Analysis of methanogenic archaeal and sulphate reducing bacterial populations in deep sediments of the Black Sea

Geomicrobiology Journal

Volumn 23, Issue 5, 2006, Pages 285-292

  Ince, Bahar Kasapgil ^a   Usenti, Iclal ^a   Eyigor, Ayse ^a   Oz, Nilgun Ayman ^a   Kolukirik, Mustafa ^b   Ince, Orhan ^b  

^a BOGAZICI UNIVERSITY   (Turkey)

^b ISTANBUL TECHNICAL UNIVERSITY   (Turkey)

Author keywords

Deep sediment; Fluorescence in situ hybridization (FISH); Methanogenic Archaea (MA); Sulfate reducing bacteria (SRB); The Black Sea

Indexed keywords

DEEP-SEA SEDIMENT; METHANOGENIC BACTERIUM; MICROBIAL COMMUNITY; RELATIVE ABUNDANCE; SULFATE-REDUCING BACTERIUM;

BLACK SEA; EURASIA;

ARCHAEA; BACTERIA (MICROORGANISMS); DESULFOBOTULUS; DESULFOCOCCUS; DESULFOSARCINA; METHANOCOCCALES;

EID: 33750008710     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450600760724     Document Type: Conference Paper

References (37)

1. Amann, R and Binder, B and Olson, R and Chisholm, S and Devereux, R and Stahl, D. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations Appl Environ Microbiol, 56, pp. 1919-1925 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 2200342&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+56%5BVolume%5D+AND+1919%5BPage+Number%5D+AND+ 1990%5BPublication+Date%5D+AND+Amann%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol= 56&iss=&firstpage=1919
2. Balba, M and Nedwell, D. (1982) Microbial metabolism of acetate, propionate and butyrate in anoxic sediments from the Colne Point saltmarsh J Gen Microbiol, 128, pp. 1415-1422 http://www.csa.com/htbin/linkabst.cgi?issn=0022-1287&vol=128&iss= &firstpage=1415
3. Bouvier, T and del Giorgio, P. (2003) Factors influencing the detection of bacterial cells using fluorescence in situ hybridization (FISH): A quantitative review of published reports FEMS Microbiol Ecol, 44, pp. 3-15http://dx.doi.org/10.1016%2FS0168-6496%2802%2900461-0 http://www.csa.com/htbin/ linkabst.cgi?issn=0168-6496&vol=44&iss=&firstpage=3
4. Canfield, D and Des Marais, D. (1991) Aerobic sulfate reduction in microbial mats Science, 251, pp. 1471-1473 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 11538266&Session=&searchQuery=Science%5BJournal+Name%5D+AND+ 251%5BVolume%5D+AND+1471%5BPage+Number%5D+AND+1991%5BPublication+Date%5D+ AND+Canfield%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0294-0337&vol=251&iss=&firstpage=1471
5. Durisch-Kaiser, E and Klauser, L and Wehrli, B and Schubert, C. (2005) Evidence of intense archaeal and bacterial methanotrophic activity in the black sea water column Appl Environ Microbiol, 71(12), pp. 8099-8106 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 16332791&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+71%5BVolume%5D+AND+8099%5BPage+Number%5D+AND+ 2005%5BPublication+Date%5D+AND+Durisch%2DKaiser%5BAuthor+ Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.71.12.8099-8106.2005 http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=71&iss=12&firstpage=8099
6. Eyigor, A.(2004) Analysis of Archaeal Diversity in the Black Sea Sediments by Fluorescence in situ Hybridization Technique Bogazici University.
7. Genc, G.(2004) Comparison of Fluff Layer Composition with the Underlying Sediments in the Black Sea Istanbul: Bogazici University.
8. Harmsen, H and Kengen, H and Akkermans, A and Stams, A and de Vos, W. (1996) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes Appl Environ Microbiol 62, pp. 1656-1663 http://www4.infotrieve.com/newmedline/ detail.asp?NameID=8633864&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+62%5BVolume%5D+AND+1656%5BPage+Number%5D+ AND+1996%5BPublication+Date%5D+AND+Harmsen%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=62&iss= &firstpage=1656
9. Isa, Z and Grusenmeyer, S and Verstraete, W. (1986) Sulfate reduction relative to methane production in high-rate anaerobic digestion: technical aspects Appl Environ Microbiol, 51, pp. 580-587 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 16347019&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+51%5BVolume%5D+AND+580%5BPage+Number%5D+AND+ 1986%5BPublication+Date%5D+AND+Isa%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=51&iss=&firstpage=580
10. Ishii, K and Mußmann, M and MacGregor, B and Aman, R. (2004) An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments FEMS Microbiol Ecol, 50, pp. 203-212 http://dx.doi.org/10.1016%2Fj.femsec.2004.06.015 http://www.csa.com/htbin/linkabst.cgi?issn=0168-6496&vol=50&iss= &firstpage=203
11. Jannasch, H.(1991) Microbial processes in the Black Sea water column and top sediment: An overview. In Black Sea oceanography. (pp. 271-286). Dordrecht: Kluwer Academic Publishers.
