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Ecological and evolutionary microbiology

This section aims to publish studies looking at all aspects of ecological and evolutionary microbiology, including microbial ecology, ecosystems, biodiversity, evolution, population genetics, phylogenetics, microbial communities and biofilms, marine and freshwater microbiology.

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  1. Acquisition of exogenous genetic material is a key event in bacterial speciation. It seems reasonable to assume that recombination of the incoming DNA into genome would be more efficient with higher levels of ...

    Authors: Hong-Xia Bao, Le Tang, Lu Yu, Xu-Yao Wang, Yang Li, Xia Deng, Yong-Guo Li, Ang Li, Da-Ling Zhu, Randal N Johnston, Gui-Rong Liu, Ye Feng and Shu-Lin Liu

    Citation: BMC Microbiology 2014 14:157

    Content type: Research article

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  2. Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, tr...

    Authors: Tong Dan, Wenjun Liu, Zhihong Sun, Qiang Lv, Haiyan Xu, Yuqin Song and Heping Zhang

    Citation: BMC Microbiology 2014 14:150

    Content type: Research article

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  3. Cereulide is a cyclic dodecadepsipeptide ionophore, produced via non-ribosomal peptide synthetases (NRPS), which in rare cases can lead to human death. Early studies had shown that emetic toxin formation belon...

    Authors: Xiaofen Mei, Kai Xu, Lingling Yang, Zhiming Yuan, Jacques Mahillon and Xiaomin Hu

    Citation: BMC Microbiology 2014 14:149

    Content type: Research article

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  4. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their c...

    Authors: Refugio Robles-Sikisaka, Mayuri Naidu, Melissa Ly, Julia Salzman, Shira R Abeles, Tobias K Boehm and David T Pride

    Citation: BMC Microbiology 2014 14:146

    Content type: Research article

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  5. Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, wh...

    Authors: Paul Purcell, Hannah Jary, Audrey Perry, John D Perry, Christopher J Stewart, Andrew Nelson, Clare Lanyon, Darren L Smith, Stephen P Cummings and Anthony De Soyza

    Citation: BMC Microbiology 2014 14:130

    Content type: Research article

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  6. Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak,

    Authors: Erin J Kelley, Elizabeth M Driebe, Kizee Etienne, Mary E Brandt, James M Schupp, John D Gillece, Jesse S Trujillo, Shawn R Lockhart, Eszter Deak, Paul S Keim and David M Engelthaler

    Citation: BMC Microbiology 2014 14:125

    Content type: Methodology article

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  7. Authors: Ana Maldonado-Contreras, Shrinivasrao P Mane, Xue-Song Zhang, Luis Pericchi, Teresa Alarcón, Monica Contreras, Bodo Linz, Martin J Blaser and María Gloria Domínguez-Bello

    Citation: BMC Microbiology 2014 14:122

    Content type: Erratum

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    The original article was published in BMC Microbiology 2013 13:211

  8. Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the coloniza...

    Authors: Simon van Vliet, Felix JH Hol, Tim Weenink, Peter Galajda and Juan E Keymer

    Citation: BMC Microbiology 2014 14:116

    Content type: Research article

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  9. Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a s...

    Authors: Aurélie Chambouvet, Cédric Berney, Sarah Romac, Stéphane Audic, Finlay Maguire, Colomban De Vargas and Thomas A Richards

    Citation: BMC Microbiology 2014 14:110

    Content type: Research article

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  10. The novel archaea belonging to Rumen Cluster C (RCC), which may play an important role in methane production in the rumen have received increased attention. However, the present information on RCC in the rumen...

    Authors: Wei Jin, Yan Fen Cheng, Sheng Yong Mao and Wei Yun Zhu

    Citation: BMC Microbiology 2014 14:104

    Content type: Research article

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  11. Cytolethal distending toxin (CDT)-producing Escherichia coli (CTEC) has been isolated from patients with gastrointestinal or urinary tract infection, and sepsis. However, the source of human infection remains unk...

    Authors: Atsushi Hinenoya, Kensuke Shima, Masahiro Asakura, Kazuhiko Nishimura, Teizo Tsukamoto, Tadasuke Ooka, Tetsuya Hayashi, Thandavarayan Ramamurthy, Shah M Faruque and Shinji Yamasaki

    Citation: BMC Microbiology 2014 14:97

    Content type: Research article

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  12. Zearalenone is a mycotoxin produced by several species of Fusarium genus, most notably Fusarium graminearum and Fusarium culmorum. This resorcylic acid lactone is one of the most important toxins causing serious ...

