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 L-K, Martinez-Garcia M, Sczyrba A, et al. (2014)
The ISME Journal 8(12): 2503-2516.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Ghylin, Trevor W.; Garcia, Sarahi L.; Moya, Francisco; Oyserman, Ben O.; Schwientek, Patrick; Forest, Katrina T.; Mutschler, James; Dwulit-Smith, Jeffrey; Chan, Leong-Keat; Martinez-Garcia, Manuel; Sczyrba, AlexanderUniBi ; Stepanauskas, Ramunas
Alle
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Technische Fakultät > Computational Metagenomics
Erscheinungsjahr
2014
Zeitschriftentitel
The ISME Journal
Band
8
Ausgabe
12
Seite(n)
2503-2516
ISSN
1751-7362
eISSN
1751-7370
Page URI
https://pub.uni-bielefeld.de/record/2689051

Zitieren

Ghylin TW, Garcia SL, Moya F, et al. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal. 2014;8(12):2503-2516.
Ghylin, T. W., Garcia, S. L., Moya, F., Oyserman, B. O., Schwientek, P., Forest, K. T., Mutschler, J., et al. (2014). Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8(12), 2503-2516. doi:10.1038/ismej.2014.135
Ghylin, Trevor W., Garcia, Sarahi L., Moya, Francisco, Oyserman, Ben O., Schwientek, Patrick, Forest, Katrina T., Mutschler, James, et al. 2014. “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”. The ISME Journal 8 (12): 2503-2516.
Ghylin, T. W., Garcia, S. L., Moya, F., Oyserman, B. O., Schwientek, P., Forest, K. T., Mutschler, J., Dwulit-Smith, J., Chan, L. - K., Martinez-Garcia, M., et al. (2014). Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal 8, 2503-2516.
Ghylin, T.W., et al., 2014. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8(12), p 2503-2516.
T.W. Ghylin, et al., “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”, The ISME Journal, vol. 8, 2014, pp. 2503-2516.
Ghylin, T.W., Garcia, S.L., Moya, F., Oyserman, B.O., Schwientek, P., Forest, K.T., Mutschler, J., Dwulit-Smith, J., Chan, L.-K., Martinez-Garcia, M., Sczyrba, A., Stepanauskas, R., Grossart, H.-P., Woyke, T., Warnecke, F., Malmstrom, R., Bertilsson, S., McMahon, K.D.: Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal. 8, 2503-2516 (2014).
Ghylin, Trevor W., Garcia, Sarahi L., Moya, Francisco, Oyserman, Ben O., Schwientek, Patrick, Forest, Katrina T., Mutschler, James, Dwulit-Smith, Jeffrey, Chan, Leong-Keat, Martinez-Garcia, Manuel, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, Warnecke, Falk, Malmstrom, Rex, Bertilsson, Stefan, and McMahon, Katherine D. “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”. The ISME Journal 8.12 (2014): 2503-2516.

