Diversity and abundance of "Pelagibacterales" (SAR11) in the Baltic Sea salinity gradient

Systematic and Applied Microbiology

Volumn 37, Issue 8, 2014, Pages 601-604

  Herlemann, Daniel P R ^a   Woelk, Jana ^a   Labrenz, Matthias ^a   Jürgens, Klaus ^a  

^a LEIBNIZ INSTITUTE FOR BALTIC SEA RESEARCH   (Germany)

Author keywords

"Pelagibacterales" (SAR11); Baltic Sea; CARD FISH probe; Mesohaline (brackish); Salinity gradient; SAR11 III

Indexed keywords

FRESH WATER; SEA WATER;

AMPLICON; ARTICLE; BACTERIAL STRAIN; BALTIC SEA; CLADISTICS; COASTAL WATERS; CONTROLLED STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; LIMIT OF DETECTION; MARINE BACTERIUM; MICROBIAL DIVERSITY; NONHUMAN; PELAGIBACTERALES; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; SALINITY; ALPHAPROTEOBACTERIA; CLASSIFICATION; GENETICS; MICROBIOLOGY; PHYSIOLOGY; SEA;

BACTERIA (MICROORGANISMS);

ALPHAPROTEOBACTERIA; OCEANS AND SEAS; PHYLOGENY; SEAWATER;

EID: 84924215579     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2014.09.002     Document Type: Article

References (37)

1. Amann R., Binder B. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 1990, 56:1919-1925.
2. Ashelford K., Chuzhanova N. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 2005, 71:7724-7736.
3. Bahr M., Hobbie J., Sogin M. Bacterial diversity in an arctic lake: a freshwater SAR11 cluster. Aquat. Microb. Ecol. 1996, 11:271-277.
4. Bergen B., Herlemann D.P.R., Labrenz M., Jürgens K. Distribution of the verrucomicrobial clade Spartobacteria along a salinity gradient in the Baltic Sea. Environ. Microbiol. Rep. 2014, (in press). 10.1111/1758-2229.12178.
5. Brown M.V., Lauro F.M., DeMaere M.Z., Muir L., Wilkins D., Thomas T., Riddle M.J., Fuhrman J.A., Andrews-Pfannkoch C., Hoffman J.M., McQuaid J.B., Allen A., Rintoul S.R., Cavicchioli R. Global biogeography of SAR11 marine bacteria. Mol. Syst. Biol. 2012, 8:595.
6. Campbell B.J., Kirchman D.L. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J. 2013, 7:210-220.
7. Daims H., Brühl A., Amann R., Schleifer K.H., Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 1999, 22:434-444.
8. Dupont C.L., Larsson J., Yooseph S., Ininbergs K., Goll J., Asplund-Samuelsson J., McCrow J.P., Celepli N., Allen L.Z., Ekman M., Lucas A.J., Hagström Å., Thiagarajan M., Brindefalk B., Richter A.R., Andersson A.F., Tenney A., Lundin D., Tovchigrechko A., Nylander J.A.A., Brami D., Badger J.H., Allen A.E., Rusch D.B., Hoffman J., Norrby E., Friedman R., Pinhassi J., Venter J.C., Bergman B. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLOS ONE 2014, 9:e89549.
9. Fuchs B.M., Glöckner F.O., Wulf J., Amann R. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 2000, 66:3603-3607.
10. Grasshoff K., Kremling K., Ehrhardt M. Methods of Seawater Analysis 1983, Verlag Chemie, Weinheim, Germany.
11. Grote J., Thrash J.C., Huggett M.J., Landry Z.C., Carini P., Giovannoni S.J., Rappe M.S. Streamlining and core genome conservation among highly divergent members of the SAR11 Clade. MBio 2012, 3. e00252-12.
12. Herlemann D., Labrenz M., Jürgens K. Transitions in bacterial communities along the 2000km salinity gradient of the Baltic Sea. ISME J. 2011, 5:1571-1579.
13. Herlemann D., Lundin D., Labrenz M. Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. MBio 2013, 4:e00569-e612.
14. Kan J., Evans S., Chen F., Suzuki M. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat. Microb. Ecol. 2008, 51:55-66.
15. Klindworth A., Pruesse E., Schweer T., Peplies J., Quast C., Horn M., Glöckner F.O. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013, 41:e1.
16. Lefort T., Gasol J.M. Global-scale distributions of marine surface bacterioplankton groups along gradients of salinity, temperature, and chlorophyll: a meta-analysis of fluorescence in situ hybridization studies. Aquat. Microb. Ecol. 2013, 70:111-130.
17. Logares R., Bråte J., Bertilsson S. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 2009, 17:414-422.
18. Lozupone C., Knight R. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:11436-11440.
19. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüssmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
20. Morris R., Rappé M., Connon S. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 2002, 420:806-810.
21. Morris R.M., Vergin K.L., Cho J.-C., Rappé M.S., Carlson C.A., Giovannoni S.J. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic time-series study site. Limnol. Oceanogr. 2005, 50:1687-1696.
22. Ngugi D., Stingl U. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro-and macrodiversity of SAR11 populations in the Red Sea. PLOS ONE 2012, 7:e50274.
23. Oh H.-M., Kang I., Lee K., Jang Y., Lim S.-I., Cho J.-C. Complete genome sequence of strain IMCC9063, belonging to SAR11 subgroup 3, isolated from the Arctic Ocean. J. Bacteriol. 2011, 193:3379-3380.
24. Oksanen J., Blanchet F.G., Kindt R., Legendre P., O'Hara R.B., Simpson G.L., Solymos P., Stevens M.H.H., Wagner H. vegan: Community Ecology Package. R Package Version. 1, r Package Version 2.0-4 2012.
25. Peplies J., Kottmann R., Ludwig W., Glöckner F.O. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 2008, 31:251-257.
26. Pernthaler A., Pernthaler J., Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 2002, 68:3094-3101.
27. Pernthaler J. Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Microbiol. 2005, 3:537-546.
28. Piwosz K., Salcher M., Zeder M. Seasonal dynamics and activity of typical freshwater bacteria in brackish waters of the Gulf of Gdansk. Limnol. Oceanogr. 2013, 58:817-826.
29. Polz M., Cavanaugh C. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64:3724-3730.
30. Quast C., Pruesse E., Yilmaz P. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013, 41:d590-d596.
31. Salcher M.M., Pernthaler J., Posch T. Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria that rule the waves (LD12). ISME J. 2011, 5:1242-1252.
32. Sekar R., Pernthaler A., Pernthaler J., Warnecke F., Posch T., Amann R. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol. 2003, 69:2928-2935.
33. Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 1996, 62:625-630.
34. Viklund J., Martijn J., Ettema T.J.G., Andersson S.G.E. Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLOS ONE 2013, 8:e78858.
35. Wallner G., Amann R., Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 1993, 14:136-143.
36. Zaremba-Niedzwiedzka K., Viklund J., Zhao W., Ast J., Sczyrba A., Woyke T., McMahon K., Bertilsson S., Stepanauskas R., Andersson S.G. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol. 2013, 14:r130.
37. Zhao Y., Temperton B., Thrash J.C., Schwalbach M.S., Vergin K.L., Landry Z.C., Ellisman M., Deerinck T., Sullivan M.B., Giovannoni S.J. Abundant SAR11 viruses in the ocean. Nature 2013, 494:357-360.