeliads are highly abundant epiphytes in neotropical forests and form a unique canopy wetland ecosystem which is involved in the global methane cycle. Although the tropical climate is characterized by high annual precipitation, the plants can face periods of restricted water. Thus, we hypothesized that water is an important controller of the archaeal community composition and the pathway of methane formation in tank bromeliads. Greenhouse experiments were established to investigate the resident and active archaeal community targeting the 16S rDNA and 16S rRNA in the tank slurry of bromeliads at three different moisture levels. Archaeal community composition and abundance were determined using terminal restriction fragment length polymorphism and quantitative PCR. Release of methane and its stable carbon isotopic signature were determined in a further incubation experiment under two moisture levels. The relative abundance of aceticlastic Methanosaetaceae increased up to 34% and that of hydrogenotrophic Methanobacteriales decreased by more than half with decreasing moisture. Furthermore, at low moisture levels, methane production was up to 100-fold lower (≤0.1-1.1 nmol gdw(-1) d(-1)) than under high moisture levels (10-15 nmol gdw(-1) d(-1)). The rapid response of the archaeal community indicates that the pathway of methane formation in bromeliad tanks may indeed be strongly susceptible to periods of drought in neotropical forest canopies.

  3. Composition of bacterial and archaeal communities during landfill refuse decomposition processes.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Zhao, Heping; Long, David T

    2015-12-01

    Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.

  4. Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

    Directory of Open Access Journals (Sweden)

    Kara Bowen De León

    2013-11-01

    Full Text Available The Heart Lake Geyser Basin (HLGB is remotely located at the base of Mount Sheridan in southern Yellowstone National Park, Wyoming, USA and is situated along Witch Creek and the northwestern shore of Heart Lake. Likely because of its location, little is known about the microbial community structure of springs in the HLGB. Bacterial and archaeal populations were monitored via small subunit (SSU rRNA gene pyrosequencing over 3 years in 3 alkaline (pH 8.5 hot springs with varying temperatures (44°C, 63°C, 75°C. The bacterial populations were generally stable over time, but varied by temperature. The dominant bacterial community changed from moderately thermophilic and photosynthetic members (Cyanobacteria and Chloroflexi at 44°C to a mixed photosynthetic and thermophilic community (Deinococcus-Thermus at 63°C and a non-photosynthetic thermophilic community at 75°C. The archaeal community was more variable across time and was predominantly a methanogenic community in the 44°C and 63°C springs and a hyperthermophilic community in the 75°C spring. The 75°C spring demonstrated large shifts in the archaeal populations and was predominantly Candidatus Nitrosocaldus, an ammonia-oxidizing crenarchaeote, in the 2007 sample, and almost exclusively Thermofilum or Candidatus Caldiarchaeum in the 2009 sample, depending on SSU rRNA gene region examined. The majority of sequences were dissimilar (≥10% different to any known organisms suggesting that HLGB possesses numerous new phylogenetic groups that warrant cultivation efforts.

  5. Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park.

    Science.gov (United States)

    Bowen De León, Kara; Gerlach, Robin; Peyton, Brent M; Fields, Matthew W

    2013-01-01

    The Heart Lake Geyser Basin (HLGB) is remotely located at the base of Mount Sheridan in southern Yellowstone National Park (YNP), Wyoming, USA and is situated along Witch Creek and the northwestern shore of Heart Lake. Likely because of its location, little is known about the microbial community structure of springs in the HLGB. Bacterial and archaeal populations were monitored via small subunit (SSU) rRNA gene pyrosequencing over 3 years in 3 alkaline (pH 8.5) hot springs with varying temperatures (44°C, 63°C, 75°C). The bacterial populations were generally stable over time, but varied by temperature. The dominant bacterial community changed from moderately thermophilic and photosynthetic members (Cyanobacteria and Chloroflexi) at 44°C to a mixed photosynthetic and thermophilic community (Deinococcus-Thermus) at 63°C and a non-photosynthetic thermophilic community at 75°C. The archaeal community was more variable across time and was predominantly a methanogenic community in the 44 and 63°C springs and a thermophilic community in the 75°C spring. The 75°C spring demonstrated large shifts in the archaeal populations and was predominantly Candidatus Nitrosocaldus, an ammonia-oxidizing crenarchaeote, in the 2007 sample, and almost exclusively Thermofilum or Candidatus Caldiarchaeum in the 2009 sample, depending on SSU rRNA gene region examined. The majority of sequences were dissimilar (≥10% different) to any known organisms suggesting that HLGB possesses numerous new phylogenetic groups that warrant cultivation efforts.

  6. Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland.

    Science.gov (United States)

    Liu, Yin; Li, Hong; Liu, Qun Fang; Li, Yan Hong

    2015-05-01

    The richness, phylogeny and composition of archaeal community associated with the roots of common reed (Phragmites australis) growing in the Beijing Cuihu Wetland, China was investigated using a 16S rDNA library. In total, 235 individual sequences were collected, and a phylogenetic analysis revealed that 69.4 and 11.5 % of clones were affiliated with the Euryarchaeota and the Crenarchaeota, respectively. In Euryarchaeota, the archaeal community was dominated by species in following genera: Methanobacterium in the order Methanobacteriales (60.7 %); Methanoregula and Methanospirillum in the order Methanomicrobiales (20.2 %), and Methanomethylovorans, Methanosarcina and Methanosaeta in the order Methanosarcinales (17.2 %). Of 27 sequences assigned to uncultured Crenarchaeota, 22 were grouped into Group 1.3, and five grouped into Group 1.1b. Hence, the archaeal communities associated with reed roots are largely involved in methane production, and, to a lesser extent, in ammonia oxidization. Quantification of the archaeal amoA gene indicated that ammonia oxidizing archaea were more numerous in the rhizosphere soil than in the root tissue or surrounding water. A total of 19.1 % of the sequences were unclassified, suggesting that many unidentified archaea are probably involved in the reed wetland ecosystem.

  7. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases.

    Science.gov (United States)

    Maita, Nobuo; Nyirenda, James; Igura, Mayumi; Kamishikiryo, Jun; Kohda, Daisuke

    2010-02-12

    Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. In the bacterium Campylobacter jejuni, a single-subunit membrane protein, PglB, catalyzes N-glycosylation. We report the 2.8 A resolution crystal structure of the C-terminal globular domain of PglB and its comparison with the previously determined structure from the archaeon Pyrococcus AglB. The two distantly related oligosaccharyltransferases share unexpected structural similarity beyond that expected from the sequence comparison. The common architecture of the putative catalytic sites revealed a new catalytic motif in PglB. Site-directed mutagenesis analyses confirmed the contribution of this motif to the catalytic function. Bacterial PglB and archaeal AglB constitute a protein family of the catalytic subunit of OST along with STT3 from eukaryotes. A structure-aided multiple sequence alignment of the STT3/PglB/AglB protein family revealed three types of OST catalytic centers. This novel classification will provide a useful framework for understanding the enzymatic properties of the OST enzymes from Eukarya, Archaea, and Bacteria.

  8. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

    Science.gov (United States)

    Yu, D; Kurola, J M; Lähde, K; Kymäläinen, M; Sinkkonen, A; Romantschuk, M

    2014-10-01

    Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

  9. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-05-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  10. Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm

    Directory of Open Access Journals (Sweden)

    Daiva Domenech Tupinambá

    2016-01-01

    Full Text Available This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7% were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area. More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.

  11. Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm.

    Science.gov (United States)

    Tupinambá, Daiva Domenech; Cantão, Maurício Egídio; Costa, Ohana Yonara Assis; Bergmann, Jessica Carvalho; Kruger, Ricardo Henrique; Kyaw, Cynthia Maria; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2016-01-01

    This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.

  12. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    Science.gov (United States)

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils. PMID:27807431

  13. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures

    DEFF Research Database (Denmark)

    Häring, Monika; Vestergaard, Gisle Alberg; Brügger, Kim;

    2005-01-01

    A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus Acidianus shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologou...... to those of other lipothrixviruses, a single tRNA(Lys) gene containing a 12-bp archaeal intron, and a 1,008-bp repeat-rich region near the center of the genome....

  14. Effects of oxytetracycline on archaeal community, and tetracycline resistance genes in anaerobic co-digestion of pig manure and wheat straw.

    Science.gov (United States)

    Wang, Xiaojuan; Pan, Hongjia; Gu, Jie; Qian, Xun; Gao, Hua; Qin, Qingjun

    2016-12-01

    In this study, the effects of different concentrations of oxytetracycline (OTC) on biogas production, archaeal community structure, and the levels of tetracycline resistance genes (TRGs) were investigated in the anaerobic co-digestion products of pig manure and wheat straw. PCR denaturing gradient gel electrophoresis analysis and real-time quantitative polymerase chain reaction (RT-qPCR) (PCR) were used to detect the archaeal community structure and the levels of four TRGs: tet(M), tet(Q), tet(W), and tet(C). The results showed that anaerobic co-digestion with OTC at concentrations of 60, 100, and 140 mg/kg (dry weight of pig manure) reduced the cumulative biogas production levels by 9.9%, 10.4%, and 14.1%, respectively, compared with that produced by the control, which lacked the antibiotic. The addition of OTC substantially modified the structure of the archaeal community. Two orders were identified by phylogenetic analysis, that is, Pseudomonadales and Methanomicrobiales, and the methanogen present during anaerobic co-digestion with OTC may have been resistant to OTC. The abundances of tet(Q) and tet(W) genes increased as the OTC concentration increased, whereas the abundances of tet(M) and tet(C) genes decreased as the OTC concentration increased.

  15. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

    Science.gov (United States)

    Wilms, Reinhard; Sass, Henrik; Köpke, Beate; Köster, Jürgen; Cypionka, Heribert; Engelen, Bert

    2006-04-01

    The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

  16. Linking the composition of bacterial and archaeal communities to characteristics of soil and flora composition in the Atlantic rainforest

    NARCIS (Netherlands)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of t

  17. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

    Science.gov (United States)

    Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, Mircea

    2013-06-01

    Next-generation sequencing has dramatically changed the landscape of microbial ecology, large-scale and in-depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.

  18. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest.

    Science.gov (United States)

    Rasche, Frank; Knapp, Daniela; Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Sessitsch, Angela

    2011-03-01

    It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups.

  19. Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium.

    Science.gov (United States)

    Colman, Daniel R; Thomas, Raquela; Maas, Kendra R; Takacs-Vesbach, Cristina D

    2015-03-01

    Recent metagenomic analyses of Yellowstone National Park (YNP) thermal spring communities suggested the presence of minor archaeal populations that simultaneous PCR-based assays using traditional 'universal' 16S rRNA gene primers failed to detect. Here we use metagenomics to identify PCR primers effective at detecting elusive members of the Archaea, assess their efficacy, and describe the diverse and novel archaeal community from a circum-neutral thermal spring from the Bechler region of YNP. We determined that a less commonly used PCR primer, Arch349F, captured more diversity in this spring than the widely used A21F primer. A search of the PCR primers against the RDP 16S rRNA gene database indicated that Arch349F also captured the largest percentage of Archaea, including 41 % more than A21F. Pyrosequencing using the Arch349F primer recovered all of the phylotypes present in the clone-based portion of the study and the metagenome of this spring in addition to several other populations of Archaea, some of which are phylogenetically novel. In contrast to the lack of amplification with traditional 16S rRNA gene primers, our comprehensive analyses suggested a diverse archaeal community in the Bechler spring, with implications for recently discovered groups such as the Geoarchaeota and other undescribed archaeal groups.

  20. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Science.gov (United States)

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (pmangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

  1. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska.

    Science.gov (United States)

    Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A G; Tiedje, James M; Zhou, Jizhong

    2015-01-01

    Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.

  2. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.

    Directory of Open Access Journals (Sweden)

    Florence Guillière

    Full Text Available While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.

  3. Preservation of Archaeal Surface Layer Structure During Mineralization

    Science.gov (United States)

    Kish, Adrienne; Miot, Jennyfer; Lombard, Carine; Guigner, Jean-Michel; Bernard, Sylvain; Zirah, Séverine; Guyot, François

    2016-05-01

    Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer “ghosts” during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.

  4. Preservation of Archaeal Surface Layer Structure During Mineralization.

    Science.gov (United States)

    Kish, Adrienne; Miot, Jennyfer; Lombard, Carine; Guigner, Jean-Michel; Bernard, Sylvain; Zirah, Séverine; Guyot, François

    2016-05-25

    Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer "ghosts" during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.

  5. Structure of the archaeal Cascade subunit Csa5

    Science.gov (United States)

    Reeks, Judith; Graham, Shirley; Anderson, Linzi; Liu, Huanting; White, Malcolm F.; Naismith, James H.

    2013-01-01

    The Cascade complex for CRISPR-mediated antiviral immunity uses CRISPR RNA (crRNA) to target invading DNA species from mobile elements such as viruses, leading to their destruction. The core of the Cascade effector complex consists of the Cas5 and Cas7 subunits, which are widely conserved in prokaryotes. Cas7 binds crRNA and forms the helical backbone of Cascade. Many archaea encode a version of the Cascade complex (denoted Type I-A) that includes a Csa5 (or small) subunit, which interacts weakly with the core proteins. Here, we report the crystal structure of the Csa5 protein from Sulfolobus solfataricus. Csa5 comprises a conserved α-helical domain with a small insertion consisting of a weakly conserved β-strand domain. In the crystal, the Csa5 monomers have multimerized into infinite helical threads. At each interface is a strictly conserved intersubunit salt bridge, deletion of which disrupts multimerization. Structural analysis indicates a shared evolutionary history among the small subunits of the CRISPR effector complexes. The same α-helical domain is found in the C-terminal domain of Cse2 (from Type I-E Cascade), while the N-terminal domain of Cse2 is found in Cmr5 of the CMR (Type III-B) effector complex. As Cmr5 shares no match with Csa5, two possibilities present themselves: selective domain loss from an ancestral Cse2 to create two new subfamilies or domain fusion of two separate families to create a new Cse2 family. A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. PMID:23846216

  6. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico).

    Science.gov (United States)

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Enríquez-Aragón, J Arturo; Estrada-Alvarado, Isabel; Hernández-Rodríguez, César; Dendooven, Luc; Marsch, Rodolfo

    2008-03-01

    The soil of the former lake Texcoco is an extreme environment localized in the valley of Mexico City, Mexico. It is highly saline and alkaline, where Na+, Cl(-), HCO3(-) and CO3(2-) are the predominant ions, with a pH ranging from 9.8 to 11.7 and electrolytic conductivities in saturation extracts from 22 to 150 dS m(-1). Metagenomic DNA from the archaeal community was extracted directly from soil and used as template to amplify 16S ribosomal gene by PCR. PCR products were used to construct gene libraries. The ribosomal library showed that the archaeal diversity included Natronococcus sp., Natronolimnobius sp., Natronobacterium sp., Natrinema sp., Natronomonas sp., Halovivax sp., "Halalkalicoccus jeotgali" and novel clades within the family of Halobacteriaceae. Four clones could not be classified. It was found that the archaeal diversity in an alkaline-saline soil of the former lake Texcoco, Mexico, was low, but showed yet uncharacterized and unclassified species.

  7. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  8. Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California).

    Science.gov (United States)

    Vigneron, Adrien; Cruaud, Perrine; Pignet, Patricia; Caprais, Jean-Claude; Cambon-Bonavita, Marie-Anne; Godfroy, Anne; Toffin, Laurent

    2013-08-01

    Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the 'BIG' cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel 'ANME-2c Sonora' lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support

  9. Persistence of bacterial and archaeal communities in sea ice through an Arctic winter.

    Science.gov (United States)

    Collins, R Eric; Rocap, Gabrielle; Deming, Jody W

    2010-07-01

    The structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. We tested these hypotheses by weekly sampling (January-March 2004) of first-year winter sea ice (Franklin Bay, Western Arctic) that experienced temperatures from -9 degrees C to -26 degrees C, generating community fingerprints and clone libraries for Bacteria and Archaea. Despite severe conditions and significant decreases in microbial abundance, no significant changes in richness or community structure were detected in the ice. Communities of Bacteria and Archaea in the ice, as in under-ice seawater, were dominated by SAR11 clade Alphaproteobacteria and Marine Group I Crenarchaeota, neither of which is known from later season sea ice. The bacterial ice library contained clones of Gammaproteobacteria from oligotrophic seawater clades (e.g. OM60, OM182) but no clones from gammaproteobacterial genera commonly detected in later season sea ice by similar methods (e.g. Colwellia, Psychrobacter). The only common sea ice bacterial genus detected in winter ice was Polaribacter. Overall, selection during ice formation and mortality during winter appear to play minor roles in the process of microbial succession that leads to distinctive spring and summer sea ice communities.

  10. Segregated Planktonic and Bottom-Dwelling Archaeal Communities in High-Temperature Acidic/Sulfuric Ponds of the Tatun Volcano Group, Northern Taiwan

    Directory of Open Access Journals (Sweden)

    Ting-Wen Cheng

    2013-01-01

    Full Text Available Geothermal environments are characterized by dynamic redox and temperature fluctuations inherited from the exposure of deeply-sourced, hot, reducing fluids to low-temperature, oxidizing ambient environments. To investigate whether microbial assemblages shifted in response to the changes of a redox state within acidic hot ponds, we collected three paired water and sediment samples from the Tatun Volcano Group, assessed metabolic roles of community members, and correlated their functional capabilities with geochemical factors along depth. Molecular analyses revealed that Sulfolobus spp., Acidianus spp. and Vulcanisaeta spp. capable of respiring elemental sulfur under oxic and/or low-oxygen conditions were the major archaeal members in planktonic communities. In contrast, obligate anaerobic Caldisphaera spp. dominated over others in bottom-dwelling communities. Bacteria were only detected in one locality wherein the majority was affiliated with microaerophilic Hydrogenobaculum spp. Cluster analyses indicated that archaeal communities associated with sediments tended to cluster together and branch off those with water. In addition, the quantities of dissolved oxygen within the water column were substantially less than those in equilibrium with atmospheric oxygen, indicating a net oxygen consumption most likely catalyzed by microbial processes. These lines of evidence suggest that the segregation of planktonic from bottom-dwelling archaeal assemblages could be accounted for by the oxygen affinities inherited in individual archaeal members. Community assemblages in geothermal ecosystems would be often underrepresented without cautious sampling of both water and sediments.

  11. Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

    NARCIS (Netherlands)

    Su, Y.; Smidt, H.; Zhu, W.Y.

    2014-01-01

    Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE) wi

  12. Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.

    Science.gov (United States)

    Xie, Wei; Zhang, Chuanlun L; Wang, Jinxiang; Chen, Yufei; Zhu, Yuanqing; de la Torre, José R; Dong, Hailiang; Hartnett, Hilairy E; Hedlund, Brian P; Klotz, Martin G

    2015-05-01

    Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.

  13. Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.

    Directory of Open Access Journals (Sweden)

    Vanessa Delfosse

    Full Text Available Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4 symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

  14. Shaping the Archaeal Cell Envelope

    Directory of Open Access Journals (Sweden)

    Albert F. Ellen

    2010-01-01

    Full Text Available Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane.

  15. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

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    Changrui Lu

    Full Text Available BACKGROUND: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. METHODOLOGY/PRINCIPAL FINDINGS: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. CONCLUSION/SIGNIFICANCE: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

  16. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Qingping; Rife, Christopher L.; Carlton, Dennis; Miller, Mitchell D.; Krishna, S. Sri; Elsliger, Marc-André; Abdubek, Polat; Astakhova, Tamara; Chiu, Hsiu-Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; van den Bedem, Henry; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.; (Scripps); (SSR); (SSRL); (JCSG); (UCSD)

    2009-08-28

    Signal transduction ATPases with numerous domains (STAND), a large class of P-loop NTPases, belong to AAA+ ATPases. They include AP(apoptotic)-ATPases (e.g., animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators), NACHT NTPases (e.g. CARD4, NAIP, Het-E-1, TLP1), and several other less well-characterized families. STAND differ from other P-loop NTPases by their unique sequence motifs, which include an hhGRExE (h, hydrophobic; x, any residue) motif at the N-terminal region, a GxP/GxxP motif at the C-terminal region of the NTPase domain, in addition to a C-terminal helical domain and additional domains such as WD40, TPR, LRR or catalytic modules. Despite significant biological interests, structural coverage of STAND proteins is very limited and only two other structures are currently known: the cell death regulators Apaf-1 and CED-4. Here, we report the crystal structure of SSO1545 from Sulfolobus solfataricus, which was determined using the semi-automated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org), as part of the National Institute of General Medical Sciences' Protein Structure Initiative (PSI). SSO1545 (NP-342973.1), a representative of the archaeal STANDs, is a member of Pfam PF01637 and encodes a protein of 356 residues with calculated molecular weight and isoelectric point of 41.7 kD and 8.2, respectively.

  17. Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal d-family DNA polymerase.