44 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.
Props R, Monsieurs P, Vandamme P, Leys N, Denef VJ, Boon N., mSphere 4(1), 2019
PMID: 30728279
Characterization of Distinct CyanoHABs-Related Modules in Microbial Recurrent Association Network.
Chun SJ, Cui Y, Lee CS, Cho AR, Baek K, Choi A, Ko SR, Lee HG, Hwang S, Oh HM, Ahn CY., Front Microbiol 10(), 2019
PMID: 31379787
Spatial heterogeneity and hydrological fluctuations drive bacterioplankton community composition in an Amazon floodplain system.
Câmara Dos Reis M, Lacativa Bagatini I, de Oliveira Vidal L, Bonnet MP, da Motta Marques D, Sarmento H., PLoS One 14(8), 2019
PMID: 31398199
Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria.
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
Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.
Tandon K, Yang SH, Wan MT, Yang CC, Baatar B, Chiu CY, Tsai JW, Liu WC, Tang SL., Microbes Environ 33(2), 2018
PMID: 29681561
Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake.
Kong Z, Kou W, Ma Y, Yu H, Ge G, Wu L., Can J Microbiol 64(11), 2018
PMID: 29791806
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.
Garcia SL, Buck M, Hamilton JJ, Wurzbacher C, Grossart HP, McMahon KD, Eiler A., mSphere 3(3), 2018
PMID: 29848762
Solving the structure-function puzzle.
Ma L, Cordero OX., Nat Microbiol 3(7), 2018
PMID: 29946162
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
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.
Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J., Microbiome 6(1), 2018
PMID: 30266101
Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.
Mehrshad M, Salcher MM, Okazaki Y, Nakano SI, Šimek K, Andrei AS, Ghai R., Microbiome 6(1), 2018
PMID: 30285851
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
Composition and copper binding properties of aquatic fulvic acids in eutrophic Taihu Lake, China.
Li W, Zhang F, Ye Q, Wu D, Wang L, Yu Y, Deng B, Du J., Chemosphere 172(), 2017
PMID: 28104558
MetaSort untangles metagenome assembly by reducing microbial community complexity.
Ji P, Zhang Y, Wang J, Zhao F., Nat Commun 8(), 2017
PMID: 28112173
The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures.
Kang I, Kim S, Islam MR, Cho JC., Sci Rep 7(), 2017
PMID: 28186143
Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China.
Li Z, Lu L, Guo J, Yang J, Zhang J, He B, Xu L., Sci Rep 7(), 2017
PMID: 28211884
Microbial profiles of a drinking water resource based on different 16S rRNA V regions during a heavy cyanobacterial bloom in Lake Taihu, China.
Zhang J, Zhu C, Guan R, Xiong Z, Zhang W, Shi J, Sheng Y, Zhu B, Tu J, Ge Q, Chen T, Lu Z., Environ Sci Pollut Res Int 24(14), 2017
PMID: 28364202
Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.
Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD., mSphere 2(3), 2017
PMID: 28680968
Competition and niche separation of pelagic bacteria in freshwater habitats.
Pernthaler J., Environ Microbiol 19(6), 2017
PMID: 28370850
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
Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course.
Tromas N, Fortin N, Bedrani L, Terrat Y, Cardoso P, Bird D, Greer CW, Shapiro BJ., ISME J 11(8), 2017
PMID: 28524869
Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.
Denef VJ, Carrick HJ, Cavaletto J, Chiang E, Johengen TH, Vanderploeg HA., mSphere 2(3), 2017
PMID: 28593195
Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment.
Baumgartner M, Roffler S, Wicker T, Pernthaler J., ISME J 11(10), 2017
PMID: 28585936
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
Periphyton effects on bacterial assemblages and harmful cyanobacterial blooms in a eutrophic freshwater lake: a mesocosm study.
Cui Y, Jin L, Ko SR, Chun SJ, Oh HS, Lee CS, Srivastava A, Oh HM, Ahn CY., Sci Rep 7(1), 2017
PMID: 28798489
Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria.
Horňák K, Kasalický V, Šimek K, Grossart HP., Environ Microbiol 19(11), 2017
PMID: 28856804
Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group.
Moon K, Kang I, Kim S, Kim SJ, Cho JC., Environ Microbiol 19(11), 2017
PMID: 28925542
Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake.
Woodhouse JN, Kinsela AS, Collins RN, Bowling LC, Honeyman GL, Holliday JK, Neilan BA., ISME J 10(6), 2016
PMID: 26636552
Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?
Ricão Canelhas M, Eiler A, Bertilsson S., FEMS Microbiol Ecol 92(2), 2016
PMID: 26738554
Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria.
Oyserman BO, Moya F, Lawson CE, Garcia AL, Vogt M, Heffernen M, Noguera DR, McMahon KD., ISME J 10(12), 2016
PMID: 27128993
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
Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.
Liu J, Fu B, Yang H, Zhao M, He B, Zhang XH., Front Microbiol 6(), 2015
PMID: 25713564
Fluorescence in situ hybridization and sequential catalyzed reporter deposition (2C-FISH) for the flow cytometric sorting of freshwater ultramicrobacteria.
Neuenschwander SM, Salcher MM, Pernthaler J., Front Microbiol 6(), 2015
PMID: 25873914
Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages.
Luo H, Thompson LR, Stingl U, Hughes AL., Mol Biol Evol 32(10), 2015
PMID: 26116859
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
A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan.
Newton RJ, McLellan SL., Front Microbiol 6(), 2015
PMID: 26483766
Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu.
Li J, Zhang J, Liu L, Fan Y, Li L, Yang Y, Lu Z, Zhang X., Sci Rep 5(), 2015
PMID: 26503553
Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River.
Ruiz-González C, Salazar G, Logares R, Proia L, Gasol JM, Sabater S., Front Microbiol 6(), 2015
PMID: 26635761
Metagenome-assembled genomes uncover a global brackish microbiome.
Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF., Genome Biol 16(), 2015
PMID: 26667648
Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation.
Denef VJ, Mueller RS, Chiang E, Liebig JR, Vanderploeg HA., Appl Environ Microbiol 82(5), 2015
PMID: 26682860

68 References

Daten bereitgestellt von Europe PubMed Central.

