Effect of storage conditions on archaeal and bacterial communities in subsurface marine sediments

Geomicrobiology Journal

Volumn 27, Issue 3, 2010, Pages 261-272

  Lin, Yu Shih ^a   Biddle, Jennifer F ^a,b   Lipp, Julius S ^a   Orcutt, Beth N ^c   Holler, Thomas ^d   Teske, Andreas ^b   Hinrichs, Kai Uwe ^a  

^a UNIVERSITY OF BREMEN   (Germany)

^b University of North Carolina at Chapel Hill   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

16S rRNA; Anaerobic oxidation of methane; ANME; Deep biosphere; Glycolipid; Intact polar lipid; McrA; Ocean drilling; Phospholipid

Indexed keywords

ANOXIC CONDITIONS; BIOSPHERE; DEEP-SEA SEDIMENT; GROWTH RATE; INFILTRATION; METHANE; MICROBIAL COMMUNITY; OCEAN DRILLING PROGRAM; OXIDATION; PHOSPHOLIPID; RNA;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 77952228973     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450903410423     Document Type: Article

References (44)

1. Batzke A, Engelen B, Sass H, Cypionka H. 2007. Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from Equatorial Pacific Ocean and Peru Margin sediments. Geomicrobiol J 24:261-273.
2. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. 2008. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105:10583-10588.
3. Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs KU. 2006. Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103: 3846-3851.
4. Brockman FJ, Kieft TL, Frederickson JK, Bjornstad BN, Li SW, Spangenburg W, Long PE. 1992. Microbiology of vadose zone paleosols in south-central Washington State. Microb Ecol 23:279-301.
5. Cragg BA, Bale SJ, Parkes RJ. 1992. A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere. Lett Appl Microbiol 15:125-128.
6. Crank J. 1975. The mathematics of diffusion, 2nd ed. Oxford: Oxford University Press. 414 p.
7. De Long EF. 1992. Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689.
8. D'Hondt S, Inagaki F, Ferdelman T, Jørgensen BB, Kato K, Kemp P, Sobecky P, Sogin M, Takai, K. 2007. Exploring subseafloor life with the Integrated Ocean Drilling Program. Sci Drill 5:26-37.
9. D'Hondt SL, Jørgensen BB, Miller DJ, et al. 2003. Proc ODP, Init Repts, 201. College Station, TX: Ocean Drilling Program.
10. Friedrich MW. 2005. Methyl-coenzyme M reductase genes: Unique functional markers for methanogenic and anaerobic methane-oxidizing archaea. Meth Enzymol 397:428-442.
11. Haldeman DL, Amy PS, Ringelberg D, White DC, Garen RE, Ghiorse WC. 1995. Microbial growth and resuscitation alter community structure after perturbation. FEMS Microbiol Ecol 17:27-38.
12. Haldeman DL, Amy PS, White DC, Ringelberg DB. 1994. Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4° C. Appl Environ Microbiol 60:2697-2703.
13. Hallam SJ, Girguis PR, Preston CM, Richardson PM, De Long EF. 2003. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:5483-5491.
14. Hansen JW, Thamdrup B, Jørgensen BB. 2000. Anoxic incubation of sediment in gas-tight plastic bags: a method for biogeochemical process studies. Mar Ecol Prog Ser 208:273-282.
15. Heizmann WR, Werner H. 1989. GasPack versus Anaerocult A-two carbon dioxide/hydrogen systems for cultivation of anaerobes. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig 270:511-516.
16. Hernandez RJ, Culter JD, Selke SEM. 2000. Plastic Packaging: Properties, Processing, Applications, and Regulations. Munich: Hanser. 425 p.
17. Hirsch P, Rades-Rohkohl E. 1988. Some special problems in the determination of viable counts of groundwater microorganisms. Microb Ecol 16:99-113.
18. House C, Cragg B, Teske A, Party SS. 2003. Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. In: D'Hondt SL, Jørgensen BB, Miller DJ, et al. Proc ODP, Init Repts, 201. College Station, TX: Ocean Drilling Program. P 1-19.
