The ISME Journal - Table of Contents alert Volume 7 Issue 3

TABLE OF CONTENTS Volume 7, Issue 3 (March 2013) In this issue Commentaries Mini-Review Original Articles Short Communications Also new AOP Sign up for e-alerts Recommend to your library Web feed Subscribe Advertisement Article Focus- Sizing up metatranscriptomics In this ISMEJ perspective Moran, Hopkinson and colleagues review the available data on transcript dynamics in environmental bacteria, and then consider the consequences of a small and transient mRNA inventory for functional metagenomic studies of microbial communities.   Commentaries Top Secondary structure improves OTU assignments of 16S rRNA gene sequences Patrick D Schloss ISME J 2013 7: 457-460; advance online publication, September 27, 2012; 10.1038/ismej.2012.102 Full Text Collaborative cloud-enabled tools allow rapid, reproducible biological insights Open Benjamin Ragan-Kelley, William Anton Walters, Daniel McDonald, Justin Riley, Brian E Granger, Antonio Gonzalez, Rob Knight, Fernando Perez and J Gregory Caporaso ISME J 2013 7: 461-464; advance online publication, October 25, 2012; 10.1038/ismej.2012.123 Full Text Microbial individuality in the natural environment M Ackermann ISME J 2013 7: 465-467; advance online publication, November 22, 2012; 10.1038/ismej.2012.131 Full Text Mini-Review Top MICROBIAL ECOLOGY AND FUNCTIONAL DIVERSITY OF NATURAL HABITATS Microbiology of Lonar Lake and other soda lakes Chakkiath Paul Antony, Deepak Kumaresan, Sindy Hunger, Harold L Drake, J Colin Murrell and Yogesh S Shouche ISME J 2013 7: 468-476; advance online publication, November 22, 2012; 10.1038/ismej.2012.137 Abstract | Full Text Original Articles Top MICROBIAL POPULATION AND COMMUNITY ECOLOGY Fungal community on decomposing leaf litter undergoes rapid successional changes Jana Voříšková and Petr Baldrian ISME J 2013 7: 477-486; advance online publication, October 11, 2012; 10.1038/ismej.2012.116 Abstract | Full Text Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network 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 and Gabriela Olmedo-Alvarez ISME J 2013 7: 487-497; advance online publication, October 25, 2012; 10.1038/ismej.2012.119 Abstract | Full Text The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale Christina Hazard, Paul Gosling, Christopher J van der Gast, Derek T Mitchell, Fiona M Doohan and Gary D Bending ISME J 2013 7: 498-508; advance online publication, October 25, 2012; 10.1038/ismej.2012.127 Abstract | Full Text Reproducibility of Vibrionaceae population structure in coastal bacterioplankton Gitta Szabo, Sarah P Preheim, Kathryn M Kauffman, Lawrence A David, Jesse Shapiro, Eric J Alm and Martin F Polz ISME J 2013 7: 509-519; advance online publication, November 22, 2012; 10.1038/ismej.2012.134 Abstract | Full Text Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages Open Cesar O Flores, Sergi Valverde and Joshua S Weitz ISME J 2013 7: 520-532; advance online publication, November 22, 2012; 10.1038/ismej.2012.135 Abstract | Full Text Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses Steven A J Declerck, Christian Winter, Jonathan B Shurin, Curtis A Suttle and Blake Matthews ISME J 2013 7: 533-542; advance online publication, November 22, 2012; 10.1038/ismej.2012.138 Abstract | Full Text INTEGRATED GENOMICS AND POST-GENOMICS APPROACHES IN MICROBIAL ECOLOGY A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal 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 and Per Halkjær Nielsen ISME J 2013 7: 543-554; advance online publication, November 22, 2012; 10.1038/ismej.2012.136 Abstract | Full Text GEOMICROBIOLOGY AND MICROBIAL CONTRIBUTIONS TO GEOCHEMICAL CYCLES Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes 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 and Fumio Inagaki ISME J 2013 7: 