    Science.gov (United States)

    Matsui, Ikuo; Matsui, Eriko; Yamasaki, Kazuhiko; Yokoyama, Hideshi

    2013-07-05

    Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  18. Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase

    Directory of Open Access Journals (Sweden)

    Hideshi Yokoyama

    2013-07-01

    Full Text Available Archaea-specific D-family DNA polymerase (PolD forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  19. Structural diversity of archaeal ether lipid and phylogenetic relationship; Ko saikin eteru shishitsu no tayosei to keito kankei

    Energy Technology Data Exchange (ETDEWEB)

    Koga, Y. [Univ. of Occupational and Environmental Health, Kitakyushu (Japan)

    1997-05-20

    Existence of ether lipids is not limited in archaea, however, ether lipids are characteristic market of archaea. Archaeal ether lipids have diverse structures and unusual features not found in other organisms. Archaeal lipids have saturated isoprenoid hydrocarbon chain ether-linked to glycerol. Tetraether type lipids with two polar groups on two sides of hydrocarbon chains are found in archaea widely. Core lipids of non-methanogenic thermophilic archaea are mainly tetraether type lipids containing inositol as a phosphate-containing polar head group. Lipids of extreme halophilic archaea are composed of diether type and glycerophosphate as polar head groups. The feature of methanogenic archaeral lipids is nitrogen-containing polar head groups. Distribution of lipid constituents is used as a chemotaxonomic marker of extreme halophiles and methanogens. The most fundamental phenotypic difference between archaea and Eubacteria is enantiomeric difference at C-2 position of glycerophosphate backbone, that is archaea have G-1-P configuration. 31 refs., 7 figs., 3 tabs.

  20. 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.

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

    Science.gov (United States)

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

    2015-02-01

    Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

  2. Pyrosequencing reveals the influence of elevated atmospheric CO2 on the composition of archaeal communities in the rhizosphere of C3 and C4 crops

    Science.gov (United States)

    Nelson, D. M.; Cann, I. K.; Mackie, R. I.

    2008-12-01

    The projected increase in atmospheric CO2 concentrations throughout the 21st century is likely to increase aboveground and belowground plant productivity and cause changes in the quantity and quality of plant root exudates, although plants using C4 photosynthesis are likely to be only affected during times of drought (Leakey et al., 2006, Plant Physiology, 140, 779). Evidence is emerging from molecular tools that these changes may influence the abundance and composition of soil microbial communities that regulate key soil processes, such as nitrogen cycling (Lesaulnier et al., 2008, Environmental Microbiology, 10, 926). However, most molecular tools are not well-suited for comparing multiple samples at great sequencing depth, which is critical when considering soil microbial communities of high diversity. To overcome these limitations we used pyrosequencing and quantitative PCR (qPCR) of two genes (the V3 region of 16S rDNA and the amoA gene) to examine intra- and inter-treatment variability in the abundance and composition of microbial communities in the rhizosphere of soybean (C3) and maize (C4) grown in field conditions under ambient (~380 ppm) and elevated (~550 ppm) CO2 using FACE (free-air concentration enrichment) technology during the 2006 growing season in central Illinois. We specifically focused on archaeal communities because of their key role in nitrification (Leininger et al., 2006, Nature, 442, 806). The majority (>97%) of recovered sequences were from members of the phylum Crenarchaeota. Principle component analysis of sequence results from the V3 and amoA genes indicated significant (p<0.05) differences in the composition of rhizosphere archaeal communities between ambient and elevated CO2 beneath soybean, but not maize. qPCR suggested no significant difference in the abundance of archaea between treatments for soybean and maize. The lack of response of archaeal community composition beneath maize to elevated CO2 is consistent with relatively high

  3. Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.

    Science.gov (United States)

    Fujihashi, Masahiro; Numoto, Nobutaka; Kobayashi, Yukiko; Mizushima, Akira; Tsujimura, Masanari; Nakamura, Akira; Kawarabayasi, Yutaka; Miki, Kunio

    2007-01-26

    UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.

  4. Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

    NARCIS (Netherlands)

    Pereira e Silva, Michele C.; Franco Dias, Armando Cavalcante; van Elsas, Jan Dirk; Salles, Joana Falcao

    2012-01-01

    Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this st

  5. Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment

    Science.gov (United States)

    Polónia, Ana Rita Moura; Cleary, Daniel Francis Richard; Freitas, Rossana; Gomes, Newton Carlos Marcial; de Voogd, Nicole Joy

    2017-01-01

    Little is known about the microbial diversity, composition and predicted functional similarities and dissimilarities between prokaryotic kingdoms and among coral reef biotopes located in close spatial proximity to one other. In this study, we compared communities of Archaea and Bacteria in two distinct biotopes, namely, the sponge Xestospongia testudinaria and sediment of the Berau reef system, Indonesia. Using a 16S rRNA gene barcoded pyrosequencing approach and a recently developed predictive metagenomic approach (PICRUSt), we tested to what extent sediment and X. testudinaria host compositionally and functionally distinct communities of Archaea and Bacteria. Although Crenarchaeota (Archaea) and Proteobacteria (Bacteria) were the dominant phyla in the microbial communities of both sediment and sponge, there were significant differences in composition between them. Biotope proved to be the main identifiable factor affecting composition. In line with the compositional differences between sediment and sponge prokaryote communities, there were also differences in predicted functions. The archaeal and bacterial communities of sediment were enriched for functions associated with the Metabolism and Environmental Information Processing categories; those of X. testudinaria were enriched for functions associated with the Genetic Information Processing category. The significant levels of concordance between archaeal and bacterial communities and the similar enrichment of these communities in the same functional categories suggests a certain degree of functional redundancy between Archaea and Bacteria in the studied biotopes, which for the sponge may result in an increased resilience to environmental perturbations.

  6. 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.

  7. Spatial patterns of bacterial and archaeal communities along the Romanche Fracture Zone (tropical Atlantic)

    NARCIS (Netherlands)

    Lekunberri, Itziar; Sintes, Eva; de Corte, Daniele; Yokokawa, Taichi; Herndl, Gerhard J.

    2013-01-01

    The composition of prokaryotic communities was determined in the meso- and bathypelagic waters funneled through the Romanche Fracture Zone (RFZ, 2 degrees 7'S, 31 degrees 79'W to 0 degrees 6'N, 14 degrees 33'W) in the tropical Atlantic. Distinct water masses were identified based on their physical a

  8. Pyrosequencing of mcrA and archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters.

    Science.gov (United States)

    Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng; Lee, Patrick K H

    2015-01-01

    Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield.

  9. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.

    Science.gov (United States)

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers.

  10. Impact of Anaerobic Phenanthrene Biodegradation on Bacterial and Archaeal Communities%菲厌氧降解对细菌和古细菌群落的影响

    Institute of Scientific and Technical Information of China (English)

    张书颖; 谢曙光

    2011-01-01

    利用TRFLP技术研究了受垃圾渗滤液污染的地下沉积物中细菌和古细菌群落在菲厌氧降解前后的变化。结果表明:细菌群落在生物降解过程中变化很大,物种丰度及Shannon-Weiner指数分别由15和2.39增加到23和2.88;古细菌群落在生物降解过程中变化较小,物种丰度及Shannon-Weiner指数变化不大。%Terminal restriction fragment length polymorphism(TRFLP) was used to investigate the change of bacterial and archaeal communities in leachate-contaminated aquifer in response to anaerobic phenanthrene biodegradation.Results show that a great change in bacterial community occurred with phenanthrene biodegradation.The ribotype and Shannon-Weiner index increase from 15 to 23,and 2.39 to 2.88 respectively.However,archaeal community only shows an insignificant change with phenanthrene biodegradation,and ribotype and Shannon-Weiner index vary slightly.

  11. Archaeal extrachromosomal genetic elements

    DEFF Research Database (Denmark)

    Wang, Haina; Peng, Nan; Shah, Shiraz Ali

    2015-01-01

    SUMMARY: Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spind......SUMMARY: Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes...

  12. Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Margarita Kambourova

    2016-01-01

    Full Text Available Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS (34% salinity, demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs assigned to 15 different genera from two orders, Halobacteriales and Haloferacales. All retrieved sequences were related to culturable halophiles or unculturable clones from saline (mostly hypersaline niches. New sequences represented 53.9% of archaeal OTUs. Some of them formed separate branches with 90% similarity to the closest neighbor. Present results significantly differed from the previous investigations in regard to the number of presented genera, the domination of some genera not reported before in such extreme niche, and the identification of previously undiscovered 16S rRNA sequences.

  13. Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

    Institute of Scientific and Technical Information of China (English)

    SU Yong; Hauke Smidt; ZHU Wei-Yun

    2014-01-01

    Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE) with two primer pairs (344fGC/519r and 519f/915rGC) and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A (mcrA) gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82°C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase (including diet factor) other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.

  14. Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane.

    Science.gov (United States)

    Singh, Durgesh Narain; Kumar, Ashok; Sarbhai, Munish Prasad; Tripathi, Anil Kumar

    2012-02-01

    Biogenic origin of the significant proportion of coal bed methane has indicated the role of microbial communities in methanogenesis. By using cultivation-independent approach, we have analysed the archaeal and bacterial community present in the formation water of an Indian coal bed at 600-700 m depth to understand their role in methanogenesis. Presence of methanogens in the formation water was inferred by epifluorescence microscopy and PCR amplification of mcrA gene. Archaeal 16S rRNA gene clone library from the formation water metagenome was dominated by methanogens showing similarity to Methanobacterium, Methanothermobacter and Methanolinea whereas the clones of bacterial 16S rRNA gene library were closely related to Azonexus, Azospira, Dechloromonas and Thauera. Thus, microbial community of the formation water consisted of predominantly hydrogenotrophic methanogens and the proteobacteria capable of nitrogen fixation, nitrate reduction and polyaromatic compound degradation. Methanogenic potential of the microbial community present in the formation water was elucidated by the production of methane in the enrichment culture, which contained 16S rRNA gene sequences showing close relatedness to the genus Methanobacterium. Microcosm using formation water as medium as well as a source of inoculum and coal as carbon source produced significant amount of methane which increased considerably by the addition of nitrite. The dominance of Diaphorobacter sp. in nitrite amended microcosm indicated their important role in supporting methanogenesis in the coal bed. This is the first study indicating existence of methanogenic and bacterial community in an Indian coal bed that is capable of in situ biotransformation of coal into methane.

  15. Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex

    Science.gov (United States)

    Wiedemann, Christoph; Szambowska, Anna; Häfner, Sabine; Ohlenschläger, Oliver; Gührs, Karl-Heinz; Görlach, Matthias

    2015-01-01

    The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. Here, we describe the solution structure of the C-terminal domains of the archaeal MCMs of Sulfolobus solfataricus (Sso) and Methanothermobacter thermautotrophicus (Mth). Those domains consist of a structurally conserved truncated winged helix (WH) domain lacking the two typical ‘wings’ of canonical WH domains. A less conserved N-terminal extension links this WH module to the MCM AAA+ domain forming the ATPase center. In the Sso MCM this linker contains a short α-helical element. Using Sso MCM mutants, including chimeric constructs containing Mth C-terminal domain elements, we show that the ATPase and helicase activity of the Sso MCM is significantly modulated by the short α-helical linker element and by N-terminal residues of the first α-helix of the truncated WH module. Finally, based on our structural and functional data, we present a docking-derived model of the Sso MCM, which implies an allosteric control of the ATPase center by the C-terminal domain. PMID:25712103

  16. S-layers at second glance? Altiarchaeal grappling hooks (hami resemble archaeal S-layer proteins in structure and sequence

    Directory of Open Access Journals (Sweden)

    Alexandra Kristin Perras

    2015-06-01

    Full Text Available The uncultivated Ca. Altiarchaeum hamiconexum (formerly known as SM1 Euryarchaeon carries highly specialized nano-grappling hooks (hami on its cell surface. Until now little is known about the major protein forming these structured fibrous cell surface appendages, the genes involved or membrane anchoring of these filaments. These aspects were analyzed in depth in this study using environmental transcriptomics combined with imaging methods. Since a laboratory culture of this archaeon is not yet available, natural biofilm samples with high Ca. A. hamiconexum abundance were used for the entire analyses. The filamentous surface appendages spanned both membranes of the cell, which are composed of glycosyl-archaeol. The hami consisted of multiple copies of the same protein, the corresponding gene of which was identified via metagenome-mapped transcriptome analysis. The hamus subunit proteins, which are likely to self-assemble due to their predicted beta sheet topology, revealed no similiarity to known microbial flagella-, archaella-, fimbriae- or pili-proteins, but a high similarity to known S-layer proteins of the archaeal phylum at their N-terminal region (47-44% identity. Our results provide new insights into the structure of the unique hami and their major protein and indicate their divergent evolution with S-layer proteins.

  17. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence.

    Science.gov (United States)

    Perras, Alexandra K; Daum, Bertram; Ziegler, Christine; Takahashi, Lynelle K; Ahmed, Musahid; Wanner, Gerhard; Klingl, Andreas; Leitinger, Gerd; Kolb-Lenz, Dagmar; Gribaldo, Simonetta; Auerbach, Anna; Mora, Maximilian; Probst, Alexander J; Bellack, Annett; Moissl-Eichinger, Christine

    2015-01-01

    The uncultivated "Candidatus Altiarchaeum hamiconexum" (formerly known as SM1 Euryarchaeon) carries highly specialized nano-grappling hooks ("hami") on its cell surface. Until now little is known about the major protein forming these structured fibrous cell surface appendages, the genes involved or membrane anchoring of these filaments. These aspects were analyzed in depth in this study using environmental transcriptomics combined with imaging methods. Since a laboratory culture of this archaeon is not yet available, natural biofilm samples with high Ca. A. hamiconexum abundance were used for the entire analyses. The filamentous surface appendages spanned both membranes of the cell, which are composed of glycosyl-archaeol. The hami consisted of multiple copies of the same protein, the corresponding gene of which was identified via metagenome-mapped transcriptome analysis. The hamus subunit proteins, which are likely to self-assemble due to their predicted beta sheet topology, revealed no similiarity to known microbial flagella-, archaella-, fimbriae- or pili-proteins, but a high similarity to known S-layer proteins of the archaeal domain at their N-terminal region (44-47% identity). Our results provide new insights into the structure of the unique hami and their major protein and indicate their divergent evolution with S-layer proteins.

  18. Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors

    KAUST Repository

    Chehab, Noura A.

    2013-06-18

    A large percentage of organic fuel consumed in a microbial fuel cell (MFC) is lost as a result of oxygen transfer through the cathode. In order to understand how this oxygen transfer affects the microbial community structure, reactors were operated in duplicate using three configurations: closed circuit (CC; with current generation), open circuit (OC; no current generation), and sealed off cathodes (SO; no current, with a solid plate placed across the cathode). Most (98 %) of the chemical oxygen demand (COD) was removed during power production in the CC reactor (maximum of 640 ± 10 mW/m 2), with a low percent of substrate converted to current (coulombic efficiency of 26.5 ± 2.1 %). Sealing the cathode reduced COD removal to 7 %, but with an open cathode, there was nearly as much COD removal by the OC reactor (94.5 %) as the CC reactor. Oxygen transfer into the reactor substantially affected the composition of the microbial communities. Based on analysis of the biofilms using 16S rRNA gene pyrosequencing, microbes most similar to Geobacter were predominant on the anodes in the CC MFC (72 % of sequences), but the most abundant bacteria were Azoarcus (42 to 47 %) in the OC reactor, and Dechloromonas (17 %) in the SO reactor. Hydrogenotrophic methanogens were most predominant, with sequences most similar to Methanobacterium in the CC and SO reactor, and Methanocorpusculum in the OC reactors. These results show that oxygen leakage through the cathode substantially alters the bacterial anode communities, and that hydrogenotrophic methanogens predominate despite high concentrations of acetate. The predominant methanogens in the CC reactor most closely resembled those in the SO reactor, demonstrating that oxygen leakage alters methanogenic as well as general bacterial communities. © 2013 Springer-Verlag Berlin Heidelberg.

  19. Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean

    NARCIS (Netherlands)

    Baltar, F.; Aristegui, J.; Gasol, J.M.; Herndl, G.J.

    2012-01-01

    We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 t

  20. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle

    DEFF Research Database (Denmark)

    Prangishvili, David; Vestergaard, Gisle Alberg; Häring, Monika;

    2006-01-01

    A novel virus, ATV, of the hyperthermophilic archaeal genus Acidianus has the unique property of undergoing a major morphological development outside of, and independently of, the host cell. Virions are extruded from host cells as lemon-shaped tail-less particles, after which they develop long...

  1. Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes.

    Science.gov (United States)

    Reeks, Judith; Graham, Shirley; Anderson, Linzi; Liu, Huanting; White, Malcolm F; Naismith, James H

    2013-05-01

    The Cascade complex for CRISPR-mediated antiviral immunity uses CRISPR RNA (crRNA) to target invading DNA species from mobile elements such as viruses, leading to their destruction. The core of the Cascade effector complex consists of the Cas5 and Cas7 subunits, which are widely conserved in prokaryotes. Cas7 binds crRNA and forms the helical backbone of Cascade. Many archaea encode a version of the Cascade complex (denoted Type I-A) that includes a Csa5 (or small) subunit, which interacts weakly with the core proteins. Here, we report the crystal structure of the Csa5 protein from Sulfolobus solfataricus. Csa5 comprises a conserved α-helical domain with a small insertion consisting of a weakly conserved β-strand domain. In the crystal, the Csa5 monomers have multimerized into infinite helical threads. At each interface is a strictly conserved intersubunit salt bridge, deletion of which disrupts multimerization. Structural analysis indicates a shared evolutionary history among the small subunits of the CRISPR effector complexes. The same α-helical domain is found in the C-terminal domain of Cse2 (from Type I-E Cascade), while the N-terminal domain of Cse2 is found in Cmr5 of the CMR (Type III-B) effector complex. As Cmr5 shares no match with Csa5, two possibilities present themselves: selective domain loss from an ancestral Cse2 to create two new subfamilies or domain fusion of two separate families to create a new Cse2 family. A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes.

  2. Crystal structure of the sugar binding domain of the archaeal transcriptional regulator TrmB.

    Science.gov (United States)

    Krug, Michael; Lee, Sung-Jae; Diederichs, Kay; Boos, Winfried; Welte, Wolfram

    2006-04-21

    TrmB is an alpha-glucoside-sensing transcriptional regulator controlling two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus furiosus. The crystal structure of an N-terminal truncated derivative of TrmB (amino acids 2-109 deleted; TrmB(delta2-109)) was solved at 1.5 A resolution. This protein has lost its DNA binding domain but has retained its sugar recognition site. The structure represents a novel sugar-binding fold. TrmB(delta2-109) bound maltose, glucose, sucrose, and maltotriose, exhibiting Kd values of 6.8, 25, 34, and 160 microM, respectively. TrmB(delta2-109) behaved as a monomer in dilute buffer solution in contrast to the full-length protein, which is a dimer. Co-crystallization with bound maltose identified a binding site involving seven amino acid residues: Ser229, Asn305, Gly320, Met321, Val324, Ile325, and Glu326. Six of these residues interact with the nonreducing glucosyl residue of maltose. The nonreducing glucosyl residue is shared by all substrates bound to TrmB, suggesting it as a common recognition motif.

  3. Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses

    DEFF Research Database (Denmark)

    Vestergaard, Gisle Alberg; Aramayo, Ricardo; Basta, Tamara;

    2008-01-01

    be assigned specific functions, including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators, and glycosyltransferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral...... genome, apparently resulting in phenotypic changes, as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include (i) large inverted terminal repeats exhibiting conserved, regularly spaced direct repeats; (ii) a highly conserved operon encoding the two major...... structural proteins; (iii) multiple overlapping open reading frames, which may be indicative of gene recoding; (iv) putative 12-bp genetic elements; and (v) partial gene sequences corresponding closely to spacer sequences of chromosomal repeat clusters....

  4. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans.

    Directory of Open Access Journals (Sweden)

    Lesley Tilleman

    Full Text Available Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20101 was mutated to Ser. The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the "more reactive" and "less reactive" conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60B9, Tyr(61B10, and Phe(93E11. Trp(60B9 and Tyr(61B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60B9, Tyr(61B10, and Phe(93E11 play a role in regulating heme/ligand affinity.

  5. 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.

  6. Temporal changes in abundance and composition of ammonia-oxidizing bacterial and archaeal communities in a drained peat soil in relation to N{sub 2}O emissions

    Energy Technology Data Exchange (ETDEWEB)

    Andert, Janet [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Microbiology; Max-Planck-Institute of Colloids and Interfaces, Potsdam (Germany); Wessen, Ella; Hallin, Sara [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Microbiology; Boerjesson, Gunnar [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Soil and Environment

    2011-12-15

    Boreal peat soils comprise about 3% of the terrestrial environments, and when drained, they become sources of the greenhouse gas nitrous oxide (N{sub 2}O). Ammonia oxidation can result in N{sub 2}O emissions, either directly or by fuelling denitrification, but we know little about the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in peat soils. Our aim was to determine temporal alterations in abundance and composition of these communities in a drained and forested peat soil in relation to N{sub 2}O emissions and ammonia oxidation activity. Materials and methods The peat was sampled at three different depths in the upper 0.5 m over a period of 9 months covering two summer and two winter samplings. Community composition and abundance were determined by T-RFLP and quantitative real-time PCR of the bacterial and archaeal amoA genes. Potential ammonia oxidation rates were measured using the chlorate inhibition technique, and in situ N{sub 2}O emission was determined using chambers. Results and discussion The soil parameters displayed little spatial and temporal heterogeneity, which probably explained why there were no depth-related effects on the abundance, composition, or activity of the ammonia oxidizers. In contrast to most terrestrial environments, the AOB dominated numerically over the AOA. Both groups changed in community composition between sampling occasions, although the AOB showed more significant seasonal signatures than the AOA. Temporal changes in abundance were only observed for the AOB, with a decrease in numbers from May to March. Such differences were not reflected by the activity or N{sub 2}O emissions. Conclusions The high ammonium concentrations in the peat soil likely favored the AOB over the AOA, and we hypothesize that they were more active than the AOA and therefore responded to climatic and environmental changes. However, other processes rather than ammonia oxidation were likely responsible for N{sub 2}O emissions at the site.

