AEM -- Table of Contents (May 15 2008, 74 [10])

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Contents: May 2008, Volume 74, Issue 10

       Microbial Ecology

       Methods

       Physiology and Biotechnology

       Public Health Microbiology

       Enzymology and Protein Engineering

       Genetics and Molecular Biology

       Evolutionary and Genomic Microbiology

       Environmental Microbiology

       Food Microbiology

       Invertebrate Microbiology

       Geomicrobiology

       Plant Microbiology

       Errata

       Author's Correction

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Microbial Ecology:

Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton
Erin J. Biers, Kui Wang, Catherine Pennington, Robert Belas, Feng Chen, and Mary Ann Moran
Appl. Environ. Microbiol. May 2008 74: 2933-2939; published ahead of print March 21, 2008, doi:10.1128/AEM.02129-07
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Unexpected Importance of Potential Parasites in the Composition of the Freshwater Small-Eukaryote Community
Cécile Lepère, Isabelle Domaizon, and Didier Debroas
Appl. Environ. Microbiol. May 2008 74: 2940-2949; published ahead of print March 21, 2008, doi:10.1128/AEM.01156-07
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Collateral Effects of Antibiotics: Carbadox and Metronidazole Induce VSH-1 and Facilitate Gene Transfer among Brachyspira hyodysenteriae Strains
Thaddeus B. Stanton, Samuel B. Humphrey, Vijay K. Sharma, and Richard L. Zuerner
Appl. Environ. Microbiol. May 2008 74: 2950-2956; published ahead of print March 21, 2008, doi:10.1128/AEM.00189-08
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Biome-Level Biogeography of Streambed Microbiota
Robert H. Findlay, Christine Yeates, Meredith A. J. Hullar, David A. Stahl, and Louis A. Kaplan
Appl. Environ. Microbiol. May 2008 74: 3014-3021; published ahead of print March 31, 2008, doi:10.1128/AEM.01809-07
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Phylogenetic Analysis of Members of the Phycodnaviridae Virus Family, Using Amplified Fragments of the Major Capsid Protein Gene
J. B. Larsen, A. Larsen, G. Bratbak, and R.-A. Sandaa
Appl. Environ. Microbiol. May 2008 74: 3048-3057; published ahead of print March 21, 2008, doi:10.1128/AEM.02548-07
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Role of Intestinal Microbiota in Transformation of Bismuth and Other Metals and Metalloids into Volatile Methyl and Hydride Derivatives in Humans and Mice
Klaus Michalke, Annette Schmidt, Britta Huber, Jörg Meyer, Margareta Sulkowski, Alfred V. Hirner, Jens Boertz, Frank Mosel, Philip Dammann, Gero Hilken, Hans J. Hedrich, Martina Dorsch, Albert W. Rettenmeier, and Reinhard Hensel
Appl. Environ. Microbiol. May 2008 74: 3069-3075; published ahead of print March 31, 2008, doi:10.1128/AEM.02933-07
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Diverse Responses of the Bivalve-Killing Dinoflagellate Heterocapsa circularisquama to Infection by a Single-Stranded RNA Virus
Hiroyuki Mizumoto, Yuji Tomaru, Yoshitake Takao, Yoko Shirai, and Keizo Nagasaki
Appl. Environ. Microbiol. May 2008 74: 3105-3111; published ahead of print March 21, 2008, doi:10.1128/AEM.02190-07
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Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fen
Alexandra Hamberger, Marcus A. Horn, Marc G. Dumont, J. Colin Murrell, and Harold L. Drake
Appl. Environ. Microbiol. May 2008 74: 3112-3120; published ahead of print March 31, 2008, doi:10.1128/AEM.00193-08
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Identification and Onion Pathogenicity of Burkholderia cepacia Complex Isolates from the Onion Rhizosphere and Onion Field Soil
Janette L. Jacobs, Anthony C. Fasi, Alban Ramette, James J. Smith, Raymond Hammerschmidt, and George W. Sundin
Appl. Environ. Microbiol. May 2008 74: 3121-3129; published ahead of print March 14, 2008, doi:10.1128/AEM.01941-07
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Ecological Dynamics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa and Its Cyanophages in Freshwater
Mitsuhiro Yoshida, Takashi Yoshida, Aki Kashima, Yukari Takashima, Naohiko Hosoda, Keizo Nagasaki, and Shingo Hiroishi
Appl. Environ. Microbiol. May 2008 74: 3269-3273; published ahead of print March 14, 2008, doi:10.1128/AEM.02240-07
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Microbes Enriched in Seawater after Addition of Coral Mucus
Elke Allers, Christina Niesner, Christian Wild, and Jakob Pernthaler
Appl. Environ. Microbiol. May 2008 74: 3274-3278; published ahead of print March 14, 2008, doi:10.1128/AEM.01870-07
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Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora
Martina Herrmann, Aaron M. Saunders, and Andreas Schramm
Appl. Environ. Microbiol. May 2008 74: 3279-3283; published ahead of print March 14, 2008, doi:10.1128/AEM.02802-07
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Methods:

Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis
Zhili He and Jizhong Zhou
Appl. Environ. Microbiol. May 2008 74: 2957-2966; published ahead of print March 14, 2008, doi:10.1128/AEM.02536-07
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Targeted Mutagenesis of Burkholderia thailandensis and Burkholderia pseudomallei through Natural Transformation of PCR Fragments
Metawee Thongdee, Larry A. Gallagher, Mark Schell, Tararaj Dharakul, Sirirurg Songsivilai, and Colin Manoil
Appl. Environ. Microbiol. May 2008 74: 2985-2989; published ahead of print February 29, 2008, doi:10.1128/AEM.00030-08
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Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms
Mark R. Liles, Lynn L. Williamson, Jitsupang Rodbumrer, Vigdis Torsvik, Robert M. Goodman, and Jo Handelsman
Appl. Environ. Microbiol. May 2008 74: 3302-3305; published ahead of print March 21, 2008, doi:10.1128/AEM.02630-07
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Use of Murine Norovirus as a Surrogate To Evaluate Resistance of Human Norovirus to Disinfectants
Gaël Belliot, Amandine Lavaux, Donya Souihel, Davide Agnello, and Pierre Pothier
Appl. Environ. Microbiol. May 2008 74: 3315-3318; published ahead of print March 31, 2008, doi:10.1128/AEM.02148-07
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Physiology and Biotechnology:

Efficient Production of L-Ribose with a Recombinant Escherichia coli Biocatalyst
Ryan D. Woodyer, Nathan J. Wymer, F. Michael Racine, Shama N. Khan, and Badal C. Saha
Appl. Environ. Microbiol. May 2008 74: 2967-2975; published ahead of print March 14, 2008, doi:10.1128/AEM.02768-07
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Comparison of Microbial and Photochemical Processes and Their Combination for Degradation of 2-Aminobenzothiazole
Andrei Bunescu, Pascale Besse-Hoggan, Martine Sancelme, Gilles Mailhot, and Anne-Marie Delort
Appl. Environ. Microbiol. May 2008 74: 2976-2984; published ahead of print February 29, 2008, doi:10.1128/AEM.01696-07
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Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas
Lisa M. Gieg, Kathleen E. Duncan, and Joseph M. Suflita
Appl. Environ. Microbiol. May 2008 74: 3022-3029; published ahead of print March 31, 2008, doi:10.1128/AEM.00119-08
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Stimulation of Zero-trans Rates of Lactose and Maltose Uptake into Yeasts by Preincubation with Hexose To Increase the Adenylate Energy Charge
Pedro M. R. Guimarães, Jyri-Pekka Multanen, Lucília Domingues, José A. Teixeira, and John Londesborough
Appl. Environ. Microbiol. May 2008 74: 3076-3084; published ahead of print March 31, 2008, doi:10.1128/AEM.00188-08
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Engineering and Analysis of a Saccharomyces cerevisiae Strain That Uses Formaldehyde as an Auxiliary Substrate
Richard J. S. Baerends, Erik de Hulster, Jan-Maarten A. Geertman, Jean-Marc Daran, Antonius J. A. van Maris, Marten Veenhuis, Ida J. van der Klei, and Jack T. Pronk
Appl. Environ. Microbiol. May 2008 74: 3182-3188; published ahead of print March 31, 2008, doi:10.1128/AEM.02858-07
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Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production
Lance Kizer, Douglas J. Pitera, Brian F. Pfleger, and Jay D. Keasling
Appl. Environ. Microbiol. May 2008 74: 3229-3241; published ahead of print March 14, 2008, doi:10.1128/AEM.02750-07
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Induction and Resuscitation of Viable Nonculturable Arcobacter butzleri Cells
M. T. Fera, T. L. Maugeri, C. Gugliandolo, E. La Camera, V. Lentini, A. Favaloro, D. Bonanno, and M. Carbone
Appl. Environ. Microbiol. May 2008 74: 3266-3268; published ahead of print March 31, 2008, doi:10.1128/AEM.00059-08
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Metabolic Engineering of Escherichia coli for L-Tyrosine Production by Expression of Genes Coding for the Chorismate Mutase Domain of the Native Chorismate Mutase-Prephenate Dehydratase and a Cyclohexadienyl Dehydrogenase from Zymomonas mobilis
María I. Chávez-Béjar, Alvaro R. Lara, Hezraí López, Georgina Hernández-Chávez, Alfredo Martinez, Octavio T. Ramírez, Francisco Bolívar, and Guillermo Gosset
Appl. Environ. Microbiol. May 2008 74: 3284-3290; published ahead of print March 14, 2008, doi:10.1128/AEM.02456-07
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High-Level Folate Production in Fermented Foods by the B₁₂ Producer Lactobacillus reuteri JCM1112
Filipe Santos, Arno Wegkamp, Willem M. de Vos, Eddy J. Smid, and Jeroen Hugenholtz
Appl. Environ. Microbiol. May 2008 74: 3291-3294; published ahead of print March 14, 2008, doi:10.1128/AEM.02719-07
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Repression of the Locus of the Enterocyte Effacement-Encoded Regulator of Gene Transcription of Escherichia coli O157:H7 by Lactobacillus reuteri Culture Supernatants Is LuxS and Strain Dependent
Ivan Jelcic, Eric Hüfner, Herbert Schmidt, and Christian Hertel
Appl. Environ. Microbiol. May 2008 74: 3310-3314; published ahead of print March 31, 2008, doi:10.1128/AEM.00072-08
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Public Health Microbiology:

Concentration of Enteroviruses, Adenoviruses, and Noroviruses from Drinking Water by Use of Glass Wool Filters
Elisabetta Lambertini, Susan K. Spencer, Phillip D. Bertz, Frank J. Loge, Burney A. Kieke, and Mark A. Borchardt
Appl. Environ. Microbiol. May 2008 74: 2990-2996; published ahead of print March 21, 2008, doi:10.1128/AEM.02246-07
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Bactericidal Effect of Solar Water Disinfection under Real Sunlight Conditions
M. Boyle, C. Sichel, P. Fernández-Ibáñez, G. B. Arias-Quiroz, M. Iriarte-Puña, A. Mercado, E. Ubomba-Jaswa, and K. G. McGuigan
Appl. Environ. Microbiol. May 2008 74: 2997-3001; published ahead of print March 21, 2008, doi:10.1128/AEM.02415-07
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Survival of Influenza Virus on Banknotes
Yves Thomas, Guido Vogel, Werner Wunderli, Patricia Suter, Mark Witschi, Daniel Koch, Caroline Tapparel, and Laurent Kaiser
Appl. Environ. Microbiol. May 2008 74: 3002-3007; published ahead of print March 21, 2008, doi:10.1128/AEM.00076-08
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Dynamics of Legionella spp. and Bacterial Populations during the Proliferation of L. pneumophila in a Cooling Tower Facility
Nathalie Wéry, Valérie Bru-Adan, Céline Minervini, Jean-Philippe Delgénes, Laurent Garrelly, and Jean-Jacques Godon
Appl. Environ. Microbiol. May 2008 74: 3030-3037; published ahead of print April 4, 2008, doi:10.1128/AEM.02760-07
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Correlation between Detection of a Plasmid and High-Level Virulence of Vibrio nigripulchritudo, a Pathogen of the Shrimp Litopenaeus stylirostris
Yann Reynaud, Denis Saulnier, Didier Mazel, Cyrille Goarant, and Frédérique Le Roux
Appl. Environ. Microbiol. May 2008 74: 3038-3047; published ahead of print March 21, 2008, doi:10.1128/AEM.02680-07
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Comparison of Methods for Processing Drinking Water Samples for the Isolation of Mycobacterium avium and Mycobacterium intracellulare
Rachel Thomson, Robyn Carter, Chris Gilpin, Chris Coulter, and Megan Hargreaves
Appl. Environ. Microbiol. May 2008 74: 3094-3098; published ahead of print March 21, 2008, doi:10.1128/AEM.02009-07
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Comparison of Transcription-Mediated Amplification and Growth-Based Methods for the Quantitation of Enterococcus Bacteria in Environmental Waters
Ceri A. Morris, A. Denene Blackwood, Marek Kirs, Neil D. Buttigieg, Rhian R. Morgan, James J. Hogan, Ian Weeks, and Rachel T. Noble
Appl. Environ. Microbiol. May 2008 74: 3319-3320; published ahead of print March 31, 2008, doi:10.1128/AEM.02623-07
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Enzymology and Protein Engineering:

