Subfossil 16S rRNA gene sequences of green sulfur bacteria in the black sea and their implications for past photic zone anoxia

Applied and Environmental Microbiology

Volumn 74, Issue 3, 2008, Pages 624-632

  Manske, Ann K ^a   Henßge, Uta ^a   Glaeser, Jens ^a,b   Overmann, Jörg ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CULTIVATION; DENATURATION; DNA; GENE EXPRESSION; OPTIMIZATION; SEDIMENTS; SULFUR;

BLACK SEA; PHOTIC ZONE ANOXIA;

BACTERIA;

BACTERIAL DNA; RNA 16S;

ANOXIC CONDITIONS; BACTERIUM; BIOINDICATOR; CLADISTICS; ELECTROKINESIS; FOSSIL RECORD; NUCLEIC ACID ANALYSIS; PALEOENVIRONMENT; RECONSTRUCTION; RNA;

ARTICLE; CHLOROBIUM; ENVIRONMENT; FOSSIL; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEROZOIC; RNA GENE; SEA;

CHLOROBI; CHLOROBIUM; DNA, BACTERIAL; FOSSILS; GENES, RRNA; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

BLACK SEA; EURASIA;

BACTERIA (MICROORGANISMS); CHLOROBI; CHLOROBIUM SP.;

EID: 38949113818     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02137-07     Document Type: Article

References (43)

