Direct in situ detection of cells in deep-sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229)

Geobiology

Volumn 2, Issue 4, 2004, Pages 217-223

  Mauclaire, Laurie ^a   Zepp, K ^b   Meister, P ^a   Mckenzie, J ^a  

^a GEOLOGICAL INSTITUTE   (Switzerland)

^b SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARMORACIA RUSTICANA; BACTERIA (MICROORGANISMS); DESULFOBACTERACEAE; DESULFOVIBRIONACEAE;

EID: 23944458436     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4677.2004.00035.x     Document Type: Article

References (35)

1. Amann RI, Binder BJ, Olsen RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16SrRNA-targeted oligonucleotide probes with flow cytometry for analysing mixed microbial populations. Applied and Environmental Microbiology 56, 1919–1925.pmid/2200342
2. Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp nov, a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. International Journal of Systematic Bacteriology 47, 515–521.pmid/9103642
3. Barnes SP, Bradbrook SD, Cragg BA, Marchesi JR, Weightman AJ, Fry JC, Parkes RJ (1998) Isolation of sulfate-reducing bacteria from deep sediment layers of the Pacific Ocean. Geomicrobiology Journal 15, 67–83.
4. Boudreau BP, Westrich JT (1984) The dependence of bacterial sulfate reduction on sulfate concentration in marine sediments. Geochimica et Cosmochimica Acta 48, 2503–2516.
5. Capone GJ, Kiene RP (1988) Comparison of microbial dynamic in marine and fresh-water sediments: contrasts in anaerobic carbon catabolism. Limnology and Oceanography 33, 725–749.
6. Chevaldonné P, Godfroy A (1997) Enumeration of microorganisms from deep-sea hydrothermal chimney samples. FEMS Microbiology Letters 146, 211–216.
7. Clarke KR, Joint IR (1986) Methodology for estimating numbers of free-living and attached bacteria in estuarine water. Applied and Environmental Microbiology 51, 1110–1120.
8. Coleman AW (1980) Enhanced detection of bacteria in natural environments by fluorochrome staining of DNA. Limnology and Oceanography 25, 948–951.
9. Cragg BA, Parkes RJ, Fry JC, Herbert RA, Wimpenny JWT, Getliff JM (1990) Bacterial biomass and activity profiles within deep sediment layers. Proceedings of the Ocean Drilling Program, Scientific Results 112, 607–619.
10. Fry JC (1990) Direct methods and biomass estimation. Methods in Microbiology 22, 41–85.
11. Glöckner FO, Mann RI, Alfreider A, Pernthaler J, Psenner R, Trebesius K, Schleifer KH (1996) An optimized in situ hybridization protocol for planktonic bacteria. Systematic and Applied Microbiology 19, 403–406.
12. Gough HL, Stahl DA (2003) Optimization of direct cell counting in sediment. Journal of Microbiological Methods 52, 39–46.pmid/12401225
13. Goulder R (1977) Attached and free bacteria in an estuary with abundant suspended solids. Journal of Applied Bacteriology 43, 399–405.
14. Hahn D, Amann RI, Ludwig W, Akkermand ADL, Schleife K-H (1992) Detection of microorganisms in soil after in situ hybridization with rRNA-targeted, fluorescently labeled oligonucleotides. Journal of General Microbiology 138, 879–887.pmid/1379623
15. Hobbie JE, Daley RJ, Jasper S (1977) Use of nucleopore filters for counting bacteria by fluorescence microscopy. Applied and Environmental Microbiology 33, 1225–1228.pmid/327932
16. House CH, Cragg BA, Teske A (2003) Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. In Proceedings of the Ocean Drilling Program, Initial Reports 201, 1–19 [CD–ROM] (eds D’Hondt SL, Jorgensen BB, Miller DJ et al). Available from: Ocean Drilling Program, Texas A & M University, College Station TX 77845–9547, USA.
17. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Applied and Environmental Microbiology 69, 7224–7235.pmid/14660370
18. Knepner RLJ Jr, Pratt JR (1994) Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present. Microbiological Reviews 58, 603–615.pmid/7854248
19. Kuwae T, Hosokawa Y (1999) Determination of abundance and biovolume of bacteria in sediments by dual staining with 4′,6-diamidino-2-phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics. Applied and Environmental Microbiology 65, 3407–3412.pmid/10427027
20. Marchesi JR, Weightman AJ, Cragg BA, Parkes RJ, Fry JC (2001) Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiology Ecology 34, 221–228.pmid/11137602
21. Mauclaire L, Marmonier P, Gibert J (1998) Sampling water and sediment in interstitial habitats: a comparison of coring and pumping techniques. Archives Fur Hydrobiologie 142, 111–123.
22. 13C-enrichment of biomarker fatty acids. Journal of Microbiological Methods 55, 635–649.pmid/14607407
23. Mermillod-Blondin F, Fauvet G, Chalamet A, Creuzé des Châtelliers M (2001) A comparison of two ultrasonic methods for detaching biofilms from natural substrata. International Review of Hydrobiology 83, 349–360.
24. Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ, Fry JC (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Programme Leg 190. Environmental Microbiology 6, 274–287.pmid/14871211
25. Parkes RJ, Cragg BA, Bale SJ, Goodman K, Rochelle PA, Fry JC, Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific ocean sediments. Nature 371, 410–413.
26. Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments. Hydrogeology Journal 8, 11–28.
27. Peduzzi S, Tonolla M, Hahn D (2003) Vertical distribution of sulfate-reducing bacteria in the chemocline of lake Cadagno, Switzerland, over an annula cycle. Aquatic Microbial Ecology 30, 295–302.
28. Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnology and Oceanography 25, 943–948.
29. Rabus R, Fukui M, Wilkes H, Widdel F (1996) Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Applied and Environmental Microbiology 62, 3605–3613.pmid/8837415
30. Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Applied and Environmental Microbiology 68, 3759–3770.pmid/12147470
31. Rochelle PA, Cragg BA, Fry JC, Parkes RJ, Weightman AJ (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiology Ecology 15, 215–226.
32. Schallenberg M, Kalff J, Rasmussen JB (1989) Solutions to problems in enumerating sediment bacteria by direct counts. Applied and Environmental Microbiology 55, 1214–1219.
33. Shipboard Scientific Party (2003a) Leg 201 Summary. In Proceedings of the Ocean Drilling Program, Initial Reports 201, 1–81[CD–ROM] (eds D’Hondt SL, Jorgensen BB, Miller DJ et al). Available from: Ocean Drilling Program, Texas A & M University, College Station TX 77845–9547, USA.
34. Shipboard Scientific Party (2003b) Site 1229. In Proceedings of the Ocean Drilling Program, Initial Reports 201, 1–78 [CD–ROM] (eds D’Hondt SL, Jorgensen BB, Miller DJ et al). Available from: Ocean Drilling Program, Texas A & M University, College Station TX 77845–9547, USA.
35. Warthmann R, Van Lith Y, Vasconcelos C, McKenzie JA, Karpoff AM (2000) Bacterially induced dolomite precipitation in anoxic culture experiments. Geology 28, 1091–1094.