  7. Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution

    DEFF Research Database (Denmark)

    Greber, Basil J; Boehringer, Daniel; Godinic-Mikulcic, Vlatka;

    2012-01-01

    Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing sever......, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea....

  8. Exploring Archaeal Communities And Genomes Across Five Deep-Sea Brine Lakes Of The Red Sea With A Focus On Methanogens

    KAUST Repository

    Guan, Yue

    2015-12-15

    The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

  9. The UCSC Archaeal Genome Browser: 2012 update.

    Science.gov (United States)

    Chan, Patricia P; Holmes, Andrew D; Smith, Andrew M; Tran, Danny; Lowe, Todd M

    2012-01-01

    The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.

  10. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

    DEFF Research Database (Denmark)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...

  11. First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for L-amino acids and R-amines.

    Science.gov (United States)

    Boyko, Konstantin M; Stekhanova, Tatiana N; Nikolaeva, Alena Yu; Mardanov, Andrey V; Rakitin, Andrey L; Ravin, Nikolai V; Bezsudnova, Ekaterina Yu; Popov, Vladimir O

    2016-03-01

    The gene TUZN1299 from the genome of the hyperthermophilic archaeon Thermoproteus uzoniensis encoding a new 32.8 kDa branched-chain amino acid aminotransferase (BCAT) was expressed in Escherichia coli. The recombinant protein TUZN1299 was purified to homogeneity in the PLP-bound form. TUZN1299 was active towards branched-chain amino acids (L-Val, L-Leu, L-Ile) and showed low but detectable activity toward (R)-alpha-methylbenzylamine. The enzyme exhibits high-temperature optimum, thermal stability, and tolerance to organic solvents. The structure of an archaeal BCAT called TUZN1299 was solved for the first time (at 2.0 Å resolution). TUZN1299 has a typical BCAT type IV fold, and the organization of its active site is similar to that of bacterial BCATs. However, there are some differences in the amino acid composition of the active site.

  12. Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China.

    Science.gov (United States)

    Dong, Minghua; Wu, Yan; Li, Qiumin; Tian, Guangliang; Yang, Bin; Li, Yingjuan; Zhang, Lijuan; Wang, Yongxia; Xiao, Wei; Yin, Fang; Zhao, Xingling; Zhang, Wudi; Cui, Xiaolong

    2015-05-01

    Understanding of the microbial community structures of the biogas digesters in different climatic regions can help improve the methane production in the fermentation process. The methanogenic archaeal diversity in four rural biogas digesters (BNA, JSA, LJA, and XGA) was investigated by a culture-independent rRNA approach in different climatic regions in Yunnan. Community structure composed of 711 clones in the all libraries. A total of 33 operational taxonomic units (OTUs) were detected, and major groups of methanogens were the orders Methanosarcinales and Methanomicrobiales. 63.2 % of all archaeal OTUs belong to the order Methanosarcinales which mostly contain acetotrophic methanogens. Methanomicrobiales (19.5 % in all OTUs) were detected in considerable number. Additionally, there were minor rates of uncultured archaea. The principal component analysis indicated that the genus Methanosaeta was mainly affected by the fermentation temperatures.

  13. Archaeal histones: dynamic and versatile genome architects

    Directory of Open Access Journals (Sweden)

    Bram Henneman

    2015-12-01

    Full Text Available Genome organization and compaction in Archaea involves different chromatin proteins, among which homologues of eukaryotic histones. Archaeal histones are considered the ancestors of their eukaryotic counterparts, which isreflected in the way they position along the genome and wrap DNA. Evolution from the archaeal modes of action to the prototypical eukaryotic nucleosome may be attributed to altered histone-histone interactions and DNA sequence determinants cooperating to yield stable multimeric structures. The identification of a new candidate phylum, proposed to be a missing link between archaea and eukaryotes, Lokiarchaeaota, may be instrumental in addressing this hypothesis.

  14. Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

    Science.gov (United States)

    Moeller, Andrew H.; Goodman, Andrew L.; Ochman, Howard

    2017-01-01

    ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis

  15. UPF201 Archaeal Specific Family Members Reveals Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

    Energy Technology Data Exchange (ETDEWEB)

    Rao, K.N.; Swaminathan, S.; Burley, S. K.

    2008-12-11

    We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel {beta}-sheet and five {alpha}-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

  16. UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA-Binding Proteins but Low Likelyhood for RNA-Binding Function

    Energy Technology Data Exchange (ETDEWEB)

    Rao, K.; Burley, S; Swaminathan, S

    2008-01-01

    We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel {beta}-sheet and five {alpha}-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

  17. UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.

    Directory of Open Access Journals (Sweden)

    Krishnamurthy N Rao

    Full Text Available We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54 to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40% and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel beta-sheet and five alpha-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

  18. Influence of fertilizer draw solution properties on the process performance and microbial community structure in a side-stream anaerobic fertilizer-drawn forward osmosis – ultrafiltration bioreactor

    KAUST Repository

    Kim, Youngjin

    2017-02-27

    In this study, a side-stream anaerobic fertilizer-drawn forward osmosis (FDFO) and ultrafiltration (UF) membrane bioreactor (MBR) hybrid system was proposed and operated for 55 days. The FDFO performance was first investigated in terms of flux decline with various fertilizers draw solution. Flux decline was very severe with all fertilizers due to the absence of aeration and the sticky property of sludge. Flux recovery by physical cleaning varied significantly amongst tested fertilizers which seriously affected biofouling in FDFO via reverse salt flux (RSF). Besides, RSF had a significant impact on nutrient accumulation in the bioreactor. These results indicated that nutrient accumulation negatively influenced the anaerobic activity. To elucidate these phenomena, bacterial and archaeal community structures were analyzed by pyrosequencing. Results showed that bacterial community structure was affected by fertilizer properties with less impact on archaeal community structure, which resulted in a reduction in biogas production and an increase in nitrogen content.

  19. 40 Years of archaeal virology: Expanding viral diversity.

    Science.gov (United States)

    Snyder, Jamie C; Bolduc, Benjamin; Young, Mark J

    2015-05-01

    The first archaeal virus was isolated over 40 years ago prior to the recognition of the three domain structure of life. In the ensuing years, our knowledge of Archaea and their viruses has increased, but they still remain the most mysterious of life's three domains. Currently, over 100 archaeal viruses have been discovered, but few have been described in biochemical or structural detail. However, those that have been characterized have revealed a new world of structural, biochemical and genetic diversity. Several model systems for studying archaeal virus-host interactions have been developed, revealing evolutionary linkages between viruses infecting the three domains of life, new viral lysis systems, and unusual features of host-virus interactions. It is likely that the study of archaeal viruses will continue to provide fertile ground for fundamental discoveries in virus diversity, structure and function.

  20. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    Science.gov (United States)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  1. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)*

    Science.gov (United States)

    Lintner, Nathanael G.; Kerou, Melina; Brumfield, Susan K.; Graham, Shirley; Liu, Huanting; Naismith, James H.; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J.; White, Malcolm F.; Lawrence, C. Martin

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli “CRISPR-associated complex for antiviral defense” (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea. PMID:21507944

  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. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China.

    Science.gov (United States)

    Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Tang, Shu-Kun; Jiang, Hong-Chen; Zhang, Chuanlun L; Dong, Hailiang; Li, Wen-Jun

    2013-04-01

    Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.

  4. A c subunit with four transmembrane helices and one ion (Na+)-binding site in an archaeal ATP synthase: implications for c ring function and structure.

    Science.gov (United States)

    Mayer, Florian; Leone, Vanessa; Langer, Julian D; Faraldo-Gómez, José D; Müller, Volker

    2012-11-16

    The ion-driven membrane rotors of ATP synthases consist of multiple copies of subunit c, forming a closed ring. Subunit c typically comprises two transmembrane helices, and the c ring features an ion-binding site in between each pair of adjacent subunits. Here, we use experimental and computational methods to study the structure and specificity of an archaeal c subunit more akin to those of V-type ATPases, namely that from Pyrococcus furiosus. The c subunit was purified by chloroform/methanol extraction and determined to be 15.8 kDa with four predicted transmembrane helices. However, labeling with DCCD as well as Na(+)-DCCD competition experiments revealed only one binding site for DCCD and Na(+), indicating that the mature c subunit of this A(1)A(O) ATP synthase is indeed of the V-type. A structural model generated computationally revealed one Na(+)-binding site within each of the c subunits, mediated by a conserved glutamate side chain alongside other coordinating groups. An intriguing second glutamate located in-between adjacent c subunits was ruled out as a functional Na(+)-binding site. Molecular dynamics simulations indicate that the c ring of P. furiosus is highly Na(+)-specific under in vivo conditions, comparable with the Na(+)-dependent V(1)V(O) ATPase from Enterococcus hirae. Interestingly, the same holds true for the c ring from the methanogenic archaeon Methanobrevibacter ruminantium, whose c subunits also feature a V-type architecture but carry two Na(+)-binding sites instead. These findings are discussed in light of their physiological relevance and with respect to the mode of ion coupling in A(1)A(O) ATP synthases.

  5. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

    Directory of Open Access Journals (Sweden)

    Anne eDaebeler

    2012-10-01

    Full Text Available The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of the associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilisation site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative PCR suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while the measured soil physico-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

  6. Tropical Aquatic Archaea Show Environment-Specific Community Composition

    Science.gov (United States)

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

    2013-01-01

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

  7. Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

    Directory of Open Access Journals (Sweden)

    Thomas Geoffrey C

    2011-05-01

    Full Text Available Abstract Background Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA comprises ~530 residues, the G isoform (MSG is ~730 residues, and this third isoform (MSH-halophilic is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. Results We have solved the structure of a malate synthase H (MSH isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. Conclusions The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C

  8. 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.

  9. Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter.

    Science.gov (United States)

    Smith, Ami M; Sharma, Deepak; Lappin-Scott, Hilary; Burton, Sara; Huber, David H

    2014-03-01

    The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.

  10. Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ

    Directory of Open Access Journals (Sweden)

    SERGIO A. COELHO-SOUZA

    2015-09-01

    Full Text Available ABSTRACTUpwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling.

  11. 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.

  12. 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.

  13. 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.

  14. Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil.

    Science.gov (United States)

    Bao, Qiongli; Huang, Yizong; Wang, Fenghua; Nie, Sanan; Nicol, Graeme W; Yao, Huaiying; Ding, Longjun

    2016-07-01

    Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

  15. 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.

  16. 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...

  17. Archaeal viruses of the sulfolobales

    DEFF Research Database (Denmark)

    Erdmann, Susanne; Garrett, Roger Antony

    2015-01-01

    Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2 with an environm......Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2...... in CRISPR loci of Sulfolobus species from a second coinfecting conjugative plasmid or virus (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012; Erdmann et al. Mol Microbiol 91:900-917, 2014). Here we describe, firstly, the isolation of archaeal virus mixtures from terrestrial hot springs...

  18. Impact of long-term Diesel Contamination on Soil Microbial Community Structure

    NARCIS (Netherlands)

    Sutton, N.B.; Maphosa, F.; Morillo, J.A.; Abu Al-Soud, W.; Langenhoff, A.A.M.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.; Smidt, H.

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical pro

  19. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Frank Roberto

    2010-03-01

    The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host numerous deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five high-temperature (> 65 oC) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved O2 and ferrous Fe. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is

  20. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

    Directory of Open Access Journals (Sweden)

    William P Inskeep

    Full Text Available The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site was obtained for five high-temperature (>65 degrees C chemotrophic microbial communities sampled from geothermal springs (or pools in Yellowstone National Park (YNP that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3 Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in

  1. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

    Science.gov (United States)

    Inskeep, William P; Rusch, Douglas B; Jay, Zackary J; Herrgard, Markus J; Kozubal, Mark A; Richardson, Toby H; Macur, Richard E; Hamamura, Natsuko; Jennings, Ryan deM; Fouke, Bruce W; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S; Badger, Jonathan H; Mathur, Eric J; Ortmann, Alice C; Bateson, Mary; Geesey, Gill; Frazier, Marvin

    2010-03-19

    The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five high-temperature (>65 degrees C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron

  2. 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.

  3. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

    Science.gov (United States)

    Inskeep, William P; Jay, Zackary J; Herrgard, Markus J; Kozubal, Mark A; Rusch, Douglas B; Tringe, Susannah G; Macur, Richard E; Jennings, Ryan deM; Boyd, Eric S; Spear, John R; Roberto, Francisco F

    2013-01-01

    Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.

  4. Phylogenetic and functional analysis of metagenome sequence from high-temperature archaeal habitats demonstrate linkages between metabolic potential and geochemistry

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-05-01

    Full Text Available Geothermal habitats in Yellowstone National Park (YNP provide an unparalled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40-45 Mbase Sanger sequencing per site was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G+C content and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH. These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high temperature systems of YNP.

  5. Shaping the Archaeal Cell Envelope

    NARCIS (Netherlands)

    Ellen, Albert F.; Zolghadr, Behnam; Driessen, Arnold M. J.; Albers, Sonja-Verena

    2010-01-01

    Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface st

  6. Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation.

    Science.gov (United States)

    Galand, Pierre E; Lovejoy, Connie; Hamilton, Andrew K; Ingram, R Grant; Pedneault, Estelle; Carmack, Eddy C

    2009-04-01

    Evidence of microbial zonation in the open ocean is rapidly accumulating, but while the distribution of communities is often described according to depth, the other physical factors structuring microbial diversity and function remain poorly understood. Here we identify three different water masses in the North Water (eastern Canadian Arctic), defined by distinct temperature and salinity characteristics, and show that they contained distinct archaeal communities. Moreover, we found that one of the water masses contained an increased abundance of the archaeal alpha-subunit of the ammonia monooxygenase gene (amoA) and accounted for 70% of the amoA gene detected overall. This indicates likely differences in putative biogeochemical capacities among different water masses. The ensemble of our results strongly suggest that the widely accepted view of depth stratification did not explain microbial diversity, but rather that parent water masses provide the framework for predicting communities and potential microbial function in an Arctic marine system. Our results emphasize that microbial distributions are strongly influenced by oceanic circulation, implying that shifting currents and water mass boundaries resulting from climate change may well impact patterns of microbial diversity by displacing whole biomes from their historic distributions. This relocation could have the potential to establish a substantially different geography of microbial-driven biogeochemical processes and associated oceanic production.

  7. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.

    Science.gov (United States)

    Galand, Pierre E; Casamayor, Emilio O; Kirchman, David L; Potvin, Marianne; Lovejoy, Connie

    2009-07-01

    The Arctic Ocean plays a critical role in controlling nutrient budgets between the Pacific and Atlantic Ocean. Archaea are key players in the nitrogen cycle and in cycling nutrients, but their community composition has been little studied in the Arctic Ocean. Here, we characterize archaeal assemblages from surface and deep Arctic water masses using massively parallel tag sequencing of the V6 region of the 16S rRNA gene. This approach gave a very high coverage of the natural communities, allowing a precise description of archaeal assemblages. This first taxonomic description of archaeal communities by tag sequencing reported so far shows that it is possible to assign an identity below phylum level to most (95%) of the archaeal V6 tags, and shows that tag sequencing is a powerful tool for resolving the diversity and distribution of specific microbes in the environment. Marine group I Crenarchaeota was overall the most abundant group in the Arctic Ocean and comprised between 27% and 63% of all tags. Group III Euryarchaeota were more abundant in deep-water masses and represented the largest archaeal group in the deep Atlantic layer of the central Arctic Ocean. Coastal surface waters, in turn, harbored more group II Euryarchaeota. Moreover, group II sequences that dominated surface waters were different from the group II sequences detected in deep waters, suggesting functional differences in closely related groups. Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea.

  8. 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...

  9. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

  10. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Science.gov (United States)

    Narihiro, Takashi; Tamaki, Hideyuki; Akiba, Aya; Takasaki, Kazuto; Nakano, Koichiro; Kamagata, Yoichi; Hanada, Satoshi; Maji, Taizo

    2014-01-01

    From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

  11. Segregated Planktonic and Bottom-Dwelling Archaeal Communities in High-Temperature Acidic/Sulfuric Ponds of the Tatun Volcano Group, Northern Taiwan

    OpenAIRE

    Ting-Wen Cheng; Pei-Ling Wang; Sheng-Rong Song; Li-Hung Lin

    2013-01-01

    Geothermal environments are characterized by dynamic redox and temperature fluctuations inherited from the exposure of deeply-sourced, hot, reducing fluids to low-temperature, oxidizing ambient environments. To investigate whether microbial assemblages shifted in response to the changes of a redox state within acidic hot ponds, we collected three paired water and sediment samples from the Tatun Volcano Group, assessed metabolic roles of community members, and correlated their functional capab...

  12. Diversity and subcellular distribution of archaeal secreted proteins

    Directory of Open Access Journals (Sweden)

    Mechthild ePohlschroder

    2012-07-01

    Full Text Available Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell-wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as archaeal kingdom-specific pathways. A more comprehensive understanding of the transport pathways and post-translational modifications of secreted archaeal proteins will also generate invaluable insights that will facilitate the identification of commercially valuable archaeal enzymes and the development of heterologous systems in which to efficiently express them.

  13. 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...

  14. 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...

  15. 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.

  16. 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.

  17. Analysis of the structure of microbial community in soils with different degrees of salinization using T-RFLP and real-time PCR techniques

    Science.gov (United States)

    Andronov, E. E.; Petrova, S. N.; Pinaev, A. G.; Pershina, E. V.; Rakhimgalieva, S. Zh.; Akhmedenov, K. M.; Gorobets, A. V.; Sergaliev, N. Kh.

    2012-02-01

    Molecular methods were used to study variation in the taxonomic structure of bacterial, archaeal, and fungal communities in soil samples taken along a salinity gradient from a solonchak in the vicinity of Lake Akkol' (Shingirlau, Kazakhstan). Soils from arable fields located 195 km from the solonchak served as the control. Total DNA was isolated from every sample and analyzed by T-RFLP and real-time PCR. Salinization was found to be the main ecological factor determining the structure of soil microbial community in the study region. The values of Simpson's index characterizing the diversity of this community proved to be similar in all the samples, which, however, significantly differed in the taxonomic composition of microorganisms. A significantly increased content of archaea was revealed in the sample with the highest salinity. The results of this study show that the structure of soil microbial community reflects specific features of a given soil and can be used as an indicator of its ecological state.

  18. 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...

  19. 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

  20. Study of microbial community structures in UASB sludge treating municipal wastewater by denaturing gradient gel electrophoresis of 16S rDNA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ying; Sunny Aiyuk; XU Hui; CHEN Guanxiong; Willy Verstraete

    2005-01-01

    The structures of microbial communities in lab-scale upflow anaerobic sludge blanket (UASB) reactors for treating municipal wastewater with different ratios of COD soluble/COD total were studied using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes.The microbial structure of the inoculum sludge obtained from a full-scale UASB reactor of treating potato processing wastewater was compared with the structures of sludges collected from three lab-scale UASB reactors after eight months feeding with raw municipal wastewater, with CEPS (chemically enhanced primary sedimentation) pretreated municipal wastewater, and with a synthetic municipal sewage, respectively. Computer-aided numerical analysis of the DGGE fingerprints showed that the bacterial community underwent major changes. The sludges for treating raw and CEPS pretreated wastewater had very similar bacterial and archaeal communities (82%and 96% similarity) but were different from that for treating the synthetic sewage. Hence, despite similar % COD in the particulate form in the synthetic and the real wastewater, the two wastewaters were selected for different microbial communities. Prominent DGGE bands of Bacteria and Archaea were purified and sequenced. The 16S rRNA gene sequences of the dominant archaeal bands found in the inoculum, and UASB sludge fed with raw sewage, CEPS pretreated wastewater, and synthetic sewage were closely associated with Methanosaeta concilii. In the UASB sludge fed with synthetic sewage, another dominant band associated with an uncultured archaeon 39-2 was found together with M. concilii.

  1. 印度尼西亚Padang Cermin热泉古菌多样性分析%Phylogenetic Diversity of Archaeal Community in the Hot Spring in Padang Cermin, Sumatra, Indonesia

    Institute of Scientific and Technical Information of China (English)

    沈继红; 宋维志; 林学政; 王帅; Dewi Seswita Zilda

    2012-01-01

    Bank range from 91. 9% to 97. 8% and all of the closest matches are from uncultured archaeal clones. Comparing with those reported in other hot springs of the world, the lower similarity of uncultivable clones indicate that the archaea in the hot spring in Padang Cermin might have some unique characters, probably being the presence of a particular archaeal community.

