ADVANCE ONLINE PUBLICATION

The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).
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July 14 2017

Perspective

Applying allometric theory to fungi

Carlos A Aguilar-Trigueros, Matthias C Rillig and Thomas W Crowther

ISME J advance online publication, July 14, 2017; doi:10.1038/ismej.2017.86

Original Article

An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community

Eeva Eronen-Rasimus, Anne-Mari Luhtanen, Janne-Markus Rintala, Bruno Delille, Gerhard Dieckmann, Antti Karkman and Jean-Louis Tison

ISME J advance online publication, July 14, 2017; doi:10.1038/ismej.2017.96

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July 11 2017

Original Articles

Optimised chronic infection models demonstrate that siderophore ‘cheating’ in Pseudomonas aeruginosa is context specific Open

Freya Harrison, Alan McNally, Ana C da Silva, Stephan Heeb and Stephen P Diggle

ISME J advance online publication, July 11, 2017; doi:10.1038/ismej.2017.103

Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy

Pawel Lycus, Kari Lovise Bøthun, Linda Bergaust, James Peele Shapleigh, Lars Reier Bakken and Åsa Frostegård

ISME J advance online publication, July 11, 2017; doi:10.1038/ismej.2017.82

Microbial survival strategies in ancient permafrost: insights from metagenomics Open

Rachel Mackelprang, Alexander Burkert, Monica Haw, Tara Mahendrarajah, Christopher H Conaway, Thomas A Douglas and Mark P Waldrop

ISME J advance online publication, July 11, 2017; doi:10.1038/ismej.2017.93

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization Open

Beate M Slaby, Thomas Hackl, Hannes Horn, Kristina Bayer and Ute Hentschel

ISME J advance online publication, July 11, 2017; doi:10.1038/ismej.2017.101

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June 23 2017

Original Articles

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community

David W Armitage

ISME J advance online publication, June 23, 2017; doi:10.1038/ismej.2017.99

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae Open

Astrid Collingro, Stephan Köstlbacher, Marc Mussmann, Ramunas Stepanauskas, Steven J Hallam and Matthias Horn

ISME J advance online publication, June 23, 2017; doi:10.1038/ismej.2017.95

Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community

Lily Momper, Sean P Jungbluth, Michael D Lee and Jan P Amend

ISME J advance online publication, June 23, 2017; doi:10.1038/ismej.2017.94

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June 16 2017

Original Article

A niche for cyanobacteria producing chlorophyll f within a microbial mat

Satoshi Ohkubo and Hideaki Miyashita

ISME J advance online publication, June 16, 2017; doi:10.1038/ismej.2017.98

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June 6 2017

Original Articles

Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment

Michael Baumgartner, Stefan Roffler, Thomas Wicker and Jakob Pernthaler

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.87

Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

Guillaume Borrel, Angela McCann, Jennifer Deane, Marta C Neto, Denise B Lynch, Jean- François Brugère and Paul W O'Toole

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.72

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

S Emilia Hannula, Elly Morriën, Mattias de Hollander, Wim H van der Putten, Johannes A van Veen and Wietse de Boer

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.90

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes Open

Yusuke Okazaki, Shohei Fujinaga, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi and Shin-ichi Nakano

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.89

Crenothrix are major methane consumers in stratified lakes Open

Kirsten Oswald, Jon S Graf, Sten Littmann, Daniela Tienken, Andreas Brand, Bernhard Wehrli, Mads Albertsen, Holger Daims, Michael Wagner, Marcel MM Kuypers, Carsten J Schubert and Jana Milucka

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.77

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

Juan E Pérez-Jaramillo, Víctor J Carrión, Mirte Bosse, Luiz F V Ferrão, Mattias de Hollander, Antonio A F Garcia, Camilo A Ramírez, Rodrigo Mendes and Jos M Raaijmakers

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.85

Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells Open

Robert W Read, Paul M Berube, Steven J Biller, Iva Neveux, Andres Cubillos-Ruiz, Sallie W Chisholm and Joseph J Grzymski

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.88

Identifying the core seed bank of a complex boreal bacterial metacommunity

Clara Ruiz-González, Juan Pablo Niño-García, Steven W Kembel and Paul A del Giorgio

ISME J advance online publication, June 6, 2017; doi:10.1038/ismej.2017.67

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June 2 2017

Mini Review

Capturing the genetic makeup of the active microbiome in situ  Open

Esther Singer, Michael Wagner and Tanja Woyke

ISME J advance online publication, June 2, 2017; doi:10.1038/ismej.2017.59

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May 26 2017

Original Articles

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA Open

Christian F Edwardson and James T Hollibaugh

ISME J advance online publication, May 26, 2017; doi:10.1038/ismej.2017.80

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding

Zehra Esra Ilhan, John K DiBaise, Nancy G Isern, David W Hoyt, Andrew K Marcus, Dae-Wook Kang, Michael D Crowell, Bruce E Rittmann and Rosa Krajmalnik-Brown

ISME J advance online publication, May 26, 2017; doi:10.1038/ismej.2017.71

Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate

Xinguo Shi, Xin Lin, Ling Li, Meizhen Li, Brian Palenik and Senjie Lin

ISME J advance online publication, May 26, 2017; doi:10.1038/ismej.2017.81

Co-evolution with Staphylococcus aureus leads to lipopolysaccharide alterations in Pseudomonas aeruginosa

