Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR

Environmental Microbiology

Volumn 8, Issue 7, 2006, Pages 1251-1260

  Schippers, Axel ^a   Neretin, Lev N ^a,b  

^a FEDERAL INSTITUTE FOR GEOSCIENCES AND NATURAL RESOURCES BGR   (Germany)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA 16S; RNA 18S;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL COUNT; DELTAPROTEOBACTERIA; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; PERU; PHYLOGENY; SEDIMENT;

ARCHAEA; COLONY COUNT, MICROBIAL; DELTAPROTEOBACTERIA; DNA, RIBOSOMAL; ECOSYSTEM; GEOLOGIC SEDIMENTS; PERU; PHYLOGENY; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; GEOBACTERACEAE; PROKARYOTA;

EID: 33745121530     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01019.x     Document Type: Article

References (46)

1. ® ribosomal RNA control reagents, VIC™ probe, protocol. Part number 4308310 Rev. C.
2. Böning P. Brumsack H.-J. Böttcher M.E. Schnetger B. Kriete C. Kallmeyer J. Borchers S.L. ( 2004) Geochemistry of Peruvian near-surface sediments. Geochim Cosmochim Acta 68 : 4429 4451.
3. Coolen M.J.L. Overmann J. ( 1998) Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl Environ Microbiol 64 : 4513 4521.
4. Coolen M.J.L. Cypionka H. Sass A.M. Sass H. Overmann J. ( 2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296 : 2407 2410.
5. Coolen M.J.L. Muyzer G. Schouten S. Volkman J.K. Sinninghe Damsté J.S. ( 2006) Sulfur and methane cycling during the Holocene in Ace Lake (Antarctica) revealed by lipid and DNA stratigraphy. In Past and Present Water Column Anoxia. NATO Science Series, IV. Earth and Environmental Sciences, Vol. 64. Neretin L.N. (ed.). Dordrecht, the Netherlands : Springer, pp. 41 65.
6. Corinaldesi C. Danovaro R. Dell'Anno A. ( 2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 71 : 46 50.
7. Cragg B.A. Parkes R.J. Fry J.C. Herbert R.A. Wimpenny J.W.T. Getliff J.M. ( 1990) Bacterial biomass and activity profiles within deep sediment layers. In Proceedings of the ODP Scientific Results, Vol. 112. Suess E. van Huene R. Emeis KC. Bourgais J. del C. Cruzado Castañeda J. De Wever P., et al. (eds). College Station, TX : Ocean Drilling Program, pp. 607 619.
8. D'Hondt S.L. Jørgensen B.B. Miller D.J. Aiello I.W. Bekins B. Blake R., et al. ( 2003) Leg 201 Initial Report - controls on microbial communities in deeply buried sediments, Eastern Equatorial Pacific and Peru Margin. Ocean Drilling Program. URL http://www-odp.tamu.edu/publications/201_IR/ 201ir.htm
9. D'Hondt S.L. Jørgensen B.B. Miller D.J. Batzke A. Blake R. Cragg B.A., et al. ( 2004) Distributions of microbial activities in deep subseafloor sediments. Science 306 : 2216 2221.
10. Dell'Anno A. Corinaldesi C. ( 2004) Degradation and turnover of extracellular DNA in marine sediments: ecological and methodological considerations. Appl Environ Microbiol 70 : 4384 4386.
11. Dell'Anno A. Fabiano M. Duineveld G.C.A. Kok A. Danovaro R. ( 1998) Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments: comparison of spectrophotometric, fluorometric, and High-Performance Liquid Chromatography methods and estimation of detrital DNA. Appl Environ Microbiol 64 : 3238 3245.
12. Demanèche S. Jocteur-Monrozier L. Quiquampoix H. Simonet P. ( 2001) Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl Environ Microbiol 67 : 293 299.
13. Harms G. Layton A.C. Dionisi H.M. Gregory I.R. Garrett V.M. Hawkins S.A., et al. ( 2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37 : 343 351.
14. Hebsgaard M.B. Phillips M.J. Willerslev E. ( 2005) Geologically ancient DNA: fact or artefact? Trends Microbiol 13 : 212 220.
15. Holmes D.E. Finneran K.T. O'Neil R.A. Lovley D.R. ( 2002) Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl Environ Microbiol 68 : 2300 2306.
16. Inagaki F. Nealson K.H. ( 2006) The paleome: letters from ancient earth. In Past and Present Water Column Anoxia. NATO Science Series, IV. Earth and Environmental Sciences, Vol. 64. Neretin L.N. (ed.). Dordrecht, the Netherlands : Springer, pp. 21 39.
17. Inagaki F. Suzuki M. Takai K. Oida H. Sakamoto T. Aoki K., et al. ( 2003) Microbial communities associated with geological horizons in costal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69 : 7224 7235.
18. Inagaki F. Okada H. Tsapin A.I. Nealson K.H. ( 2005) The Paleome: a sedimentary genetic record of past microbial communities. Astrobiology 5 : 141 153.
