Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart H-P, Woyke T, Warnecke F (2012)
The ISME journal 7(1): 137-147.

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Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.
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The ISME journal
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7
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137-147
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Garcia SL, McMahon KD, Martinez-Garcia M, et al. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal. 2012;7(1):137-147.
Garcia, S. L., McMahon, K. D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., Stepanauskas, R., Grossart, H. - P., et al. (2012). Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal, 7(1), 137-147. doi:10.1038/ismej.2012.86
Garcia, S. L., McMahon, K. D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., Stepanauskas, R., Grossart, H. - P., Woyke, T., and Warnecke, F. (2012). Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal 7, 137-147.
Garcia, S.L., et al., 2012. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal, 7(1), p 137-147.
S.L. Garcia, et al., “Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton”, The ISME journal, vol. 7, 2012, pp. 137-147.
Garcia, S.L., McMahon, K.D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., Stepanauskas, R., Grossart, H.-P., Woyke, T., Warnecke, F.: Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal. 7, 137-147 (2012).
Garcia, Sarahi L, McMahon, Katherine D, Martinez-Garcia, Manuel, Srivastava, Abhishek, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, and Warnecke, Falk. “Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton”. The ISME journal 7.1 (2012): 137-147.

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Daten bereitgestellt von Europe PubMed Central.

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Neuenschwander SM, Ghai R, Pernthaler J, Salcher MM., ISME J 12(1), 2018
PMID: 29027997
Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake.
Salmaso N, Albanese D, Capelli C, Boscaini A, Pindo M, Donati C., Microb Ecol 76(1), 2018
PMID: 29192335
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations.
Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD., ISME J 12(3), 2018
PMID: 29222442
Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau.
Aguilar P, Dorador C, Vila I, Sommaruga R., FEMS Microbiol Ecol 94(3), 2018
PMID: 29346530
Ecology and evolution of metabolic cross-feeding interactions in bacteria.
D'Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C., Nat Prod Rep 35(5), 2018
PMID: 29799048
Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay.
Maresca JA, Miller KJ, Keffer JL, Sabanayagam CR, Campbell BJ., Appl Environ Microbiol 84(13), 2018
PMID: 29703736
Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution.
Lacombe-Harvey MÈ, Brzezinski R, Beaulieu C., Appl Microbiol Biotechnol 102(17), 2018
PMID: 29931600
Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community.
Chaudhary A, Kauser I, Ray A, Poretsky R., mSphere 3(4), 2018
PMID: 29976643
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.
Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD., mSphere 3(5), 2018
PMID: 30185512
acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal.
Dwulit-Smith JR, Hamilton JJ, Stevenson DM, He S, Oyserman BO, Moya-Flores F, Garcia SL, Amador-Noguez D, McMahon KD, Forest KT., Appl Environ Microbiol 84(24), 2018
PMID: 30315080
Seasonality of freshwater bacterioplankton diversity in two tropical shallow lakes from the Brazilian Atlantic Forest.
Ávila MP, Staehr PA, Barbosa FAR, Chartone-Souza E, Nascimento AMA., FEMS Microbiol Ecol 93(1), 2017
PMID: 27797965
Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA).
Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH., PLoS One 12(5), 2017
PMID: 28493994
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.
Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, Malmstrom RR, Forest KT, McMahon KD., mSystems 2(4), 2017
PMID: 28861526
Parallel genome reduction in symbionts descended from closely related free-living bacteria.
Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ., Nat Ecol Evol 1(8), 2017
PMID: 29046583
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.
Eiler A, Mondav R, Sinclair L, Fernandez-Vidal L, Scofield DG, Schwientek P, Martinez-Garcia M, Torrents D, McMahon KD, Andersson SG, Stepanauskas R, Woyke T, Bertilsson S., ISME J 10(8), 2016
PMID: 26784354
Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico.
Mason OU, Canter EJ, Gillies LE, Paisie TK, Roberts BJ., Front Microbiol 7(), 2016
PMID: 27458442
Experimental Evolution of Metabolic Dependency in Bacteria.
D'Souza G, Kost C., PLoS Genet 12(11), 2016
PMID: 27814362
Resistant microbial cooccurrence patterns inferred by network topology.
Peura S, Bertilsson S, Jones RI, Eiler A., Appl Environ Microbiol 81(6), 2015
PMID: 25576616
Dissolved organic monomer partitioning among bacterial groups in two oligotrophic lakes.
Pérez MT, Rofner C, Sommaruga R., Environ Microbiol Rep 7(2), 2015
PMID: 25403482
Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.
Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D., ISME J 9(4), 2015
PMID: 25303714
Bacterial diversity along a 2600 km river continuum.
Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AK, Farnleitner AH, Eiler A., Environ Microbiol 17(12), 2015
PMID: 25922985
Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.
Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F., Mol Ecol 24(17), 2015
PMID: 26179741
Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.
Satinsky BM, Fortunato CS, Doherty M, Smith CB, Sharma S, Ward ND, Krusche AV, Yager PL, Richey JE, Moran MA, Crump BC., Microbiome 3(), 2015
PMID: 26353777
Successful enrichment of the ubiquitous freshwater acI Actinobacteria.
Garcia SL, McMahon KD, Grossart HP, Warnecke F., Environ Microbiol Rep 6(1), 2014
PMID: 24596259
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.
Eiler A, Zaremba-Niedzwiedzka K, Martínez-García M, McMahon KD, Stepanauskas R, Andersson SG, Bertilsson S., Environ Microbiol 16(9), 2014
PMID: 24118837
Contrasting effects of singlet oxygen and hydrogen peroxide on bacterial community composition in a humic lake.
Glaeser SP, Berghoff BA, Stratmann V, Grossart HP, Glaeser J., PLoS One 9(3), 2014
PMID: 24667441
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning.
Krause S, Le Roux X, Niklaus PA, Van Bodegom PM, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier PL., Front Microbiol 5(), 2014
PMID: 24904563
Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.
Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U., Int J Syst Evol Microbiol 64(pt 9), 2014
PMID: 24984700
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.
Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD., ISME J 8(12), 2014
PMID: 25093637
Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon.
Eckert EM, Baumgartner M, Huber IM, Pernthaler J., Environ Microbiol 15(7), 2013
PMID: 23413977
Depth-discrete profiles of bacterial communities reveal pronounced spatio-temporal dynamics related to lake stratification.
Garcia SL, Salka I, Grossart HP, Warnecke F., Environ Microbiol Rep 5(4), 2013
PMID: 23864569
Cyanobacterial toxin degrading bacteria: who are they?
Kormas KA, Lymperopoulou DS., Biomed Res Int 2013(), 2013
PMID: 23841072
Bacterial chitin degradation-mechanisms and ecophysiological strategies.
Beier S, Bertilsson S., Front Microbiol 4(), 2013
PMID: 23785358

65 References

Daten bereitgestellt von Europe PubMed Central.