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

    Science.gov (United States)

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

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

  3. Global occurrence of archaeal amoA genes in terrestrial hot springs.

    Science.gov (United States)

    Zhang, Chuanlun L; Ye, Qi; Huang, Zhiyong; Li, Wenjun; Chen, Jinquan; Song, Zhaoqi; Zhao, Weidong; Bagwell, Christopher; Inskeep, William P; Ross, Christian; Gao, Lei; Wiegel, Juergen; Romanek, Christopher S; Shock, Everett L; Hedlund, Brian P

    2008-10-01

    Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86 degrees C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were

  4. Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

    Directory of Open Access Journals (Sweden)

    Henry eMueller

    2015-03-01

    Full Text Available Endophytes have an intimate and often symbiotic interaction with their hosts. Less is known about the composition and function of endophytes in trees. In order to evaluate our hypothesis that plant genotype and origin have a strong impact on both, endophytes of leaves from 10 Olea europaea L. cultivars from the Mediterranean basin growing at a single agricultural site in Spain and from nine wild olive trees located in natural habitats in Greece, Cyprus and on Madeira Island were studied. The composition of the bacterial endophytic communities as revealed by 16S rRNA gene amplicon sequencing and the subsequent PCoA analysis showed a strong correlation to the plant genotypes. The bacterial distribution patterns were congruent with the plant origins in Eastern and Western areas of the Mediterranean basin. Subsequently, the endophytic microbiome of wild olives was shown to be closely related to those of cultivated olives of the corresponding geographic origins. The olive leaf endosphere harbored mostly Proteobacteria, followed by Firmicutes, Actinobacteria and Bacteroidetes. The detection of a high portion of archaeal taxa belonging to the phyla Thaumarchaeota, Crenarchaeota and Euryarchaeota in the amplicon libraries was an unexpected discovery, which was confirmed by quantitative real-time PCR revealing an archaeal portion of up to 35.8%. Although the function of these Archaea for their host plant remains speculative, this finding suggests a significant relevance of archaeal endophytes for plant-microbe interactions. In addition, the antagonistic potential of culturable endophytes was determined; all isolates with antagonistic activity against the olive-pathogenic fungus Verticillium dahliae Kleb. belong to Bacillus amyloliquefaciens. In contrast to the specific global structural diversity, BOX-fingerprints of the antagonistic Bacillus isolates were highly similar and independent of the olive genotype from which they were isolated.

  5. 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.

  6. 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...

  7. 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

  8. 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

  9. 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

  10. 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

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

    KAUST Repository

    Bougouffa, Salim

    2013-03-29

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

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

    Science.gov (United States)

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

    2012-01-01

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

  13. Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

    Science.gov (United States)

    Danielsson, Rebecca; Dicksved, Johan; Sun, Li; Gonda, Horacio; Müller, Bettina; Schnürer, Anna; Bertilsson, Jan

    2017-01-01

    Methane (CH4) is produced as an end product from feed fermentation in the rumen. Yield of CH4 varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH4 emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH4 emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH4 emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters (P Fermentation pattern of volatile fatty acids showed that proportion of propionate was higher in cluster L, while proportion of butyrate was higher in cluster H. No difference was found in milk production or organic matter digestibility between cows. Cows in cluster L had lower CH4/kg energy corrected milk (ECM) compared to cows in cluster H, 8.3 compared to 9.7 g CH4/kg ECM, showing that low CH4 cows utilized the feed more efficient for milk production which might indicate a more efficient microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations. PMID:28261182

  14. 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

  15. 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.

  16. 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....

  17. 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...

  18. 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.

  19. 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…

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

    Science.gov (United States)

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

    2007-01-01

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

  1. 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.

  2. 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...

  3. 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.

  4. 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.

  5. 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.

  6. Structural and functional changes with depth in microbial communities in a tropical Malaysian peat swamp forest.

    Science.gov (United States)

    Jackson, Colin R; Liew, Kong Cheng; Yule, Catherine M

    2009-04-01

    Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. Denaturing gradient gel electrophoresis profiles of amplified 16S ribosomal ribonucleic acid (rRNA) gene fragments showed that different depths harbored different bacterial assemblages and that Archaea appeared to be limited to the deeper samples. Cloning and sequencing of longer 16S rRNA gene fragments suggested reduced microbial diversity in the deeper samples compared to the surface. Bacterial clone libraries were largely dominated by ribotypes affiliated with the Acidobacteria, which accounted for at least 27-54% of the sequences obtained. All of the sequenced representatives from the archaeal clone libraries were Crenarchaeota. Activities of microbial extracellular enzymes involved in carbon, nitrogen, and phosphorus cycling declined appreciably with depth, the only exception being peroxidase. These results show that tropical peat swamp forests are unusual systems with microbial assemblages dominated by members of the Acidobacteria and Crenarchaeota. Microbial communities show clear changes with depth, and most microbial activity is likely confined to populations in the upper few centimeters, the site of new leaf litter fall, rather than the deeper, older, peat layers.

  7. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    Science.gov (United States)

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

  8. Hyperthermophilic Archaeal Viruses as Novel Nanoplatforms

    DEFF Research Database (Denmark)

    Uldahl, Kristine Buch

    of a broad range of genetic and chemical engineering methods, viral research has expanded. Viruses are now emerging as nanoplatforms with applications in materials science and medicine. A great challenge in biomedicine is the targeting of therapeutics to specific locations in the body in order to increase...... nanoplatforms than mammalian viruses because they cannot proliferate in humans and hence are less likely to trigger adverse effects. Another group of viruses that fits this criterion is archaeal viruses yet their potential remains untapped. As a group, archaeal viruses offer distinct advantages such as unique...... hyperthermophilic archaeal viruses, SMV1 and SSV2 and cells of human origin. This chapter provides the first results demonstrating that archaeal viruses can be taken up and internalized by human cells, thus indicating a potential as intracellular delivery agents. Chapter III investigates SMV1 particles as potential...

  9. Archaeal Enzymes and Applications in Industrial Biocatalysts.

    Science.gov (United States)

    Littlechild, Jennifer A

    2015-01-01

    Archaeal enzymes are playing an important role in industrial biotechnology. Many representatives of organisms living in "extreme" conditions, the so-called Extremophiles, belong to the archaeal kingdom of life. This paper will review studies carried by the Exeter group and others regarding archaeal enzymes that have important applications in commercial biocatalysis. Some of these biocatalysts are already being used in large scale industrial processes for the production of optically pure drug intermediates and amino acids and their analogues. Other enzymes have been characterised at laboratory scale regarding their substrate specificity and properties for potential industrial application. The increasing availability of DNA sequences from new archaeal species and metagenomes will provide a continuing resource to identify new enzymes of commercial interest using both bioinformatics and screening approaches.

  10. Archaeal Enzymes and Applications in Industrial Biocatalysts

    Directory of Open Access Journals (Sweden)

    Jennifer A. Littlechild

    2015-01-01

    Full Text Available Archaeal enzymes are playing an important role in industrial biotechnology. Many representatives of organisms living in “extreme” conditions, the so-called Extremophiles, belong to the archaeal kingdom of life. This paper will review studies carried by the Exeter group and others regarding archaeal enzymes that have important applications in commercial biocatalysis. Some of these biocatalysts are already being used in large scale industrial processes for the production of optically pure drug intermediates and amino acids and their analogues. Other enzymes have been characterised at laboratory scale regarding their substrate specificity and properties for potential industrial application. The increasing availability of DNA sequences from new archaeal species and metagenomes will provide a continuing resource to identify new enzymes of commercial interest using both bioinformatics and screening approaches.

  11. 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.

  12. The UCSC Archaeal Genome Browser: 2012 update

    OpenAIRE

    Chan, Patricia P.; Holmes, Andrew D.; Smith, Andrew M.; Tran, Danny; Lowe, Todd M.

    2011-01-01

    The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of ...

  13. Archaeal S-layer glycoproteins: Post-translational modification in the face of extremes

    Directory of Open Access Journals (Sweden)

    Jerry eEichler

    2014-11-01

    Full Text Available Corresponding to the sole or basic component of the surface (S-layer surrounding the archaeal cell in most known cases, S-layer glycoproteins are in direct contact with the harsh environments that characterize niches where Archaea can thrive. Accordingly, early work examining archaeal S-layer glycoproteins focused on identifying those properties that allow members of this group of proteins to maintain their structural integrity in the face of extremes of temperature, pH and salinity, as well as other physical challenges. However, with expansion of the list of archaeal strains serving as model systems, as well as growth in the number of molecular tools available for the manipulation of these strains, studies on archaeal S-layer glycoproteins are currently more likely to consider the various post-translational modifications these polypeptides undergo. For instance, archaeal S-layer glycoproteins can undergo proteolytic cleavage, both N- and O-glycosylation, lipid-modification and oligomerization. In this mini-review, recent findings related to the post-translational modification of archaeal S-layer glycoproteins are considered.

  14. 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.

  15. Microbial community changes in aquifer sediment microcosm for anaerobic anthracene biodegradation under methanogenic condition

    Institute of Scientific and Technical Information of China (English)

    Rui Wan; Shuying Zhang; Shuguang Xie

    2012-01-01

    The widespread distribution of polycyclic aromatic hydrocarbons(PAHs)in groundwater has become an important environmental issue.Knowledge of microbial community changes could aid in identification of particular microorganisms that are capable of degrading PAHs in contaminated aquifers.Therefore,16S rRNA gene clone library analysis was used to identify the archaeal and bacterial communities in an aquifer sediment microcosm used for anaerobic anthracene degradation under methanogenic conditions.A remarkable shift of the archaeal community structure occurred after anaerobic anthracene degradation,but the types of the abundant bacterial phyla did not change.However,a decrease of both archaeal and bacterial diversity was observed.Bacterial genera Bacillus,Rhodococcus and Herbaspirillum might have links with anaerobic anthracene degradation,suggesting a role of microbial consortia.This work might add some new information for understanding the mechanism of PAH degradation under methanogenic conditions.

  16. Microbial community structural analysis of an expanded granular sludge bed (EGSB) reactor for beet sugar industrial wastewater (BSIW) treatment.

    Science.gov (United States)

    Ambuchi, John Justo; Liu, Junfeng; Wang, Haiman; Shan, Lili; Zhou, Xiangtong; Mohammed, Mohammed O A; Feng, Yujie

    2016-05-01

    A looming global energy crisis has directly increased biomethanation processes using anaerobic digestion technology. However, much knowledge on the microbial community structure, their distribution within the digester and related functions remains extremely scanty and unavailable in some cases, yet very valuable in the improvement of the anaerobic bioprocesses. Using pyrosequencing technique based on Miseq PE 3000, microbial community population profiles were determined in an operated mesophilic expanded granular sludge bed (EGSB) reactor treating beet sugar industrial wastewater (BSIW) in the laboratory scale. Further, the distribution of the organisms in the lower, middle and upper sections within the reactor was examined. To our knowledge, this kind of analysis of the microbial community in a reactor treating BSIW is the first of its kind. A total of 44,204 non-chimeric reads with average length beyond 450 bp were yielded. Both bacterial and archaeal communities were identified with archaea predominance (60 %) observed in the middle section. Bayesian classifier yielded 164 families with only 0.73 % sequences which could not be classified to any taxa at family level. The overall phylum predominance in the reactor showed Firmicutes, Euryarchaeota, Chloroflexi, Proteobacteria and Bacteroidetes in the descending order. Our results clearly demonstrate a highly diverse microbial community population of an anaerobic reactor treating BSIW, with distinct distribution levels within the reactor.

  17. 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.

  18. Taxonomies of networks from community structure

    Science.gov (United States)

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

    2012-09-01

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

  19. Global analysis of viral infection in an archaeal model system

    Directory of Open Access Journals (Sweden)

    Walid S. Maaty

    2012-12-01

    Full Text Available The origin and evolutionary relationship of viruses is poorly understood. This makes archaeal virus-host of particular interest because the hosts generally root near the base of phylogenetic trees, while some of the viruses have clear structural similarities to those that infect prokaryotic and eukaryotic cells. Despite the advantageous position for use in evolutionary studies, little is known about archaeal viruses or how they interact with their hosts, compared to viruses of bacteria and eukaryotes. In addition, many archaeal viruses have been isolated from extreme environments and present a unique opportunity for elucidating factors that are important for existence at the extremes.. In this article we focus on virus-host interactions using a proteomics approach to study Sulfolobus Turreted Icosahedral Virus (STIV infection of Sulfolobus solfataricus P2. Using cultures grown from the ATCC cell stock, a single cycle of STIV infection was sampled 6 times over a 72 hr period. More than 700 proteins were identified throughout the course of the experiments. Seventy one host proteins were found to change by nearly two-fold (p<0.05 with 40 becoming more abundant and 31 less abundant. The modulated proteins represent 30 different cell pathways and 14 COG groups. 2D gel analysis showed that changes in post translational modifications were a common feature of the affected proteins. The results from these studies showed that the prokaryotic antiviral adaptive immune system CRISPR associated proteins (CAS proteins were regulated in response to the virus infection. It was found that regulated proteins come from mRNAs with a shorter than average half-life. In addition, activity-based protein profiling (ABPP profiling on 2D gels showed caspase, hydrolase and tyrosine phosphatase enzyme activity labeling at the protein isoform level. Together, this data provides a more detailed global view of archaeal cellular responses to viral infection, demonstrates the

  20. Impact of long-term diesel contamination on soil microbial community structure

    DEFF Research Database (Denmark)

    Sutton, Nora; Maphosa, Farai; Morillo, Jose

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical...... properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean...... samples showed higher diversity than contaminated samples (P

  1. 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

  2. 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.

  3. Protein Adaptations in Archaeal Extremophiles

    Directory of Open Access Journals (Sweden)

    Christopher J. Reed

    2013-01-01

    Full Text Available Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.

  4. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Directory of Open Access Journals (Sweden)

    Yuguang Zhang

    Full Text Available Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05 at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05 correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05 to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback

  5. Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands

    Directory of Open Access Journals (Sweden)

    Chelsea J Carey

    2015-05-01

    Full Text Available Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to environmental change, yet little is known about how microbial structure and function respond to multiple disturbances, or whether multiple environmental changes lead to unanticipated interactive effects. Our study used experimental semi-arid grassland plots in a Mediterranean-climate to determine how soil microbial communities in a seasonally variable ecosystem respond to one, two, or three simultaneous environmental changes: exotic plant invasion, plant invasion + vegetation clipping (to simulate common management practices like mowing or livestock grazing, plant invasion + nitrogen (N fertilization, and plant invasion + clipping + N fertilization. We examined microbial community structure 5-6 years after plot establishment via sequencing of >1 million 16S rRNA genes. Abiotic soil properties (soil moisture, temperature, pH, and inorganic N and microbial functioning (nitrification and denitrification potentials were also measured and showed treatment-induced shifts, including altered NO3- availability, temperature, and nitrification potential. Despite these changes, bacterial and archaeal communities showed little variation in composition and diversity across treatments. Even communities in plots exposed to three interacting environmental changes were similar to those in restored native grassland plots. Historical exposure to large seasonal and inter-annual variations in key soil properties, in addition to prior site cultivation, may select for a functionally plastic or largely dormant microbial community, resulting in a microbial community that is structurally robust to single and multiple environmental changes.

  6. 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.

  7. Bacterial, archaeal and fungal succession in the forefield of a receding glacier.

    Science.gov (United States)

    Zumsteg, Anita; Luster, Jörg; Göransson, Hans; Smittenberg, Rienk H; Brunner, Ivano; Bernasconi, Stefano M; Zeyer, Josef; Frey, Beat

    2012-04-01

    Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefield.

  8. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

    DEFF Research Database (Denmark)

    Inskeep, William P; Jay, Zackary J; Herrgard, Markus;

    2013-01-01

    Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high......-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.......4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and...

  9. 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.

  10. 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 ...

  11. 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…

  12. 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 ...

  13. 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…

  14. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

    NARCIS (Netherlands)

    Daebeler, A.; Gansen, M.; Frenzel, P.

    2013-01-01

    The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly

  15. Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes

    Science.gov (United States)

    Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Boldyrev, Ivan A.; Efremov, Roman G.

    2014-12-01

    Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and ``branched'' hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

  16. Archaeal type IV pili and their involvement in biofilm formation

    Directory of Open Access Journals (Sweden)

    Rianne eEsquivel

    2015-03-01

    Full Text Available Type IV pili are ancient proteinaceous structures present on the cell surface of species in nearly all bacterial and archaeal phyla. These filaments are involved in a diverse array of critical cellular processes. While the core components of the pilus biosynthesis machinery are highly conserved, type IV pilins, the structural subunits of pili, share little sequence homology. However, the conserved structure of the signal peptides of these pilus subunits has allowed the development of prediction programs that accurately detect the processing sites recognized by bacterial and archaeal prepilin peptidases. Using these programs, the genomes of organisms from both prokaryotic domains have been shown to encode a diverse set of putative type IV pilins. Recently, in vivo studies in model archaea representing the euryarchaeal and crenarchaeal kingdoms confirmed that several of these pilins are incorporated into type IV adhesion pili. In addition to facilitating surface adhesion, these in vivo studies also showed that several predicted pilins are required for additional functions that are critical to biofilm formation. Examples include the subunits of Sulfolobus acidocaldarius Ups pili, which are induced by exposure to UV light and promote cell aggregation and conjugation, and a subset of the Haloferax volcanii adhesion pilins, which play a critical role in microcolony formation while other pilins inhibit this process. The recent discovery of novel pilin functions such as the ability of haloarchaeal adhesion pilins to regulate swimming motility rather than being unique to organisms that inhabit high salt environments may point to novel prokaryotic regulatory pathways. In this review, we will discuss recent advances in our understanding of the functional roles played by archaeal type IV adhesion pili and their subunits, with particular emphasis on their involvement in biofilm formation.

  17. A putative viral defence mechanism in archaeal cells

    Directory of Open Access Journals (Sweden)

    Reidun Lillestøl

    2006-01-01

    Full Text Available Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer-repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA-based may be evolutionarily related to the interference RNA systems (siRNA and miRNA, which are common in eukarya. Here, we analyze all the current data on archaeal repeat clusters and provide some new insights into their diverse structures, transcriptional properties and mode of structural development. The results are consistent with larger cluster transcripts being processed at the centers of the repeat sequences and being further trimmed by exonucleases to yield a dominant, intracellular RNA species, which corresponds approximately to the size of a spacer. Furthermore, analysis of the extensive clusters of Sulfolobus solfataricus strains P1 and P2B provides support for the presence of a flanking sequence adjoining a cluster being a prerequisite for the incorporation of new spacer-repeat units, which occurs between the flanking sequence and the cluster. An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/.

  18. 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.

  19. Archaeal promoter architecture and mechanism of gene activation

    DEFF Research Database (Denmark)

    Peng, Nan; Ao, Xiang; Liang, Yun Xiang;

    2011-01-01

    Sulfolobus solfataricus and Sulfolobus islandicus contain several genes exhibiting D-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. At sequence level, only two highly conserved cis elements are present on the promoters: a regulatory...... element named ara box directing arabinose-inducible expression and the basal promoter element TATA, serving as the binding site for the TATA-binding protein. Strikingly, these promoters possess a modular structure that allows an essentially inactive basal promoter to be strongly activated. The invoked...

  20. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

    Science.gov (United States)

    Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

    2013-04-01

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  1. Electroporation of archaeal lipid membranes using MD simulations.

    Science.gov (United States)

    Polak, Andraž; Tarek, Mounir; Tomšič, Matija; Valant, Janez; Ulrih, Nataša Poklar; Jamnik, Andrej; Kramar, Peter; Miklavčič, Damijan

    2014-12-01

    Molecular dynamics (MD) simulations were used to investigate the electroporation of archaeal lipid bilayers when subjected to high transmembrane voltages induced by a charge imbalance, mimicking therefore millisecond electric pulse experiments. The structural characteristics of the bilayer, a 9:91 mol% 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) were compared to small angle X-ray scattering data. A rather good agreement of the electron density profiles at temperatures of 298 and 343 K was found assessing therefore the validity of the protocols and force fields used in simulations. Compared to dipalmitoyl-phosphatidylcholine (DPPC), the electroporation threshold for the bilayer was found to increase from ~2 V to 4.3 V at 323 K, and to 5.2 V at 298 K. Comparing the electroporation thresholds of the archaeal lipids to those of simple diphytanoyl-phosphatidylcholine (DPhPC) bilayers (2.5 V at 323 K) allowed one to trace back the stability of the membranes to the structure of their lipid head groups. Addition of DPPC in amounts of 50 mol% to the archaeal lipid bilayers decreases their stability and lowers the electroporation thresholds to 3.8 V and 4.1 V at respectively 323 and 298 K. The present study therefore shows how membrane compositions can be selected to cover a wide range of responses to electric stimuli. This provides new routes for the design of liposomes that can be efficiently used as drug delivery carriers, as the selection of their composition allows one to tune in their electroporation threshold for subsequent release of their load.

  2. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    Science.gov (United States)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  3. Archaeal viruses-novel, diverse and enigmatic

    DEFF Research Database (Denmark)

    Peng, Xu; Garrett, Roger Antony; She, Qunxin

    2012-01-01

    Recent research has revealed a remarkable diversity of viruses in archaeal-rich environments where spindles, spheres, filaments and rods are common, together with other exceptional morphotypes never recorded previously. Moreover, their double-stranded DNA genomes carry very few genes exhibiting...

  4. Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

    Science.gov (United States)

    Bengtson, Per; Sterngren, Anna E; Rousk, Johannes

    2012-08-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

  5. 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.

  6. Environmental drivers of soil microbial community structure and function at the Avon River Critical Zone Observatory.

    Science.gov (United States)

    Gleeson, Deirdre; Mathes, Falko; Farrell, Mark; Leopold, Matthias

    2016-11-15

    The Critical Zone is defined as the thin, permeable layer from the tops of the trees to the bottom of the bedrock that sustains terrestrial life on Earth. The geometry and shape of the various weathering zones are known as the critical zone architecture. At the centre of the Critical Zone are soils and the microorganisms that inhabit them. In Western Australia, the million-year-old stable weathering history and more recent lateral erosion during the past hundreds of thousands of years have created a geomorphic setting where deep weathering zones are now exposed on the surface along the flanks of many lateritic hills. These old weathering zones provide diverse physical and chemical properties that influence near surface pedologic conditions and thus likely shape current surface microbiology. Here, we present data derived from a small lateritic hill on the UWA Farm Ridgefield. Spatial soil sampling revealed the contrasting distribution patterns of simple soil parameters such as pH (CaCl2) and electric conductivity. These are clearly linked with underlying changes of the critical zone architecture and show a strong contrast with low values of pH3.3 at the top of the hill to pH5.3 at the bottom. These parameters were identified as major drivers of microbial spatial variability in terms of bacterial and archaeal community composition but not abundance. In addition, we used sensitive (14)C labelling to assess turnover of three model organic nitrogen compounds - an important biogeochemical functional trait relating to nutrient availability. Though generally rapid and in the order of rates reported elsewhere (t½10h). In conclusion, we have shown that the weathering and erosion history of ancient Western Australia affects the surface pedology and has consequences for microbial community structure and function.

