Publications

Bienhold C, Boetius A, Ramette A. The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISMEJ doi: 10.1038/ismej.2011.140.

Gobet A, Böer SI, Huse SM, van Beusekom JEE, Quince C, Sogin ML, Boetius A, Ramette A. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISMEJ doi:10.1038/ismej.2011.132

Abed RMM, Ramette A, Hübner V, De Dekker P, de Beer D. Microbial diversity of eolian dust sources from saline lake sediments and biological soil crusts in arid Southern Australia. FEMS Microbiology Ecology. DOI: 10.1111/j.1574-6941.2011.01289.x

Schöttner S, Wild C, Hoffmann F, Boetius A, Ramette A (2012). Spatial scales of bacterial diversity in cold-water coral reef ecosystems. PLoS ONE 7(3): e32093. doi:10.1371/journal.pone.0032093

Kostadinov I, Kottmann R, Ramette A, Waldmann J, Buttigieg PL, Glöckner FO (2011) Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. Microbial Informatics and Experimentation 1:9

Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Mark Welch DB, Martiny JBH, Sogin M, Boetius A, Ramette A (2011). Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6(9): e24570

Schöttner S, Pfitzner B, Grünke S, Rasheed M, Wild C, Ramette A (2011) Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea. Environmental Microbiology 13(7): 1815-1826

Ramette A, Frapolli M, Fischer-Le Saux M, Gruffaz C, Meyer JM, Défago G, Sutra L, Moënne-Loccoz Y (2011). Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Systematic and Applied Microbiology. 34(3):180-188

Rossel PE, Elvert M, Ramette A, Boetius A, Hinrichs KU (2011) Factors controlling the distribution of anaerobic methanotrophic communities in marine environments: Evidence from intact polar membrane lipids. Geochimica et Cosmochimica Acta 75(1):164-184

Bru D, Ramette A, Saby NPA, Dequiedt S, Ranjard L, Jolivet C, Arrouays D, Philippot L (2011) Determinants of the distribution of nitrogen-cycling microbial communities at the landscape-scale. ISME Journal 5: 532-542

Orcutt BN, Samantha BJ, Kleindienst S, Knittel K, Ramette A, Reitz A, Samarkin V, Treude T, and Boetius A (2010) Impact of natural oil and higher hydrocarbons on microbial diversity, distribution and activity in Gulf of Mexico cold seep sediments. Deep-Sea Research II, 57:2008–2021

Amaral-Zettler L, Artigas LF, Baross J, Bharathi PAL, Boetius A, Chandramohan D, Herndl G, Kogure K, Neal P, Pedrós-Alió C, Ramette A, Schouten S, Stal L, Thessen A, de Leeuw J, Sogin ML (2010) A Global Census of Marine Microbes. In 'Life in the World’s Oceans' (Ed. AD McIntyre), Blackwell Publishing [book chapter]

Meziti A, Ramette A, Mente E, Kormas K (2010) Temporal shifts of the Norway lobster (Nephrops norvegicus) gut bacterial communities. FEMS Microbiology Ecology 74(2): 472–484

Alonso C, Gómez-Pereira P, Ramette A, Ortega L, Fuchs BM, Rudolf A (2010) Multilevel diversity analysis of bacterial communities along the environmental gradient Rio de la Plata-South Atlantic Ocean. Aquatic Microbial Ecology 61:57–72

Verna C, Ramette A, Wiklund H, Dahlgren TG, Glover AG, Gaill F, Dubilier N (2010) High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic. Environmental Microbiology. 12(8): 2355– 2370

Santillano D, Boetius A, Ramette A (2010) Improved dsrA-based Terminal Restriction Fragment Length Polymorphism analysis of sulfate-reducing bacteria. Applied and Environmental Microbiology 76(15): 5308–5311

Gobet A, Quince C, Ramette A (2010). Multivariate Cutoff Level Analysis (MultiCoLA) of Large Community Datasets. Nucleic Acids Research 38 (15): e155

Grünke S, Lichtschlag A, de Beer D, Kuypers M, Lösekann-Behrens T, Ramette A and Boetius A (2010) Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats. ISME Journal 4: 1031–1043

Knief C, Ramette A, Frances L, Alonso-Blanco C, and Vorholt JA (2010) Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME Journal 4: 719–728

Petersen JM, Ramette A, Lott C, Cambon-Bonavita MA, Zbinden M, and Dubilier N (2010) Dual symbiosis of the vent shrimp Rimicaris exoculata with filamentous Gamma- and Epsilonproteobacteria at four Mid-Atlantic Ridge hydrothermal vent fields. Environmental Microbiology 12(8): 2204–2218