12. Jorgensen, B. (1982) Mineralisation of organic matter in the sea-bed - the role of sulfate reduction Nature, 296, pp. 643-645 http://dx.doi.org/10.1038%2F296643a0 http://www.csa.com/htbin/linkabst.cgi?issn=0028-0887&vol=296&iss= &firstpage=643
13. Knittel, K and Lösekann, T and Boetius, A and Kort, R and Amann, R. (2005) Diversity and distribution of methanotrophic Archaea at cold seeps Appl Environ Microbiol, 71(1), pp. 467-479 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 15640223&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+71%5BVolume%5D+AND+467%5BPage+Number%5D+AND+ 2005%5BPublication+Date%5D+AND+Knittel%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.71.1.467-479.2005 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=71&iss= 1&firstpage=467
14. Lathe, R. (1985) Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations J Mol Biol, 183, pp. 1-12 http://www4.infotrieve.com/newmedline/ detail.asp?NameID=4009718&Session=&searchQuery=J+Mol+ Biol%5BJournal+Name%5D+AND+183%5BVolume%5D+AND+1%5BPage+Number%5D+AND+ 1985%5BPublication+Date%5D+AND+Lathe%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1016%2F0022-2836%2885%2990276-1 http://www.csa.com/htbin/linkabst.cgi?issn=0960-0760&vol=183&iss= &firstpage=1
15. Llobet-Brossa, E and Rosselló-Mora, R and Amann, R. (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization Appl Environ Microbiol, 64, pp. 2691-2696 http://www4.infotrieve.com/newmedline/ detail.asp?NameID=9647850&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+64%5BVolume%5D+AND+2691%5BPage+Number%5D+ AND+1998%5BPublication+Date%5D+AND+Llobet%2DBrossa%5BAuthor+ Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=64&iss=&firstpage=2691
16. Loring, D and Rantala, R. (1992) Manual for the geochemical analyses of marine sediments and suspended particulate matter Earth Sci Rev, 32, pp. 235-283 http://dx.doi.org/10.1016%2F0012-8252%2892%2990001-A http://www.csa.com/htbin/linkabst.cgi?issn=0012-8252&vol=32&iss= &firstpage=235
17. Lovley, D and Dawyer, D and Klug, M. (1982) Kinetic analysis of competition between sulfate reducers and methanogens for hydrogen in sediments Appl Environ Microbiol, 43, pp. 1373-1379 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 16346033&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+43%5BVolume%5D+AND+1373%5BPage+Number%5D+AND+ 1982%5BPublication+Date%5D+AND+Lovley%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=43&iss=&firstpage=1373
18. Manz, W and Amann, R and Ludwig, W and Wagner, M and Schleifer, K. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: Problems and solutions System Appl Microbiol, 15, pp. 593-600 http://www.csa.com/htbin/linkabst.cgi?issn=0723-2020&vol= 15&iss=&firstpage=593
19. Moter, A and Gobel, U. (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms J Microbiol Meth, 41, pp. 85-112 http://dx.doi.org/10.1016%2FS0167-7012%2800%2900152-4 http://www.csa.com/htbin/linkabst.cgi?issn=0167-7012&vol= 41&iss=&firstpage=85
20. Morita, R.(1997) Bacteria in oligotrophic environments: starvation-survival lifestyle. New York: Chapman & Hall.
21. Murray, J and Konovalov, S and Oguz, T and Besiktepe, S and Tugrul, S and Yakushev, E.(2003). 2001 R/V Knorr Cruise: New observations and Variations in the structure of the suboxic zone. Proceeding of the 'Second International Conference on Oceanography of the Eastern Medirratean and Black Sea: Similarities and Differences of Two Interconnected Basins', In Oceanography of the Eastern Mediterranean and Black Sea [pp. 545-557].
22. Nielsen, P. (1987) Biofilm dynamics and kinetics during high-rate sulfate reduction under anaerobic conditions Appl Environ Microbiol, 53, pp. 27-32 http://www4.infotrieve.com/newmedline/ detail.asp?NameID=16347263&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+53%5BVolume%5D+AND+27%5BPage+Number%5D+ AND+1987%5BPublication+Date%5D+AND+Nielsen%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=53&iss= &firstpage=27
23. Pimenov, N and Ivanova, A. (2005) Anaerobic methane oxidation and sulfate reduction in bacterial mats of coral-like carbonate structures in the Black Sea Mikrobiologiia, 74(3), pp. 420-429 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 16119857&Session=&searchQuery=Mikrobiologiia%5BJournal+Name%5D+ AND+74%5BVolume%5D+AND+420%5BPage+Number%5D+AND+2005%5BPublication+ Date%5D+AND+Pimenov%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0130-6758&vol=74&iss= 3&firstpage=420
24. Raskin, L and Stromley, J and Ritmann, B and Stahl, D. (1994) Group specific 16s rRNA hybridization probes to describe natural communities of methanogens Appl Environ Microbiol, 60, pp. 1232-1240 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 7517128&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+60%5BVolume%5D+AND+1232%5BPage+Number%5D+AND+ 1994%5BPublication+Date%5D+AND+Raskin%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=60&iss= &firstpage=1232