Mikael Tognon, Thilo Köhler, Bartosz G Gdaniec, Youai Hao, Joseph S Lam, Marie Beaume, Alexandre Luscher, Angus Buckling and Christian van Delden

ISME J advance online publication, May 26, 2017; doi:10.1038/ismej.2017.83

Short Communication

The endobacterium of an arbuscular mycorrhizal fungus modulates the expression of its toxin–antitoxin systems during the life cycle of its host

Alessandra Salvioli di Fossalunga, Justine Lipuma, Francesco Venice, Laurence Dupont and Paola Bonfante

ISME J advance online publication, May 26, 2017; doi:10.1038/ismej.2017.84

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May 23 2017

Original Articles

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean Open

Kyle R Frischkorn, Mónica Rouco, Benjamin A S Van Mooy and Sonya T Dyhrman

ISME J advance online publication, May 23, 2017; doi:10.1038/ismej.2017.74

A tale of two risks: smoking, diabetes and the subgingival microbiome Open

Sukirth M Ganesan, Vinayak Joshi, Megan Fellows, Shareef M Dabdoub, Haikady N Nagaraja, Benjamin O'Donnell, Neeta Rohit Deshpande and Purnima S Kumar

ISME J advance online publication, May 23, 2017; doi:10.1038/ismej.2017.73

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations

Felix Goldschmidt, Roland R Regoes and David R Johnson

ISME J advance online publication, May 23, 2017; doi:10.1038/ismej.2017.76

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling

Linwei Wu, Yunfeng Yang, Shiping Wang, Haowei Yue, Qiaoyan Lin, Yigang Hu, Zhili He, Joy D Van Nostrand, Lauren Hale, Xiangzhen Li, Jack A Gilbert and Jizhong Zhou

ISME J advance online publication, May 23, 2017; doi:10.1038/ismej.2017.75

Short Communication

Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria

Isabel Ferrera, Olga Sánchez, Eva Kolářová, Michal Koblížek and Josep M Gasol

ISME J advance online publication, May 23, 2017; doi:10.1038/ismej.2017.79

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May 19 2017

Original Articles

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass Open

Tulika Arora, Florian Seyfried, Neil G Docherty, Valentina Tremaroli, Carel W le Roux, Rosie Perkins and Fredrik Bäckhed

ISME J advance online publication, May 19, 2017; doi:10.1038/ismej.2017.70

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus

Nadav Kashtan, Sara E Roggensack, Jessie W Berta-Thompson, Maor Grinberg, Ramunas Stepanauskas and Sallie W Chisholm

ISME J advance online publication, May 19, 2017; doi:10.1038/ismej.2017.64

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis Open

Ramon Terrado, Alexis L Pasulka, Alle A-Y Lie, Victoria J Orphan, Karla B Heidelberg and David A Caron

ISME J advance online publication, May 19, 2017; doi:10.1038/ismej.2017.68

Succession in the petroleum reservoir microbiome through an oil field production lifecycle Open

Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head and Nicolas Tsesmetzis

ISME J advance online publication, May 19, 2017; doi:10.1038/ismej.2017.78

Short Communication

In situ light responses of the proteorhodopsin-bearing Antarctic sea-ice bacterium, Psychroflexus torques

David J Burr, Andrew Martin, Elizabeth W Maas and Ken G Ryan

ISME J advance online publication, May 19, 2017; doi:10.1038/ismej.2017.65

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May 16 2017

Winogradsky Review

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations

Richard E Lenski

ISME J advance online publication, May 16, 2017; doi:10.1038/ismej.2017.69

Perspective

Microbial contributions to the persistence of coral reefs Open

Nicole S Webster and Thorsten B H Reusch

ISME J advance online publication, May 16, 2017; doi:10.1038/ismej.2017.66

Original Article

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes Open

Laura Baldo, Joan Lluís Pretus, Joan Lluís Riera, Zuzana Musilova, Arnold Roger Bitja Nyom and Walter Salzburger

ISME J advance online publication, May 16, 2017; doi:10.1038/ismej.2017.62

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May 12 2017

Original Article

Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera Open

Bob G Blasdel, Anne Chevallereau, Marc Monot, Rob Lavigne and Laurent Debarbieux

ISME J advance online publication, May 12, 2017; doi:10.1038/ismej.2017.63

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May 5 2017

Perspective

Multi-stability and the origin of microbial community types Open

Didier Gonze, Leo Lahti, Jeroen Raes and Karoline Faust

ISME J advance online publication, May 5, 2017; doi:10.1038/ismej.2017.60

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April 21 2017

Original Article

Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs Open

Raisa Mäkipää, Tiina Rajala, Dmitry Schigel, Katja T Rinne, Taina Pennanen, Nerea Abrego and Otso Ovaskainen

ISME J advance online publication, April 21, 2017; doi:10.1038/ismej.2017.57

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April 14 2017

Perspective

Soil aggregates as massively concurrent evolutionary incubators Open

Matthias C Rillig, Ludo AH Muller and Anika Lehmann

ISME J advance online publication, April 14, 2017; doi:10.1038/ismej.2017.56