Publikationen 2012/11

Yilmaz P, Iversen MH, Hankeln W, Kottmann R, Quast C, Glöckner FO (2012) Ecological structuring of bacterial and archaeal taxa in surface ocean waters. FEMS Microbiol Ecol 81:373-385 (DOI: 10.1111/j.1574-6941.2012.01357)

Voigt B, Hieu CX, Hempel K, Becher D, Schluter R, Teeling H, Glöckner FO, Amann R, Hecker M, Schweder T (2012) Cell surface proteome of the marine planctomycete Rhodopirellula baltica. Proteomics 12:1781-1791(DOI:10.1002/pmic.201100512)

Tuama EO, Deck J, Droge G, Doring M, Field D, Kottmann R, Ma J, Mori H, Morrison N, Sterk P, Sugawara H, Wieczorek J, Wu L, Yilmaz P (2012) Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012). Stand Genomic Sci 7:166-170 (DOI: 10.4056/sigs.3166513)

Teeling H, Glöckner FO (2012) Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. Brief. Bioinform. 13:728-742 (DOI: 10.1093/bib/bbs039)

Teeling H et al. (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336:608-611 (DOI: 10.1126/science.1218344)

Santos F, Yarza P, Parro V, Meseguer I, Rossello-Mora R, Anton J (2012) Culture-independent approaches for studying viruses from hypersaline environments. Appl Environ Microbiol 78:1635-1643 (DOI: 10.1128/AEM.07175-11)

Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EO, San Gil I, Wooley J (2012) RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011. Stand Genomic Sci 7:153-158 (DOI:10.4056/sigs.3146509)

Robbins RJ, Beach J, Blum S, Dawyndt P, Deck J, Kottmann R, Morrison N, Tuama EO, San Gil I, Vieglas D, Wieczorek J, Wooley J (2012) RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011. Stand Genomic Sci 7:171-174 (DOI:10.4056/sigs.3176515)

Robbins RJ et al. (2012) RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. Stand Genomic Sci 7:159-165 (DOI: 10.4056/sigs.3156511)

Radom M, Rybarczyk A, Kottmann R, Formanowicz P, Szachniuk M, Glöckner FO, Rebholz-Schuhmann D, Blazewicz J (2012) Poseidon: An information retrieval and extraction system for metagenomic marine science. Ecological Informatics 12:10-15 (DOI:10.1016/j.ecoinf.2012.07.003)

Pruesse E, Peplies J, Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829 (DOI: 10.1093/bioinformatics/bts252)

Lenk S, Moraru C, Hahnke S, Arnds J, Richter M, Kube M, Reinhardt R, Brinkhoff T, Harder J, Amann R, Mussmann M (2012) Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. ISME J 6:2178-2187 (DOI:10.1038/ismej.2012.66)

Kleiner M et al. (2012) Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci U S A 109:E1173-1182 (DOI: 10.1073/pnas.1121198109)

Jogler C, Waldmann J, Huang X, Jogler M, Glöckner FO, Mascher T, Kolter R (2012) Planctomycetes Comparative Genomics: Identification of Proteins Likely Involved in Morphogenesis, Cell Division and Signal Transduction. J Bacteriol 2012:21 (DOI:10.1128/JB.01325-12)

Ionescu D et al. (2012) Microbial and chemical characterization of underwater fresh water springs in the Dead Sea. PLoS One 7:e38319 (DOI: 10.1371/journal.pone.0038319)

Grote J, Schott T, Bruckner CG, Glöckner FO, Jost G, Teeling H, Labrenz M, Jürgens K (2012) Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc. Natl. Acad. Sci. USA 109:506-510 (DOI: 10.1073/pnas.1111262109)

Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H, Waldmann J, Richter M, Barbe V, Bataille E, Glöckner FO, Amann R (2012) Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ. Microbiol. 14:52-66 (DOI:10.1111/j.1462-2920.2011.02555)