19. Imhof A, Heinzer I. 1996. Continuous monitoring of oxygen concentrations in several systems for cultivation of anaerobic bacteria. J Clin Microbiol 34:1646-1648.
20. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D'Hondt S, Jørgensen BB. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103:2815-2820.
21. Koga Y, Morii H. 2005. Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects. Biosci Biotechnol Biochem 69:2019-2034.
22. Koga Y, Nakano M. 2008. A dendrogram of archaea based on lipid component parts composition and its relationship to rRNA phylogeny. System Appl Microbiol 31:169-182.
23. Kraal P, Slomp CP, Forster A, Kuypers MMM, Sluijs A. 2009. Pyrite oxidation during sample storage determines phosphorus fractionation in carbonate-poor anoxic sediments. Geochim Cosmochim Acta 73:3277-3290.
24. Kumar S, Dudley J, Nei M, Tamura K. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9: 299-306.
25. Lever MA, Alperin M, Engelen B, Inagaki F, Nakagawa S, Steinsbu BO, Teske A, IODP Expedition 301 Scientists. 2006. Trends in basalt and sediment core contamination during IODP Expedition 301. Geomicrobiol J 23: 517-530.
26. Lipp JS, Morono Y, Inagaki F, Hinrichs KU. 2008. Significant contribution of archaea to extant biomass in marine subsurface sediments. Nature 454:991-994.
27. Musslewhite CL, Swift D, Gilpen J, McInerney MJ. 2007. Spatial variability of sulfate reduction in a shallow aquifer. Environ Microbiol 9: 2810-2819.
28. Orcutt B, Boetius A, Elvert M, Samarkin V, Joye SB. 2005. Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta 69:4267-4281.
29. Oremland RS, Polcin S. 1982. Methanogenesis and sulfate reduction: Competitive and noncompetitive substrates in estuarine sediments. Appl Environ Microbiol 66: 1270-1276.
30. Parkes RJ, Cragg BA, Wellsbury P. 2000. Recent studies on bacterial populations and processes in subseafloor sediments: A review. Hydrogeol J 8: 11-28.
31. Riedel M, Collet TS, Malone MJ, the Expedition 311 Scientists. 2006. Proc IODP, 311. Washington, DC: IODP Management International, Inc.
32. 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 Microbiol Ecol 15: 215-226.
33. Rossel PE, Lipp JS, Fredricks HF, Arnds J, Boetius A, Elvert M, Hinrichs KU. 2008. Intact polar lipids of anaerobic methanotrophic archaea and associated bacteria. Org Geochem 39:992-999.
34. Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, Parkes RJ, Jørgensen BB. 2005. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861-864.
35. Singer PC, Stumm W. 1970. Acidic mine drainage: The rate-determining step. Science 167: 1121-1123.
36. Smith DC, Spivack AJ, Fisk MR, Haveman SA, Staudigel H. 2000. Tracerbased estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol J 17:207-219.
37. Sørensen KB, Teske A. 2006. Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72: 4596-4603.
38. Sturt HF, Summons RE, Smith K, Elvert M, Hinrichs KU. 2004. Intact polar membrane lipids in prokaryotes and sediments deciphered by highperformance liquid chromatography/electrospray ionization multistage mass spectrometry-new biomarkers for biogeochemistry and microbial ecology. Rapid Commun Mass Spectrom 18:617-628.
39. Tabatabai MA. 1974. A rapid method for determination of sulfate in water samples. Environ Lett 7:237-243.
40. Teske A, Hinrichs KU, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68:1994-2007.
41. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673-4680.
42. Tréhu AM, Bohrmann G, Rack FR, Torres ME, et al. 2003. Proc ODP, Init Repts, 204. College Station, TX: Ocean Drilling Program.
43. Valentine D. 2007. Adaptations to energy stress dictate the ecology and evolution of the archaea. Nature Rev Microbiol 5:316-323.
44. Widdel F, Bak F. 1992. Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M., Harder W, Schleifer KH, editors. The Prokaryotes. New York: Springer. P 3352-3378.