    Authors: Delfina Popiel, Grzegorz Koczyk, Adam Dawidziuk, Karolina Gromadzka, Lidia Blaszczyk and Jerzy Chelkowski

    Citation: BMC Microbiology 2014 14:82

    Content type: Research article

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  13. Commensal bacteria are a reservoir for antimicrobial-resistance genes. In the Netherlands, bacteria producing Extended Spectrum Beta-Lactamases (ESBL) are found on chicken-meat and in the gut of broilers at a ...

    Authors: Egil AJ Fischer, Cindy M Dierikx, Alieda van Essen-Zandbergen, Herman JW van Roermund, Dik J Mevius, Arjan Stegeman and Don Klinkenberg

    Citation: BMC Microbiology 2014 14:77

    Content type: Research article

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  14. Taylorella equigenitalis is the causative agent of contagious equine metritis, a sexually-transmitted infection of Equidae characterised in infected mares by abundant mucopurulent vaginal discharge and a variabl...

    Authors: Julie Allombert, Anne Vianney, Claire Laugier, Sandrine Petry and Laurent Hébert

    Citation: BMC Microbiology 2014 14:69

    Content type: Research article

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  15. Generalist bacterial pathogens, with the ability for environmental survival and growth, often face variable conditions during their outside-host period. Abiotic factors (such as nutrient deprivation) act as se...

    Authors: Lotta-Riina Sundberg, Heidi M T Kunttu and E Tellervo Valtonen

    Citation: BMC Microbiology 2014 14:67

    Content type: Research article

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  16. Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the recent evolution of two clinically relev...

    Authors: Ewa Sadowy and Aneta Luczkiewicz

    Citation: BMC Microbiology 2014 14:66

    Content type: Research article

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  17. Smokers are more prone to oral infections than are non-smokers. Cigarette smoke reaches the host cells but also microorganisms present in the oral cavity. The contact between cigarette smoke and oral bacteria ...

    Authors: Abdelhabib Semlali, Kerstin Killer, Humidah Alanazi, Witold Chmielewski and Mahmoud Rouabhia

    Citation: BMC Microbiology 2014 14:61

    Content type: Research article

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  18. Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between dif...

    Authors: Sara Urmersbach, Thomas Alter, Madura Sanjeevani Gonsal Koralage, Lisa Sperling, Gunnar Gerdts, Ute Messelhäusser and Stephan Huehn

    Citation: BMC Microbiology 2014 14:59

    Content type: Research article

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  19. Mixed microbial infections of the respiratory tracts with P. aeruginosa and A. fumigatus capable of producing biofilms are commonly found in cystic fibrosis patients. The primary objective of this study was to de...

    Authors: Elias K Manavathu, Dora L Vager and Jose A Vazquez

    Citation: BMC Microbiology 2014 14:53

    Content type: Research article

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  20. Meyerozyma guilliermondii (anamorph Candida guilliermondii) and Meyerozyma caribbica (anamorph Candida fermentati) are closely related species of the genetically heterogenous M. guilliermondii complex. Conventio...

    Authors: Wahengbam Romi, Santosh Keisam, Giasuddin Ahmed and Kumaraswamy Jeyaram

    Citation: BMC Microbiology 2014 14:52

    Content type: Methodology article

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  21. Imbalanced feeding regimes may initiate gastrointestinal and metabolic diseases in endangered felids kept in captivity such as cheetahs. Given the crucial role of the host’s intestinal microbiota in feed ferme...

    Authors: Anne AMJ Becker, Myriam Hesta, Joke Hollants, Geert PJ Janssens and Geert Huys

    Citation: BMC Microbiology 2014 14:43

    Content type: Research article

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  22. Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as th...

    Authors: Talima Pearson, Heidie M Hornstra, Remy Hilsabeck, Lauren T Gates, Sonora M Olivas, Dawn M Birdsell, Carina M Hall, Sabrina German, James M Cook, Meagan L Seymour, Rachael A Priestley, Ashley V Kondas, Christine L Clark Friedman, Erin P Price, James M Schupp, Cindy M Liu…

    Citation: BMC Microbiology 2014 14:41

    Content type: Research article

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  23. The potential for the human gut microbiota to serve as a reservoir for antibiotic resistance genes has been the subject of recent discussion. However, this has yet to be investigated using a rapid PCR-based ap...

    Authors: Fiona Fouhy, R Paul Ross, Gerald F Fitzgerald, Catherine Stanton and Paul D Cotter

    Citation: BMC Microbiology 2014 14:25

    Content type: Research article

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  24. Histoplasma capsulatum and Pneumocystis organisms cause host infections primarily affecting the lung tissue. H. capsulatum is endemic in the United States of America and Latin American countries. In special envi...

