ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

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Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea (2013)

Alvaro Orell; Eveline Peeters; Victoria Vassen; Silke Jachlewski; Sven Schalles; Bettina Siebers; Sonja-Verena Albers

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea The ISME Journal 7, 1886 (October 2013). doi:10.1038/ismej.2013.68 Authors: Alvaro Orell, Eveline Peeters, Victoria Vassen, Silke Jachlewski, Sven Schalles, Bettina Siebers & Sonja-Verena Albers

Keywords: archaeabiofilm formationcell motilityEPStranscriptional regulation

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Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology (2013)

Martin von Bergen; Nico Jehmlich; Martin Taubert; Carsten Vogt; Felipe Bastida; Florian-Alexander Herbst; Frank Schmidt; Hans-Hermann Richnow; Jana Seifert

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology The ISME Journal 7, 1877 (October 2013). doi:10.1038/ismej.2013.78 Authors: Martin von Bergen, Nico Jehmlich, Martin Taubert, Carsten Vogt, Felipe Bastida, Florian-Alexander Herbst, Frank Schmidt, Hans-Hermann Richnow & Jana Seifert

Keywords: quantitative metaproteomicslabel-free quantificationspectral countingstable isotope probingprotein-SIPfunctional microbial community

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3

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The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis (2013)

Adam C-N Wong; John M Chaston; Angela E Douglas

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis The ISME Journal 7, 1922 (October 2013). doi:10.1038/ismej.2013.86 Authors: Adam C-N Wong, John M Chaston & Angela E Douglas

Keywords: Acetobactercore microbiotaDrosophilagut microbiotaLactobactillussymbiosis

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4

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Diversity of protists and bacteria determines predation performance and stability (2013)

Muhammad Saleem; Ingo Fetzer; Hauke Harms; Antonis Chatzinotas

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Diversity of protists and bacteria determines predation performance and stability The ISME Journal 7, 1912 (October 2013). doi:10.1038/ismej.2013.95 Authors: Muhammad Saleem, Ingo Fetzer, Hauke Harms & Antonis Chatzinotas

Keywords: microbial diversity and ecosystem functioningprotist-bacteria interactionstrophic interactionsmicrobial model systemspredator-prey

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Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin (2013)

Caroline S Fortunato; Alexander Eiler; Lydie Herfort; Joseph A Needoba; Tawnya D Peterson; Byron C Crump

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin The ISME Journal 7, 1899 (October 2013). doi:10.1038/ismej.2013.79 Authors: Caroline S Fortunato, Alexander Eiler, Lydie Herfort, Joseph A Needoba, Tawnya D Peterson & Byron C Crump

Keywords: 16S ampliconbiogeographylcoastal oceangradientindicator

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6

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Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake (2013)

Sheree Yau; Federico M Lauro; Timothy J Williams; Matthew Z De; Maere; Mark V Brown; John Rich; John AE Gibson; Ricardo Cavicchioli

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake The ISME Journal 7, 1944 (October 2013). doi:10.1038/ismej.2013.69 Authors: Sheree Yau, Federico M Lauro, Timothy J Williams, Matthew Z DeMaere, Mark V Brown, John Rich, John AE Gibson & Ricardo Cavicchioli

Keywords: metagenomicsOrganic LakeAntarctic microbial ecologynutrient cyclesdimethylsulfide

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7

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Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling (2013)

Brett J Baker; Cody S Sheik; Chris A Taylor; Sunit Jain; Ashwini Bhasi; James D Cavalcoli; Gregory J Dick

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling The ISME Journal 7, 1962 (October 2013). doi:10.1038/ismej.2013.85 Authors: Brett J Baker, Cody S Sheik, Chris A Taylor, Sunit Jain, Ashwini Bhasi, James D Cavalcoli & Gregory J Dick

Keywords: Archaeadeep seatranscriptomicsnitrificationAlteromonasNitrospirae

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8

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Specific carbonate–microbe interactions in the modern microbialites of Lake Alchichica (Mexico) (2013)

Emmanuelle Gérard; Bénédicte Ménez; Estelle Couradeau; David Moreira; Karim Benzerara; Rosaluz Tavera; Purificación López-García

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Specific carbonate–microbe interactions in the modern microbialites of Lake Alchichica (Mexico) The ISME Journal 7, 1997 (October 2013). doi:10.1038/ismej.2013.81 Authors: Emmanuelle Gérard, Bénédicte Ménez, Estelle Couradeau, David Moreira, Karim Benzerara, Rosaluz Tavera & Purificación López-García

Keywords: microbialitesPleurocapsalesaragonitehydromagnesiteRaman spectroscopyconfocal laser scanning microscopy

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9

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A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice (2013)

A Marcobal; P C Kashyap; T A Nelson; P A Aronov; M S Donia; A Spormann; M A Fischbach; J L Sonnenburg

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice The ISME Journal 7, 1933 (October 2013). doi:10.1038/ismej.2013.89 Authors: A Marcobal, P C Kashyap, T A Nelson, P A Aronov, M S Donia, A Spormann, M A Fischbach & J L Sonnenburg

Keywords: metabolomicshumanized micegut microbiotaUPLC-MS

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10

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Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits (2013)

David Goudenège; Yannick Labreuche; Evelyne Krin; Dominique Ansquer; Sophie Mangenot; Alexandra Calteau; Claudine Médigue; Didier Mazel; Martin F Polz; Frédérique Le Roux

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits The ISME Journal 7, 1985 (October 2013). doi:10.1038/ismej.2013.90 Authors: David Goudenège, Yannick Labreuche, Evelyne Krin, Dominique Ansquer, Sophie Mangenot, Alexandra Calteau, Claudine Médigue, Didier Mazel, Martin F Polz & Frédérique Le Roux

Keywords: horizontal gene transfernigritoxinphylogenyshrimpvirulencevibrio

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11

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Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus (2013)

F Rineau; F Shah; M M Smits; P Persson; T Johansson; R Carleer; C Troein; A Tunlid

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus The ISME Journal 7, 2010 (October 2013). doi:10.1038/ismej.2013.91 Authors: F Rineau, F Shah, M M Smits, P Persson, T Johansson, R Carleer, C Troein & A Tunlid

Keywords: carbon and nitrogen cyclingectomycorrhizanitrogen assimilationorganic matter degradationcarbon availability

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12

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Can we detect oceanic biodiversity hotspots from space? (2013)

Silvia De Monte; Alice Soccodato; Séverine Alvain; Francesco d'Ovidio

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Can we detect oceanic biodiversity hotspots from space? The ISME Journal 7, 2054 (October 2013). doi:10.1038/ismej.2013.72 Authors: Silvia De Monte, Alice Soccodato, Séverine Alvain & Francesco d'Ovidio

Keywords: biodiversitybiogeographyremote sensingglobal oceansstirring

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13

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The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities (2013)

Yong-Jin Lee; Joy D van Nostrand; Qichao Tu; Zhenmei Lu; Lei Cheng; Tong Yuan; Ye Deng; Michelle Q Carter; Zhili He; Liyou Wu; Fang Yang; Jian Xu; Jizhong Zhou

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities The ISME Journal 7, 1974 (October 2013). doi:10.1038/ismej.2013.88 Authors: Yong-Jin Lee, Joy D van Nostrand, Qichao Tu, Zhenmei Lu, Lei Cheng, Tong Yuan, Ye Deng, Michelle Q Carter, Zhili He, Liyou Wu, Fang Yang, Jian Xu & Jizhong Zhou

Keywords: virulence genesfunctional gene arrayclimate warmingoil-contaminationcaries

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14

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Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea (2013)

Rachel E A Horak; Wei Qin; Andy J Schauer; E Virginia Armbrust; Anitra E Ingalls; James W Moffett; David A Stahl; Allan H Devol