  7. Archaeal type IV pili and their involvement in biofilm formation.

    Science.gov (United States)

    Pohlschroder, Mechthild; Esquivel, Rianne N

    2015-01-01

    Type IV pili are ancient proteinaceous structures present on the cell surface of species in nearly all bacterial and archaeal phyla. These filaments, which are required for a diverse array of important cellular processes, are assembled employing a conserved set of core components. While type IV pilins, the structural subunits of pili, share little sequence homology, their signal peptides are structurally conserved allowing for in silico prediction. Recently, in vivo studies in model archaea representing the euryarchaeal and crenarchaeal kingdoms confirmed that several of these pilins are incorporated into type IV adhesion pili. In addition to facilitating surface adhesion, these in vivo studies also showed that several predicted pilins are required for additional functions that are critical to biofilm formation. Examples include the subunits of Sulfolobus acidocaldarius Ups pili, which are induced by exposure to UV light and promote cell aggregation and conjugation, and a subset of the Haloferax volcanii adhesion pilins, which play a critical role in microcolony formation while other pilins inhibit this process. The recent discovery of novel pilin functions such as the ability of haloarchaeal adhesion pilins to regulate swimming motility may point to novel regulatory pathways conserved across prokaryotic domains. In this review, we will discuss recent advances in our understanding of the functional roles played by archaeal type IV adhesion pili and their subunits, with particular emphasis on their involvement in biofilm formation.

  8. Non-extremophilic 'extremophiles' - Archaeal dominance in the subsurface and their implication for life

    Science.gov (United States)

    Reitschuler, Christoph; Lins, Philipp; Illmer, Paul

    2014-05-01

    Archaea - besides bacteria and eukaryota constituting the third big domain of life - were so far regarded as typical inhabitants of extreme environments, as indicated by the name (Archaeon, Greek: 'original', 'primal'). Previous research and cultivation successes were basically carried out in habitats characterized by extreme temperature, pH and salinity regimes. Such extreme conditions, as expected at the beginning of the Earth's evolution, are occasionally also prevalent on extraterrestrial planets and moons and make the Archaeal domain a key group to be studied concerning life's evolution and the most likely pioneer organisms to colonize environments that are regarded as hostile. However, in recent years it became obvious that Archaea, in particular non-extremophilic species, can be found almost ubiquitously in marine, freshwater, terrestrial and also subsurface habitats and occasionally outnumber other microbial domains and hold key positions in globally relevant energy and nutrient cycles. Besides extreme environments - the big question remains how to define a parameter as extreme - subsurface and cave environments present a window to the past, where adaptions to early life's conditions can be studied and how microbiomes may be structured in a habitat that represents a refugium on extraterrestrial celestial bodies, were surface conditions might be at first sight too extreme for life. The lower part of the alpine Hundsalm cave in Tyrol (Austria) offered a unique opportunity to study an almost pristine cave habitat, which is separated from the touristic part of the ice cave. The main focus of our research was laid on the microbial communities that were supposed to be in connection with secondary carbonate precipitations ('moonmilk'). For the ascertainment of these so far poorly evaluated structures a multiple approach assessment was chosen to generate a virtually complete picture of these subsurface microbiomes. Thereby, a combination of different cultivation

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China.

    Science.gov (United States)

    Huang, Qiuyuan; Dong, Christina Z; Dong, Raymond M; Jiang, Hongchen; Wang, Shang; Wang, Genhou; Fang, Bin; Ding, Xiaoxue; Niu, Lu; Li, Xin; Zhang, Chuanlun; Dong, Hailiang

    2011-09-01

    The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.

  16. 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…

  17. 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…

  18. 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

  19. Familial relationships in hyperthermo- and acidophilic archaeal viruses

    DEFF Research Database (Denmark)

    Happonen, Lotta Johanna; Redder, Peter; Peng, Xu;

    2010-01-01

    Archaea often live in extreme, harsh environments such as acidic hot springs and hypersaline waters. To date, only two icosahedrally symmetric, membrane-containing archaeal viruses, SH1 and Sulfolobus turreted icosahedral virus (STIV), have been described in detail. We report the sequence and three......-dimensional structure of a third such virus isolated from a hyperthermoacidophilic crenarchaeon, Sulfolobus strain G4ST-2. Characterization of this new isolate revealed it to be similar to STIV on the levels of genome and structural organization. The genome organization indicates that these two viruses have diverged...... from a common ancestor. Interestingly, the prominent surface turrets of the two viruses are strikingly different. By sequencing and mass spectrometry, we mapped several large insertions and deletions in the known structural proteins that could account for these differences and showed that both viruses...

  20. 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.

  1. 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.  

  2. 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.

  3. Archaeal diversity and the extent of iron and manganese pyritization in sediments from a tropical mangrove creek (Cardoso Island, Brazil)

    Science.gov (United States)

    Otero, X. L.; Lucheta, A. R.; Ferreira, T. O.; Huerta-Díaz, M. A.; Lambais, M. R.

    2014-06-01

    Even though several studies on the geochemical processes occurring in mangrove soils and sediments have been performed, information on the diversity of Archaea and their functional roles in these ecosystems, especially in subsurface environments, is scarce. In this study, we have analyzed the depth distribution of Archaea and their possible relationships with the geochemical transformations of Fe and Mn in a sediment core from a tropical mangrove creek, using 16S rRNA gene profiling and sequential extraction of different forms of Fe and Mn. A significant shift in the archaeal community structure was observed in the lower layers (90-100 cm), coinciding with a clear decrease in total organic carbon (TOC) content and an increase in the percentage of sand. The comparison of the archaeal communities showed a dominance of methanogenic Euryarchaeota in the upper layers (0-20 cm), whereas Crenarchaeota was the most abundant taxon in the lower layers. The dominance of methanogenic Euryarchaeota in the upper layer of the sediment suggests the occurrence of methanogenesis in anoxic microenvironments. The concentrations of Fe-oxyhydroxides in the profile were very low, and showed positive correlation with the concentrations of pyrite and degrees of Fe and Mn pyritization. Additionally, a partial decoupling of pyrite formation from organic matter concentration was observed, suggesting excessive Fe pyritization. This overpyritization of Fe can be explained either by the anoxic oxidation of methane by sulfate and/or by detrital pyrite tidal transportation from the surrounding mangrove soils. The higher pyritization levels observed in deeper layers of the creek sediment were also in agreement with its Pleistocenic origin.

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

    Directory of Open Access Journals (Sweden)

    Jia Hou Chin

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

  5. 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

  6. 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.

  7. Useful scars: Physics of the capsids of archaeal viruses

    Science.gov (United States)

    Perotti, L. E.; Dharmavaram, S.; Klug, W. S.; Marian, J.; Rudnick, J.; Bruinsma, R. F.

    2016-07-01

    We propose a physical model for the capsids of tailed archaeal viruses as viscoelastic membranes under tension. The fluidity is generated by thermal motion of scarlike structures that are an intrinsic feature of the ground state of large particle arrays covering surfaces with nonzero Gauss curvature. The tension is generated by a combination of the osmotic pressure of the enclosed genome and an extension force generated by filamentous structure formation that drives the formation of the tails. In continuum theory, the capsid has the shape of a surface of constant mean curvature: an unduloid. Particle arrays covering unduloids are shown to exhibit pronounced subdiffusive and diffusive single-particle transport at temperatures that are well below the melting temperature of defect-free particle arrays on a surface with zero Gauss curvature.

  8. 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.

  9. 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.

  10. 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...

  11. Identification of archaeal proteins that affect the exosome function in vitro

    Directory of Open Access Journals (Sweden)

    Palhano Fernando L

    2010-05-01

    Full Text Available Abstract Background The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. Results Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. Conclusions Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.

  12. 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…

  13. 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

  14. 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…

  15. 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

  16. 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.

  17. 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...

  18. 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...

  19. Archaeal CRISPR-based immune systems

    DEFF Research Database (Denmark)

    Garrett, Roger A; Vestergaard, Gisle Alberg; Shah, Shiraz Ali

    2011-01-01

    CRISPR (clustered regularly interspaced short palindromic repeats)-based immune systems are essentially modular with three primary functions: the excision and integration of new spacers, the processing of CRISPR transcripts to yield mature CRISPR RNAs (crRNAs), and the targeting and cleavage...... of foreign nucleic acid. The primary target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA in vitro. The archaeal CRISPR systems tend to be both diverse and complex. Here we examine evidence...... of CRISPR loci and the evidence for intergenomic exchange of CRISPR systems....

  20. 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.

  1. 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.

  2. 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.

  3. Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

    Science.gov (United States)

    Rodríguez-Marconi, Susana; De la Iglesia, Rodrigo; Díez, Beatriz; Fonseca, Cássio A.; Hajdu, Eduardo; Trefault, Nicole

    2015-01-01

    Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems. PMID:26421612

  4. Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

    Directory of Open Access Journals (Sweden)

    Takahito Mukai

    2017-02-01

    Full Text Available The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS and tryptophanyl-tRNA synthetase (TrpRS predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A. The TrpRS-A open reading frames (ORFs are always associated with another ORF (named ORF1 encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.

  5. Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

    Science.gov (United States)

    Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

    2014-01-01

    Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost

  6. Comparative study of subseafloor microbial community structures in deeply buried coral fossils and sediment matrices from the Challenger Mound in the Porcupine Seabight

    Directory of Open Access Journals (Sweden)

    Tatsuhiko eHoshino

    2011-11-01

    Full Text Available Subseafloor sedimentary environments harbor remarkably diverse microbial communities. However, it remains unknown if the deeply buried fossils in these sediments play ecological roles in deep microbial habitats, or whether the microbial communities inhabiting such fossils differ from those in the surrounding sediment matrix. Here we compare the community structures of subseafloor microbes in coldwater coral carbonates (Madrepora oculata and Lophelia pertusa and the clay matrix. Samples were obtained from the Challenger Mound in the Porcupine Seabight at Site U1317 Hole A during the Integrated Ocean Drilling Program Expedition 307. DNA was extracted from coral fossils and the surrounding sedimentary matrix at 4, 20 and 105 meters below the seafloor. 16S rRNA genes of Bacteria and Archaea were amplified by PCR, and a total of 213,792 16S rRNA gene-tagged sequences were analyzed. At the phylum level, dominant microbial components in both habitats consisted of Proteobacteria, Firmicutes, Nitrospirae, Chloroflexi and Miscellaneous Crenarchaeota Group (MCG at all three of the depths examined. However, at the genus and/or species level (similarity threshold 97.0%, the community compositions were found to be very different, with 69-75% and 46-57% of bacterial and archaeal phylotypes not overlapping in coral fossils and the clay matrix, respectively. Species richness analysis revealed that bacterial communities were generally more diverse than archaea, and that the diversity scores of coral fossils were lower than those in sediment matrix. However, the evenness of microbial communities was not significantly different in all the samples examined. No eukaryotic DNA sequences, such as 18S rRNA genes, were obtained from the corals. The findings suggested that, even at the same or similar depths, the sedimentological characteristics of a habitat are important factors affecting microbial diversity and community structure in deep subseafloor sedimentary

  7. Comparative study of subseafloor microbial community structures in deeply buried coral fossils and sediment matrices from the challenger mound in the porcupine seabight.

    Science.gov (United States)

    Hoshino, Tatsuhiko; Morono, Yuki; Terada, Takeshi; Imachi, Hiroyuki; Ferdelman, Timothy G; Inagaki, Fumio

    2011-01-01

    Subseafloor sedimentary environments harbor remarkably diverse microbial communities. However, it remains unknown if the deeply buried fossils in these sediments play ecological roles in deep microbial habitats, or whether the microbial communities inhabiting such fossils differ from those in the surrounding sediment matrix. Here we compare the community structures of subseafloor microbes in cold-water coral carbonates (Madrepora oculata and Lophelia pertusa) and the clay matrix. Samples were obtained from the Challenger Mound in the Porcupine Seabight at Site U1317 Hole A during the Integrated Ocean Drilling Program Expedition 307. DNA was extracted from coral fossils and the surrounding sedimentary matrix at 4, 20, and 105 m below the seafloor. 16S rRNA genes of Bacteria and Archaea were amplified by PCR, and a total of 213,792 16S rRNA gene-tagged sequences were analyzed. At the phylum level, dominant microbial components in both habitats consisted of Proteobacteria, Firmicutes, Nitrospirae, Chloroflexi, and Miscellaneous Crenarchaeota Group (MCG) at all three of the depths examined. However, at the genus and/or species level (similarity threshold 97.0%), the community compositions were found to be very different, with 69-75 and 46-57% of bacterial and archaeal phylotypes not overlapping in coral fossils and the clay matrix, respectively. Species richness analysis revealed that bacterial communities were generally more diverse than archaea, and that the diversity scores of coral fossils were lower than those in sediment matrix. However, the evenness of microbial communities was not significantly different in all the samples examined. No eukaryotic DNA sequences, such as 18S rRNA genes, were obtained from the corals. The findings suggested that, even at the same or similar depths, the sedimentological characteristics of a habitat are important factors affecting microbial diversity and community structure in deep subseafloor sedimentary habitats.

  8. 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.

  9. 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

  10. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

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

  11. Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

    OpenAIRE

    Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan Georges Philippe; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Barry A Cragg; Parkes, Ronald John; Joy D Van Nostrand; He, Zhili; Zhou, Jizhong; Toffin, Laurent

    2014-01-01

    International audience; Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PC...

  12. The archaeal Ced system imports DNA

    Science.gov (United States)

    van Wolferen, Marleen; Wagner, Alexander; van der Does, Chris; Albers, Sonja-Verena

    2016-01-01

    The intercellular transfer of DNA is a phenomenon that occurs in all domains of life and is a major driving force of evolution. Upon UV-light treatment, cells of the crenarchaeal genus Sulfolobus express Ups pili, which initiate cell aggregate formation. Within these aggregates, chromosomal DNA, which is used for the repair of DNA double-strand breaks, is exchanged. Because so far no clear homologs of bacterial DNA transporters have been identified among the genomes of Archaea, the mechanisms of archaeal DNA transport have remained a puzzling and underinvestigated topic. Here we identify saci_0568 and saci_0748, two genes from Sulfolobus acidocaldarius that are highly induced upon UV treatment, encoding a transmembrane protein and a membrane-bound VirB4/HerA homolog, respectively. DNA transfer assays showed that both proteins are essential for DNA transfer between Sulfolobus cells and act downstream of the Ups pili system. Our results moreover revealed that the system is involved in the import of DNA rather than the export. We therefore propose that both Saci_0568 and Saci_0748 are part of a previously unidentified DNA importer. Given the fact that we found this transporter system to be widely spread among the Crenarchaeota, we propose to name it the Crenarchaeal system for exchange of DNA (Ced). In this study we have for the first time to our knowledge described an archaeal DNA transporter. PMID:26884154

  13. 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.

  14. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

    Science.gov (United States)

    Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

    2013-06-01

    The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

  15. 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.

  16. 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.

  17. 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.

  18. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    KAUST Repository

    Cao, Huiluo

    2015-07-21

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  19. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    Directory of Open Access Journals (Sweden)

    Huiluo eCao

    2015-07-01

    Full Text Available The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of ammonia oxidizing archaea in different habitats (water versus sediment potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  20. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    Science.gov (United States)

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

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

    Science.gov (United States)

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

    2006-04-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  3. 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

  4. 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...

  5. 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....

  6. Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil.

    Science.gov (United States)

    Cunha, Isabel S; Barreto, Cristine C; Costa, Ohana Y A; Bomfim, Marco A; Castro, Alinne P; Kruger, Ricardo H; Quirino, Betania F

    2011-06-01

    Most studies present in the literature about the rumen microbiome have focused on cattle and sheep. This is the first report of the characterization of the bacterial and archaeal communities present in the liquid and solid-associated fractions of the rumen from free ranging Moxotó breed goats using 16S rRNA gene libraries. PCR was used to amplify the 16S rRNA gene with bacterial and archaeal universal primers and sequences from each library constructed were obtained. Sequences of Bacteria from the phyla Bacteroidetes and Firmicutes were predominant. The overall dominant classes in the rumen were Clostridia and Bacteroidia, which are known to play a role in plant fiber degradation in other ruminants. Unclassified Bacteria accounted for 4.7% of the liquid fraction sequences and 16.4% of the solid fraction sequences. From the archaeal libraries only sequences from the phylum Euryarcheota were identified and were assigned to the class Methanobacteria of the genera Methanobrevibacter and Methanosphaera. A group of Archaea not previously known to be associated with the rumen was identified: uncultured methanogens belonging to the "uncultured marine bacteria" groups II and III. The local water contained high salt concentrations and this may explain the presence of these groups in the Moxotó goat rumen.

  7. Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage.

    Science.gov (United States)

    Langer, Susanne G; Ahmed, Sharif; Einfalt, Daniel; Bengelsdorf, Frank R; Kazda, Marian

    2015-09-01

    Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here, we describe the functional redundancy and structural changes of involved microbial communities in four lab-scale continuously stirred tank reactors (CSTRs, 39°C, 12 L volume) supplied with different mixtures of maize silage (MS) and sugar beet silage (SBS) over 80 days. Continuously stirred tank reactors were fed with mixtures of MS and SBS in volatile solid ratios of 1:0 (Continuous Fermenter (CF) 1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kgVS m(-3)  d(-1) ) and showed similar biogas production rates in all reactors. The compositions of bacterial and archaeal communities were analysed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. Especially pronounced were changes in the archaeal composition towards Methanosarcina with increasing proportion of SBS, while Methanosaeta declined simultaneously. Compositional shifts within the microbial communities did not influence the respective biogas production rates indicating that these communities adapted to environmental conditions induced by different feedstock mixtures. The diverse microbial communities optimized their metabolism in a way that ensured efficient biogas production.

  8. Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

    Science.gov (United States)

    Langer, Susanne G; Ahmed, Sharif; Einfalt, Daniel; Bengelsdorf, Frank R; Kazda, Marian

    2015-01-01

    Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here, we describe the functional redundancy and structural changes of involved microbial communities in four lab-scale continuously stirred tank reactors (CSTRs, 39°C, 12 L volume) supplied with different mixtures of maize silage (MS) and sugar beet silage (SBS) over 80 days. Continuously stirred tank reactors were fed with mixtures of MS and SBS in volatile solid ratios of 1:0 (Continuous Fermenter (CF) 1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kgVS m−3 d−1) and showed similar biogas production rates in all reactors. The compositions of bacterial and archaeal communities were analysed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. Especially pronounced were changes in the archaeal composition towards Methanosarcina with increasing proportion of SBS, while Methanosaeta declined simultaneously. Compositional shifts within the microbial communities did not influence the respective biogas production rates indicating that these communities adapted to environmental conditions induced by different feedstock mixtures. The diverse microbial communities optimized their metabolism in a way that ensured efficient biogas production. PMID:26200922

  9. 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.

  10. 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 $S_{gc}$...

  11. A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model.

    Science.gov (United States)

    Min, Wonki; Angileri, Francesca; Luo, Haibin; Lauria, Antonino; Shanmugasundaram, Maruda; Almerico, Anna Maria; Cappello, Francesco; de Macario, Everly Conway; Lednev, Igor K; Macario, Alberto J L; Robb, Frank T

    2014-10-27

    Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, causes neuropathy. Knowledge is scarce on the impact of this and other mutations upon the chaperone's structure and functions. To make progress, experimental models must be developed. We used an archaeal mutant homolog and demonstrated that the His147Arg mutant has impaired oligomeric assembly, ATPase activity, and defective protein homeostasis functions. These results establish for the first time that a human chaperonin gene defect can be reproduced and studied at the molecular level with an archaeal homolog. The major advantage of the system, consisting of rings with eight identical subunits, is that it amplifies the effects of a mutation as compared with the human counterpart, in which just one subunit per ring is defective. Therefore, the slight deficit of a non-lethal mutation can be detected and characterized.

  12. Archaeal Diversity in Biofilm Technologies Applied to Treat Urban and Industrial Wastewater: Recent Advances and Future Prospects

    Directory of Open Access Journals (Sweden)

    Jesús González-López

    2013-09-01

    Full Text Available Biological wastewater treatment (WWT frequently relies on biofilms for the removal of anthropogenic contaminants. The use of inert carrier materials to support biofilm development is often required, although under certain operating conditions microorganisms yield structures called granules, dense aggregates of self-immobilized cells with the characteristics of biofilms maintained in suspension. Molecular techniques have been successfully applied in recent years to identify the prokaryotic communities inhabiting biofilms in WWT plants. Although methanogenic Archaea are widely acknowledged as key players for the degradation of organic matter in anaerobic bioreactors, other biotechnological functions fulfilled by Archaea are less explored, and research on their significance and potential for WWT is largely needed. In addition, the occurrence of biofilms in WWT plants can sometimes be a source of operational problems. This is the case for membrane bioreactors (MBR, an advanced technology that combines conventional biological treatment with membrane filtration, which is strongly limited by biofouling, defined as the undesirable accumulation of microbial biofilms and other materials on membrane surfaces. The prevalence and spatial distribution of archaeal communities in biofilm-based WWT as well as their role in biofouling are reviewed here, in order to illustrate the significance of this prokaryotic cellular lineage in engineered environments devoted to WWT.

