Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea

Applied and Environmental Microbiology

Volumn 72, Issue 4, 2006, Pages 3079-3083

  Kirkpatrick, John ^a   Oakley, Brian ^b   Fuchsman, Clara ^a   Srinivasan, Sujatha ^b   Staley, James T ^b   Murray, James W ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; GENES; NUTRITION; OXIDATION; REDOX REACTIONS; RNA;

LOCAL NUTRIENTS; PHYLOTYPE DIVERSITY; PLANCTOMYCETES; SUBOXIC ZONE;

BACTERIA;

OXYGEN; RNA 16S;

AQUATIC COMMUNITY; BACTERIUM; BIODIVERSITY; DENITRIFICATION; GENE EXPRESSION; NITROGEN CYCLE; NUTRIENT DYNAMICS;

ARTICLE; BACTERIUM; GENE SEQUENCE; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT; OXIDATION REDUCTION REACTION; PHYLOGENY; PLANCTOMYCETES; SEA; UNINDEXED SEQUENCE; WATER SAMPLING;

BACTERIA, ANAEROBIC; DNA, BACTERIAL; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; OXIDATION-REDUCTION; OXYGEN; PHYLOGENY; QUATERNARY AMMONIUM COMPOUNDS; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

BLACK SEA; EURASIA;

BACTERIA (MICROORGANISMS); PLANCTOMYCETES;

EID: 33646112155     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.72.4.3079-3083.2006     Document Type: Article

References (36)

1. Anbar, A. D., and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:1137-1142.
2. Armstrong, F. A., C. R. Stearns, and J. D. H. Strickland. 1967. The measurement of upwelling and subsequent biological processes by means of the Technicon AutoAnalyzer and associated equipment. Deep-Sea Res. 14:381-389.
3. Chistoserdova, L., C. Jenkins, M. G. Kalyuzhnaya, C. J. Marx, A. Lapidus, J. A. Vorholt, J. T. Staley, and M. E. Lidstrom. 2004. The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol. Biol. Evol. 21:1234-1241.
4. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new auto-aligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443.
5. 2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422:606-608.
6. Damsté, J. S. S., M. Strous, W. I. C. Rijpstra, E. C. Hopmans, J. A. J. Geenevasen, A. C. T. van Duin, L. A. van Niftrik, and M. S. M. Jetten. 2002. Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419:708-712.
7. Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
8. Fuerst, J. A. 1995. The planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141:1493-1506.
9. Fuerst, J. A., H. G. Gwilliam, M. Lindsay, A. Lichanska, C. Belcher, J. E. Vickers, and P. Hugenholtz. 1997. Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Appl. Environ. Microbiol. 63:254-262.
10. Fuerst, J. A. 2005. Intracellular compartmentation in planctomycetes. Annu. Rev. Microbiol. 59:299-328.
11. Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70:845-849.
12. Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.
13. Kuypers, M. M. M., A. O. Sliekers, G. Lavik, M. Schmid, B. B. Jørgensen, J. G. Kuenen, J. S. Sinninghe Damsté, M. Strous, and M. S. M. Jetten. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608-611.
14. Kuypers, M. M. M, G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. B. Jørgensen, and M. S. M. Jetten. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 102:6478-6483.
15. Lachavanne, J.-B., and R. Juge. 1997. Land-inland water ecotones as transitional systems of particularly high biodiversity: towards a synthesis, p. 277-297. In J.-B. Lachavanne and R. Juge (ed.), Biodiversity in land-inland water ecotones. UNESCO, Paris, France.
16. Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:5072-5078.
17. Lindsay, M. R., R. I. Webb, M. Strous, M. S. M. Jetten, M. K. Butler, R. J. Forde, and J. A. Fuerst. 2001. Cell compartmentalization in planctomycetes: novel types of structural organization for the bacterial cell. Arch. Microbiol. 175:413-429.
18. Murray, J. W., L. A. Codispoti, and G. E. Friederich. 1995. Oxidation-reduction environments: the suboxic zone in the Black Sea, p. 157-176. In C. P. Huang, C. O'Melia, and J. J. Morgan (ed.), Aquatic chemistry. American Chemical Society, Washington, D.C.
19. 15N signatures of nitrogen transformations in the suboxic zone of the Black Sea. Oceanography 18:36-47.
20. Neef, A., R. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266.
21. Nicholas, K. B., H. B. Nicholas, Jr., and D. W. Deerfield II. 31 July 1997, posting date. GeneDoc: analysis and visualization of genetic variation. EMBnet.news 4. [Online.] http://www.ebi.ac.uk/embnet.news/vol4_2/genedoc.html.
22. Pearson, A., M. Budin, and J. J. Brocks. 2003. Phylogenetic biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus. Proc. Natl. Acad. Sci. USA 100:15352-15357.
23. Rysgaard, S., and R. N. Glud. 2004. Anaerobic N2 production in Arctic sea ice. Limnol. Oceanogr. 49:86-94.
24. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
26. Schmid, M., S. Schmitz-Esser, M. Jetten, and M. Wagner. 2001. 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ. Microbiol. 3:450-459.
27. Schmid, M., K. Walsh, R. Webb, W. I. C. Rijpstra, K. van de Pas-Schoonen, M. J. Verbruggen, T. Hill, B. Moffett, J. Fuerst, S. Schouten, J. S. Sinninghe Damsté, J. Harris, P. Shaw, M. Jetten, and M. Strous. 2003. Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria. Syst. Appl. Microbiol. 26:529-538.
28. Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, M. Jetten, J. W. Metzger, K.-H. Schleifer, and M. Wagner. 2000. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst. Appl. Microbiol. 23:93-106.
29. Slawyk, G., and J. J. MacIsaac. 1972. Comparison of two automated ammonium methods in a region of coastal upwelling. Deep-Sea Res. 19:521-524.
30. Smith, T. B., S. Kark, C. J. Schneider, R. K. Wayne, and C. Moritz. 2001. Biodiversity hotspots and beyond: the need for preserving environmental transitions. Trends Ecol. Evol. 16:431.
31. Strous, M., J. A. Fuerst, E. H. M. Kramer, S. Logemann, G. Muyzer, K. T. van de Pas-Schoonen, R. Webb, J. Gijs Kuenen, and M. S. M. Jetten. 1999. Missing lithotroph identified as new planctomycete. Nature 400:446-449.
32. 2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl. Environ. Microbiol. 68:1312-1318.
33. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
34. Van de Peer, Y., and R. De Wachter. 1997. Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Appl. Biosci. 13:227-230.
35. Vetriani, C., H. V. Tran, and L. J. Kerkhof. 2003. Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Appl. Environ. Microbiol. 69:6481-6488.
36. Wang, J., C. Jenkins, R. I. Webb, and J. A. Fuerst. 2002. Isolation of Gemmata-like and Isosphaera-like bacteria from soil and freshwater. Appl. Environ. Microbiol. 68:417-422.