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea The ISME Journal 7, 2023 (October 2013). doi:10.1038/ismej.2013.75 Authors: Rachel E A Horak, Wei Qin, Andy J Schauer, E Virginia Armbrust, Anitra E Ingalls, James W Moffett, David A Stahl & Allan H Devol

Keywords: amoAammonia oxidationKmmarine ArchaeaQ10

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15

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Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling (2013)

Brett J Baker; Cody S Sheik; Chris A Taylor; Sunit Jain; Ashwini Bhasi; James D Cavalcoli; Gregory J Dick

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling The ISME Journal 7, 2060 (October 2013). doi:10.1038/ismej.2013.101 Authors: Brett J Baker, Cody S Sheik, Chris A Taylor, Sunit Jain, Ashwini Bhasi, James D Cavalcoli & Gregory J Dick

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16

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Chytrid epidemics may increase genetic diversity of a diatom spring-bloom (2013)

Alena S Gsell; Lisette N de Senerpont Domis; Koen JF Verhoeven; Ellen van Donk; Bastiaan W Ibelings

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Chytrid epidemics may increase genetic diversity of a diatom spring-bloom The ISME Journal 7, 2057 (October 2013). doi:10.1038/ismej.2013.73 Authors: Alena S Gsell, Lisette N de Senerpont Domis, Koen JF Verhoeven, Ellen van Donk & Bastiaan W Ibelings

Keywords: beta-dispersionchytriddiatomgenetic diversityparasitism

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17

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A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli (2013)

Katherine Phan; Thomas Ferenci

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli The ISME Journal 7, 2034 (October 2013). doi:10.1038/ismej.2013.82 Authors: Katherine Phan & Thomas Ferenci

Keywords: bacterial diversitytrade-offsnutrient uptakeouter membranesantibiotic susceptibility

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18

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Linking microbial community structure to β-glucosidic function in soil aggregates (2013)

Vanessa L Bailey; Sarah J Fansler; James C Stegen; Lee Ann McCue

Springer Nature

In: ISME Journal

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Publication Date: 2013-09-25

Description: Linking microbial community structure to β-glucosidic function in soil aggregates The ISME Journal 7, 2044 (October 2013). doi:10.1038/ismej.2013.87 Authors: Vanessa L Bailey, Sarah J Fansler, James C Stegen & Lee Ann McCue

Keywords: microbial communitydiversity16S pyrosequencingbeta-glucosidasesoil aggregatesATP

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19

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Secondary structure improves OTU assignments of 16S rRNA gene sequences (2013)

Patrick D Schloss

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Secondary structure improves OTU assignments of 16S rRNA gene sequences The ISME Journal 7, 457 (March 2013). doi:10.1038/ismej.2012.102 Author: Patrick D Schloss

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20

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Collaborative cloud-enabled tools allow rapid, reproducible biological insights (2013)

Benjamin Ragan-Kelley; William Anton Walters; Daniel McDonald; Justin Riley; Brian E Granger; Antonio Gonzalez; Rob Knight; Fernando Perez; J Gregory Caporaso

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Collaborative cloud-enabled tools allow rapid, reproducible biological insights The ISME Journal 7, 461 (March 2013). doi:10.1038/ismej.2012.123 Authors: Benjamin Ragan-Kelley, William Anton Walters, Daniel McDonald, Justin Riley, Brian E Granger, Antonio Gonzalez, Rob Knight, Fernando Perez & J Gregory Caporaso

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21

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Microbial individuality in the natural environment (2013)

M Ackermann

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Microbial individuality in the natural environment The ISME Journal 7, 465 (March 2013). doi:10.1038/ismej.2012.131 Author: M Ackermann

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22

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Microbiology of Lonar Lake and other soda lakes (2013)

Chakkiath Paul Antony; Deepak Kumaresan; Sindy Hunger; Harold L Drake; J Colin Murrell; Yogesh S Shouche

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Microbiology of Lonar Lake and other soda lakes The ISME Journal 7, 468 (March 2013). doi:10.1038/ismej.2012.137 Authors: Chakkiath Paul Antony, Deepak Kumaresan, Sindy Hunger, Harold L Drake, J Colin Murrell & Yogesh S Shouche

Keywords: Lonar Lakesoda lakesalkaliphilesstable-isotope probingmicrobial prospecting

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23

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Fungal community on decomposing leaf litter undergoes rapid successional changes (2013)

Jana VoříškováPetr Baldrian

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Fungal community on decomposing leaf litter undergoes rapid successional changes The ISME Journal 7, 477 (March 2013). doi:10.1038/ismej.2012.116 Authors: Jana Voříšková & Petr Baldrian

Keywords: fungilitter decompositioncelluloseendophytetemperate forests

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24

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Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network (2013)

Rocío-Anaís Pérez-Gutiérrez; Varinia López-RamírezÁfrica Islas; Luis David Alcaraz; Ismael Hernández-González; Beatriz Carely Luna Olivera; Moisés Santillán; Luis E Eguiarte; Valeria Souza; Michael Travisano; Gabriela Olmedo-Alvarez

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network The ISME Journal 7, 487 (March 2013). doi:10.1038/ismej.2012.119 Authors: Rocío-Anaís Pérez-Gutiérrez, Varinia López-Ramírez, África Islas, Luis David Alcaraz, Ismael Hernández-González, Beatriz Carely Luna Olivera, Moisés Santillán, Luis E Eguiarte, Valeria Souza, Michael Travisano & Gabriela Olmedo-Alvarez

Keywords: antagonism networkcommunity assemblageinterference interactionsantagonistic interactionslocal communitiesself-organization

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The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale (2013)

Christina Hazard; Paul Gosling; Christopher J van der Gast; Derek T Mitchell; Fiona M Doohan; Gary D Bending

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale The ISME Journal 7, 498 (March 2013). doi:10.1038/ismej.2012.127 Authors: Christina Hazard, Paul Gosling, Christopher J van der Gast, Derek T Mitchell, Fiona M Doohan & Gary D Bending

Keywords: arbuscular mycorrhizal fungibiogeographydiversityhost preferenceland usesoil type

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Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses (2013)

Steven A J Declerck; Christian Winter; Jonathan B Shurin; Curtis A Suttle; Blake Matthews

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses The ISME Journal 7, 533 (March 2013). doi:10.1038/ismej.2012.138 Authors: Steven A J Declerck, Christian Winter, Jonathan B Shurin, Curtis A Suttle & Blake Matthews

Keywords: virusesbacteriametacommunityexperimentdispersal limitationpatch heterogeneity

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Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium (2013)

Paul Carini; Laura Steindler; Sara Beszteri; Stephen J Giovannoni

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium The ISME Journal 7, 592 (March 2013). doi:10.1038/ismej.2012.122 Authors: Paul Carini, Laura Steindler, Sara Beszteri & Stephen J Giovannoni

Keywords: alaninegenome streamliningglycolatephytoplankton

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Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades (2013)

Robert T Green; Jonathan D Todd; Andrew W B Johnston

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades The ISME Journal 7, 581 (March 2013). doi:10.1038/ismej.2012.140 Authors: Robert T Green, Jonathan D Todd & Andrew W B Johnston

Keywords: manganeseMntXMurregulationRoseobactersSAR11SAR116SitABCDVibrio

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Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens (2013)

Yeshi Yin; Yu Wang; Liying Zhu; Wei Liu; Ningbo Liao; Mizu Jiang; Baoli Zhu; Hongwei D Yu; Charlie Xiang; Xin Wang

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens The ISME Journal 7, 615 (March 2013). doi:10.1038/ismej.2012.128 Authors: Yeshi Yin, Yu Wang, Liying Zhu, Wei Liu, Ningbo Liao, Mizu Jiang, Baoli Zhu, Hongwei D Yu, Charlie Xiang & Xin Wang