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

    Directory of Open Access Journals (Sweden)

    Katherine E Fish

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

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

    Science.gov (United States)

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

    2015-01-01

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

  15. A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure.

    Science.gov (United States)

    Sun, Bo; Wang, Feng; Jiang, Yuji; Li, Yun; Dong, Zhixin; Li, Zhongpei; Zhang, Xue-Xian

    2014-04-01

    The spatial patterns of microbial communities are largely determined by the combined effects of historical contingencies and contemporary environmental disturbances, but their relative importance remains poorly understood. Empirical biogeographic data currently available are mostly based on the traditional method of observational survey, which typically involves comparing indigenous microbial communities across spatial scales. Here, we report a long-term soil transplantation experiment, whereby the same two soils (red Acrisol and purple Cambisol from Yingtan) were placed into two geographic locations of ∼1000 km apart (i.e., Yingtan in the mid-subtropical region and Fengqiu in warm-temperate region; both located in China). Twenty years after the transplantation, the resulting soil microbial communities were subject to high-throughput 454 pyrosequencing analysis of 16S and 18S rRNA genes. Additionally, bacteria and archaea involved in nitrogen cycling were estimated using clone library analysis of four genes: archaeal amoA, bacterial amoA,nirK, and nifH. Data of subsequent phylogenetic analysis show that bacteria, fungi, and other microbial eukaryotes, as well as the nitrogen cycling genes, are grouped primarily by the factor of geographic location rather than soil type. Moreover, a shift of microbial communities toward those in local soil (i.e., Chao soil in Fengqiu) has been observed. The results thus suggest that the historical effects persistent in the soil microbial communities can be largely erased by contemporary disturbance within a short period of 20 years, implicating weak effects of historical contingencies on the structure and composition of microbial communities in the soil.

  16. 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.

  17. A Method for Identification of Selenoprotein Genes in Archaeal Genomes

    Institute of Scientific and Technical Information of China (English)

    Mingfeng Li; Yanzhao Huang; Yi Xiao

    2009-01-01

    The genetic codon UGA has a dual function: serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should be a real selenoprotein gene. The result shows that Asec-Prediction is effective for the prediction of archaeal selenoprotein genes.

  18. 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

  19. 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....

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

    OpenAIRE

    Hardoim, Cristiane C. P.; Rodrigo Costa

    2014-01-01

    Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is ...

  6. 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...

  7. Carcass mass has little influence on the structure of gravesoil microbial communities.

    Science.gov (United States)

    Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob

    2016-01-01

    Little is known about how variables, such as carcass mass, affect the succession pattern of microbes in soils during decomposition. To investigate the effects of carcass mass on the soil microbial community, soils associated with swine (Sus scrofa domesticus) carcasses of four different masses were sampled until the 15th day of decomposition during the month of June in a pasture near Lincoln, Nebraska. Soils underneath swine of 1, 20, 40, and 50 kg masses were investigated in triplicate, as well as control sites not associated with a carcass. Soil microbial communities were characterized by sequencing the archaeal, bacterial (16S), and eukaryotic (18S) rRNA genes in soil samples. We conclude that time of decomposition was a significant influence on the microbial community, but carcass mass was not. The gravesoil associated with 1 kg mass carcasses differs most compared to the gravesoil associated with other carcass masses. We also identify the 15 most abundant bacterial and eukaryotic taxa, and discuss changes in their abundance as carcass decomposition progressed. Finally, we show significant decreases in alpha diversity for carcasses of differing mass in pre-carcass rupture (days 0, 1, 2, 4, 5, and 6 postmortem) versus post-carcass rupture (days 9 and 15 postmortem) microbial communities.

  8. Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines.

    Science.gov (United States)

    Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R; Wang, Shang; Hou, Weiguo; Li, Gaoyuan; Wu, Geng; Solis, Ramonito; Arcilla, Carlo A; Abrajano, Teofilo; Dong, Hailiang

    2013-09-01

    The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.

  9. The Primary Results of Analyses on The Archaeal and Bacterial Diversity of Active Cave Environments Settled in Limestones at Southern Turkey

    Science.gov (United States)

    Tok, Ezgi; Kurt, Halil; Tunga Akarsubasi, A.

    2016-04-01

    The microbial diversity of cave sediments which are obtained from three different caves named Insuyu, Balatini and Altınbeşik located at Southern Turkey has been investigated using molecular methods for biomineralization . The total number of 22 samples were taken in duplicates from the critical zones of the caves at where the water activity is observed all year round. Microbial communities were monitored by 16S rRNA gene based PCR-DGGE (Polymerase Chain Reaction - Denaturating Gradient Gel Electrophoresis) methodology. DNA were extracted from the samples by The PowerSoil® DNA Isolation Kit (MO BIO Laboratories inc., CA) with the modifications on the producer's protocol. The synthetic DNA molecule poly-dIdC was used to increase the yield of PCR amplification via blocking the reaction between CaCO3 and DNA molecules. Thereafter samples were amplified by using both Archaeal and Bacterial universal primers (ref). Subsequently, archaeal and bacterial diversities in cave sediments, were investigated to be able to compare with respect to their similarities by using DGGE. DGGE patterns were analysed with BioNumerics software 5.1. Similarity matrix and dendograms of the DGGE profiles were generated based on the Dice correlation coefficient (band-based) and unweighted pair-group method with arithmetic mean (UPGMA). The structural diversity of the microbial community was examined by the Shannon index of general diversity (H). Similtaneously, geochemical analyses of the sediment samples were performed within the scope of this study. Total organic carbon (TOC), x-ray diffraction spectroscopy (XRD) and x-ray fluorescence spectroscopy (XRF) analysis of sediments were also implemented. The extensive results will be obtained at the next stages of the study currently carried on.

  10. [Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing].

    Science.gov (United States)

    Karaevskaia, E S; Demchenko, L S; Demidov, N É; Rivkina, E M; Bulat, S A; Gilichinskiĭ, D A

    2014-01-01

    Archaeal communities of permafrost deposits of King George Island and Bunger Hills Oasis (Antarctica) differing in the content of biogenic methane were analyzed using clone libraries of two 16S rRNA gene regions. Phylotypes belonging to methanogenic archaea were identified in all horizons.

  11. Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep.

    Directory of Open Access Journals (Sweden)

    Karen G Lloyd

    Full Text Available BACKGROUND: Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118 in the Gulf of Mexico. High process rates within the mat ( approximately 400 cm and approximately 10 cm from the mat's edge contrasted with sharply diminished activity at approximately 50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase and mcrA (methyl coenzyme M reductase mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae and methane-cycling archaea (ANME-1 and ANME-2 were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12-20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. CONCLUSIONS/SIGNIFICANCE: The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and

  12. Rumen microbial communities influence metabolic phenotypes in lambs

    DEFF Research Database (Denmark)

    Morgavi, Diego P.; Rahahao-Paris, Estelle; Popova, Milka

    2015-01-01

    and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted...... the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult...... sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure...

  13. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

    Energy Technology Data Exchange (ETDEWEB)

    Flores, Gilberto E [Portland State University; Campbell, James H [ORNL; Kirshtein, Julie D [United States Geological Survey, Reston, VA; Meneghin, Jennifer [Portland State University; Podar, Mircea [ORNL; Steinberg, Joshua [Oregon Episcopal School, Portland, OR; Seewald, Jeffrey S [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Tivey, Margaret Kingston [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Voytek, Mary A [United States Geological Survey & National Aeronautics and Space Administration; Reysenbach, Anna-Louise [Portland State University; Yang, Zamin Koo [ORNL

    2011-01-01

    To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37 17'N, 32 16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36 13'N, 33 54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

  14. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge.

    Science.gov (United States)

    Flores, Gilberto E; Campbell, James H; Kirshtein, Julie D; Meneghin, Jennifer; Podar, Mircea; Steinberg, Joshua I; Seewald, Jeffrey S; Tivey, Margaret Kingston; Voytek, Mary A; Yang, Zamin K; Reysenbach, Anna-Louise

    2011-08-01

    To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

  15. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

    Science.gov (United States)

    Flores, Gilberto E.; Campbell, James H.; Kirshtein, Julie D.; Meneghin, Jennifer; Podar, Mircea; Steinberg, Joshua I.; Seewald, Jeffrey S.; Tivey, Margaret Kingston; Voytek, Mary A.; Yang, Zamin K.; Reysenbach, Anna-Louise

    2011-01-01

    To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

  16. Changes of soil prokaryotic communities after clear-cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes.

    Science.gov (United States)

    Zhang, Xiao; Liu, Shirong; Li, Xiangzhen; Wang, Jingxin; Ding, Qiong; Wang, Hui; Tian, Chao; Yao, Minjie; An, Jiaxing; Huang, Yongtao

    2016-03-01

    To understand the temporal responses of soil prokaryotic communities to clear-cutting disturbance, we examined the changes in soil bacterial and archaeal community composition, structure and diversity along a chronosequence of forest successional restoration using high-throughput 16S rRNA gene sequencing. Our results demonstrated that clear-cutting significantly altered soil bacterial community structure, while no significant shifts of soil archaeal communities were observed. The hypothesis that soil bacterial communities would become similar to those of surrounding intact primary forest with natural regeneration was supported by the shifts in the bacterial community composition and structure. Bacterial community diversity patterns induced by clear-cutting were consistent with the intermediate disturbance hypothesis. Dynamics of bacterial communities was mostly driven by soil properties, which collectively explained more than 70% of the variation in bacterial community composition. Community assembly data revealed that clear-cutting promoted the importance of the deterministic processes in shaping bacterial communities, coinciding with the resultant low resource environments. But assembly processes in the secondary forest returned a similar level compared to the intact primary forest. These findings suggest that bacterial community dynamics may be predictable during the natural recovery process.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. Control of temperature on microbial community structure in hot springs of the Tibetan Plateau.

    Directory of Open Access Journals (Sweden)

    Shang Wang

    Full Text Available The Tibetan Plateau in Northwest China hosts a number of hot springs that represent a biodiversity hotspot for thermophiles, yet their diversity and relationship to environmental conditions are poorly explored in these habitats. In this study we investigated microbial diversity and community composition in 13 Tibetan hot springs with a wide range of temperatures (22.1-75°C and other geochemical conditions by using the 16S rRNA gene pyrosequencing approach. Bacteria (10(8-10(11 copy/g; 42 bacterial phyla in Tibetan hot springs were more abundant and far more diverse than Archaea (10(7-10(10 copy/g; 5 archaeal phyla. The dominant bacterial phyla systematically varied with temperature. Moderate temperatures (75-66°C favored Aquificae, GAL35, and novel Bacteria, whereas low temperatures (60-22.1°C selected for Deinococcus-Thermus, Cyanobacteria, and Chloroflexi. The relative abundance of Aquificae was correlated positively with temperature, but the abundances of Deinococcus-Thermus, Cyanobacteria, and Chloroflexi were negatively correlated with temperature. Cyanobacteria and Chloroflexi were abundant in Tibetan hot springs and their abundances were positively correlated at low temperatures (55-43°C but negatively correlated at moderate temperatures (75-55°C. These correlation patterns suggest a complex physiological relationship between these two phyla. Most archaeal sequences were related to Crenarchaeota with only a few related to Euryarchaeota and Thaumarchaeota. Despite the fact that microbial composition in Tibetan hot springs was strongly shaped by temperature, microbial diversity (richness, evenness and Shannon diversity was not significantly correlated with temperature change. The results of this study expand our current understanding of microbial ecology in Tibetan hot springs and provide a basis for a global comparison.

  3. Control of temperature on microbial community structure in hot springs of the Tibetan Plateau.

    Science.gov (United States)

    Wang, Shang; Hou, Weiguo; Dong, Hailiang; Jiang, Hongchen; Huang, Liuqin; Wu, Geng; Zhang, Chuanlun; Song, Zhaoqi; Zhang, Yong; Ren, Huilei; Zhang, Jing; Zhang, Li

    2013-01-01

    The Tibetan Plateau in Northwest China hosts a number of hot springs that represent a biodiversity hotspot for thermophiles, yet their diversity and relationship to environmental conditions are poorly explored in these habitats. In this study we investigated microbial diversity and community composition in 13 Tibetan hot springs with a wide range of temperatures (22.1-75°C) and other geochemical conditions by using the 16S rRNA gene pyrosequencing approach. Bacteria (10(8)-10(11) copy/g; 42 bacterial phyla) in Tibetan hot springs were more abundant and far more diverse than Archaea (10(7)-10(10) copy/g; 5 archaeal phyla). The dominant bacterial phyla systematically varied with temperature. Moderate temperatures (75-66°C) favored Aquificae, GAL35, and novel Bacteria, whereas low temperatures (60-22.1°C) selected for Deinococcus-Thermus, Cyanobacteria, and Chloroflexi. The relative abundance of Aquificae was correlated positively with temperature, but the abundances of Deinococcus-Thermus, Cyanobacteria, and Chloroflexi were negatively correlated with temperature. Cyanobacteria and Chloroflexi were abundant in Tibetan hot springs and their abundances were positively correlated at low temperatures (55-43°C) but negatively correlated at moderate temperatures (75-55°C). These correlation patterns suggest a complex physiological relationship between these two phyla. Most archaeal sequences were related to Crenarchaeota with only a few related to Euryarchaeota and Thaumarchaeota. Despite the fact that microbial composition in Tibetan hot springs was strongly shaped by temperature, microbial diversity (richness, evenness and Shannon diversity) was not significantly correlated with temperature change. The results of this study expand our current understanding of microbial ecology in Tibetan hot springs and provide a basis for a global comparison.

  4. Archaeal communities of Arctic methane-containing permafrost.

    Science.gov (United States)

    Shcherbakova, Victoria; Yoshimura, Yoshitaka; Ryzhmanova, Yana; Taguchi, Yukihiro; Segawa, Takahiro; Oshurkova, Victoria; Rivkina, Elizaveta

    2016-10-01

    In the present study, we used culture-independent methods to investigate the diversity of methanogenic archaea and their distribution in five permafrost samples collected from a borehole in the Kolyma River Lowland (north-east of Russia). Total DNA was extracted from methane-containing permafrost samples of different age and amplified by PCR. The resulting DNA fragments were cloned. Phylogenetic analysis of the sequences showed the presence of archaea in all studied samples; 60%-95% of sequences belonged to the Euryarchaeota. Methanogenic archaea were novel representatives of Methanosarcinales, Methanomicrobiales, Methanobacteriales and Methanocellales orders. Bathyarchaeota (Miscellaneous Crenarchaeota Group) representatives were found among nonmethanogenic archaea in all the samples studied. The Thaumarchaeota representatives were not found in the upper sample, whereas Woesearchaeota (formerly DHVEG-6) were found in the three deepest samples. Unexpectedly, the greatest diversity of archaea was observed at a depth of 22.3 m, probably due to the availability of the labile organic carbon and/or due to the migration of the microbial cells during the freezing front towards the bottom.

  5. 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...

  6. Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection.

    Science.gov (United States)

    Sinapah, Sylvie; Wu, Shiying; Chen, Yu; Pettersson, B M Fredrik; Gopalan, Venkat; Kirsebom, Leif A

    2011-02-01

    RNase P is a catalytic ribonucleoprotein primarily involved in tRNA biogenesis. Archaeal RNase P comprises a catalytic RNase P RNA (RPR) and at least four protein cofactors (RPPs), which function as two binary complexes (POP5•RPP30 and RPP21• RPP29). Exploiting the ability to assemble a functional Pyrococcus furiosus (Pfu) RNase P in vitro, we examined the role of RPPs in influencing substrate recognition by the RPR. We first demonstrate that Pfu RPR, like its bacterial and eukaryal counterparts, cleaves model hairpin loop substrates albeit at rates 90- to 200-fold lower when compared with cleavage by bacterial RPR, highlighting the functionally comparable catalytic cores in bacterial and archaeal RPRs. By investigating cleavage-site selection exhibited by Pfu RPR (±RPPs) with various model substrates missing consensus-recognition elements, we determined substrate features whose recognition is facilitated by either POP5•RPP30 or RPP21•RPP29 (directly or indirectly via the RPR). Our results also revealed that Pfu RPR + RPP21•RPP29 displays substrate-recognition properties coinciding with those of the bacterial RPR-alone reaction rather than the Pfu RPR, and that this behaviour is attributable to structural differences in the substrate-specificity domains of bacterial and archaeal RPRs. Moreover, our data reveal a hierarchy in recognition elements that dictates cleavage-site selection by archaeal RNase P.

  7. 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.

  8. 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.

  9. Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano.

    Science.gov (United States)

    Lazar, Cassandre Sara; L'haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

    2011-05-01

    Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

  10. Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, S.; Akiyama, M.; Naganuma, T.; Fujioka, M.; Nako, M.; Ishijima, Y. [Northern Advancement Center for Science and Technology, Hokkaido (Japan)

    2007-12-15

    We investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843-907 m below ground level in northern Japan; additionally, we studied the {delta}{sup 13}C and {delta} {sup 2}H ({delta}D) of coal-bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N{sub 2} gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, AMOVA analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N{sub 2} injection into the coal seam might affect the cycling of matter by methanogens in situ.

  11. 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.

  12. 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.

  13. Competition for space and the structure of ecological communities

    CERN Document Server

    Yodzis, Peter

    1978-01-01

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

  14. Functional analysis of archaeal MBF1 by complementation studies in yeast

    Directory of Open Access Journals (Sweden)

    Siebers Bettina

    2011-03-01

    Full Text Available Abstract Background Multiprotein-bridging factor 1 (MBF1 is a transcriptional co-activator that bridges a sequence-specific activator (basic-leucine zipper (bZIP like proteins (e.g. Gcn4 in yeast or steroid/nuclear-hormone receptor family (e.g. FTZ-F1 in insect and the TATA-box binding protein (TBP in Eukaryotes. MBF1 is absent in Bacteria, but is well- conserved in Eukaryotes and Archaea and harbors a C-terminal Cro-like Helix Turn Helix (HTH domain, which is the only highly conserved, classical HTH domain that is vertically inherited in all Eukaryotes and Archaea. The main structural difference between archaeal MBF1 (aMBF1 and eukaryotic MBF1 is the presence of a Zn ribbon motif in aMBF1. In addition MBF1 interacting activators are absent in the archaeal domain. To study the function and therefore the evolutionary conservation of MBF1 and its single domains complementation studies in yeast (mbf1Δ as well as domain swap experiments between aMBF1 and yMbf1 were performed. Results In contrast to previous reports for eukaryotic MBF1 (i.e. Arabidopsis thaliana, insect and human the two archaeal MBF1 orthologs, TMBF1 from the hyperthermophile Thermoproteus tenax and MMBF1 from the mesophile Methanosarcina mazei were not functional for complementation of an Saccharomyces cerevisiae mutant lacking Mbf1 (mbf1Δ. Of twelve chimeric proteins representing different combinations of the N-terminal, core domain, and the C-terminal extension from yeast and aMBF1, only the chimeric MBF1 comprising the yeast N-terminal and core domain fused to the archaeal C-terminal part was able to restore full wild-type activity of MBF1. However, as reported previously for Bombyx mori, the C-terminal part of yeast Mbf1 was shown to be not essential for function. In addition phylogenetic analyses revealed a common distribution of MBF1 in all Archaea with available genome sequence, except of two of the three Thaumarchaeota; Cenarchaeum symbiosum A and Nitrosopumilus maritimus

  15. 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.

  16. Viral Predation and Host Immunity Structure Microbial Communities in a Terrestrial Deep Subsurface, Hydraulically Fractured Shale System

    Science.gov (United States)

    Daly, R. A.; Mouser, P. J.; Trexler, R.; Wrighton, K. C.

    2014-12-01

    Despite a growing appreciation for the ecological role of viruses in marine and gut systems, little is known about their role in the terrestrial deep (> 2000 m) subsurface. We used assembly-based metagenomics to examine the viral component in fluids from hydraulically fractured Marcellus shale gas wells. Here we reconstructed microbial and viral genomes from samples collected 7, 82, and 328 days post fracturing. Viruses accounted for 4.14%, 0.92% and 0.59% of the sample reads that mapped to the assembly. We identified 6 complete, circularized viral genomes and an additional 92 viral contigs > 5 kb with a maximum contig size of 73.6 kb. A BLAST comparison to NCBI viral genomes revealed that 85% of viral contigs had significant hits to the viral order Caudovirales, with 43% of sequences belonging to the family Siphoviridae, 38% to Myoviridae, and 12% to Podoviridae. Enrichment of Caudovirales viruses was supported by a large number of predicted proteins characteristic of tailed viruses including terminases (TerL), tape measure, tail formation, and baseplate related proteins. The viral contigs included evidence of lytic and temperate lifestyles, with the 7 day sample having the greatest number of detected lytic viruses. Notably in this sample, the most abundant virus was lytic and its inferred host, a member of the Vibrionaceae, was not detected at later time points. Analyses of CRISPR sequences (a viral and foreign DNA immune system in bacteria and archaea), linked 18 viral contigs to hosts. CRISPR linkages increased through time and all bacterial and archaeal genomes recovered in the final time point had genes for CRISPR-mediated viral defense. The majority of CRISPR sequences linked phage genomes to several Halanaerobium strains, which are the dominant and persisting members of the community inferred to be responsible for carbon and sulfur cycling in these shales. Network analysis revealed that several viruses were present in the 82 and 328 day samples; this viral

  17. 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.