Schauer R, Bienhold C, Ramette A, and Harder J (2010) Bacterial diversity and biogeography in deep-sea sediments of the South Atlantic Ocean. ISME Journal 4: 159–170

Zhao S, Ramette A, Niu GL, Liu H, Zhou NY (2009) Effects of nitrobenzene contamination and of bioaugmentation on nitrification and ammonia-oxidizing bacteria in soil. FEMS Microbiology Ecology 70(2): 159-167 [link]

Kanzog C, Ramette A (2009) Microbial colonisation of artificial and deep-sea sediments in the Arctic Ocean. Marine Ecology- An evolutionary perspective 30(4):391-404 [link]

Böer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, Ramette A (2009)Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. The ISME Journal 3:780-791 [link]

Ramette A (2009) Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol 75(8): 2495-2505  [link]

Schöttner S, Hoffmann F, Wild C, Rapp HT, Boetius A, Ramette A (2009) Inter- and intra-habitat bacterial diversity associated with cold-water corals. The ISME Journal 3: 756-759 [link]

Ramette A, Boetius A (2009) How to use a crystal ball in environmental microbiology: developing new ways to explore complex datasets. Environ Microbiol Reports 1(1):3-26 [link]

Ramette A, Tiedje JM, Boetius A (2009) Impact of space, time and complex environments on microbial communities. Clinical Microbiology and Infection 15(s1):60-62 [link]

Kanzog C, Ramette A, Quéric NV, Klages M (2009) Response of benthic microbial communities to chitin enrichment: an in situ study in the deep Arctic Ocean. Polar Biology 32: 105-112. [link]

Amaral-Zettler L, Peplies, J., Ramette A, Fuchs, B., Wolfgang Ludwige,W. Glöckner, F.O. (2008) Proceedings of the international workshop on Ribosomal RNA technology, April 7–9, 2008, Bremen, Germany. Systematic and Applied Microbiology 31: 258-268 [link]

Jacobs JL, Fasi AC, Ramette A, Smith JJ, Hammerschmidt R, Sundin GW (2008) Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil. Appl Environ Microbiol 74: 3121-3129 [link]

Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiology Ecology 62:142-160 [link]

Ramette A, Tiedje JM (2007) Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci USA. 104: 2761-2766 [link]

Ramette A, Tiedje JM (2007) Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microbial Ecology 53 (2): 197-207 [link]

Ramette A, Moënne-Loccoz Y, Défago G (2006) Genetic diversity and biocontrol potential of fluorescent pseudomonads producing phloroglucinols and hydrogen cyanide from Swiss soils naturally suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco. FEMS Microbiol. Ecol. 55 (3): 369-381 [link]

Payne GW, Ramette A, Rose HL, Weightman AJ, Jones TH, Tiedje JM, Mahenthiralingam E (2006) Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species. FEMS Microbiol. Lett. 259 (1): 126-132. [link]

Konstantinidis K, Ramette A, Tiedje JM (2006) Toward a more robust assessment of intra-species diversity using fewer genetic markers. Appl. Environ. Microbiol. 72, 7286-7293 [link]

Konstantinidis KT, Ramette A, Tiedje JM. (2006). The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci. 361(1475):1929-40 [link]

Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA. 103(42):15280-7 [link]

Ramette A, LiPuma JJ, Tiedje JM (2005) Species abundance and diversity of Burkholderia cepacia complex in the environment. Appl. Environ. Microbiol. 71 (3): 1193-1201 [link]

Ramette A, Frapolli M, Défago G, and Moënne-Loccoz Y (2003) Phylogeny of HCN synthase-encoding hcnBC genes in biocontrol fluorescent pseudomonads and its relationship with host plant species and HCN synthesis ability. Mol. Plant-Microbe Interact. 16(6):525-535 [link]

Ramette A, Moënne-Loccoz Y, and Défago G (2003) Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiol. Ecol. 44: 35-43 [link]

Wang CX, Ramette A, Punjasamarnwong P, Zala M, Natsch A, Moënne-Loccoz Y, Défago G (2001) Cosmopolitan distribution of phlD-containing dicotyledonous crop-associated biocontrol pseudomonads of worldwide origin. FEMS Microbiol. Ecol. 37: 105-116 [link]

Ramette A, Moënne-Loccoz Y, Défago G (2001) Polymorphism of the polyketide synthase gene phlD in biocontrol fluorescent pseudomonads producing 2,4-diacetylphloroglucinol and comparison of PhlD with plant polyketide synthases. Mol. Plant-Microbe Interact. 14(5): 639-652 [link]