Keywords: distributiondiversityphylogenetic relationshipssegmented filamentous bacteria

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Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park (2013)

Mark A Kozubal; Margaret Romine; Ryan de; M Jennings; Zack J Jay; Susannah G Tringe; Doug B Rusch; Jacob P Beam; Lee Ann McCue; William P Inskeep

Springer Nature

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Publication Date: 2013-02-20

Description: Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park The ISME Journal 7, 622 (March 2013). doi:10.1038/ismej.2012.132 Authors: Mark A Kozubal, Margaret Romine, Ryan deM Jennings, Zack J Jay, Susannah G Tringe, Doug B Rusch, Jacob P Beam, Lee Ann McCue & William P Inskeep

Keywords: extremophilesgeothermalYellowstone National Parkheme copper oxidasecarbon monoxideiron-oxides

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Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages (2013)

Cesar O Flores; Sergi Valverde; Joshua S Weitz

Springer Nature

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Publication Date: 2013-02-20

Description: Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages The ISME Journal 7, 520 (March 2013). doi:10.1038/ismej.2012.135 Authors: Cesar O Flores, Sergi Valverde & Joshua S Weitz

Keywords: microbial ecologyvirusesbiogeographynetworks

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Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm (2013)

Alexander J Probst; Hoi-Ying N Holman; Todd Z De; Santis; Gary L Andersen; Giovanni Birarda; Hans A Bechtel; Yvette M Piceno; Maria Sonnleitner; Kasthuri Venkateswaran; Christine Moissl-Eichinger

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In: ISME Journal

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Publication Date: 2013-02-20

Description: Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm The ISME Journal 7, 635 (March 2013). doi:10.1038/ismej.2012.133 Authors: Alexander J Probst, Hoi-Ying N Holman, Todd Z DeSantis, Gary L Andersen, Giovanni Birarda, Hans A Bechtel, Yvette M Piceno, Maria Sonnleitner, Kasthuri Venkateswaran & Christine Moissl-Eichinger

Keywords: Archaeamicrobial ecologyPhyloChipSR-FTIRSRBCTC

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A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA (2013)

Emily L Kara; Paul C Hanson; Yu Hen Hu; Luke Winslow; Katherine D McMahon

Springer Nature

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Publication Date: 2013-02-20

Description: A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA The ISME Journal 7, 680 (March 2013). doi:10.1038/ismej.2012.118 Authors: Emily L Kara, Paul C Hanson, Yu Hen Hu, Luke Winslow & Katherine D McMahon

Keywords: aquatic communitytemporal dynamicsseasonal dynamicslocal similarity analysisnetwork analysisdiversity

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Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean (2013)

Joanna L Dixon; Stephanie Sargeant; Philip D Nightingale; J Colin Murrell

Springer Nature

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Publication Date: 2013-02-20

Description: Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean The ISME Journal 7, 568 (March 2013). doi:10.1038/ismej.2012.130 Authors: Joanna L Dixon, Stephanie Sargeant, Philip D Nightingale & J Colin Murrell

Keywords: methanol uptakeoligotrophic gyresupwellingchlorophyll amethylotrophic bacterialoss rates

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A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal (2013)

Rikke Kristiansen; Hien Thi Thu Nguyen; Aaron Marc Saunders; Jeppe Lund Nielsen; Reinhard Wimmer; Vang Quy Le; Simon Jon McIlroy; Steve Petrovski; Robert J Seviour; Alexandra Calteau; Kåre Lehmann Nielsen; Per Halkjær Nielsen

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Publication Date: 2013-02-20

Description: A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal The ISME Journal 7, 543 (March 2013). doi:10.1038/ismej.2012.136 Authors: Rikke Kristiansen, Hien Thi Thu Nguyen, Aaron Marc Saunders, Jeppe Lund Nielsen, Reinhard Wimmer, Vang Quy Le, Simon Jon McIlroy, Steve Petrovski, Robert J Seviour, Alexandra Calteau, Kåre Lehmann Nielsen & Per Halkjær Nielsen

Keywords: enhanced biological phosphorus removalTetrasphaerametabolic modelgenomic sequencing

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Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes (2013)

Katsunori Yanagawa; Yuki Morono; Dirk de Beer; Matthias Haeckel; Michinari Sunamura; Taiki Futagami; Tatsuhiko Hoshino; Takeshi Terada; Ko-ichi Nakamura; Tetsuro Urabe; Gregor Rehder; Antje Boetius; Fumio Inagaki

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Publication Date: 2013-02-20

Description: Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes The ISME Journal 7, 555 (March 2013). doi:10.1038/ismej.2012.124 Authors: Katsunori Yanagawa, Yuki Morono, Dirk de Beer, Matthias Haeckel, Michinari Sunamura, Taiki Futagami, Tatsuhiko Hoshino, Takeshi Terada, Ko-ichi Nakamura, Tetsuro Urabe, Gregor Rehder, Antje Boetius & Fumio Inagaki

Keywords: CO2 seeplow pHanaerobic oxidation of methaneacidophilic sulfate reduction

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Reproducibility of Vibrionaceae population structure in coastal bacterioplankton (2013)

Gitta Szabo; Sarah P Preheim; Kathryn M Kauffman; Lawrence A David; Jesse Shapiro; Eric J Alm; Martin F Polz

Springer Nature

In: ISME Journal

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Publication Date: 2013-02-20

Description: Reproducibility of Vibrionaceae population structure in coastal bacterioplankton The ISME Journal 7, 509 (March 2013). doi:10.1038/ismej.2012.134 Authors: Gitta Szabo, Sarah P Preheim, Kathryn M Kauffman, Lawrence A David, Jesse Shapiro, Eric J Alm & Martin F Polz

Keywords: population structure and dynamicscommunity assemblyniche

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Global biogeography of highly diverse protistan communities in soil (2013)

Scott T Bates; Jose C Clemente; Gilberto E Flores; William Anthony Walters; Laura Wegener Parfrey; Rob Knight; Noah Fierer

Springer Nature

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Publication Date: 2013-02-20

Description: Global biogeography of highly diverse protistan communities in soil The ISME Journal 7, 652 (March 2013). doi:10.1038/ismej.2012.147 Authors: Scott T Bates, Jose C Clemente, Gilberto E Flores, William Anthony Walters, Laura Wegener Parfrey, Rob Knight & Noah Fierer

Keywords: biodiversitybiogeographymicrobial ecologysoil protists

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Are we missing half of the viruses in the ocean? (2013)

Grieg F Steward; Alexander I Culley; Jaclyn A Mueller; Elisha M Wood-Charlson; Mahdi Belcaid; Guylaine Poisson

Springer Nature

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Publication Date: 2013-02-20

Description: Are we missing half of the viruses in the ocean? The ISME Journal 7, 672 (March 2013). doi:10.1038/ismej.2012.121 Authors: Grieg F Steward, Alexander I Culley, Jaclyn A Mueller, Elisha M Wood-Charlson, Mahdi Belcaid & Guylaine Poisson

Keywords: RNA virusesDNA virusesvirioplanktonmarineseawaterabundancemetagenome

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Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre (2013)

Paola R Gómez-Pereira; Manuela Hartmann; Carolina Grob; Glen A Tarran; Adrian P Martin; Bernhard M Fuchs; David J Scanlan; Mikhail V Zubkov

Springer Nature

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Publication Date: 2013-02-20

Description: Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre The ISME Journal 7, 603 (March 2013). doi:10.1038/ismej.2012.126 Authors: Paola R Gómez-Pereira, Manuela Hartmann, Carolina Grob, Glen A Tarran, Adrian P Martin, Bernhard M Fuchs, David J Scanlan & Mikhail V Zubkov

Keywords: SAR11Prochlorococcuslight stimulationflow cytometric sortingradioisotope tracingATP and amino-acid uptake

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Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone (2013)