Garcia-Aljaro C, Balleste E, Rossello-Mora R, Cifuentes A, Richter M, Blanch AR (2012) Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries. Syst Appl Microbiol 35:374-379 (DOI:10.1016/j.syapm.2012.06.007)

Fernandez-Guerra A, Casamayor EO (2012) Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers. PLoS One 7:e47330 (DOI:10.1371/journal.pone.0047330)

Fernandez-Gomez B, Fernandez-Guerra A, Casamayor EO, Gonzalez JM, Pedros-Alio C, Acinas SG (2012) Patterns and architecture of genomic islands in marine bacteria. BMC Genomics 13:347 (DOI:10.1186/1471-2164-13-347)

Davies N, Field D, Glöckner FO, Network TGO (2012) Sequencing data: A genomic network to monitor Earth. Nature 481:145-145 (DOI:10.1038/481145a)

Bulgarelli D et al. (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91-95 (DOI:10.1038/nature11336)

Boujelben I, Yarza P, Almansa C, Villamor J, Maalej S, Anton J, Santos F (2012) Virioplankton community structure in Tunisian solar salterns. Appl Environ Microbiol 78:7429-7437 (DOI:10.1128/AEM.01793-12)

Barberan A, Fernandez-Guerra A, Bohannan BJ, Casamayor EO (2012) Exploration of community traits as ecological markers in microbial metagenomes. Mol Ecol 21:1909-1917 (DOI:10.1111/j.1365-294X.2011.05383)

Yilmaz P, Kottmann R, Pruesse E, Quast C, Glöckner FO (2011) Analysis of 23S rRNA genes in metagenomes - a case study from the Global Ocean Sampling Expedition. Syst. Appl. Microbiol. 34:462-469 (DOI:10.1016/j.syapm.2011.04.005)

Yilmaz P et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29:415-420 (DOI:10.1038/nbt.1823)

Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone S-A, Glöckner FO, Field D (2011) The genomic standards consortium: bringing standards to life for microbial ecology. Isme J. 5:1565–1567 (DOI:10.1038/ismej.2011.39)

Westram R, Bader K, Pruesse E, Kumar Y, Meier H, Glöckner FO, Ludwig W (2011) ARB: a software environment for sequence data. In: de Bruijn FJ (ed) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. John Wiley & Sons, Inc., pp 399-406 (DOI:10.1002/9781118010518.ch46)

Weber M, Teeling H, Huang SX, Waldmann J, Kassabgy M, Fuchs BM, Klindworth A, Klockow C, Wichels A, Gerdts G, Amann R, Glöckner FO (2011) Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. Isme J. 5:918-928 (DOI:10.1038/ismej.2010.180)

Suarez-Suarez A, Lopez-Lopez A, Tovar-Sanchez A, Yarza P, Orfila A, Terrados J, Arnds J, Marques S, Niemann H, Schmitt-Kopplin P, Amann R, Rossello-Mora R (2011) Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment. Environ Microbiol 13:1488-1499 (DOI:10.1111/j.1462-2920.2011.02451.x)

Schattenhofer M, Wulf J, Kostadinov I, Glöckner FO, Zubkov MV, Fuchs BM (2011) Phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the North Atlantic Ocean. Syst. Appl. Microbiol. 34:470-475 (DOI:10.1016/j.syapm.2011.01.008)

Pruesse E, Quast C, Yilmaz P, Ludwig W, Peplies J, Glöckner FO (2011) SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB. In: de Bruijn FJ (ed) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley, Hoboken, NJ, USA (DOI:10.1002/9781118010518.ch45)

Munoz R, Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer K-H, Glöckner FO, Rossello-Mora R (2011) Release LTPs104 of the All-Species Living Tree. Syst. Appl. Microbiol. 34:169-170 (DOI:10.1016/j.syapm.2011.03.001)

Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D (2011) Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. SIGS 4:286-292 (DOI:10.4056/sigs.1344279)