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
Reconstitution of gloeobacter rhodopsin with echinenone: role of the 4-keto group.
Balashov SP, Imasheva ES, Choi AR, Jung KH, Liaaen-Jensen S, Lanyi JK., Biochemistry 49(45), 2010
PMID: 20942439
Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton
Beier S, Bertilsson S., 2011
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
Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium.
Carini P, Steindler L, Beszteri S, Giovannoni SJ., ISME J 7(3), 2012
PMID: 23096402
Transcriptome analysis of agmatine and putrescine catabolism in Pseudomonas aeruginosa PAO1.
Chou HT, Kwon DH, Hegazy M, Lu CD., J. Bacteriol. 190(6), 2008
PMID: 18192388
Characterization and a role of Pseudomonas aeruginosa spermidine dehydrogenase in polyamine catabolism.
Dasu VV, Nakada Y, Ohnishi-Kameyama M, Kimura K, Itoh Y., Microbiology (Reading, Engl.) 152(Pt 8), 2006
PMID: 16849793
The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times.
DeLong EF, Beja O., PLoS Biol. 8(4), 2010
PMID: 20436957
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
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
Accelerated Profile HMM Searches.
Eddy SR., PLoS Comput. Biol. 7(10), 2011
PMID: 22039361
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
Eiler A, Zaremba-Niedzwiedzka K, Andersson SGE, Martinez-Garcia M, McMahon KD, Stepanauskas R., 2013
Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes.
Fuser G, Steinbuchel A., Macromol Biosci 7(3), 2007
PMID: 17390395
Successful enrichment of the ubiquitous freshwater acI Actinobacteria.
Garcia SL, McMahon KD, Grossart HP, Warnecke F., Environ Microbiol Rep 6(1), 2013
PMID: 24596259
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 HP, Woyke T, Warnecke F., ISME J 7(1), 2012
PMID: 22810059
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
Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC.
Ghai R, McMahon KD, Rodriguez-Valera F., Environ Microbiol Rep 4(1), 2011
PMID: 23757226
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
Light stimulates growth of proteorhodopsin-containing marine Flavobacteria.
Gomez-Consarnau L, Gonzalez JM, Coll-Llado M, Gourdon P, Pascher T, Neutze R, Pedros-Alio C, Pinhassi J., Nature 445(7124), 2007
PMID: 17215843
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
Streamlining and core genome conservation among highly divergent members of the SAR11 clade.
Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappe MS., MBio 3(5), 2012
PMID: 22991429
Pathogenicity islands and the evolution of microbes.
Hacker J, Kaper JB., Annu. Rev. Microbiol. 54(), 2000
PMID: 11018140
Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems.
Humbert JF, Dorigo U, Cecchi P, Le Berre B, Debroas D, Bouvy M., Environ. Microbiol. 11(9), 2009
PMID: 19508336
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
Reconstitution of Gloeobacter violaceus rhodopsin with a light-harvesting carotenoid antenna.
Imasheva ES, Balashov SP, Choi AR, Jung KH, Lanyi JK., Biochemistry 48(46), 2009
PMID: 19842712
Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes.
Jones SE, Newton RJ, McMahon KD., Environ. Microbiol. 11(9), 2009
PMID: 19558514
Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.
Konstantinidis KT, Tiedje JM., Curr. Opin. Microbiol. 10(5), 2007
PMID: 17923431
Evaluation of non-cyanobacterial genome sequences for occurrence of genes encoding proteins homologous to cyanophycin synthetase and cloning of an active cyanophycin synthetase from Acinetobacter sp. strain DSM 587.
Krehenbrink M, Oppermann-Sanio FB, Steinbuchel A., Arch. Microbiol. 177(5), 2002
PMID: 11976746
ARB: a software environment for sequence data.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH., Nucleic Acids Res. 32(4), 2004
PMID: 14985472
Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.
Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, Lanyi JK., Proc. Natl. Acad. Sci. U.S.A. 105(43), 2008
PMID: 18922772