Xinyu Li; Ye Deng; Qi Li; Caiyan Lu; Jingjing Wang; Huiwen Zhang; Jianguo Zhu; Jizhong Zhou; Zhili He

Springer Nature

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Publication Date: 2013-02-20

Description: Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone The ISME Journal 7, 660 (March 2013). doi:10.1038/ismej.2012.120 Authors: Xinyu Li, Ye Deng, Qi Li, Caiyan Lu, Jingjing Wang, Huiwen Zhang, Jianguo Zhu, Jizhong Zhou & Zhili He

Keywords: elevated ozonefunctional generhizosphere microbial communitywheat cultivar

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Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean (2013)

J Michael Beman; Joy Leilei Shih; Brian N Popp

Springer Nature

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Publication Date: 2013-10-23

Description: Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean The ISME Journal 7, 2192 (November 2013). doi:10.1038/ismej.2013.96 Authors: J Michael Beman, Joy Leilei Shih & Brian N Popp

Keywords: nitrificationnitrite oxidationnitrospinaoxygen minimum zonepyrosequencing

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Responses of soil bacterial and fungal communities to extreme desiccation and rewetting (2013)

Romain L Barnard; Catherine A Osborne; Mary K Firestone

Springer Nature

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Publication Date: 2013-10-23

Description: Responses of soil bacterial and fungal communities to extreme desiccation and rewetting The ISME Journal 7, 2229 (November 2013). doi:10.1038/ismej.2013.104 Authors: Romain L Barnard, Catherine A Osborne & Mary K Firestone

Keywords: rRNArDNArpoBpyrosequencingqPCRMediterranean grassland

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Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses (2013)

Steven J Blazewicz; Romain L Barnard; Rebecca A Daly; Mary K Firestone

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Publication Date: 2013-10-23

Description: Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses The ISME Journal 7, 2061 (November 2013). doi:10.1038/ismej.2013.102 Authors: Steven J Blazewicz, Romain L Barnard, Rebecca A Daly & Mary K Firestone

Keywords: community rRNAmicrobial activitymicrobial growthribosomesenvironmental samplesecosystem processes

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Multifactorial diversity sustains microbial community stability (2013)

Oylum Erkus; Victor CL de Jager; Maciej Spus; Ingrid J van Alen-Boerrigter; Irma MH van Rijswijck; Lucie Hazelwood; Patrick WM Janssen; Sacha AFT van Hijum; Michiel Kleerebezem; Eddy J Smid

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Publication Date: 2013-10-23

Description: Multifactorial diversity sustains microbial community stability The ISME Journal 7, 2126 (November 2013). doi:10.1038/ismej.2013.108 Authors: Oylum Erkus, Victor CL de Jager, Maciej Spus, Ingrid J van Alen-Boerrigter, Irma MH van Rijswijck, Lucie Hazelwood, Patrick WM Janssen, Sacha AFT van Hijum, Michiel Kleerebezem & Eddy J Smid

Keywords: genetic diversitymetagenomicsmicrobial communityphage predationstability

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Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model (2013)

Jonathan McCafferty; Marcus Mühlbauer; Raad Z Gharaibeh; Janelle C Arthur; Ernesto Perez-Chanona; Wei Sha; Christian Jobin; Anthony A Fodor

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Publication Date: 2013-10-23

Description: Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model The ISME Journal 7, 2116 (November 2013). doi:10.1038/ismej.2013.106 Authors: Jonathan McCafferty, Marcus Mühlbauer, Raad Z Gharaibeh, Janelle C Arthur, Ernesto Perez-Chanona, Wei Sha, Christian Jobin & Anthony A Fodor

Keywords: cagetimesuccessionmicrobiomemixed linear models

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Microbial minorities modulate methane consumption through niche partitioning (2013)

Paul LE Bodelier; Marion Meima-Franke; Cornelis A Hordijk; Anne K Steenbergh; Mariet M Hefting; Levente Bodrossy; Martin von Bergen; Jana Seifert

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Publication Date: 2013-10-23

Description: Microbial minorities modulate methane consumption through niche partitioning The ISME Journal 7, 2214 (November 2013). doi:10.1038/ismej.2013.99 Authors: Paul LE Bodelier, Marion Meima-Franke, Cornelis A Hordijk, Anne K Steenbergh, Mariet M Hefting, Levente Bodrossy, Martin von Bergen & Jana Seifert

Keywords: biodiversity–ecosystem functioning ; methane oxidationstable isotope labelingproteomicswetlands

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Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP (2013)

Tony Gutierrez; David R Singleton; David Berry; Tingting Yang; Michael D Aitken; Andreas Teske

Springer Nature

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Publication Date: 2013-10-23

Description: Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP The ISME Journal 7, 2091 (November 2013). doi:10.1038/ismej.2013.98 Authors: Tony Gutierrez, David R Singleton, David Berry, Tingting Yang, Michael D Aitken & Andreas Teske

Keywords: biodegradationDeepwater HorizonGulf of Mexicomarine bacteriapolycyclic aromatic hydrocarbonsstable-isotope probing

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Quantifying community assembly processes and identifying features that impose them (2013)

James C Stegen; Xueju Lin; Jim K Fredrickson; Xingyuan Chen; David W Kennedy; Christopher J Murray; Mark L Rockhold; Allan Konopka

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Publication Date: 2013-10-23

Description: Quantifying community assembly processes and identifying features that impose them The ISME Journal 7, 2069 (November 2013). doi:10.1038/ismej.2013.93 Authors: James C Stegen, Xueju Lin, Jim K Fredrickson, Xingyuan Chen, David W Kennedy, Christopher J Murray, Mark L Rockhold & Allan Konopka

Keywords: metacommunity assemblyHanford Siteneutral theoryniche theorynull modelsphylogenetic beta diversity

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Evidence for successional development in Antarctic hypolithic bacterial communities (2013)

Thulani P Makhalanyane; Angel Valverde; Nils-Kåre Birkeland; Stephen C Cary; I Marla Tuffin; Don A Cowan

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Publication Date: 2013-10-23

Description: Evidence for successional development in Antarctic hypolithic bacterial communities The ISME Journal 7, 2080 (November 2013). doi:10.1038/ismej.2013.94 Authors: Thulani P Makhalanyane, Angel Valverde, Nils-Kåre Birkeland, Stephen C Cary, I Marla Tuffin & Don A Cowan

Keywords: Antarcticacommunity assemblyhypolithspyrosequencingsoilsuccessionT-RFLP

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Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent (2013)

Shi Feng; Shane M Powell; Richard Wilson; John P Bowman

Springer Nature

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Publication Date: 2013-10-23

Description: Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent The ISME Journal 7, 2206 (November 2013). doi:10.1038/ismej.2013.97 Authors: Shi Feng, Shane M Powell, Richard Wilson & John P Bowman

Keywords: post-transcriptional regulationproteomicsproteorhodopsinsalinity stresssea-ice

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The protective role of endogenous bacterial communities in chironomid egg masses and larvae (2013)

Yigal Senderovich; Malka Halpern

Springer Nature

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Publication Date: 2013-10-23

Description: The protective role of endogenous bacterial communities in chironomid egg masses and larvae The ISME Journal 7, 2147 (November 2013). doi:10.1038/ismej.2013.100 Authors: Yigal Senderovich & Malka Halpern

Keywords: Chironomidegg masslarvaepyrosequensingpollutantKoch postulatesmetaldetoxification

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Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust (2013)

Lara Rajeev; Ulisses Nunes da Rocha; Niels Klitgord; Eric G Luning; Julian Fortney; Seth D Axen; Patrick M Shih; Nicholas J Bouskill; Benjamin P Bowen; Cheryl A Kerfeld; Ferran Garcia-Pichel; Eoin L Brodie; Trent R Northen; Aindrila Mukhopadhyay

Springer Nature

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Publication Date: 2013-10-23

