TABLE OF CONTENTS
Volume 3, Issue 2 (February 2009)
Perspective
The role of microorganisms in coral bleaching
Eugene Rosenberg, Ariel Kushmaro, Esti Kramarsky-Winter, Ehud Banin and Loya Yossi
ISME J 3: 139-146; advance online publication, November 13, 2008; doi:10.1038/ismej.2008.104
Original Articles
Microbial Population and Community Ecology
Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea
Daniele De Corte, Taichi Yokokawa, Marta M Varela, Hélène Agogué and Gerhard J Herndl
ISME J 3: 147-158; advance online publication, September 25, 2008; doi:10.1038/ismej.2008.94
Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon
Luis R Comolli, Brett J Baker, Kenneth H Downing, Cristina E Siegerist and Jillian F Banfield
ISME J 3: 159-167; advance online publication, October 23, 2008; doi:10.1038/ismej.2008.99
Selective progressive response of soil microbial community to wild oat roots
Kristen M DeAngelis, Eoin L Brodie, Todd Z DeSantis, Gary L Andersen, Steven E Lindow and Mary K Firestone
ISME J 3: 168-178; advance online publication, November 13, 2008; doi:10.1038/ismej.2008.103
Microbe-Microbe and Microbe-Host Interactions
Shotgun metaproteomics of the human distal gut microbiota
Nathan C Verberkmoes, Alison L Russell, Manesh Shah, Adam Godzik, Magnus Rosenquist, Jonas Halfvarson, Mark G Lefsrud, Juha Apajalahti, Curt Tysk, Robert L Hettich and Janet K Jansson
ISME J 3: 179-189; advance online publication, October 30, 2008; doi:10.1038/ismej.2008.108
Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi
Sachie Höppener-Ogawa, Johan HJ Leveau, Johannes A van Veen and Wietse De Boer
ISME J 3: 190-198; advance online publication, October 16, 2008; doi:10.1038/ismej.2008.97
Evolutionary Genetics
A comparison of homologous recombination rates in bacteria and archaea
Michiel Vos and Xavier Didelot
ISME J 3: 199-208; advance online publication, October 2, 2008; doi:10.1038/ismej.2008.93
Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons?
Michael R Gillings, Duan Xuejun, Simon A Hardwick, Marita P Holley and H W Stokes
ISME J 3: 209-215; advance online publication, October 16, 2008; doi:10.1038/ismej.2008.98
Integrated Genomics and Post-Genomics Approaches in Microbial Ecology
Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments
Dawn E Holmes, Regina A O'Neil, Milind A Chavan, Lucie A N'Guessan, Helen A Vrionis, Lorrie A Perpetua, M Juliana Larrahondo, Raymond DiDonato, Anna Liu and Derek R Lovley
ISME J 3: 216-230; advance online publication, October 9, 2008; doi:10.1038/ismej.2008.89
Geomicrobiology and Microbial Contributions to Geochemical Cycles
Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts
Olivia U Mason, Carol A Di Meo-Savoie, Joy D Van Nostrand, Jizhong Zhou, Martin R Fisk and Stephen J Giovannoni
ISME J 3: 231-242; advance online publication, October 9, 2008; doi:10.1038/ismej.2008.92
Microbial Ecology and Functional Diversity of Natural Habitats
Functional metagenomics reveals diverse 
-lactamases in a remote Alaskan soil
Heather K Allen, Luke A Moe, Jitsupang Rodbumrer, Andra Gaarder and Jo Handelsman
ISME J 3: 243-251; advance online publication, October 9, 2008; doi:10.1038/ismej.2008.86
Effects of temperature on growth rate and gross growth efficiency of an Antarctic bacterivorous protist
Julie M Rose, Neil M Vora, Peter D Countway, Rebecca J Gast and David A Caron
ISME J 3: 252-260; advance online publication, October 9, 2008; doi:10.1038/ismej.2008.96
Short Communications
Microbe-Microbe and Microbe-Host Interactions
Interaction of Salmonella enterica with basil and other salad leaves
Cedric N Berger, Robert K Shaw, Derek J Brown, Henry Mather, Simon Clare, Gordon Dougan, Mark J Pallen and Gad Frankel
ISME J 3: 261-265; advance online publication, October 2, 2008; doi:10.1038/ismej.2008.95
Microbial Ecology and Functional Diversity of Natural Habitats
Natural acidophilic biofilm communities reflect distinct organismal and functional organization
Paul Wilmes, Jonathan P Remis, Mona Hwang, Manfred Auer, Michael P Thelen and Jillian F Banfield
ISME J 3: 266-270; advance online publication, October 9, 2008; doi:10.1038/ismej.2008.90