Magnuson JJ, Kratz TK, Benson BJ., 2006
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV., Genome Res. 9(7), 1999
PMID: 10413400
IMG: the Integrated Microbial Genomes database and comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC., Nucleic Acids Res. 40(Database issue), 2012
PMID: 22194640
Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.
Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF., Proc. Natl. Acad. Sci. U.S.A. 104(13), 2007
PMID: 17372221
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
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
Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes.
Newton RJ, Kent AD, Triplett EW, McMahon KD., Environ. Microbiol. 8(6), 2006
PMID: 16689717
Isolation of cyanophycin-degrading bacteria, cloning and characterization of an extracellular cyanophycinase gene (cphE) from Pseudomonas anguilliseptica strain BI. The cphE gene from P. anguilliseptica BI encodes a cyanophycinhydrolyzing enzyme.
Obst M, Oppermann-Sanio FB, Luftmann H, Steinbuchel A., J. Biol. Chem. 277(28), 2002
PMID: 11986309
Isolation and characterization of gram-positive cyanophycin-degrading bacteria-kinetic studies on cyanophycin depolymerase activity in aerobic bacteria.
Obst M, Sallam A, Luftmann H, Steinbuchel A., Biomacromolecules 5(1), 2004
PMID: 14715021
Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements.
Perez MT, Hortnagl P, Sommaruga R., Environ. Microbiol. 12(1), 2009
PMID: 19725866
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon.
Poretsky RS, Sun S, Mou X, Moran MA., Environ. Microbiol. 12(3), 2009
PMID: 19930445
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
The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22127870
Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartic acid (cyanophycin): molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme.
Richter R, Hejazi M, Kraft R, Ziegler K, Lockau W., Eur. J. Biochem. 263(1), 1999
PMID: 10429200
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.
Riedel T, Gomez-Consarnau L, Tomasch J, Martin M, Jarek M, Gonzalez JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Goker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Dobler I., PLoS ONE 8(3), 2013
PMID: 23526944
Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization.
Rocha EP., Genome Res. 14(11), 2004
PMID: 15479947
Contrasting dynamics in activity and community composition of free-living and particle-associated bacteria in spring
Rösel S, Grossart H., 2012
The Transporter Classification Database: recent advances.
Saier MH Jr, Yen MR, Noto K, Tamang DG, Elkan C., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19022853
Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake
Salcher MM, Pernthaler J, Posch T., 2010
In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake.
Salcher MM, Posch T, Pernthaler J., ISME J 7(5), 2012
PMID: 23235289
Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters.
Salka I, Wurzbacher C, Garcia SL, Labrenz M, Jurgens K, Grossart HP., Environ. Microbiol. 16(2), 2013
PMID: 23841943
Production optimization of cyanophycinase ChpEal from Pseudomonas alcaligenes DIP1.
Sallam A, Kalkandzhiev D, Steinbuchel A., AMB Express 1(1), 2011
PMID: 22060187
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
Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.
Sharma AK, Zhaxybayeva O, Papke RT, Doolittle WF., Environ. Microbiol. 10(4), 2008
PMID: 18218036
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Sharp PM, Li WH., Nucleic Acids Res. 15(3), 1987
PMID: 3547335
A rapid bootstrap algorithm for the RAxML Web servers.
Stamatakis A, Hoover P, Rougemont J., Syst. Biol. 57(5), 2008
PMID: 18853362
Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration.
Steindler L, Schwalbach MS, Smith DP, Chan F, Giovannoni SJ., PLoS ONE 6(5), 2011
PMID: 21573025
Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method.
Tada Y, Grossart HP., ISME J 8(2), 2013
PMID: 23985742
Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin.
Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R., PLoS ONE 8(5), 2013
PMID: 23671678
Selenite and tellurite reduction by Shewanella oneidensis.
Klonowska A, Heulin T, Vermeglio A., Appl. Environ. Microbiol. 71(9), 2005
PMID: 16151159
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
Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences.
Wu X, Xi W, Ye W, Yang H., FEMS Microbiol. Ecol. 61(1), 2007
PMID: 17506827
Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler.
Wurzbacher C, Salka I, Grossart HP., Environ Microbiol Rep 4(5), 2012
PMID: 23760893
Effect of bacteria from the bottom water layer of lake Baikal on degradation of diatoms
Zakharova YR, Kurilkina MI, Likhoshvay AV, Shishlyannikov SM, Kalyuzhnaya OV, Petrova DP., 2013
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 25093637
PubMed | Europe PMC

Suchen in

Google Scholar