555-567; advance online publication, October 25, 2012; 10.1038/ismej.2012.124 Abstract | Full Text Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean Joanna L Dixon, Stephanie Sargeant, Philip D Nightingale and J Colin Murrell ISME J 2013 7: 568-580; advance online publication, November 22, 2012; 10.1038/ismej.2012.130 Abstract | Full Text Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades Robert T Green, Jonathan D Todd and Andrew W B Johnston ISME J 2013 7: 581-591; advance online publication, November 29, 2012; 10.1038/ismej.2012.140 Abstract | Full Text MICROBIAL ECOLOGY AND FUNCTIONAL DIVERSITY OF NATURAL HABITATS Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium Paul Carini, Laura Steindler, Sara Beszteri and Stephen J Giovannoni ISME J 2013 7: 592-602; advance online publication, October 25, 2012; 10.1038/ismej.2012.122 Abstract | Full Text Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre Paola R Gómez-Pereira, Manuela Hartmann, Carolina Grob, Glen A Tarran, Adrian P Martin, Bernhard M Fuchs, David J Scanlan and Mikhail V Zubkov ISME J 2013 7: 603-614; advance online publication, October 25, 2012; 10.1038/ismej.2012.126 Abstract | Full Text Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens Yeshi Yin, Yu Wang, Liying Zhu, Wei Liu, Ningbo Liao, Mizu Jiang, Baoli Zhu, Hongwei D Yu, Charlie Xiang and Xin Wang ISME J 2013 7: 615-621; advance online publication, November 15, 2012; 10.1038/ismej.2012.128 Abstract | Full Text Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park Mark A Kozubal, Margaret Romine, Ryan deM Jennings, Zack J Jay, Susannah G Tringe, Doug B Rusch, Jacob P Beam, Lee Ann McCue and William P Inskeep ISME J 2013 7: 622-634; advance online publication, November 15, 2012; 10.1038/ismej.2012.132 Abstract | Full Text Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm 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 and Christine Moissl-Eichinger ISME J 2013 7: 635-651; advance online publication, November 22, 2012; 10.1038/ismej.2012.133 Abstract | Full Text Global biogeography of highly diverse protistan communities in soil Open Scott T Bates, Jose C Clemente, Gilberto E Flores, William Anthony Walters, Laura Wegener Parfrey, Rob Knight and Noah Fierer ISME J 2013 7: 652-659; advance online publication, December 13, 2012; 10.1038/ismej.2012.147 Abstract | Full Text MICROBIAL ECOSYSTEM IMPACTS Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone Xinyu Li, Ye Deng, Qi Li, Caiyan Lu, Jingjing Wang, Huiwen Zhang, Jianguo Zhu, Jizhong Zhou and Zhili He ISME J 2013 7: 660-671; advance online publication, November 15, 2012; 10.1038/ismej.2012.120 Abstract | Full Text Short Communications Top MICROBIAL POPULATION AND COMMUNITY ECOLOGY Are we missing half of the viruses in the ocean? Open Grieg F Steward, Alexander I Culley, Jaclyn A Mueller, Elisha M Wood-Charlson, Mahdi Belcaid and Guylaine Poisson ISME J 2013 7: 672-679; advance online publication, November 15, 2012; 10.1038/ismej.2012.121 Abstract | Full Text MICROBIAL ECOLOGY AND FUNCTIONAL DIVERSITY OF NATURAL HABITATS A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA Emily L Kara, Paul C Hanson, Yu Hen Hu, Luke Winslow and Katherine D McMahon ISME J 2013 7: 680-684; advance online publication, October 11, 2012; 10.1038/ismej.2012.118 Abstract | Full Text Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events Please note that you need to be a subscriber or site-licence holder to enjoy full-text access to The ISME Journal. In order to do so, please purchase a subscription. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact our registration department. For print subscription enquiries, please contact our subscription department. For other enquiries, please contact our customer feedback department. 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