    Authors: Antonio E González-González, Cécile M Aliouat-Denis, José A Ramírez-Bárcenas, Christine Demanche, Muriel Pottier, Laura E Carreto-Binaghi, Haroon Akbar, Sandra Derouiche, Magalie Chabé, El Moukhtar Aliouat, Eduardo Dei-Cas and Maria Lucia Taylor

    Citation: BMC Microbiology 2014 14:23

    Content type: Research article

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  25. A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutation...

    Authors: Sean Michael Carroll, Katherine S Xue and Christopher J Marx

    Citation: BMC Microbiology 2014 14:2

    Content type: Research article

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  26. This work provides the first description of the bacterial population of the lung microbiota in mice. The aim of this study was to examine the lung microbiome in mice, the most used animal model for inflammator...

    Authors: Kenneth Klingenberg Barfod, Michael Roggenbuck, Lars Hestbjerg Hansen, Susanne Schjørring, Søren Thor Larsen, Søren Johannes Sørensen and Karen Angeliki Krogfelt

    Citation: BMC Microbiology 2013 13:303

    Content type: Research article

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  27. Pine wilt disease (PWD) caused by the pinewood nematode Bursaphelenchus xylophilus is one of the most serious forest diseases in the world. The role of B. xylophilus-associated bacteria in PWD and their interacti...

    Authors: Cláudia S L Vicente, Yoriko Ikuyo, Manuel Mota and Koichi Hasegawa

    Citation: BMC Microbiology 2013 13:299

    Content type: Research article

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  28. Our observation that in the Mexican Salmonella Typhimurium population none of the ST19 and ST213 strains harbored both the Salmonella virulence plasmid (pSTV) and the prevalent IncA/C plasmid (pA/C) led us to hyp...

    Authors: Magdalena Wiesner, Marcos Fernández-Mora, Miguel A Cevallos, Crispín Zavala-Alvarado, Mussaret B Zaidi, Edmundo Calva and Claudia Silva

    Citation: BMC Microbiology 2013 13:264

    Content type: Research article

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  29. Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-orga...

    Authors: Hannah M Doll, David W Armitage, Rebecca A Daly, Joanne B Emerson, Daniela S Aliaga Goltsman, Alexis P Yelton, Jennifer Kerekes, Mary K Firestone and Matthew D Potts

    Citation: BMC Microbiology 2013 13:259

    Content type: Research article

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  30. Production and wild animals are major sources of human salmonellosis and animals raised for food also play an important role in transmission of antimicrobial resistant Salmonella strains to humans. Furthermore, i...

    Authors: Assèta Kagambèga, Taru Lienemann, Laura Aulu, Alfred S Traoré, Nicolas Barro, Anja Siitonen and Kaisa Haukka

    Citation: BMC Microbiology 2013 13:253

    Content type: Research article

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  31. Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity how...

    Authors: Karl Mathias Wegner, Nils Volkenborn, Hannes Peter and Alexander Eiler

    Citation: BMC Microbiology 2013 13:252

    Content type: Research article

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  32. The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific s...

    Authors: Bastiaan Star, Thomas HA Haverkamp, Sissel Jentoft and Kjetill S Jakobsen

    Citation: BMC Microbiology 2013 13:248

    Content type: Research article

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  33. Oxyspirura petrowi appears to be emerging as a nematode parasite that could negatively impact Northern Bobwhite quail individuals and populations within Texas and other regions of the United States. Despite this ...

    Authors: Lixin Xiang, Fengguang Guo, Haili Zhang, Lloyd LaCoste, Dale Rollins, Andrea Bruno, Alan M Fedynich and Guan Zhu

    Citation: BMC Microbiology 2013 13:233

    Content type: Research article

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  34. Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori (hpE...

    Authors: Ana Maldonado-Contreras, Shrinivasrao P Mane, Xue-Song Zhang, Luis Pericchi, Teresa Alarcón, Monica Contreras, Bodo Linz, Martin J Blaser and María Gloria Domínguez-Bello

    Citation: BMC Microbiology 2013 13:211

    Content type: Research article

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    The Erratum to this article has been published in BMC Microbiology 2014 14:122

  35. Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with differ...

    Authors: Yan He, Ben-Jie Zhou, Guan-Hua Deng, Xiao-Tao Jiang, Hai Zhang and Hong-Wei Zhou

    Citation: BMC Microbiology 2013 13:208

    Content type: Research article

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  36. The white rhinoceros is on the verge of extinction with less than 20,200 animals remaining in the wild. In order to better protect these endangered animals, it is necessary to better understand their digestive...

    Authors: Yu-heng Luo, André-Denis G Wright, You-long Li, Hua Li, Qi-hong Yang, Ling-juan Luo and Ming-xian Yang

    Citation: BMC Microbiology 2013 13:207

    Content type: Research article

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  37. Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil micro...