Description: Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust The ISME Journal 7, 2178 (November 2013). doi:10.1038/ismej.2013.83 Authors: Lara Rajeev, Ulisses Nunes da Rocha, Niels Klitgord, Eric G Luning, Julian Fortney, Seth D Axen, Patrick M Shih, Nicholas J Bouskill, Benjamin P Bowen, Cheryl A Kerfeld, Ferran Garcia-Pichel, Eoin L Brodie, Trent R Northen & Aindrila Mukhopadhyay

Keywords: biological soil crustdesiccation survivaldormancyMicrocoleus vaginatuspulsed-activity eventresuscitation

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Low temperature delays timing and enhances the cost of nitrogen fixation in the unicellular cyanobacterium Cyanothece (2013)

Verena S Brauer; Maayke Stomp; Camillo Rosso; Sebastiaan AM van Beusekom; Barbara Emmerich; Lucas J Stal; Jef Huisman

Springer Nature

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Publication Date: 2013-10-23

Description: Low temperature delays timing and enhances the cost of nitrogen fixation in the unicellular cyanobacterium Cyanothece The ISME Journal 7, 2105 (November 2013). doi:10.1038/ismej.2013.103 Authors: Verena S Brauer, Maayke Stomp, Camillo Rosso, Sebastiaan AM van Beusekom, Barbara Emmerich, Lucas J Stal & Jef Huisman

Keywords: climate changeday–night cyclenitrogenasenitrogen fixationrespirationunicellular cyanobacteria

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Acetate oxidation by syntrophic association between Geobacter sulfurreducens and a hydrogen-utilizing exoelectrogen (2013)

Zen-ichiro Kimura; Satoshi Okabe

Springer Nature

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Publication Date: 2013-07-24

Description: Acetate oxidation by syntrophic association between Geobacter sulfurreducens and a hydrogen-utilizing exoelectrogen The ISME Journal 7, 1472 (August 2013). doi:10.1038/ismej.2013.40 Authors: Zen-ichiro Kimura & Satoshi Okabe

Keywords: syntrophic acetate oxidationGeobacterHydrogenophagamicrobial fuel cellinterspecies hydrogen transfer

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Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria (2013)

Karel Šimek; Vojtěch KasalickýJan Jezbera; Karel Horňák; Jiří Nedoma; Martin W Hahn; David Bass; Steffen Jost; Jens Boenigk

Springer Nature

In: ISME Journal

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Publication Date: 2013-07-24

Description: Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria The ISME Journal 7, 1519 (August 2013). doi:10.1038/ismej.2013.57 Authors: Karel Šimek, Vojtěch Kasalický, Jan Jezbera, Karel Horňák, Jiří Nedoma, Martin W Hahn, David Bass, Steffen Jost & Jens Boenigk

Keywords: flagellate community compositionfreshwaterflagellate growthfood quality of bacteriaLimnohabitans454 pyrosequencing

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Chlamydomonas reinhardtii thermal tolerance enhancement mediated by a mutualistic interaction with vitamin B12-producing bacteria (2013)

Bo Xie; Shawn Bishop; Dan Stessman; David Wright; Martin H Spalding; Larry J Halverson

Springer Nature

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Description: Chlamydomonas reinhardtii thermal tolerance enhancement mediated by a mutualistic interaction with vitamin B12-producing bacteria The ISME Journal 7, 1544 (August 2013). doi:10.1038/ismej.2013.43 Authors: Bo Xie, Shawn Bishop, Dan Stessman, David Wright, Martin H Spalding & Larry J Halverson

Keywords: bacteria–algae interactionscobalamin-independent methionine synthasecobalamin-dependent methionine synthasegene regulationstress tolerancevitamin B12

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Loss in microbial diversity affects nitrogen cycling in soil (2013)

Laurent Philippot; Aymé Spor; Catherine Hénault; David Bru; Florian Bizouard; Christopher M Jones; Amadou Sarr; Pierre-Alain Maron

Springer Nature

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Description: Loss in microbial diversity affects nitrogen cycling in soil The ISME Journal 7, 1609 (August 2013). doi:10.1038/ismej.2013.34 Authors: Laurent Philippot, Aymé Spor, Catherine Hénault, David Bru, Florian Bizouard, Christopher M Jones, Amadou Sarr & Pierre-Alain Maron

Keywords: biodiversityecosystem functioningdenitrificationfunctional redundancynitrogen cyclingsoil

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Microbial biodiversity in glacier-fed streams (2013)

Linda Wilhelm; Gabriel A Singer; Christina Fasching; Tom J Battin; Katharina Besemer

Springer Nature

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Publication Date: 2013-07-24

Description: Microbial biodiversity in glacier-fed streams The ISME Journal 7, 1651 (August 2013). doi:10.1038/ismej.2013.44 Authors: Linda Wilhelm, Gabriel A Singer, Christina Fasching, Tom J Battin & Katharina Besemer

Keywords: Biofilmglacier-fed streamsmicrobial diversityclimate changemetacommunity ecology

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Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea (2013)

Ricardo J Eloy Alves; Wolfgang Wanek; Anna Zappe; Andreas Richter; Mette M Svenning; Christa Schleper; Tim Urich

Springer Nature

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Description: Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea The ISME Journal 7, 1620 (August 2013). doi:10.1038/ismej.2013.35 Authors: Ricardo J Eloy Alves, Wolfgang Wanek, Anna Zappe, Andreas Richter, Mette M Svenning, Christa Schleper & Tim Urich

Keywords: ammonia-oxidizing archaeaarctic soilsamoAThaumarchaeotanitrification15N pool dilution

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Temporal variability in soil microbial communities across land-use types (2013)

Christian L Lauber; Kelly S Ramirez; Zach Aanderud; Jay Lennon; Noah Fierer

Springer Nature

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Publication Date: 2013-07-24

Description: Temporal variability in soil microbial communities across land-use types The ISME Journal 7, 1641 (August 2013). doi:10.1038/ismej.2013.50 Authors: Christian L Lauber, Kelly S Ramirez, Zach Aanderud, Jay Lennon & Noah Fierer

Keywords: temporal diversity16S rRNApyrosequencingland usesoil moisturebiogeochemistry

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Mesoscale distribution and functional diversity of picoeukaryotes in the first-year sea ice of the Canadian Arctic (2013)

Kasia Piwosz; Józef Maria Wiktor; Andrea Niemi; Agnieszka Tatarek; Christine Michel

Springer Nature

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Description: Mesoscale distribution and functional diversity of picoeukaryotes in the first-year sea ice of the Canadian Arctic The ISME Journal 7, 1461 (August 2013). doi:10.1038/ismej.2013.39 Authors: Kasia Piwosz, Józef Maria Wiktor, Andrea Niemi, Agnieszka Tatarek & Christine Michel

Keywords: first-year sea icepicoeukaryoteschlorophytescryptophytesstramenopilesSyndiniales Group II

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Bacterial community structure on two alpine debris-covered glaciers and biogeography of Polaromonas phylotypes (2013)

Andrea Franzetti; Valeria Tatangelo; Isabella Gandolfi; Valentina Bertolini; Giuseppina Bestetti; Guglielmina Diolaiuti; Carlo D'Agata; Claudia Mihalcea; Claudio Smiraglia; Roberto Ambrosini

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Description: Bacterial community structure on two alpine debris-covered glaciers and biogeography of Polaromonas phylotypes The ISME Journal 7, 1483 (August 2013). doi:10.1038/ismej.2013.48 Authors: Andrea Franzetti, Valeria Tatangelo, Isabella Gandolfi, Valentina Bertolini, Giuseppina Bestetti, Guglielmina Diolaiuti, Carlo D'Agata, Claudia Mihalcea, Claudio Smiraglia & Roberto Ambrosini

Keywords: biogeographycolonizationIlluminapsychrophilessoil developmentsuccession