1. Anbar, A. D., and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:1137-1142.
2. Beatty, J. T., J. Overmann, M. T. Lince, A. K. Manske, A. S. Lang, R. E. Blankenship, C. L. Van Dover, T. A. Martinson, and F. G. Plumley. 2005. An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proc. Natl. Acad. Sci. USA 102:9306-9310.
3. Codispoti, L. A., G. E. Friederich, J. W. Murray, and C. M. Sakamoto. 1991. Chemical variability in the Black Sea: implications of continuous vertical profiles that penetrated the oxic/anoxic interface. Deep-Sea Res. 38(Suppl. 2):S691-S710.
4. Coolen, M. J. L., and J. Overmann. 1998. Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl. Environ. Microbiol. 64:4513-4521.
5. Coolen, M. J. L., and J. Overmann. 2007. 217,000 year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment. Environ. Microbiol. 9:238-249.
6. Coolen, M. J. L., H. Cypionka, A. Smock, H. Sass, and J. Overmann. 2002. Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296:2407-2410.
7. Degens, E. T., and D. A. Ross. 1972. Chronology of the Black Sea over the last 25,000 years. Chem. Geol. 10:1-16.
8. Degens, E. T., and P. Stoffers. 1976. Stratified waters as a key to the past. Nature 263:22-27.
9. Eder, W., M. Schmidt, M. Koch, D. Garbe-Schönberg, and R. Huber. 2002. Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea. Environ. Microbiol. 4:758-763.
10. Freeman, K. H., S. G. Wakeham, and J. M. Hayes. 1994. Predictive isotopic biogeochemistry: hydrocarbons from anoxic marine basins. Org. Geochem. 21:629-644.
11. Fuhrman, J. A., D. E. Comeau, Å. Hagström, and A. M. Chan. 1988. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl. Environ. Microbiol. 54:1426-1429.
12. Gich, F., J. Garcia-Gil, and J. Overmann. 2001. Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch. Microbiol. 177:1-10.
13. Glaeser, J., and J. Overmann. 2004. Biogeography, evolution, and diversity of epibionts in phototrophic consortia. Appl. Environ. Microbiol. 70:4821-4830.
14. Goffredi, S. K., A. Warén, V. J. Orphan, C. van Dover, and R. C. Vrijenhoek. 2004. Novel forms of structural integration between microbes and a hydrothermal vent gastropod from the Indian Ocean. Appl. Environ. Microbiol. 70:3082-3290.
15. Gorlenko, V. M., P. V. Mikheev, I. I. Rusanov, N. V. Pimenov, and M. V. Ivanov. 2005. 2005. Ecophysiological properties of photosynthetic bacteria from the Black Sea chemocline zone. Microbiology (New York) 74:201-209.
16. Hashwa, F. A., and H. G. Trüper. 1978. Viable phototrophic bacteria from the Black-Sea bottom. Helgol. Wiss. Meeresunters. 31:249-253.
17. Hay, B. J. 1988. Sediment accumulation in the central western Black Sea over the past 5,100 years. Paleoceanography 3:491-508.
18. Hay, B. J., and M. A. Arthur. 1991. Sediment deposition in the Holocene Black Sea. Deep-Sea Res. 38(Suppl. 2):1211-1235.
19. Imhoff, J. F. 2003. Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences. Int. J. Syst. Evol. Microbiol. 53:941-951.
20. Kohnen, M. E. L., J. S. Sinninghe Damsté, and J. W. DeLeeuw. 1991. Biases from natural sulphurization in palaeoenvironmental reconstruction based on hydrocarbon biomarker distribution. Nature 349:775-778.
21. Konovalov, S. K., L. I. Ivanov, and A. S. Samodurov. 2001. Fluxes and budgets of sulphide and ammonia in the Black Sea anoxic layer. J. Mar. Syst. 31:203-216.
22. Ludwig, W., O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger, J. Neumann, M., Bachleitner, and K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
23. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
24. Manske, A. K., J. Glaeser, M. M. M. Kuypers, and J. Overmann. 2005. Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 meters in the Black Sea. Appl. Environ. Microbiol. 71:8049-8060.
25. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
26. Muyzer, G., S. Hottenträger, A. Teske, and C. Waver. 1995. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - a new molecular approach to analyse the genetic diversity of mixed microbial communities, p. 3.4.4.1-3.4.4.22. In A. D. L. Akkermans, J. D. Van Elsas, and F. J. De Bruijn (ed.), Molecular microbial ecology manual, 2nd ed. Kluwer, Dordrecht, The Netherlands.
27. Overmann, J. 1991. Standortspezifische Anpassung bei phototrophen Schwefelbakterien. Konstanzer Dissertationen Bd. 321. Hartung-Gorre, Konstanz, Germany.
28. Overmann, J., and N. Pfennig. 1989. Pelodictyon phaeoclathratiforme sp. nov., a new brown-colored member of the Chlorobiaceae forming net-like colonies. Arch. Microbiol. 152:401-406.
29. Overmann, J., and C. Tuschak. 1997. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch. Microbiol. 167:302-309.
30. Overmann, J., and A. K. Manske. 2006. Anoxygenic phototrophic bacteria in the Black Sea, p. 543-561. In L. Neretin (ed.), Past and present water column anoxia. NATO ASI series. Springer-Verlag, Berlin, Germany.
31. Overmann, J., H. Cypionka, and N. Pfennig. 1992. An extremely low-light-adapted green sulfur bacterium from the Black Sea. Limnol. Oceanogr. 37:150-155.
32. Overmann, J., M. J. L. Coolen, and C. Tuschak. 1999. Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch. Microbiol. 172:83-94.
33. Repeta, D. J. 1993. A high resolution historical record of Holocene anoxygenic primary production in the Black Sea. Geochim. Cosmochim. Acta 57:4337-4342.
34. Repeta, D. J., and D. J. Simpson. 1991. The distribution and recycling of chlorophyll, bacteriochlorophyll and carotenoids in the Black Sea. Deep-Sea Res. 38:969-984.
35. Repeta, D. J., D. J. Simpson, B. B. Jørgensen, and H. W. Jannasch. 1989. Evidence for anoxygenic photosynthesis from the distribution of bacteriochlorophylls in the Black Sea. Nature 342:69-72.
36. Rosell-Melé, A., M. A. Maslin, J. R. Maxwell, and P. Schaefer. 1997. Biomarker evidence for "Heinrich" events. Geochim. Cosmochim. Acta 61:1671-1678.
37. Schwarz, J. I. K., W. Eckert, and R. Conrad. 2007. Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst. Appl. Microbiol. 30:239-254.
38. Sinninghe Damsté, J. S., S. G. Wakeham, M. E. L. Kohnen, J. M. Hayes, and J. W. de Leeuw. 1993. A 6,000-year sedimentary molecular record of chemocline excursions in the Black Sea. Nature 362:827-829.
39. Sorokin, Y. I. 2002. The Black Sea. Ecology and oceanography. Backhuys Publishers, Leiden, The Netherlands.
40. Summons, R. E., and T. G. Powell. 1987. Identification of aryl isoprenoids in source rocks and crude oils: biological markers for the green sulfur bacteria. Geochim. Cosmochim. Acta 51:557-566.
41. Ulrich, A. C., and E. A. Edwards. 2003. Physiological and molecular characterization of anaerobic benzene-degrading mixed cultures. Environ. Microbiol. 5:92-102.
42. von Wintzingerode, F., B. Selent, W. Hegemann, and U. B. Göbel. 1999. Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl. Environ. Microbiol. 65:283-286.
43. Wakeham, S. G., J. S. Sinninghe Damsté, M. E. L. Kohnen, and J. W. DeLeeuw. 1995. Organic sulfur compounds formed during early diagenesis in Black Sea sediments. Geochim. Cosmochim. Acta 59:521-533.