Intra- and inter-lake variability of free-living and particle-associated Actinobacteria communities.
Allgaier M, Bruckner S, Jaspers E, Grossart HP., Environ. Microbiol. 9(11), 2007
PMID: 17922757
Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany.
Allgaier M, Grossart HP., Appl. Environ. Microbiol. 72(5), 2006
PMID: 16672495
Microbial extracellular enzymes and the marine carbon cycle.
Arnosti C., Ann Rev Mar Sci 3(), 2011
PMID: 21329211
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.
Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Medigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM., Genome Res. 19(6), 2009
PMID: 19270083
Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton
Beier S, Bertilsson S., 2011
DSN depletion is a simple method to remove selected transcripts from cDNA populations.
Bogdanova EA, Shagina IA, Mudrik E, Ivanov I, Amon P, Vagner LL, Lukyanov SA, Shagin DA., Mol. Biotechnol. 41(3), 2009
PMID: 19127453
Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake.
Buck U, Grossart HP, Amann R, Pernthaler J., Environ. Microbiol. 11(7), 2009
PMID: 19320716
BLAST+: architecture and applications
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K., 2009
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18838391
The oxidative environment and protein damage
Davies MJ., 2005
Comprehensive human genome amplification using multiple displacement amplification.
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS., Proc. Natl. Acad. Sci. U.S.A. 99(8), 2002
PMID: 11959976
Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget--France).
Debroas D, Humbert JF, Enault F, Bronner G, Faubladier M, Cornillot E., Environ. Microbiol. 11(9), 2009
PMID: 19558513
Peroxiredoxins in bacterial antioxidant defense
Dubbs JM, Mongkolsuk S., 2007
Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom.
Eckert EM, Salcher MM, Posch T, Eugster B, Pernthaler J., Environ. Microbiol. 14(3), 2011
PMID: 22082109
Coherent dynamics and association networks among lake bacterioplankton taxa.
Eiler A, Heinrich F, Bertilsson S., ISME J 6(2), 2011
PMID: 21881616
What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH.
Fleming EJ, Langdon AE, Martinez-Garcia M, Stepanauskas R, Poulton NJ, Masland ED, Emerson D., PLoS ONE 6(3), 2011
PMID: 21437234
Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC
Ghai R, McMahon KD, Rodriguez-Valera F., 2011
Metagenomics of the water column in the pristine upper course of the Amazon river.
Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F., PLoS ONE 6(8), 2011
PMID: 21915244
Genome streamlining in a cosmopolitan oceanic bacterium.
Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappe MS, Short JM, Carrington JC, Mathur EJ., Science 309(5738), 2005
PMID: 16109880
Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria.
Glockner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A, Amann R., Appl. Environ. Microbiol. 66(11), 2000
PMID: 11055963
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB., Proc. Natl. Acad. Sci. U.S.A. 108(4), 2010
PMID: 21187386
Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.
Gomez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, Gonzalez JM, Pinhassi J., PLoS Biol. 8(4), 2010
PMID: 20436956
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria).
Gonzalez JM, Fernandez-Gomez B, Fernandez-Guerra A, Gomez-Consarnau L, Sanchez O, Coll-Llado M, Del Campo J, Escudero L, Rodriguez-Martinez R, Alonso-Saez L, Latasa M, Paulsen I, Nedashkovskaya O, Lekunberri I, Pinhassi J, Pedros-Alio C., Proc. Natl. Acad. Sci. U.S.A. 105(25), 2008
PMID: 18552178
Effect of nutrient loading on bacterioplankton community composition in Lake Mesocosms
Haukka K, Kolmonen E, Hyder R, Hietala J, Vakkilainen K, Kairesalo T., 2006
Capturing diversity of marine heterotrophic protists: one cell at a time.
Heywood JL, Sieracki ME, Bellows W, Poulton NJ, Stepanauskas R., ISME J 5(4), 2010
PMID: 20962875
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
Genetic engineering for improved xylose fermentation by yeasts recent progress in bioconversion of lignocellulosics
Jeffries T, Shi N-Q., 1999
‘Candidatus Planktophila limnetica', an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton
Jezbera J, Sharma AK, Brandt U, Doolittle WF, Hahn MW., 2009
The SWISS-MODEL Repository and associated resources.
Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18931379
The trophic-dynamic aspect of ecology
Lindeman RL., 1942
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
Lowe TM, Eddy SR., 1997