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A meta-analysis of changes in bacterial and archaeal communities with time (2013)

Ashley Shade; J Gregory Caporaso; Jo Handelsman; Rob Knight; Noah Fierer

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Description: A meta-analysis of changes in bacterial and archaeal communities with time The ISME Journal 7, 1493 (August 2013). doi:10.1038/ismej.2013.54 Authors: Ashley Shade, J Gregory Caporaso, Jo Handelsman, Rob Knight & Noah Fierer

Keywords: similarity-decayspecies–time relationshipbeta diversity16S rRNAturnoverhigh-throughput sequencing

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Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters (2013)

Christian Winter; Blake Matthews; Curtis A Suttle

Springer Nature

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Description: Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters The ISME Journal 7, 1507 (August 2013). doi:10.1038/ismej.2013.56 Authors: Christian Winter, Blake Matthews & Curtis A Suttle

Keywords: metacommunity frameworkoceanprokaryotesvirusesdispersal

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The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia (2013)

Andrea M Sass; Crystal Schmerk; Kirsty Agnoli; Phillip J Norville; Leo Eberl; Miguel A Valvano; Eshwar Mahenthiralingam

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Description: The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia The ISME Journal 7, 1568 (August 2013). doi:10.1038/ismej.2013.36 Authors: Andrea M Sass, Crystal Schmerk, Kirsty Agnoli, Phillip J Norville, Leo Eberl, Miguel A Valvano & Eshwar Mahenthiralingam

Keywords: anoxiaBurkholderiapathogenicitypersistencesurvivaltranscriptomics

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Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3 (2013)

Dheeraj Kanaparthi; Bianca Pommerenke; Peter Casper; Marc G Dumont

Springer Nature

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Description: Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3 The ISME Journal 7, 1582 (August 2013). doi:10.1038/ismej.2013.38 Authors: Dheeraj Kanaparthi, Bianca Pommerenke, Peter Casper & Marc G Dumont

Keywords: TM3 group Actinobacteriachemolithotrophic nitrate-dependent Fe(II) oxidationstable isotope probing (SIP)pyrosequencing

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Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California) (2013)

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

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Description: Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California) The ISME Journal 7, 1595 (August 2013). doi:10.1038/ismej.2013.18 Authors: Adrien Vigneron, Perrine Cruaud, Patricia Pignet, Jean-Claude Caprais, Marie-Anne Cambon-Bonavita, Anne Godfroy & Laurent Toffin

Keywords: ANMEAOMArchaeaFISHQ-PCRSonora Margin

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Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns (2013)

Raquel Rodríguez-Martínez; Gabrielle Rocap; Guillem Salazar; Ramon Massana

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Description: Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns The ISME Journal 7, 1531 (August 2013). doi:10.1038/ismej.2013.53 Authors: Raquel Rodríguez-Martínez, Gabrielle Rocap, Guillem Salazar & Ramon Massana

Keywords: biogeographyITS1ARISAtemperaturefixation indexMAST-4

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Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts (2013)

J G Sanders; R A Beinart; F J Stewart; E F Delong; P R Girguis

Springer Nature

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Description: Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts The ISME Journal 7, 1556 (August 2013). doi:10.1038/ismej.2013.45 Authors: J G Sanders, R A Beinart, F J Stewart, E F Delong & P R Girguis

Keywords: symbiosishydrothermal ventsmetatranscriptomicschemoautotrophyAlviniconcha

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Diatom assemblages promote ice formation in large lakes (2013)

N A D'souza; Y Kawarasaki; J D Gantz; R E Lee; B F N Beall; Y M Shtarkman; Z A Koçer; S O Rogers; H Wildschutte; G S Bullerjahn; R M L McKay

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Description: Diatom assemblages promote ice formation in large lakes The ISME Journal 7, 1632 (August 2013). doi:10.1038/ismej.2013.49 Authors: N A D'souza, Y Kawarasaki, J D Gantz, R E Lee, B F N Beall, Y M Shtarkman, Z A Koçer, S O Rogers, H Wildschutte, G S Bullerjahn & R M L McKay

Keywords: diatomsice nucleationlakePseudomonas

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Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients (2013)

Paul G Dennis; Justin Seymour; Kimber Kumbun; Gene W Tyson

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Description: Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients The ISME Journal 7, 1661 (August 2013). doi:10.1038/ismej.2013.47 Authors: Paul G Dennis, Justin Seymour, Kimber Kumbun & Gene W Tyson

Keywords: chemotaxismicrobial communities16S rRNA geneinorganic substrates

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Heterogeneity in the nutrient limitation of different bacterioplankton groups in the Eastern Mediterranean Sea (2013)

Marta Sebastián; Josep M Gasol

Springer Nature

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Publication Date: 2013-07-24

Description: Heterogeneity in the nutrient limitation of different bacterioplankton groups in the Eastern Mediterranean Sea The ISME Journal 7, 1665 (August 2013). doi:10.1038/ismej.2013.42 Authors: Marta Sebastián & Josep M Gasol

Keywords: nutrient limitationheterotrophic bacteriaphosphorusMediterranean SeaMARFISH

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Ocean currents shape the microbiome of Arctic marine sediments (2013)

Leila J Hamdan; Richard B Coffin; Masoumeh Sikaroodi; Jens Greinert; Tina Treude; Patrick M Gillevet

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Publication Date: 2013-03-20

Description: Ocean currents shape the microbiome of Arctic marine sediments The ISME Journal 7, 685 (April 2013). doi:10.1038/ismej.2012.143 Authors: Leila J Hamdan, Richard B Coffin, Masoumeh Sikaroodi, Jens Greinert, Tina Treude & Patrick M Gillevet

Keywords: Arcticbiogeographymethanemicrobiomesedimentwater

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Reducing bias in bacterial community analysis of lower respiratory infections (2013)

Geraint B Rogers; Leah Cuthbertson; Lucas R Hoffman; Peter AC Wing; Christopher Pope; Danny A P Hooftman; Andrew K Lilley; Anna Oliver; Mary P Carroll; Kenneth D Bruce; Christopher J van der Gast

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Description: Reducing bias in bacterial community analysis of lower respiratory infections The ISME Journal 7, 697 (April 2013). doi:10.1038/ismej.2012.145 Authors: Geraint B Rogers, Leah Cuthbertson, Lucas R Hoffman, Peter AC Wing, Christopher Pope, Danny A P Hooftman, Andrew K Lilley, Anna Oliver, Mary P Carroll, Kenneth D Bruce & Christopher J van der Gast

Keywords: propidium monoazidepyrosequencingmetacommunityquantitative PCRcystic fibrosiscommonness and rarity

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The chemical interactome space between the human host and the genetically defined gut metabotypes (2013)

Ulrik Plesner Jacobsen; Henrik Bjørn Nielsen; Falk Hildebrand; Jeroen Raes; Thomas Sicheritz-Ponten; Irene Kouskoumvekaki; Gianni Panagiotou

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Description: The chemical interactome space between the human host and the genetically defined gut metabotypes The ISME Journal 7, 730 (April 2013). doi:10.1038/ismej.2012.141 Authors: Ulrik Plesner Jacobsen, Henrik Bjørn Nielsen, Falk Hildebrand, Jeroen Raes, Thomas Sicheritz-Ponten, Irene Kouskoumvekaki & Gianni Panagiotou

Keywords: microbiomemetabolic networkdrugsprotein interactionsdiseases

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Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities (2013)

Jessica K Cole; Joseph P Peacock; Jeremy A Dodsworth; Amanda J Williams; Daniel B Thompson; Hailiang Dong; Geng Wu; Brian P Hedlund

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Description: Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities The ISME Journal 7, 718 (April 2013). doi:10.1038/ismej.2012.157 Authors: Jessica K Cole, Joseph P Peacock, Jeremy A Dodsworth, Amanda J Williams, Daniel B Thompson, Hailiang Dong, Geng Wu & Brian P Hedlund