  18. 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

  19. 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.

  20. Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the arctic mid-ocean spreading ridge

    Directory of Open Access Journals (Sweden)

    Steffen Leth eJørgensen

    2013-10-01

    Full Text Available In marine sediments archaea often constitute a considerable part of the microbial community, of which the Deep Sea Archaeal Group (DSAG is one of the most predominant. Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is unknown. Here we show that the relative abundance of DSAG marker genes can be correlated with geochemical parameters, allowing prediction of both the potential electron donors and acceptors of these organisms. We estimated the abundance of 16S rRNA genes from Archaea, Bacteria and DSAG in 52 sediment horizons from two cores collected at the slow-spreading Arctic Mid-Ocean Ridge, using qPCR. The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ~ 50% of the total microbial community. The quantitative data were correlated to 30 different geophysical and geochemical parameters obtained from the same sediment horizons. We observed a significant correlation between the relative abundance of DSAG 16S rRNA genes and the content of organic carbon (p < 0.0001. Further, significant co-variation with iron oxide, and dissolved iron and manganese (all p < 0.0000, indicated a direct or indirect link to iron and manganese cycling. Neither of these parameters correlated with the relative abundance of archaeal or bacterial 16S rRNA genes, nor did any other major electron donor or acceptor measured. Phylogenetic analysis of DSAG 16S rRNA gene sequences reveals three monophyletic lineages with no apparent habitat-specific distribution. In this study we support the hypothesis that members of the DSAG are tightly linked to the content of organic carbon and directly or indirectly involved in the cycling of iron and/or manganese compounds. Further, we provide a molecular tool to assess their abundance in environmental samples and enrichment cultures.

  1. 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.

  2. 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.

  3. [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.

  4. 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.

  5. 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).

  6. 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.

  7. Microbial community composition controls the effects of climate change on methane emission from rice paddies.

    Science.gov (United States)

    Liu, Guang Cheng; Tokida, Takesi; Matsunami, Toshinori; Nakamura, Hirofumi; Okada, Masumi; Sameshima, Ryoji; Hasegawa, Toshihiro; Sugiyama, Shu-Ichi

    2012-12-01

    Rice paddies are one of the most important sources of CH4 emission from the terrestrial ecosystem. A Free-air CO2 Enrichment (FACE) experiment, which included a soil warming treatment, was conducted in a rice paddy at Shizukuishi, Japan. In this study, the changes in CH4 emission from a rice paddy, caused by global climate change, were explored in relation to the structural changes that have occurred in the methanogenic archaeal communities found in the soil and roots. The composition of the archaeal community was examined by terminal restriction fragment length polymorphism (T-RFLP) using the 16S rRNA gene, while its abundance was measured by real-time PCR using the methyl coenzyme M reductase (mcrA) gene. The archaeal community in the roots showed considerable change, characterized by the dominance of hydrogenotrophic methanogens and a corresponding decrease in acetoclastic methanogens. Seasonal changes in CH4 flux were closely related to the changes in methanogen abundance in the roots. Elevated CO2 caused an increase in root mass, which increased the abundance of methanogens leading to a rise in CH4 emissions. However, soil warming stimulated CH4 emissions by increasing CH4 production per individual methanogen. These results demonstrated that climate warming stimulates CH4 emission in a rice paddy by altering the abundance and activity of methanogenic archaea in the roots.

  8. Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins

    Directory of Open Access Journals (Sweden)

    David S. Shin

    2014-01-01

    Full Text Available As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.

  9. 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…

  10. 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.

  11. 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.

  12. Models of Metabolic Community Structure in Martian Habitable Environments: Constraints from a Terrestrial Analog Acid-Sulfate Fumarole Environment, Cerro Negro Volcano, Nicaragua

    Science.gov (United States)

    Rogers, K. L.; McCollom, T. M.; Hynek, B. M.

    2014-12-01

    Microbial habitability in extreme environments on Earth is described by microscale geochemical conditions that constrain metabolic niches in concert with long-term habitat stability that is governed by dynamic geologic processes. Using terrestrial analogs to identify habitable martian environments requires correlating microscale geochemical constraints with reconstructions of past martian environments that are based on global-scale observations. While past martian environments can be characterized by primary parameters (e.g. pH, redox, mineralogy, thermal history), microbial habitability on Earth is a complex function of both primary and derived parameters (e.g. metabolic reaction energetics, chemical & thermal gradients, flow dynamics). In recent years we have been investigating acid-sulfate fumaroles at the Mars analog site, Cerro Negro Volcano, Nicaragua, where habitability is constrained by steep thermal gradients, spatially- and temporally-variable vent dynamics, and limited water and nutrient availability. The most common niche identified thus far is found in fumaroles that host mixed photosynthetic and chemosynthetic endolithic microbial communities. One such endolith is dominated by acidic red algae (Cyanidiales), aerobic bacterial heterotrophs (Ktedonobacteria), and archaeal thermoacidophiles (Hyperthermus, Caldisphaera, and Thermofilum). An analysis of the metabolic structure suggests that primary production by the red algae supports the growth of heterotrophic thermoacidophiles. Diversification among the chemoheterotrophs with respect to temperature and oxygen tolerance suggests community adaptation to environmental gradients or variable venting dynamics. Furthermore, individual cells within the endolith are silica-encrusted, providing the possibility for biosignature formation and preservation. Putative hydrothermal environments on early Mars with similar conditions could have supported endolithic communities with comparable metabolic strategies. Even

  13. 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.

  14. [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

  15. Massive activation of archaeal defense genes during viral infection

    NARCIS (Netherlands)

    Quax, T.E.F.; Voet, M.; Sismeiro, O.; Dillies, M.A.; Jagla, B.; Coppée, J.Y.; Sezonov, G.; Forterre, P.; Oost, van der J.; Lavigne, R.; Prangishvili, D.

    2013-01-01

    Archaeal viruses display unusually high genetic and morphological diversity. Studies of these viruses proved to be instrumental for the expansion of knowledge on viral diversity and evolution. The Sulfolobus islandicus rod-shaped virus 2 (SIRV2) is a model to study virus-host interactions in Archaea

  16. 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...

  17. Dissolved Organic Nitrogen Composition and Reactivity as a Function of Surface Vegetation and Microbial Community Structure in Northern Minnesota Peatlands

    Science.gov (United States)

    Cooper, W. T.; Tfaily, M.; Podgorski, D.; Chanton, J.; Lin, X.; Kostka, J. E.

    2012-12-01

    Peatlands sequester one-third of all soil carbon and currently act as major sinks of atmospheric carbon dioxide. The ability to predict or simulate the fate of stored carbon in response to climatic disruption remains hampered by our limited understanding of the controls of carbon and nitrogen turnover and the composition and functioning of peatland microbial communities. Recent studies using some advanced analytical chemistry and microbial sequencing techniques, in particular ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) (Chanton et al., 2009; D'Andrilli J, et al.,2010) and bacterial/archaeal 16S rRNA sequencing (Lin X., et al., 2012) suggest that differences in enhanced carbon storage in northern peatlands that have been attributed to an inhibition of microbial metabolism can be identified and understood using this combined molecular-genetic approach. However, these studies have focused exclusively on dissolved organic carbon (DOC). In this presentation we report on similar molecular- and genetic-based studies that link microbial community structure and activity to the composition and reactivity of dissolved organic nitrogen (DON) in bog and fen sites dominated by contrasting plant species. These sites were located in the Glacial Lake Agassiz Peatland (GLAP) and Spruce and Peatland Response under Climatic and Environmental Change (SPRUCE) project area, both located in Northern Minnesota. Our study of DON reactivity was made possible by the recognition that positive- mode Atmospheric Pressure Photoionization (APPI) coupled to FT-ICR MS was able to selectively visualize the low-abundance organic nitrogen that is usually undetectable in the large background of dissolved organic carbon. This work was supported by grants from the National Science Foundation (NSF-EAR-0628349, NSF-DMR-06-54118) and Department of Energy (DE-SC0007144). Chanton JP, et al. (2008). Global Biogeochem Cy 22: GB4022, doi:4010.1029/2008GB003274. D

  18. 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.

  19. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

    Energy Technology Data Exchange (ETDEWEB)

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Li, Yu-You, E-mail: yyli@epl1.civil.tohoku.ac.jp [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi’an University of Architecture and Technology, Xi’an (China)

    2015-09-15

    Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S{sub in} in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.

  20. Diversity in prokaryotic glycosylation: an archaeal-derived N-linked glycan contains legionaminic acid.

    Science.gov (United States)

    Kandiba, Lina; Aitio, Olli; Helin, Jari; Guan, Ziqiang; Permi, Perttu; Bamford, Dennis H; Eichler, Jerry; Roine, Elina

    2012-05-01

    VP4, the major structural protein of the haloarchaeal pleomorphic virus, HRPV-1, is glycosylated. To define the glycan structure attached to this protein, oligosaccharides released by β-elimination were analysed by mass spectrometry and nuclear magnetic resonance spectroscopy. Such analyses showed that the major VP4-derived glycan is a pentasaccharide comprising glucose, glucuronic acid, mannose, sulphated glucuronic acid and a terminal 5-N-formyl-legionaminic acid residue. This is the first observation of legionaminic acid, a sialic acid-like sugar, in an archaeal-derived glycan structure. The importance of this residue for viral infection was demonstrated upon incubation with N-acetylneuraminic acid, a similar monosaccharide. Such treatment reduced progeny virus production by half 4 h post infection. LC-ESI/MS analysis confirmed the presence of pentasaccharide precursors on two different VP4-derived peptides bearing the N-glycosylation signal, NTT. The same sites modified by the native host, Halorubrum sp. strain PV6, were also recognized by the Haloferax volcanii N-glycosylation apparatus, as determined by LC-ESI/MS of heterologously expressed VP4. Here, however, the N-linked pentasaccharide was the same as shown to decorate the S-layer glycoprotein in this species. Hence, N-glycosylation of the haloarchaeal viral protein, VP4, is host-specific. These results thus present additional examples of archaeal N-glycosylation diversity and show the ability of Archaea to modify heterologously expressed proteins.

  1. 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.

  2. Microbial community structure and dynamics in two-stage vs single-stage thermophilic anaerobic digestion of mixed swine slurry and market bio-waste.

    Science.gov (United States)

    Merlino, Giuseppe; Rizzi, Aurora; Schievano, Andrea; Tenca, Alberto; Scaglia, Barbara; Oberti, Roberto; Adani, Fabrizio; Daffonchio, Daniele

    2013-04-15

    The microbial community of a thermophilic two-stage process was monitored during two-months operation and compared to a conventional single-stage process. Qualitative and quantitative microbial dynamics were analysed by Denaturing Gradient Gel Electrophoresis (DGGE) and real-time PCR techniques, respectively. The bacterial community was dominated by heat-shock resistant, spore-forming clostridia in the two-stage process, whereas a more diverse and dynamic community (Firmicutes, Bacteroidetes, Synergistes) was observed in the single-stage process. A significant evolution of bacterial community occurred over time in the acidogenic phase of the two-phase process with the selection of few dominant species associated to stable hydrogen production. The archaeal community, dominated by the acetoclastic Methanosarcinales in both methanogen reactors, showed a significant diversity change in the single-stage process after a period of adaptation to the feeding conditions, compared to a constant stability in the methanogenic reactor of the two-stage process. The more diverse and dynamic bacterial and archaeal community of single-stage process compared to the two-stage process accounted for the best degradation activity, and consequently the best performance, in this reactor. The microbiological perspective proved a useful tool for a better understanding and comparison of anaerobic digestion processes.

  3. 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.

  4. 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.

  5. 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...

  6. 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...

  7. 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

  8. 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.

  9. 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.

  10. Co-expression and co-purification of archaeal and eukaryal box C/D RNPs.

    Directory of Open Access Journals (Sweden)

    Yu Peng

    Full Text Available Box C/D ribonucleoprotein particles (RNPs are 2'-O-methylation enzymes required for maturation of ribosomal and small nuclear RNA. Previous biochemical and structural studies of the box C/D RNPs were limited by the unavailability of purified intact RNPs. We developed a bacterial co-expression strategy based on the combined use of a multi-gene expression system and a tRNA-scaffold construct that allowed the expression and purification of homogeneous archaeal and human box C/D RNPs. While the co-expressed and co-purified archaeal box C/D RNP was found to be fully active in a 2'-O-methylation assay, the intact human U14 box C/D RNP showed no detectable catalytic activity, consistent with the earlier findings that assembly of eukaryotic box C/D RNPs is nonspontaneous and requires additional protein factors. Our systems provide a means for further biochemical and structural characterization of box C/D RNPs and their assembly factors.

  11. Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea.

    Science.gov (United States)

    Giménez, María I; Cerletti, Micaela; De Castro, Rosana E

    2015-01-01

    The function of membrane proteases range from general house-keeping to regulation of cellular processes. Although the biological role of these enzymes in archaea is poorly understood, some of them are implicated in the biogenesis of the archaeal cell envelope and surface structures. The membrane-bound ATP-dependent Lon protease is essential for cell viability and affects membrane carotenoid content in Haloferax volcanii. At least two different proteases are needed in this archaeon to accomplish the posttranslational modifications of the S-layer glycoprotein. The rhomboid protease RhoII is involved in the N-glycosylation of the S-layer protein with a sulfoquinovose-containing oligosaccharide while archaeosortase ArtA mediates the proteolytic processing coupled-lipid modification of this glycoprotein facilitating its attachment to the archaeal cell surface. Interestingly, two different signal peptidase I homologs exist in H. volcanii, Sec11a and Sec11b, which likely play distinct physiological roles. Type IV prepilin peptidase PibD processes flagellin/pilin precursors, being essential for the biogenesis and function of the archaellum and other cell surface structures in H. volcanii.

  12. Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea

    Directory of Open Access Journals (Sweden)

    Maria Ines Giménez

    2015-02-01

    Full Text Available The function of membrane proteases range from general house-keeping to regulation of cellular processes. Although the biological role of these enzymes in archaea is poorly understood, some of them are implicated in the biogenesis of the archaeal cell envelope and surface structures. The membrane-bound ATP-dependent Lon protease is essential for cell viability and affects membrane carotenoid content in Haloferax volcanii. At least two different proteases are needed in this archaeon to accomplish the posttranslational modifications of the S-layer glycoprotein. The rhomboid protease RhoII is involved in the N-glycosylation of the S-layer protein with a sulfoquinovose-containing oligosaccharide while archaeosortase ArtA mediates the proteolytic processing coupled-lipid modification of this glycoprotein facilitating its attachment to the archaeal cell surface. Interestingly, two different signal peptidase I homologs exist in H. volcanii, Sec11a and Sec11b, which likely play distinct physiological roles. Type IV prepilin peptidase PibD processes flagellin/pilin precursors, being essential for the biogenesis and function of the archaellum and other cell surface structures in H. volcanii.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. Archaeal lipids in oral delivery of therapeutic peptides

    DEFF Research Database (Denmark)

    Jacobsen, Ann-Christin; Jensen, Sara M; Fricker, Gert;

    2017-01-01

    tetraether lipids. The inherent chemical stability and unique membrane-spanning characteristics of tetraether lipids render them interesting for oral drug delivery purposes. Archaeal lipids form liposomes spontaneously (archaeosomes) and may be incorporated in conventional liposomes (mixed vesicles). Both...... types of liposomes are promising to protect their drug cargo, such as therapeutic peptides, against the acidic environment of the stomach and proteolytic degradation in the intestine. They appear to withstand lipolytic enzymes and bile salts and may thus deliver orally administered therapeutic peptides...... to distant sections of the intestine or to the colon, where they may be absorbed, eventually by the help of absorption enhancers. Archaeal lipids and their semisynthetic derivatives may thus serve as biological source for the next generation oral drug delivery systems. The aim of this review is to present...

  19. An analysis of amino acid sequences surrounding archaeal glycoprotein sequons.

    Science.gov (United States)

    Abu-Qarn, Mehtap; Eichler, Jerry

    2007-05-01

    Despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the N-glycosylation process in Archaea. As in Eukarya and Bacteria, archaeal N-glycosylation takes place at the Asn residues of Asn-X-Ser/Thr sequons. Since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. As yet, the contribution to N-glycosylation made by sequon-bordering residues and other related factors in Archaea remains unaddressed. In the following, the surroundings of Asn residues confirmed by experiment as modified were analyzed in an attempt to define sequence rules and requirements for archaeal N-glycosylation.

  20. An analysis of amino acid sequences surrounding archaeal glycoprotein sequons

    Directory of Open Access Journals (Sweden)

    Mehtap Abu-Qarn

    2006-01-01

    Full Text Available Despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the N-glycosylation process in Archaea. As in Eukarya and Bacteria, archaeal N-glycosylation takes place at the Asn residues of Asn-X-Ser/Thr sequons. Since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. As yet, the contribution to N-glycosylation made by sequon-bordering residues and other related factors in Archaea remains unaddressed. In the following, the surroundings of Asn residues confirmed by experiment as modified were analyzed in an attempt to define sequence rules and requirements for archaeal N-glycosylation.

  1. 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.

  2. An analysis of amino acid sequences surrounding archaeal glycoprotein sequons

    OpenAIRE

    Mehtap Abu-Qarn; Jerry Eichler

    2006-01-01

    Despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the N-glycosylation process in Archaea. As in Eukarya and Bacteria, archaeal N-glycosylation takes place at the Asn residues of Asn-X-Ser/Thr sequons. Since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. As yet, t...

  3. 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.

  4. Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems

    Science.gov (United States)

    Tiquia, Sonia M.

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

  5. 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.

  6. 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

  7. 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.

  8. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  9. 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.

  10. A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities.

    Science.gov (United States)

    Pycke, B F G; Etchebehere, C; Van de Caveye, P; Negroni, A; Verstraete, W; Boon, N

    2011-01-01

    This study describes the microbial community richness, -dynamics, and -organization of four full-scale anaerobic digesters during a time-course study of 45 days. The microbial community was analyzed using a Bacteria- and Archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism approach. Clustering analysis separated meso- and thermophilic reactors for both archaeal and bacterial communities. Regardless of the operating temperature, each installation possessed a distinct community profile. For both microbial domains, about 8 dominant terminal-restriction fragments could be observed, with a minimum of 4 and a maximum of 14. The bacterial community organization (a coefficient which describes the specific degree of evenness) showed a factor 2 more variation in the mesophilic reactors, compared with the thermophilic ones. The archaeal community structure of the mesophilic UASB reactor was found to be more stable. The community composition was highly dynamic for Bacteria and Archaea, with a rate of change between 20-50% per 15 days. This study illustrated that microbial communities in full-scale anaerobic digesters are unique to the installation and that community properties are dynamic. Converging complex microbial processes such as anaerobic digestion which rely on a multitude of microbial teams apparently can be highly dynamic.

  11. 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…

  12. 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...

  13. Effect of continuous oleate addition on microbial communities involved in anaerobic digestion process

    DEFF Research Database (Denmark)

    Baserba, Manel Garrido; Angelidaki, Irini; Karakashev, Dimitar Borisov

    2012-01-01

    In the present study, the microbial diversity in anaerobic reactors, continuously exposed to oleate, added to a manure reactor influent, was investigated. Relative changes in archaeal community were less remarkable in comparison to changes in bacterial community indicating that dominant archaeal ...... a comprehensive picture on oleate degrading microbial communities in high organic strength wastewater. The findings might be utilized for development of strategies for biogas production from lipid-riched wastes....

  14. 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…

  15. 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.

  16. 利用小亚基核糖体RNA技术分析温室黄瓜近根土壤古菌和真菌多样性%Diversity analysis of archaeal and fungal communities in adjacent cucumber root soil samples in greenhouse by small-subunit rRNA gene cloning

    Institute of Scientific and Technical Information of China (English)

    赵志祥; 芦晓飞; 陈国华; 茆振川; 杨宇红; 刘二明; 谢丙炎

    2011-01-01

    土壤古菌和真菌在温室生态系统是仅次于细菌的微生物,具有类似于细菌的重要生态功能.通过构建古菌16S rRNA和真菌18S rRNA基因克隆文库,分析温室黄瓜近根土壤古菌和真菌群落结构组成,为开发利用温室这一特殊的生态环境中丰富的微生物资源以及理解微生物与植物间的互作提供参考依据.采用研磨-冻融-溶菌酶-蛋白酶K-SDS热处理以及CTAB处理等理化方法,提取和纯化微生物总DNA,构建古菌16S rRNA和真菌18S rRNA基因克隆文库.利用DOTUR软件将古菌和真菌序列按照相似性97%的标准分成若干个可操作分类单元(OTUs).土壤古菌克隆文库主要包括泉古菌门和未分类的古菌两大类,并有少部分广域古菌类群,所有泉古菌均属于热变形菌纲,共45个OTUs;真菌克隆文库包括真菌门的大多数亚门真菌,共24个OTUs,未发现担子菌亚门真菌.古菌多样性比较丰富,且发现少量的广域古菌(甲烷菌),这一情况可能与温室长期高温高湿,高有机质含量,土壤处于缺氧环境有关;土壤真菌的优势种群为子囊菌,占到土壤真菌的80%以上,这可能与绝大多数植物真菌性病害属于土传病害,通过菌丝体、菌核或子囊壳在土壤病残体中越冬有一定的关系.%Soil archaea and fungi play important roles in the greenhouse soil ecosystem. To develop and apply rich microbial resources in greenhouse ecological environment, and to understand the interaction between microbes and plants, we constructed archaeal 16S rRNA and fungai 18S rRNA gene libraries to analyze the compositions of archaeal and fungal communityies. Total greenhouse soil DNA was directly extracted and purified by skiving-thawing-lysozyme-proteinase K-SDS hot treatment and treatment of cetyltriethylammnonium bromide (CTAB). After PCR amplification, retrieving, ligating, transforming, screening of white clones, archaeal 16S rRNA and fungai 18S rRNA gene libraries were

  17. 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...