    Authors: Florence Kurth, Katharina Zeitler, Lasse Feldhahn, Thomas R Neu, Tilmann Weber, Václav Krištůfek, Tesfaye Wubet, Sylvie Herrmann, François Buscot and Mika T Tarkka

    Citation: BMC Microbiology 2013 13:205

    Content type: Research article

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  38. It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced...

    Authors: Jing Li, Ivan Nasidze, Dominique Quinque, Mingkun Li, Hans-Peter Horz, Claudine André, Rosa M Garriga, Michel Halbwax, Anne Fischer and Mark Stoneking

    Citation: BMC Microbiology 2013 13:204

    Content type: Research article

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  39. Pseudomonas aeruginosa populations within the cystic fibrosis lung exhibit extensive phenotypic and genetic diversification. The resultant population diversity is thought to be crucial to the persistence of infec...

    Authors: Elli A Wright, Joanne L Fothergill, Steve Paterson, Michael A Brockhurst and Craig Winstanley

    Citation: BMC Microbiology 2013 13:170

    Content type: Research article

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  40. Araucariaceae are important forest trees of the southern hemisphere. Life expectancy of their seedlings can largely be reduced by fungal infections. In this study we have isolated and characterized such a fung...

    Authors: Fernando Rostirolla Dalmas, Leandro Astarita, Luigi DeFilippis, Elisabeth Magel, Hans-Peter Fiedler, Robert Bauer and Rüdiger Hampp

    Citation: BMC Microbiology 2013 13:168

    Content type: Research article

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  41. Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimi...

    Authors: Helen ML Wimalarathna, Judith F Richardson, Andy J Lawson, Richard Elson, Richard Meldrum, Christine L Little, Martin CJ Maiden, Noel D McCarthy and Samuel K Sheppard

    Citation: BMC Microbiology 2013 13:160

    Content type: Research article

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  42. Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it i...

    Authors: Zhi Peng Li, Han Lu Liu, Guang Yu Li, Kun Bao, Kai Ying Wang, Chao Xu, Yi Feng Yang, Fu He Yang and André-Denis G Wright

    Citation: BMC Microbiology 2013 13:151

    Content type: Research article

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  43. Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recr...

    Authors: Alexandra Stock, Virginia Edgcomb, William Orsi, Sabine Filker, Hans-Werner Breiner, Michail M Yakimov and Thorsten Stoeck

    Citation: BMC Microbiology 2013 13:150

    Content type: Research article

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  44. The current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (CLPP) analysis.

    Authors: Wenxiong Lin, Linkun Wu, Sheng Lin, Aijia Zhang, Mingming Zhou, Rui Lin, Haibin Wang, Jun Chen, Zhixing Zhang and Ruiyu Lin

    Citation: BMC Microbiology 2013 13:135

    Content type: Research article

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  45. Cansiliella servadeii (Coleoptera) is an endemic troglobite living in deep carbonate caves in North-Eastern Italy. The beetle constantly moves and browses in its preferred habitat (consisting in flowing water and...

    Authors: Maurizio G Paoletti, Luca Mazzon, Isabel Martinez-Sañudo, Mauro Simonato, Mattia Beggio, Angelo Leandro Dreon, Alberto Pamio, Mauro Brilli, Luca Dorigo, Annette Summers Engel, Alessandra Tondello, Barbara Baldan, Giuseppe Concheri and Andrea Squartini

    Citation: BMC Microbiology 2013 13:129

    Content type: Research article

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  46. Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected ...

    Authors: Joanna Zaluga, Pieter Stragier, Johan Van Vaerenbergh, Martine Maes and Paul De Vos

    Citation: BMC Microbiology 2013 13:126

    Content type: Research article

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  47. Elevated atmospheric CO2 (eCO2) has been shown to have significant effects on terrestrial ecosystems. However, little is known about its influence on the structure, composition, and functional potential of soil m...

    Authors: Meiying Xu, Zhili He, Ye Deng, Liyou Wu, Joy D van Nostrand, Sarah E Hobbie, Peter B Reich and Jizhong Zhou

    Citation: BMC Microbiology 2013 13:124

    Content type: Research article

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  48. Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Wit...

    Authors: Stefan Spring, Thomas Riedel, Cathrin Spröer, Shi Yan, Jens Harder and Bernhard M Fuchs

    Citation: BMC Microbiology 2013 13:118

    Content type: Research article

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  49. Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap howev...

    Authors: Andrea R Ottesen, Antonio González Peña, James R White, James B Pettengill, Cong Li, Sarah Allard, Steven Rideout, Marc Allard, Thomas Hill, Peter Evans, Errol Strain, Steven Musser, Rob Knight and Eric Brown

    Citation: BMC Microbiology 2013 13:114

    Content type: Research article

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