Keywords: archaeabacteriapyrosequencingthermophilesGreat Basinmicrobial community

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Microbiota conservation and BMI signatures in adult monozygotic twins (2013)

Sebastian Tims; Catherine Derom; Daisy M Jonkers; Robert Vlietinck; Wim H Saris; Michiel Kleerebezem; Willem M de Vos; Erwin G Zoetendal

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Description: Microbiota conservation and BMI signatures in adult monozygotic twins The ISME Journal 7, 707 (April 2013). doi:10.1038/ismej.2012.146 Authors: Sebastian Tims, Catherine Derom, Daisy M Jonkers, Robert Vlietinck, Wim H Saris, Michiel Kleerebezem, Willem M de Vos & Erwin G Zoetendal

Keywords: BMI signaturesdiscordant BMIgastrointestinal tractmicrobiotamonozygotic twins

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Microbial metabolic exchange in 3D (2013)

Jeramie D Watrous; Vanessa V Phelan; Cheng-Chih Hsu; Wilna J Moree; Brendan M Duggan; Theodore Alexandrov; Pieter C Dorrestein

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Description: Microbial metabolic exchange in 3D The ISME Journal 7, 770 (April 2013). doi:10.1038/ismej.2012.155 Authors: Jeramie D Watrous, Vanessa V Phelan, Cheng-Chih Hsu, Wilna J Moree, Brendan M Duggan, Theodore Alexandrov & Pieter C Dorrestein

Keywords: MALDIimaging mass spectrometrymicrobial interactions

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Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon (2013)

Sahar El Aidy; Muriel Derrien; Claire A Merrifield; Florence Levenez; Joël DoréMark V Boekschoten; Jan Dekker; Elaine Holmes; Erwin G Zoetendal; Peter van Baarlen; Sandrine P Claus; Michiel Kleerebezem

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Description: Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon The ISME Journal 7, 743 (April 2013). doi:10.1038/ismej.2012.142 Authors: Sahar El Aidy, Muriel Derrien, Claire A Merrifield, Florence Levenez, Joël Doré, Mark V Boekschoten, Jan Dekker, Elaine Holmes, Erwin G Zoetendal, Peter van Baarlen, Sandrine P Claus & Michiel Kleerebezem

Keywords: C57BL6 J germfree micemicrobiotatranscriptomemetabonome

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Phylogenetic conservatism of functional traits in microorganisms (2013)

Adam C Martiny; Kathleen Treseder; Gordon Pusch

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Description: Phylogenetic conservatism of functional traits in microorganisms The ISME Journal 7, 830 (April 2013). doi:10.1038/ismej.2012.160 Authors: Adam C Martiny, Kathleen Treseder & Gordon Pusch

Keywords: PhylogenomicsSEEDtraitslateral gene transferBiologconsenTRAIT

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Metabolic activity of subterranean microbial communities in deep granitic groundwater supplemented with methane and H2 (2013)

Karsten Pedersen

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Description: Metabolic activity of subterranean microbial communities in deep granitic groundwater supplemented with methane and H2 The ISME Journal 7, 839 (April 2013). doi:10.1038/ismej.2012.144 Author: Karsten Pedersen

Keywords: acetateAMOATPredox potentialbacteriophagemicroarray

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Microbial hitchhikers on intercontinental dust: catching a lift in Chad (2013)

Jocelyne Favet; Ales Lapanje; Adriana Giongo; Suzanne Kennedy; Yin-Yin Aung; Arlette Cattaneo; Austin G Davis-Richardson; Christopher T Brown; Renate Kort; Hans-Jürgen Brumsack; Bernhard Schnetger; Adrian Chappell; Jaap Kroijenga; Andreas Beck; Karin Schwibbert; Ahmed H Mohamed; Timothy Kirchner; Patricia Dorr de Quadros; Eric W Triplett; William J Broughton; Anna A Gorbushina

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Publication Date: 2013-03-20

Description: Microbial hitchhikers on intercontinental dust: catching a lift in Chad The ISME Journal 7, 850 (April 2013). doi:10.1038/ismej.2012.152 Authors: Jocelyne Favet, Ales Lapanje, Adriana Giongo, Suzanne Kennedy, Yin-Yin Aung, Arlette Cattaneo, Austin G Davis-Richardson, Christopher T Brown, Renate Kort, Hans-Jürgen Brumsack, Bernhard Schnetger, Adrian Chappell, Jaap Kroijenga, Andreas Beck, Karin Schwibbert, Ahmed H Mohamed, Timothy Kirchner, Patricia Dorr de Quadros, Eric W Triplett, William J Broughton & Anna A Gorbushina

Keywords: aeolianhigh throughput sequencingBodélé DepressionRepublic of Chadwind erosion

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Microbial composition affects the functioning of estuarine sediments (2013)

Heather E Reed; Jennifer BH Martiny

Springer Nature

In: ISME Journal

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Publication Date: 2013-03-20

Description: Microbial composition affects the functioning of estuarine sediments The ISME Journal 7, 868 (April 2013). doi:10.1038/ismej.2012.154 Authors: Heather E Reed & Jennifer BH Martiny

Keywords: ecosystem functioningcommon gardenreciprocal transplantestuary

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An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice (2013)

Na Fei; Liping Zhao

Springer Nature

In: ISME Journal

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Publication Date: 2013-03-20

Description: An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice The ISME Journal 7, 880 (April 2013). doi:10.1038/ismej.2012.153 Authors: Na Fei & Liping Zhao

Keywords: gut microbiotagermfree miceendotoxin-producing bacteriumobesityinsulin resistancehigh-fat diet

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86

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Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community (2013)

Kim M Handley; Nathan C Ver; Berkmoes; Carl I Steefel; Kenneth H Williams; Itai Sharon; Christopher S Miller; Kyle R Frischkorn; Karuna Chourey; Brian C Thomas; Manesh B Shah; Philip E Long; Robert L Hettich; Jillian F Banfield

Springer Nature

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Publication Date: 2013-03-20

Description: Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community The ISME Journal 7, 800 (April 2013). doi:10.1038/ismej.2012.148 Authors: Kim M Handley, Nathan C VerBerkmoes, Carl I Steefel, Kenneth H Williams, Itai Sharon, Christopher S Miller, Kyle R Frischkorn, Karuna Chourey, Brian C Thomas, Manesh B Shah, Philip E Long, Robert L Hettich & Jillian F Banfield

Keywords: autotrophmetagenomicsproteomicssedimentsubsurfacesyntrophy

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87

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By their genes ye shall know them: genomic signatures of predatory bacteria (2013)

Zohar Pasternak; Shmuel Pietrokovski; Or Rotem; Uri Gophna; Mor N Lurie-Weinberger; Edouard Jurkevitch

Springer Nature

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Publication Date: 2013-03-20

Description: By their genes ye shall know them: genomic signatures of predatory bacteria The ISME Journal 7, 756 (April 2013). doi:10.1038/ismej.2012.149 Authors: Zohar Pasternak, Shmuel Pietrokovski, Or Rotem, Uri Gophna, Mor N Lurie-Weinberger & Edouard Jurkevitch

Keywords: microbial predatorsbacterial predationcomparative genomicsBdellovibrio

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Bacterial colonization of Hydra hatchlings follows a robust temporal pattern (2013)

Sören Franzenburg; Sebastian Fraune; Philipp M Altrock; Sven Künzel; John F Baines; Arne Traulsen; Thomas CG Bosch

Springer Nature

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Publication Date: 2013-03-20

Description: Bacterial colonization of Hydra hatchlings follows a robust temporal pattern The ISME Journal 7, 781 (April 2013). doi:10.1038/ismej.2012.156 Authors: Sören Franzenburg, Sebastian Fraune, Philipp M Altrock, Sven Künzel, John F Baines, Arne Traulsen & Thomas CG Bosch