  18. 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.

  19. 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.

  20. 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...

  1. 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...

  2. 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...

  3. Novel archaeal adhesion pilins with a conserved N terminus.

    Science.gov (United States)

    Esquivel, Rianne N; Xu, Rachel; Pohlschroder, Mechthild

    2013-09-01

    Type IV pili play important roles in a wide array of processes, including surface adhesion and twitching motility. Although archaeal genomes encode a diverse set of type IV pilus subunits, the functions for most remain unknown. We have now characterized six Haloferax volcanii pilins, PilA[1-6], each containing an identical 30-amino-acid N-terminal hydrophobic motif that is part of a larger highly conserved domain of unknown function (Duf1628). Deletion mutants lacking up to five of the six pilin genes display no significant adhesion defects; however, H. volcanii lacking all six pilins (ΔpilA[1-6]) does not adhere to glass or plastic. Consistent with these results, the expression of any one of these pilins in trans is sufficient to produce functional pili in the ΔpilA[1-6] strain. PilA1His and PilA2His only partially rescue this phenotype, whereas ΔpilA[1-6] strains expressing PilA3His or PilA4His adhere even more strongly than the parental strain. Most surprisingly, expressing either PilA5His or PilA6His in the ΔpilA[1-6] strain results in microcolony formation. A hybrid protein in which the conserved N terminus of the mature PilA1His is replaced with the corresponding N domain of FlgA1 is processed by the prepilin peptidase, but it does not assemble functional pili, leading us to conclude that Duf1628 can be annotated as the N terminus of archaeal PilA adhesion pilins. Finally, the pilin prediction program, FlaFind, which was trained primarily on archaeal flagellin sequences, was successfully refined to more accurately predict pilins based on the in vivo verification of PilA[1-6].

  4. 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.

  5. 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

  6. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Science.gov (United States)

    Holman, Devin B; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills.

  7. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Directory of Open Access Journals (Sweden)

    Devin B Holman

    Full Text Available Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills.

  8. Factors affecting Archaeal Lipid Compositions of the Sulfolobus Species

    Science.gov (United States)

    He, L.; Han, J.; Wei, Y.; Lin, L.; Wei, Y.; Zhang, C.

    2010-12-01

    Temperature is the best known variable affecting the distribution of the archaeal glycerol dibiphytanyl glycerol tetraethers (GDGTs) in marine and freshwater systems. Other variables such as pH, ionic strength, or bicarbonate concentration may also affect archaeal GDGTs in terrestrial systems. Studies of pure cultures can help us pinpoint the specific effects these variables may have on archaeal lipid distribution in natural environments. In this study, three Sulfolobus species (HG4, HB5-2, HB9-6) isolated from Tengchong hot springs (pH 2-3, temperature 73-90°C) in China were used to investigate the effects of temperature, pH, substrate, and type of strain on the composition of GDGTs. Results showed that increase in temperature had negative effects on the relative contents of GDGT-0 (no cyclopentyl rings), GDGT-1 (one cyclopentyl ring), GDGT-2 and GDGT-3 but positive effects on GDGT-4, GDGT-4', GDGT-5 and GDGT-5'. Increase in pH, on the other hand, had negative effects on GDGT-0, GDGT-1, GDGT-4', GDGT-5 and GDGT-5', and positive effects on GDGT-3 and GDGT-4. GDGT-2 remained relatively constant with changing pH. When the HG4 was grown on different substrates, GDGT-5 was five time more abundant in sucrose-grown cultures than in yeast extract- or sulfur- grown cultures, suggesting that carbohydrates may stimulate the production of GDGT-5. For all three species, the ring index (average number of rings) of GDGTs correlated positively with incubation temperature. In HG4, ring index was much lower at optimal pH (3.5) than at other pH values. Ring index of HB5-2 or HB9-6 is higher than that of HG4, suggesting that speciation may affect the degree of cyclization of GDGT of the Sulfolobus. These results indicate that individual archaeal lipids respond differently to changes in environmental variables, which may be also species specific.

  9. Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment

    KAUST Repository

    Jeong, Sanghyun

    2016-03-03

    Membrane bioreactors (MBRs) were operated on-site for 56 d with different powdered activated carbon (PAC) dosages of 0, 1.5 and 5.0 g/L to pretreat seawater for reverse osmosis desalination. It was hypothesized that PAC would stimulate adsorption and biological degradation of organic compounds. The microbial communities responsible for biofouling on microfiltration (MF) membranes and biological organic removal in MBR were assessed using terminal restriction fragment length polymorphism fingerprinting and 454-pyrosequencing. The PAC addition improved assimilable organic carbon removal (53-59%), and resulted in reduced biofouling development on MF (> 50%) with only a marginal development in trans-membrane pressure. Interestingly, the bacterial community composition was significantly differentiated by the PAC addition. Cyanobacterium, Pelagibaca and Maricoccus were dominant in the PAC-free conditions, while Thiothrix and Sphingomonas were presumably responsible for the better reactor performances in PAC-added conditions. In contrast, the archaeal communities were consistent with predominance of Candidatus Nitrosopumilus. These data therefore show that the addition of PAC can improve MBR performance by developing different bacterial species, controlling AOC and associated biofouling on the membranes.

  10. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.

    Science.gov (United States)

    Briggs, Brandon R; Brodie, Eoin L; Tom, Lauren M; Dong, Hailiang; Jiang, Hongchen; Huang, Qiuyuan; Wang, Shang; Hou, Weiguo; Wu, Geng; Huang, Liuquin; Hedlund, Brian P; Zhang, Chuanlun; Dijkstra, Paul; Hungate, Bruce A

    2014-06-01

    Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.

  11. Effect of pesticides on microbial communities in container aquatic habitats

    Science.gov (United States)

    Muturi, Ephantus J.; Donthu, Ravi Kiran; Fields, Christopher J.; Moise, Imelda K.; Kim, Chang-Hyun

    2017-01-01

    Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats. MiSeq sequencing of the V4 region of both bacterial and archaeal 16S rRNA gene was used to characterize the microbial communities of indoor microcosms that were either exposed to each pesticide alone, a mix of herbicides, a mix of insecticides, or a mix of all five insecticides. Individual insecticides but not herbicides reduced the microbial diversity and richness and two insecticides, carbaryl and permethrin, also altered the microbial community structure. A mixture of herbicides had no effect on microbial diversity or structure but a mixture of insecticides or all five pesticides reduced microbial diversity and altered the community structure. These findings suggest that exposure of aquatic ecosystems to individual pesticides or their mixtures can disrupt aquatic microbial communities and there is need to decipher how these changes affect resident macroinvertebrate communities. PMID:28300212

  12. Effect of pesticides on microbial communities in container aquatic habitats.

    Science.gov (United States)

    Muturi, Ephantus J; Donthu, Ravi Kiran; Fields, Christopher J; Moise, Imelda K; Kim, Chang-Hyun

    2017-03-16

    Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats. MiSeq sequencing of the V4 region of both bacterial and archaeal 16S rRNA gene was used to characterize the microbial communities of indoor microcosms that were either exposed to each pesticide alone, a mix of herbicides, a mix of insecticides, or a mix of all five insecticides. Individual insecticides but not herbicides reduced the microbial diversity and richness and two insecticides, carbaryl and permethrin, also altered the microbial community structure. A mixture of herbicides had no effect on microbial diversity or structure but a mixture of insecticides or all five pesticides reduced microbial diversity and altered the community structure. These findings suggest that exposure of aquatic ecosystems to individual pesticides or their mixtures can disrupt aquatic microbial communities and there is need to decipher how these changes affect resident macroinvertebrate communities.

  13. Bacterial and archaeal phylogenetic diversity of a cold sulfur-rich spring on the shoreline of Lake Erie, Michigan

    Science.gov (United States)

    Chaudhary, A.; Haack, S.K.; Duris, J.W.; Marsh, T.L.

    2009-01-01

    Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H2, 5.4 nM; CH4, 2.70 ??M) with concentrations of S2- (0.03 mM), SO42- (14.8 mM), Ca2+ (15.7 mM), and HCO3- (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

  14. Bacterial and archaeal phylogenetic diversity of a cold sulfur-rich spring on the shoreline of Lake Erie, Michigan.

    Science.gov (United States)

    Chaudhary, Anita; Haack, Sheridan Kidd; Duris, Joseph W; Marsh, Terence L

    2009-08-01

    Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H(2), 5.4 nM; CH(4), 2.70 microM) with concentrations of S(2-) (0.03 mM), SO(4)(2-) (14.8 mM), Ca(2+) (15.7 mM), and HCO(3)(-) (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments.

  15. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

    Directory of Open Access Journals (Sweden)

    Yang Yi-Fan

    2007-03-01

    Full Text Available Abstract Background Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. Results This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs and Translation Initiation Sites (TISs. The former is based on a linguistic "Entropy Density Profile" (EDP model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. Conclusion Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.

  16. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

    Science.gov (United States)

    Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

    2013-01-01

    Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data

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

    Indian Academy of Sciences (India)

    Quang Manh Vu; Tri Tien Nguyen

    2000-12-01

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

  18. Analyses of in vivo interactions between transcription factors and the archaeal RNA polymerase.

    Science.gov (United States)

    Walker, Julie E; Santangelo, Thomas J

    2015-09-15

    Transcription factors regulate the activities of RNA polymerase (RNAP) at each stage of the transcription cycle. Many basal transcription factors with common ancestry are employed in eukaryotic and archaeal systems that directly bind to RNAP and influence intramolecular movements of RNAP and modulate DNA or RNA interactions. We describe and employ a flexible methodology to directly probe and quantify the binding of transcription factors to RNAP in vivo. We demonstrate that binding of the conserved and essential archaeal transcription factor TFE to the archaeal RNAP is directed, in part, by interactions with the RpoE subunit of RNAP. As the surfaces involved are conserved in many eukaryotic and archaeal systems, the identified TFE-RNAP interactions are likely conserved in archaeal-eukaryal systems and represent an important point of contact that can influence the efficiency of transcription initiation.

  19. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.

    Science.gov (United States)

    Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A; Parkes, John R; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Toffin, Laurent

    2014-01-01

    Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.

  20. Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

    Science.gov (United States)

    Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

    2014-01-01

    Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Archaeal viruses multiply: temporal screening in a solar saltern.

    Science.gov (United States)

    Atanasova, Nina S; Demina, Tatiana A; Buivydas, Andrius; Bamford, Dennis H; Oksanen, Hanna M

    2015-04-10

    Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.

  7. Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern

    Directory of Open Access Journals (Sweden)

    Nina S. Atanasova

    2015-04-01

    Full Text Available Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010. Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26. This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.

  8. Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology

    Directory of Open Access Journals (Sweden)

    Cecilia R. Chambers

    2015-01-01

    Full Text Available With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments. We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.

  9. Two distinct microbial communities revealed in the sponge Cinachyrella

    Directory of Open Access Journals (Sweden)

    Marie Laure Cuvelier

    2014-11-01

    Full Text Available Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes, which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1 with low diversity (Shannon-Weiner index: 3.73 ± 0.22 and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25. Hosts’ 28S rDNA sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences present in low abundance or below detection limits (<0.07% in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5% and 22.4% of SG1 and SG2’s total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.

  10. Archaeal populations in two distinct sedimentary facies of the subsurface of the Dead Sea.

    Science.gov (United States)

    Thomas, C; Ionescu, D; Ariztegui, D

    2014-10-01

    Archaeal metabolism was studied in aragonitic and gypsum facies of the Dead Sea subsurface using high-throughput DNA sequencing. We show that the communities are well adapted to the peculiar environment of the Dead Sea subsurface. They harbor the necessary genes to deal with osmotic pressure using high- and low-salt-in strategies, and to cope with unusually high concentrations of heavy metals. Methanogenesis was identified for the first time in the Dead Sea and appears to be an important metabolism in the aragonite sediment. Fermentation of residual organic matter, probably performed by some members of the Halobacteria class is common to both types of sediments. The latter group represents more than 95% of the taxonomically identifiable Archaea in the metagenome of the gypsum sediment. The potential for sulfur reduction has also been revealed and is associated in the sediment with EPS degradation and Fe-S mineralization as revealed by SEM imaging. Overall, we show that distinct communities of Archaea are associated with the two different facies of the Dead Sea, and are adapted to the harsh chemistry of its subsurface, in different ways.

  11. 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…

  12. 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....

  13. 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

  14. 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

  15. 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…

  16. 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...

  17. 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

  18. 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...

  19. Effects of Oxytetracycline on Methane Production and the Microbial Communities During Anaerobic Digestion of Cow Manure

    Institute of Scientific and Technical Information of China (English)

    KE Xin; WANG Chun-yong; LI Run-dong; ZHANG Yun

    2014-01-01

    The effects of different concentrations of oxytetracycline (OTC) on the dynamics of bacterial and archaeal communities during the mesophilic anaerobic digestion (37°C) of cow manure were investigated. Before anaerobic digestion, OTC was added to digesters at concentrations of 20, 50, and 80 mg L-1, respectively. Compared with no-antibiotic control, all methane productions underwent different levels of inhibition at different concentrations of OTC. Changes in the bacterial and archaeal communities were discussed by using PCR-denaturing gradient gel electrophoresis (DGGE). Results showed that OTC affected the richness and diversity of bacterial and archaeal communities. The bacterial genus Flavobacterium and an uncultured bacterium (JN256083.1) were detected throughout the entire process of anaerobic digestion and seemed to be the functional bacteria. Methanobrevibacter boviskoreani and an uncultured archaeon (FJ230982.1) dominated the archaeal communities during anaerobic digestion. These microorganisms may have high resistance to OTC and may play vital roles in methane production.

  20. 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/.

  1. [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.

  2. 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)

  3. 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...

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. [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.

  19. 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.

  20. Immunogenic properties of archaeal species found in bioaerosols.

    Directory of Open Access Journals (Sweden)

    Pascale Blais Lecours

    Full Text Available The etiology of bioaerosol-related pulmonary diseases remains poorly understood. Recently, archaea emerged as prominent airborne components of agricultural environments, but the consequences of airway exposure to archaea remain unknown. Since subcomponents of archaea can be immunogenic, we used a murine model to study the pulmonary immune responses to two archaeal species found in agricultural facilities: Methanobrevibacter smithii (MBS and Methanosphaera stadtmanae (MSS. Mice were administered intranasally with 6.25, 25 or 100 µg of MBS or MSS, once daily, 3 days a week, for 3 weeks. MSS induced more severe histopathological alterations than MBS with perivascular accumulation of granulocytes, pronounced thickening of the alveolar septa, alveolar macrophages accumulation and increased perivascular mononucleated cell accumulation. Analyses of bronchoalveolar lavage fluids revealed up to 3 times greater leukocyte accumulation with MSS compared to MBS. Instillation of 100 µg of MBS or MSS caused predominant accumulation of monocyte/macrophages (4.5×10(5 and 4.8×10(5 cells/ml respectively followed by CD4(+ T cells (1.38×10(5 and 1.94×10(5 cells/ml respectively, B cells (0.73×10(5 and 1.28×10(5 cells/ml respectively, and CD8(+ T cells (0.20×10(5 and 0.31×10(5 cells/ml respectively in the airways. Both archaeal species induced similar titers of antigen-specific IgGs in plasma. MSS but not MBS caused an accumulation of eosinophils and neutrophils in the lungs, which surprisingly, correlated inversely with the size of the inoculum. Stronger immunogenicity of MSS was confirmed by a 3 fold higher accumulation of myeloid dendritic cells in the airways, compared to MBS. Thus, the dose and species of archaea determine the magnitude and nature of the pulmonary immune response. This is the first report of an immunomodulatory role of archaeal species found in bioaerosols.

  1. Comparison Of A Laboratory Consortium That Dechlorinates TCE To Ethene To The Field Community From Which It Was Derived

    Energy Technology Data Exchange (ETDEWEB)

    T. Wood; K. S. Sorenson; D. E. Cummings

    2004-12-01

    Sodium lactate additions to a trichloroethene (TCE) residual source area in deep, fractured basalt at a U.S. Department of Energy site have resulted in the enrichment of the indigenous microbial community, the complete dechlorination of nearly all aqueous-phase TCE to ethene, and the continued depletion of the residual source since 1999. The bacterial and archaeal consortia in groundwater obtained from the residual source were assessed by using PCR-amplified 16S rRNA genes. A clone library of bacterial amplicons was predominated by those from members of the class Clostridia (57 of 93 clones), of which a phylotype most similar to that of the homoacetogen Acetobacterium sp. strain HAAP-1 was most abundant (32 of 93 clones). The remaining Bacteria consisted of phylotypes affiliated with Sphingobacteria, Bacteroides, Spirochaetes, Mollicutes, and Proteobacteria and candidate divisions OP11 and OP3. The two proteobacterial phylotypes were most similar to those of the known dechlorinators Trichlorobacter thiogenes and Sulfurospirillum multivorans. Although not represented by the bacterial clones generated with broad-specificity bacterial primers, a Dehalococcoides-like phylotype was identified with genus-specific primers. Only four distinct phylotypes were detected in the groundwater archaeal library, including predominantly a clone affiliated with the strictly acetoclastic methanogen Methanosaeta concilii (24 of 43 clones). A mixed culture that completely dechlorinates TCE to ethene was enriched from this groundwater, and both communities were characterized by terminal restriction fragment length polymorphism (T-RFLP). According to T-RFLP, the laboratory enrichment community was less diverse overall than the groundwater community, with 22 unique phylotypes as opposed to 43 and a higher percentage of Clostridia, including the Acetobacterium population. Bioreactor archaeal structure was very similar to that of the groundwater community, suggesting that methane is

  2. A Dechlorinating Community Resulting From In Situ Biostimulation of a TCE-contaminated Deep Fracture Basalt Aquifer

    Energy Technology Data Exchange (ETDEWEB)

    T. Wood; D. E. Cummings

    2004-12-01

    Sodium lactate additions to a trichloroethene (TCE) residual source area in deep, fractured basalt at a U.S. Department of Energy site have resulted in the enrichment of the indigenous microbial community, the complete dechlorination of nearly all aqueous-phase TCE to ethene, and the continued depletion of the residual source since 1999. The bacterial and archaeal consortia in groundwater obtained from the residual source were assessed by using PCR-amplified 16S rRNA genes. A clone library of bacterial amplicons was predominated by those from members of the class Clostridia (57 of 93 clones), of which a phylotype most similar to that of the homoacetogen Acetobacterium sp. strain HAAP-1 was most abundant (32 of 93 clones). The remaining Bacteria consisted of phylotypes affiliated with Sphingobacteria, Bacteroides, Spirochaetes, Mollicutes, and Proteobacteria and candidate divisions OP11 and OP3. The two proteobacterial phylotypes were most similar to those of the known dechlorinators Trichlorobacter thiogenes and Sulfurospirillum multivorans. Although not represented by the bacterial clones generated with broad-specificity bacterial primers, a Dehalococcoides-like phylotype was identified with genus-specific primers. Only four distinct phylotypes were detected in the groundwater archaeal library, including predominantly a clone affiliated with the strictly acetoclastic methanogen Methanosaeta concilii (24 of 43 clones). A mixed culture that completely dechlorinates TCE to ethene was enriched from this groundwater, and both communities were characterized by terminal restriction fragment length polymorphism (T-RFLP). According to T-RFLP, the laboratory enrichment community was less diverse overall than the groundwater community, with 22 unique phylotypes as opposed to 43 and a higher percentage of Clostridia, including the Acetobacterium population. Bioreactor archaeal structure was very similar to that of the groundwater community, suggesting that methane is

  3. 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.

  4. Magnetic Au Nanoparticles on Archaeal S-Layer Ghosts as Templates

    Directory of Open Access Journals (Sweden)

    Sonja Selenska-Pobell

    2011-10-01

    Full Text Available Cell‐ghosts representing empty cells of the archaeon Sulfolobus acidocaldarius, consisting only of their highly ordered and unusually stable outermost proteinaceous surface layer (S‐layer, were used as templates for Au nanoparticles fabrication. The properties of these archaeal Au nanoparticles differ significantly from those produced earlier by us onto bacterial S‐layer sheets. The archaeal Au nanoparticles, with a size of about 2.5 nm, consist exclusively of metallic Au(0, while those produced on the bacterial S‐layer had a size of about 4 nm and represented a mixture of Au(0 and Au(III in the ratio of 40 to 60 %. The most impressive feature of the archaeal Au nanoparticles is that they are strongly paramagnetic, in contrast to the bacterial ones and also to bulk gold. SQUID magnetometry and XMCD measurements demonstrated that the archaeal Au nanoparticles possess a rather large magnetic moment of about 0.1 µB/atom. HR‐ TEM‐EDX analysis revealed that the archaeal Au nanoparticles are linked to the sulfur atoms of the thiol groups of the amino acid cysteine, characteristic only for archaeal S‐layers. This is the first study demonstrating the formation of such unusually strong magnetic Au nanoparticles on a non‐modified archaeal S‐layer.

  5. 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.

  6. 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...

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on