19. Inagaki F. Nunoura T. Nakagawa S. Teske A. Lever M. Lauer A., et al. ( 2006) In search of the deep biosphere: biogeographical distribution and diversity of microbes in deep marine sediments associated with methane hydrates on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103 : 2815 2820.
20. Jørgensen B.B. D'Hondt S.L. Miller D.J., eds. ( 2005) Proc. ODP, Sci. Results, 201. URL http://www-odp.tamu.edu/publications/201_SR/201sr.htm
21. Kepner R.L., Jr Pratt J.R. ( 1994) Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present. Microbiol Rev 58 : 603 615.
22. Klappenbach J.L. Saxman P.R. Cole J.R. Schmidt T.M. ( 2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acid Res 29 : 181 184.
23. Knittel K. Boetius A. Lemke A. Eilers H. Lochte K. Pfannkuche O., et al. ( 2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia margin, Oregon). Geomicrobiol J 20 : 269 294.
24. Kondo R. Nedwell D.B. Purdy K.J. de Queiroz Silva S. ( 2004) Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiol J 21 : 145 157.
25. Kormas K. Ar, Smith D.C. Edgcomb V. Teske A. ( 2003) Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45 : 115 125.
26. Kudrass H.R., ed. ( 2000) Cruise report SO147 Peru Upwelling: Valparaiso-Callao, 29.05.-03.07.2000. Hannover, Germany : BGR Hannover.
27. Lee Y.-J. Wagner I.D. Brice M.E. Kevbrin V.V. Mills G.L. Romanek C.S. Wiegel J. ( 2005) Thermosediminibacter oceani gen. nov., sp. nov. & Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. Extremophiles 9 : 375 383.
28. Leloup J. Quillet L. Oger C. Boust D. Petit F. ( 2004) Molecular quantification of sulfate-reducing microorganisms (carrying dsr AB genes) by competitive PCR in estuarine sediments. FEMS Microbiol Ecol 47 : 207 214.
29. Lydolph M.C. Jacobsen J. Arctander P. Gilbert M.T.P. Gilichinsky D.A. Hansen A.J., et al. ( 2005) Beringian paleoecology inferred from permafrost-preserved fungal DNA. Appl Environ Microbiol 71 : 1012 1017.
30. Nadkarni M. Martin F.E. Jacques N.A. Hunter N. ( 2002) Determination of bacterial load by real-time PCR using a broad range (universal) probe and primer set. Microbiology 148 : 257 266.
31. Newberry C.J. Webster G. Cragg B.A. Parkes R.J. Weightman A.J. Fry J. ( 2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol 6 : 274 287.
32. Parkes R.J. Cragg B.A. Bale S.J. Getliff J.M. Goodman K. Rochelle P.A., et al. ( 1994) Deep bacterial biosphere in Pacific Ocean sediments. Nature 371 : 410 413.
33. Parkes R.J. Cragg B.A. Wellsbury P. ( 2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8 : 11 28.
34. Parkes R.J. Webster G. Cragg B.A. Weightman A.J. Newberry C.J. Ferdelman T.G., et al. 2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436 : 390 394.
35. Ramakers C. Ruijter J.M. Deprez R.H.L. Moorman A.F.M. ( 2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339 : 62 66.
36. Romanowski G. Lorenz M.G. Wackernagel W. ( 1991) Adsorption of plasmid DNA to mineral surfaces and protection against DNase I. Appl Environ Microbiol 57 : 1057 1061.
37. Ravenschlag K. Sahm K. Knoblauch C. Jørgensen B.B. Amann R. ( 2000) Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments. Appl Environ Microbiol 66 : 3592 3602.
38. Ravenschlag K. Sahm K. Amann R. ( 2001) Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Appl Environ Microbiol 67 : 387 395.
39. Sahm K. MacGregor B.J. Jørgensen B.B. Stahl D.A. ( 1999) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1 : 65 74.
40. Schippers A. Neretin L.N. Kallmeyer J. Ferdelman T.G. Cragg B.A. Parkes R.J. Jørgensen B.B. ( 2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433 : 861 864.
41. Sørensen K.B. Lauer A. Teske A. ( 2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2 : 151 161.
42. Takai K. Horikoshi K. ( 2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66 : 5066 5072.
43. Teske A.P. ( 2005) The deep subsurface biosphere is alive and well. Trends Microbiol 13 : 402 404.
44. Webster G. Newberry C.J. Fry J.C. Weightman A.J. ( 2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J Microbiol Methods 55 : 155 164.
45. Webster G. Parkes R.J. Fry J.C. Weightman A.J. ( 2004) Widespread occurrence of a novel division of bacteria identified by 16S rDNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70 : 5708 5713.
46. Whitman W.B. Coleman D.C. Wiebe W.J. ( 1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95 : 6578 6583.