CDD: a Conserved Domain Database for the functional annotation of proteins.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21109532
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR., Proc. Natl. Acad. Sci. U.S.A. 104(29), 2007
PMID: 17620602
IMG ER: a system for microbial genome annotation expert review and curation.
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC., Bioinformatics 25(17), 2009
PMID: 19561336
Unveiling in situ interactions between marine protists and bacteria through single cell sequencing.
Martinez-Garcia M, Brazel D, Poulton NJ, Swan BK, Gomez ML, Masland D, Sieracki ME, Stepanauskas R., ISME J 6(3), 2011
PMID: 21938022
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.
Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R., ISME J 6(1), 2011
PMID: 21716306
Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
PMID: 19307242
A guide to the natural history of freshwater lake bacteria.
Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S., Microbiol. Mol. Biol. Rev. 75(1), 2011
PMID: 21372319
Phylogenetic ecology of the freshwater Actinobacteria acI lineage.
Newton RJ, Jones SE, Helmus MR, McMahon KD., Appl. Environ. Microbiol. 73(22), 2007
PMID: 17827330
CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC., 2010
Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture.
Pernthaler J, Posch T, Simek K, Vrba J, Pernthaler A, Glockner FO, Nubel U, Psenner R, Amann R., Appl. Environ. Microbiol. 67(5), 2001
PMID: 11319094
SignalP 4.0: discriminating signal peptides from transmembrane regions.
Petersen TN, Brunak S, von Heijne G, Nielsen H., Nat. Methods 8(10), 2011
PMID: 21959131
Comparative analyses of actinobacterial genomic fragments from Lake Kinneret.
Philosof A, Sabehi G, Beja O., Environ. Microbiol. 11(12), 2009
PMID: 19678830
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO., Nucleic Acids Res. 35(21), 2007
PMID: 17947321
Prediction of effective genome size in metagenomic samples.
Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P., Genome Biol. 8(1), 2007
PMID: 17224063
Genomic DNA amplification from a single bacterium.
Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS., Appl. Environ. Microbiol. 71(6), 2005
PMID: 15933038
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC., PLoS Biol. 5(3), 2007
PMID: 17355176
Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria.
Sharma AK, Sommerfeld K, Bullerjahn GS, Matteson AR, Wilhelm SW, Jezbera J, Brandt U, Doolittle WF, Hahn MW., ISME J 3(6), 2009
PMID: 19242530
PROSITE, a protein domain database for functional characterization and annotation.
Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19858104
Proposal for a New Hierarchic Classification System, Actinobacteria classis nov
Stackebrandt E, Rainey FA, Ward-Rainey NL., 1997
A Rapid Bootstrap Algorithm for the RAxML Web Servers
Stamatakis A, Hoover P, Rougemont J., 2008
Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time.
Stepanauskas R, Sieracki ME., Proc. Natl. Acad. Sci. U.S.A. 104(21), 2007
PMID: 17502618
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.
Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21045053
Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland ED, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R., Science 333(6047), 2011
PMID: 21885783
Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114.
Tang KH, Feng X, Tang YJ, Blankenship RE., PLoS ONE 4(10), 2009
PMID: 19794911
Do mycobacteria produce endospores?
Traag BA, Driks A, Stragier P, Bitter W, Broussard G, Hatfull G, Chu F, Adams KN, Ramakrishnan L, Losick R., Proc. Natl. Acad. Sci. U.S.A. 107(2), 2009
PMID: 20080769
Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages.
Warnecke F, Amann R, Pernthaler J., Environ. Microbiol. 6(3), 2004
PMID: 14871208
Abundances, identity, and growth state of actinobacteria in mountain lakes of different UV transparency.
Warnecke F, Sommaruga R, Sekar R, Hofer JS, Pernthaler J., Appl. Environ. Microbiol. 71(9), 2005
PMID: 16151148
Decontamination of MDA reagents for single cell whole genome amplification.
Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng JF., PLoS ONE 6(10), 2011
PMID: 22028825
Assembling the marine metagenome, one cell at a time.
Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R., PLoS ONE 4(4), 2009
PMID: 19390573
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
Sequencing genomes from single cells by polymerase cloning.
Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM., Nat. Biotechnol. 24(6), 2006
PMID: 16732271

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