25. Ravenschlag, K and Sahm, K and Amann, R. (2001) Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard) Appl Environ Microbiol, 67, pp. 387-395 http://www4.infotrieve.com/newmedline/detail.asp?NameID= 11133470&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+67%5BVolume%5D+AND+387%5BPage+Number%5D+AND+ 2001%5BPublication+Date%5D+AND+Ravenschlag%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.67.1.387-395.2001 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=67&iss= &firstpage=387
26. Ravenschlag, K and Sahm, K and Knoblauch, C and Jøgensen, B and Amann, R. (2000) Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments Appl Environ Microbiol, 66, pp. 3592-3602. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 10919825&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+66%5BVolume%5D+AND+3592%5BPage+Number%5D+AND+ 2000%5BPublication+Date%5D+AND+Ravenschlag%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.66.8.3592-3602.2000 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=66&iss= &firstpage=3592
27. Reitner, J and Peckmann, J and Blumenberg, M and Michaelis, W and Reimer, A and Thiel, V. (2005) Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments Palaeogeogr Palaeoclimatol Palaeoecol, 227, pp. 18-30. http://dx.doi.org/ 10.1016%2Fj.palaeo.2005.04.033 http://www.csa.com/htbin/ linkabst.cgi?issn=0031-0182&vol=227&iss=&firstpage=18
28. Risatti, J and Capman, W and Stahl, D. (1994) Community structure of a microbial mat: The phylogenetic dimension Proc Natl Acad Sci, 91, pp. 10173-10177. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 7937858&Session=&searchQuery=Proc+Natl+Acad+Sci%5BJournal+ Name%5D+AND+91%5BVolume%5D+AND+10173%5BPage+Number%5D+AND+ 1994%5BPublication+Date%5D+AND+Risatti%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1073%2Fpnas.91.21.10173 http://www.csa.com/htbin/linkabst.cgi?issn=0027-8424&vol= 91&iss=&firstpage=10173
29. Usenti, I.(2004) Determination of Sulfate Reducing Bacterial Population in the Black Sea Sediments by Flourescence In Situ Hybridization Technique. Istanbul: Bogazici University.
30. Uysal, T.(2004) Examination of Nutrient Profiles in the Black Sea. Istanbul: Bogazici University.
31. Wagner, M and Asmus, B and Hartmann, A and Hutzler, P and Amann, R. (1994) In situ analysis of microbial consortia in activated sludge using fluorescently labelled rRNA-targeted oligonucleotide probes and confocal scanning laser microscopy J Microbiol, 176, pp. 181-187. http://www.csa.com/htbin/linkabst.cgi?issn=0021-5139&vol= 176&iss=&firstpage=181
32. Wagner, M and Horn, M and Daims, H. (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes Curr Opin Microbiol, 6, pp. 302-309. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 12831908&Session=&searchQuery=Curr+Opin+Microbiol%5BJournal+ Name%5D+AND+6%5BVolume%5D+AND+302%5BPage+Number%5D+AND+ 2003%5BPublication+Date%5D+AND+Wagner%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1016%2FS1369-5274%2803%2900054-7 http://www.csa.com/htbin/ linkabst.cgi?issn=1369-5274&vol=6&iss=&firstpage=302
33. Weinbauer, M and Beckmann and Hofle, M. (1998) Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria Appl Environ Microbiol, 164, pp. 5000-5003. http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=164&iss=&firstpage=5000
34. 2 reduction vs acetate fermentation isotope evidence ;Geochim Cosmochim Acta, 50, pp. 693-709. http://dx.doi.org/ 10.1016%2F0016-7037%2886%2990346-7 http://www.csa.com/htbin/ linkabst.cgi?issn=0046-564X&vol=50&iss=&firstpage=693
35. Winfrey, M and Ward, D. (1983) Substrates for sulfate reduction and methane production in intertidal sediments Appl Environ Microbiol, 45, pp. 193-199. http://www4.infotrieve.com/newmedline/ detail.asp?NameID=16346165&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+45%5BVolume%5D+AND+193%5BPage+Number%5D+ AND+1983%5BPublication+Date%5D+AND+Winfrey%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=45&iss= &firstpage=193
36. Winfrey, M and Zeikus, J. (1977) Effect of sulfate on carbon and electron flow during microbial methanogenesis in freshwater sediments Appl Environ Microbiol, 33, pp. 275-281. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 848951&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+33%5BVolume%5D+AND+275%5BPage+Number%5D+AND+ 1977%5BPublication+Date%5D+AND+Winfrey%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=33&iss= &firstpage=275
37. Yoda, M and Kitagawa, M and Miyaji, Y. (1987) Long term competition between sulfate-reducing and methane-producing bacteria for acetate in an anaerobic biofilm Water Res, 21, pp. 1547-1556. http://dx.doi.org/10.1016%2F0043-1354%2887%2990140-0 http://www.csa.com/htbin/ linkabst.cgi?issn=0436-4163&vol=21&iss=&firstpage=1547