Ludwig W, Yilmaz P, Glöckner FO (2011) The Use of rRNA Gene Sequence Data in the Classification and Identification of Prokaryotes. In: Rainey F, Oren A (eds) Methods in Microbiology, Vol 38: Taxonomy of Prokaryotes. Elsevier Ltd, pp 349-384 (DOI:10.1016/B978-0-12-387730-7.00016-4)

Lohsse A, Ullrich S, Katzmann E, Borg S, Wanner G, Richter M, Voigt B, Schweder T, Schuler D (2011) Functional analysis of the magnetosome island in Magnetospirillum gryphiswaldense: the mamAB operon is sufficient for magnetite biomineralization. PLoS One 6:e25561 (DOI: 10.1371/journal.pone.0025561)

Kostadinov I, Kottmann R, Ramette A, Waldmann J, Buttigieg PL, Glöckner F (2011) Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. Microbial Informatics and Experimentation 1:9 (DOI: 10.1186/2042-5783-1-9)

Jogler C, Glöckner FO, Kolter R (2011) Characterization of Planctomyces limnophilus and development of genetic tools for Its manipulation. Establish It as a model species for the phylum Planctomycetes. Appl. Environ. Microbiol. 77:5826-5829 (DOI:10.1128/AEM.05132-11)

Hankeln W, Wendel NJ, Gerken J, Waldmann J, Buttigieg PL, Kostadinov I, Kottmann R, Yilmaz P, Glöckner FO (2011) CDinFusion--submission-ready, on-line integration of sequence and contextual data. PLoS One 6:e24797 (DOI:10.1371/journal.pone.0024797)

Gonzalez JM, Pinhassi J, Fernandez-Gomez B, Coll-Llado M, Gonzalez-Velazquez M, Puigbo P, Jaenicke S, Gomez-Consarnau L, Fernandez-Guerra A, Goesmann A, Pedros-Alio C (2011) Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Appl Environ Microbiol 77:8676-8686 (DOI:10.1128/AEM.06152-11)

Gomez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H, Waldmann J, Richter M, Barbe V, Bataille E, Glöckner FO, Amann R (2011) Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol 14:52-66 (DOI:10.1111/j.1462-2920.2011.02555.x)

Glöckner FO, Kottmann R (2011) MIxS: neue Standards für Sequenz- und Umweltdaten. BIOspektrum 17:710-711 (DOI:
10.1007/s12268-011-0115-2)

Glöckner FO (2011) Globale Volkszählung. Laborjournal 6:46-48 

Garcia JA, Fernandez-Guerra A, Casamayor EO (2011) A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes. Molecular phylogenetics and evolution 61:650-658 (DOI:10.1016/j.ympev.2011.08.011)

Field D, Kottmann R, Morrison N, Sterk P (2011) A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium. Stand Genomic Sci 5:194 (DOI:10.4056/sigs.2295087)

Field D et al. (2011) The Genomic Standards Consortium. PLoS. Biol. 9:e1001088 (DOI: 10.1371/journal.pbio.1001088)

Ferrer M, Werner J, Chernikova TN, Bargiela R, Fernandez L, La Cono V, Waldmann J, Teeling H, Golyshina OV, Glöckner FO, Yakimov MM, Golyshin PN (2011) Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study. Environ Microbiol 14:268-281(DOI:10.1111/j.1462-2920.2011.02634.x)

Ferrer M et al. (2011) Taxonomic and functional metagenomic profiling of the microbial community in the anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, Central Spain). Microb Ecol 62:824-837 (DOI:10.1007/s00248-011-9903-y)

Duhaime MB, Kottmann R, Field D, Glöckner FO (2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. SIGS 4:271-285 (DOI:10.4056/sigs.621069)

Barberan A, Fernandez-Guerra A, Auguet JC, Galand PE, Casamayor EO (2011) Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol Ecol 20:1988-1996 (DOI:10.1111/j.1365-294X.2011.05057.x)