Keywords: bacterial dynamicscnidarianshost–microbe interactionmicrobiota

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Significant variation in transformation frequency in Streptococcus pneumoniae (2013)

Benjamin A Evans; Daniel E Rozen

Springer Nature

In: ISME Journal

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Publication Date: 2013-03-20

Description: Significant variation in transformation frequency in Streptococcus pneumoniae The ISME Journal 7, 791 (April 2013). doi:10.1038/ismej.2012.170 Authors: Benjamin A Evans & Daniel E Rozen

Keywords: Streptococcus pneumoniaetransformationcompetencefitness-associated recombination

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Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics (2013)

Luke C Burow; Dagmar Woebken; Ian PG Marshall; Erika A Lindquist; Brad M Bebout; Leslie Prufert-Bebout; Tori M Hoehler; Susannah G Tringe; Jennifer Pett-Ridge; Peter K Weber; Alfred M Spormann; Steven W Singer

Springer Nature

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Publication Date: 2013-03-20

Description: Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics The ISME Journal 7, 817 (April 2013). doi:10.1038/ismej.2012.150 Authors: Luke C Burow, Dagmar Woebken, Ian PG Marshall, Erika A Lindquist, Brad M Bebout, Leslie Prufert-Bebout, Tori M Hoehler, Susannah G Tringe, Jennifer Pett-Ridge, Peter K Weber, Alfred M Spormann & Steven W Singer

Keywords: metatranscriptomicsNanoSIMSanoxic carbon fluxfermentationglycogen

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Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism (2013)

Sasha G Tetu; Katy Breakwell; Liam D H Elbourne; Andrew J Holmes; Michael R Gillings; Ian T Paulsen

Springer Nature

In: ISME Journal

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Publication Date: 2013-05-22

Description: Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism The ISME Journal 7, 1227 (June 2013). doi:10.1038/ismej.2013.14 Authors: Sasha G Tetu, Katy Breakwell, Liam D H Elbourne, Andrew J Holmes, Michael R Gillings & Ian T Paulsen

Keywords: ammonia oxidising archaea (AOA)chemolithotrophymetagenomicsmicrobial communitynitrogen cyclingNullarbor caves

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Community-wide plasmid gene mobilization and selection (2013)

Vladimir Sentchilo; Antonia P Mayer; Lionel Guy; Ryo Miyazaki; Susannah Green Tringe; Kerrie Barry; Stephanie Malfatti; Alexander Goessmann; Marc Robinson-Rechavi; Jan R van der Meer

Springer Nature

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Publication Date: 2013-05-22

Description: Community-wide plasmid gene mobilization and selection The ISME Journal 7, 1173 (June 2013). doi:10.1038/ismej.2013.13 Authors: Vladimir Sentchilo, Antonia P Mayer, Lionel Guy, Ryo Miyazaki, Susannah Green Tringe, Kerrie Barry, Stephanie Malfatti, Alexander Goessmann, Marc Robinson-Rechavi & Jan R van der Meer

Keywords: metagenomic studiesmobilome

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Shift from widespread symbiont infection of host tissues to specific colonization of gills in juvenile deep-sea mussels (2013)

Cecilia Wentrup; Annelie Wendeberg; Julie Y Huang; Christian Borowski; Nicole Dubilier

Springer Nature

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Publication Date: 2013-05-22

Description: Shift from widespread symbiont infection of host tissues to specific colonization of gills in juvenile deep-sea mussels The ISME Journal 7, 1244 (June 2013). doi:10.1038/ismej.2013.5 Authors: Cecilia Wentrup, Annelie Wendeberg, Julie Y Huang, Christian Borowski & Nicole Dubilier

Keywords: BathymodiolusMid-Atlantic Ridgesymbiont transmissionhydrothermal vents

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Microbiology of Lonar Lake and other soda lakes (2013)

Chakkiath Paul Antony; Deepak Kumaresan; Sindy Hunger; Harold L Drake; J Colin Murrell; Yogesh S Shouche

Springer Nature

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Publication Date: 2013-05-22

Description: Microbiology of Lonar Lake and other soda lakes The ISME Journal 7, 1252 (June 2013). doi:10.1038/ismej.2013.22 Authors: Chakkiath Paul Antony, Deepak Kumaresan, Sindy Hunger, Harold L Drake, J Colin Murrell & Yogesh S Shouche

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The species-rich assemblages of tintinnids (marine planktonic protists) are structured by mouth size (2013)

John R Dolan; Michael R Landry; Mark E Ritchie

Springer Nature

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Publication Date: 2013-05-22

Description: The species-rich assemblages of tintinnids (marine planktonic protists) are structured by mouth size The ISME Journal 7, 1237 (June 2013). doi:10.1038/ismej.2013.23 Authors: John R Dolan, Michael R Landry & Mark E Ritchie

Keywords: biodiversityciliaterare speciesspecies packingtintinnida

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Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1 (2013)

Nadia C S Mykytczuk; Simon J Foote; Chris R Omelon; Gordon Southam; Charles W Greer; Lyle G Whyte

Springer Nature

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Publication Date: 2013-05-22

Description: Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1 The ISME Journal 7, 1211 (June 2013). doi:10.1038/ismej.2013.8 Authors: Nadia C S Mykytczuk, Simon J Foote, Chris R Omelon, Gordon Southam, Charles W Greer & Lyle G Whyte

Keywords: cryophilepermafrostcold-activecold/osmotic adaptationsubzero environments

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Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades (2013)

David M Baker; Jason P Andras; Adán Guillermo Jordán-Garza; Marilyn L Fogel

Springer Nature

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Publication Date: 2013-05-22

Description: Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades The ISME Journal 7, 1248 (June 2013). doi:10.1038/ismej.2013.12 Authors: David M Baker, Jason P Andras, Adán Guillermo Jordán-Garza & Marilyn L Fogel

Keywords: nitrogencoralsymbiosistemperatureSymbiodiniumstable isotopes

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Exploring the bovine rumen bacterial community from birth to adulthood (2013)

Elie Jami; Adi Israel; Assaf Kotser; Itzhak Mizrahi

Springer Nature

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Publication Date: 2013-05-22

Description: Exploring the bovine rumen bacterial community from birth to adulthood The ISME Journal 7, 1069 (June 2013). doi:10.1038/ismej.2013.2 Authors: Elie Jami, Adi Israel, Assaf Kotser & Itzhak Mizrahi

Keywords: gut colonizationgut microbiotamicrobial ecologymicrobiomerumen microbiology

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Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species (2013)

Alexander F Koeppel; Joel O Wertheim; Laura Barone; Nicole Gentile; Danny Krizanc; Frederick M Cohan

Springer Nature

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Publication Date: 2013-05-22

Description: Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species The ISME Journal 7, 1080 (June 2013). doi:10.1038/ismej.2013.3 Authors: Alexander F Koeppel, Joel O Wertheim, Laura Barone, Nicole Gentile, Danny Krizanc & Frederick M Cohan

Keywords: anagenesisbacteriacladogenesisecotypelaboratory evolutionspeciation

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Robust estimation of microbial diversity in theory and in practice (2013)

Bart Haegeman; Jérôme Hamelin; John Moriarty; Peter Neal; Jonathan Dushoff; Joshua S Weitz

Springer Nature

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Publication Date: 2013-05-22

Description: Robust estimation of microbial diversity in theory and in practice The ISME Journal 7, 1092 (June 2013). doi:10.1038/ismej.2013.10 Authors: Bart Haegeman, Jérôme Hamelin, John Moriarty, Peter Neal, Jonathan Dushoff & Joshua S Weitz

Keywords: Chao estimatorHill diversitiesmetagenomicsShannon diversitySimpson diversityspecies abundance distribution

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