Conversion Shift of D-Fructose to D-Psicose for Enzyme-Catalyzed Epimerization by Addition of Borate
Nam-Hee Kim, Hye-Jung Kim, Dong-Il Kang, Ki-Woong Jeong, Jung-Kul Lee, Yangmee Kim, and Deok-Kun Oh
Appl. Environ. Microbiol. May 2008 74: 3008-3013; published ahead of print March 31, 2008, doi:10.1128/AEM.00249-08
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Genetics and Molecular Biology:

Discovering the Hidden Secondary Metabolome of Myxococcus xanthus: a Study of Intraspecific Diversity
Daniel Krug, Gabriela Zurek, Ole Revermann, Michiel Vos, Gregory J. Velicer, and Rolf Müller
Appl. Environ. Microbiol. May 2008 74: 3058-3068; published ahead of print March 31, 2008, doi:10.1128/AEM.02863-07
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Shuttle Vector Expression in Thermococcus kodakaraensis: Contributions of cis Elements to Protein Synthesis in a Hyperthermophilic Archaeon
Thomas J. Santangelo, L'ubomíra Cubonová, and John N. Reeve
Appl. Environ. Microbiol. May 2008 74: 3099-3104; published ahead of print March 31, 2008, doi:10.1128/AEM.00305-08
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Heterogeneous Selection in a Spatially Structured Environment Affects Fitness Tradeoffs of Plasmid Carriage in Pseudomonads
Frances R. Slater, Kenneth D. Bruce, Richard J. Ellis, Andrew K. Lilley, and Sarah L. Turner
Appl. Environ. Microbiol. May 2008 74: 3189-3197; published ahead of print March 31, 2008, doi:10.1128/AEM.02383-07
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Characterization of Endogenous Plasmids from Lactobacillus salivarius UCC118
Fang Fang, Sarah Flynn, Yin Li, Marcus J. Claesson, Jan-Peter van Pijkeren, J. Kevin Collins, Douwe van Sinderen, and Paul W. O'Toole
Appl. Environ. Microbiol. May 2008 74: 3216-3228; published ahead of print April 4, 2008, doi:10.1128/AEM.02631-07
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Evolutionary and Genomic Microbiology:

Isolation and Identification of Rhizoxin Analogs from Pseudomonas fluorescens Pf-5 by Using a Genomic Mining Strategy
Joyce E. Loper, Marcella D. Henkels, Brenda T. Shaffer, Frederick A. Valeriote, and Harald Gross
Appl. Environ. Microbiol. May 2008 74: 3085-3093; published ahead of print March 14, 2008, doi:10.1128/AEM.02848-07
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Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome
Margaret F. Romine, Timothy S. Carlson, Angela D. Norbeck, Lee Ann McCue, and Mary S. Lipton
Appl. Environ. Microbiol. May 2008 74: 3257-3265; published ahead of print March 31, 2008, doi:10.1128/AEM.02720-07
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Environmental Microbiology:

Isolation of the Exoelectrogenic Bacterium Ochrobactrum anthropi YZ-1 by Using a U-Tube Microbial Fuel Cell
Yi Zuo, Defeng Xing, John M. Regan, and Bruce E. Logan
Appl. Environ. Microbiol. May 2008 74: 3130-3137; published ahead of print March 21, 2008, doi:10.1128/AEM.02732-07
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Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS
Sebastian Behrens, Tina Lösekann, Jennifer Pett-Ridge, Peter K. Weber, Wing-On Ng, Bradley S. Stevenson, Ian D. Hutcheon, David A. Relman, and Alfred M. Spormann
Appl. Environ. Microbiol. May 2008 74: 3143-3150; published ahead of print March 21, 2008, doi:10.1128/AEM.00191-08
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Food Microbiology:

Impact of Vacuum Cooling on Escherichia coli O157:H7 Infiltration into Lettuce Tissue
Haiping Li, Mehrdad Tajkarimi, and Bennie I. Osburn
Appl. Environ. Microbiol. May 2008 74: 3138-3142; published ahead of print March 14, 2008, doi:10.1128/AEM.02811-07
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Development of a Microbial Time/Temperature Indicator Prototype for Monitoring the Microbiological Quality of Chilled Foods
Hariklia Vaikousi, Costas G. Biliaderis, and Konstantinos P. Koutsoumanis
Appl. Environ. Microbiol. May 2008 74: 3242-3250; published ahead of print March 7, 2008, doi:10.1128/AEM.02717-07
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Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR
Kazuhiko Maeta, Tomoya Ochi, Keisuke Tokimoto, Norihiro Shimomura, Nitaro Maekawa, Nobuhisa Kawaguchi, Makoto Nakaya, Yutaka Kitamoto, and Tadanori Aimi
Appl. Environ. Microbiol. May 2008 74: 3306-3309; published ahead of print March 31, 2008, doi:10.1128/AEM.02082-07
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Invertebrate Microbiology:

Characterization and Growth of Polymorphic Rickettsia felis in a Tick Cell Line
Piyanate Sunyakumthorn, Apichai Bourchookarn, Walairat Pornwiroon, Connie David, Steven A. Barker, and Kevin R. Macaluso
Appl. Environ. Microbiol. May 2008 74: 3151-3158; published ahead of print March 21, 2008, doi:10.1128/AEM.00025-08
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Drosophila melanogaster Mounts a Unique Immune Response to the Rhabdovirus Sigma virus
C. W. Tsai, E. A. McGraw, E.-D. Ammar, R. G. Dietzgen, and S. A. Hogenhout
Appl. Environ. Microbiol. May 2008 74: 3251-3256; published ahead of print March 31, 2008, doi:10.1128/AEM.02248-07
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Geomicrobiology:

Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments
Denise M. Akob, Heath J. Mills, Thomas M. Gihring, Lee Kerkhof, Joseph W. Stucki, Alexandre S. Anastácio, Kuk-Jeong Chin, Kirsten Küsel, Anthony V. Palumbo, David B. Watson, and Joel E. Kostka
Appl. Environ. Microbiol. May 2008 74: 3159-3170; published ahead of print March 31, 2008, doi:10.1128/AEM.02881-07
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Biogeochemistry and Community Composition of Iron- and Sulfur-Precipitating Microbial Mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean)
Enoma O. Omoregie, Vincent Mastalerz, Gert de Lange, Kristina L. Straub, Andreas Kappler, Hans Røy, Alina Stadnitskaia, Jean-Paul Foucher, and Antje Boetius
Appl. Environ. Microbiol. May 2008 74: 3198-3215; published ahead of print March 31, 2008, doi:10.1128/AEM.01751-07
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Plant Microbiology:

Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain
Shuangchun Yan, Haijie Liu, Toni J. Mohr, Jenny Jenrette, Rossella Chiodini, Massimo Zaccardelli, João C. Setubal, and Boris A. Vinatzer
Appl. Environ. Microbiol. May 2008 74: 3171-3181; published ahead of print March 31, 2008, doi:10.1128/AEM.00180-08
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Assessment of the Genetic Diversity of Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans as a Basis To Identify Putative Pathogenicity Genes and a Type III Secretion System of the SPI-1 Family by Multiple Suppression Subtractive Hybridizations
Seyed Mehdi Alavi, Saeideh Sanjari, Fabien Durand, Chrystelle Brin, Charles Manceau, and Stéphane Poussier
Appl. Environ. Microbiol. May 2008 74: 3295-3301; published ahead of print March 21, 2008, doi:10.1128/AEM.02507-07
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Errata:

ERRATUM

Appl. Environ. Microbiol. May 2008 74: 3321
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Author's Correction:

Role of Iron in Human Serum Resistance of the Clinical and Environmental Vibrio vulnificus Genotypes
Ryan W. Bogard and James D. Oliver
Appl. Environ. Microbiol. May 2008 74: 3322
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To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.