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.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ;
Abstract / Bemerkung
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.
Erscheinungsjahr
Zeitschriftentitel
The ISME journal
Band
7
Zeitschriftennummer
1
Seite
137-147
ISSN
eISSN
PUB-ID

Zitieren

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.

36 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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
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.

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), 2010
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), 2011
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), 2010
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

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22810059
PubMed | Europe PMC

Suchen in

Google Scholar