New insight into stratification of anaerobic methanotrophs in cold seep sediments

FEMS Microbiology Ecology

Volumn 78, Issue 2, 2011, Pages 233-243

  Roalkvam, Irene ^a   Jørgensen, Steffen Leth ^a   Chen, Yifeng ^b   Stokke, Runar ^a   Dahle, Håkon ^a   Hocking, William Peter ^a   Lanzén, Anders ^a   Haflidason, Haflidi ^a   Steen, Ida Helene ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b GUANGZHOU INSTITUTE OF GEOCHEMISTRY   (China)

Author keywords

ANME 1; Pyrosequencing; Stratification

Indexed keywords

METHANE; RNA 16S; SEA WATER;

ABUNDANCE; ANOXIC CONDITIONS; BACTERIUM; INTERSPECIFIC INTERACTION; METHANE; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; MICROBIAL MAT; OXIDATION; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REAL TIME; SEEPAGE;

ANAEROBIC GROWTH; ARTICLE; BACTERIUM; BIOFILM; CLASSIFICATION; DELTAPROTEOBACTERIA; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; REAL TIME POLYMERASE CHAIN REACTION; SEDIMENT;

ANAEROBIOSIS; BACTERIA; BIOFILMS; DELTAPROTEOBACTERIA; GEOLOGIC SEDIMENTS; METHANE; MOLECULAR SEQUENCE DATA; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER;

NORWAY;

CANDIDATE DIVISION JS1; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; METHYLOCOCCALES; SULFUROVUM;

EID: 80054109698     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01153.x     Document Type: Article

References (71)

1. Amann RI, Ludwig W & Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev59: 143-169.
2. Boetius A, Ravenschlag K, Schubert CJet al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature407: 623-626.
3. Brazelton WJ, Schrenk MO, Kelley DS & Baross JA (2006) Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microb72: 6257-6270.
4. Campbell BJ, Engel AS, Porter ML & Takai K (2006) The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4: 458-468.
5. 13C of dissolved inorganic carbon in Pockmark G11, offshore Mid-Norway. Chem Geol275: 127-138.
6. Christensen H, Hansen M & Sorensen J (1999) Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl Environ Microb65: 1753-1761.
7. Daims HBA, Amann R, Schleifer KH & Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444.
8. Edwards U, Rogall T, Blocker H, Emde M & Bottger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res17: 7843-7853.
9. Einen J, Thorseth IH & Ovreas L (2008) Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy. FEMS Microbiol Lett282: 182-187.
10. Fang J, Shizuka A, Kato C & Schouten S (2006) Microbial diversity of cold-seep sediments in Sagami Bay, Japan, as determined by 16S rRNA gene and lipid analyses. FEMS Microbiol Ecol57: 429-441.
11. Glaubitz S, Labrenz M, Jost G & Jurgens K (2010) Diversity of active chemolithoautotrophic prokaryotes in the sulfidic zone of a Black Sea pelagic redoxcline as determined by rRNA-based stable isotope probing. FEMS Microbiol Ecol74: 32-41.
12. Glöckner FO, Amann R, Alfreider A, Pernthaler J, Psenner R, Trebesius K & Schleifer KH (1996) An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst Appl Microbiol19: 403-406.
13. Harrison BK, Zhang H, Berelson W & Orphan VJ (2009) Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microb75: 1487-1499.
14. Heijs SK, Haese RR, van der Wielen PW, Forney LJ & van Elsas JD (2007) Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb Ecol53: 384-398.
15. Hinrichs KU, Hayes JM, Sylva SP, Brewer PG & DeLong EF (1999) Methane-consuming archaebacteria in marine sediments. Nature398: 802-805.
16. Hjelstuen BO, Haflidason H, Sejrup HP & Nygard A (2010) Sedimentary and structural control on pockmark development-evidence from the Nyegga pockmark field, NW European margin. Geo-Mar Lett30: 221-230.
17. Hoehler TM, Alperin MJ, Albert DB & Martens CS (1994) Field and laboratory studies of methane oxidation in an anoxic marine sediment - evidence for a methanogen-sulfate reducer consortium. Global Biogeochem Cy8: 451-463.
18. Hovland M, Svensen H, Forsberg CF, Johansen H, Fichler C, Fossa JH, Jonsson R & Rueslatten H (2005) Complex pockmarks with carbonate-ridges off mid-Norway: Products of sediment degassing. Mar Geol 218: 191-206.
19. 2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol73: 526-537.
20. Huson DH, Auch AF, Qi J & Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res17: 377-386.
21. Inagaki F, Takai K, Kobayashi H, Nealson KH & Horikoshi K (2003) Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing epsilon-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Micr53: 1801-1805.
22. Inagaki F, Takai K, Nealson KH & Horikoshi K (2004) Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. Int J Syst Evol Micr54: 1477-1482.
23. Inagaki F, Nunoura T, Nakagawa Set al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. P Natl Acad Sci USA103: 2815-2820.
24. Ivanov M, Mazzini A, Blinova V, Kozlova E, Laberg JS, Matveeva T, Taviani M & Kaskov N (2010) Seep mounds on the Southern Wiring Plateau (offshore Norway). Mar Petrol Geol27: 1235-1261.
25. Jagersma GC, Meulepas RJ, Heikamp-de Jong I, Gieteling J, Klimiuk A, Schouten S, Damste JS, Lens PN & Stams AJ (2009) Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environ Microbiol11: 3223-3232.
26. Knittel K & Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63: 311-334.
27. Knittel K, Lösekann T, Boetius A, Kort R & Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microb71: 467-479.
28. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB & Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature437: 543-546.
29. Kvenvolden KA, Ginsburg GD & Soloviev VA (1993) Worldwide distribution of subaquatic gas hydrates. Geo-Mar Lett13: 32-40.
30. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E & Goodfellow M, eds), pp. 115-175. Wiley, New York, NY.
31. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML & Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. P Natl Acad Sci USA82: 6955-6959.
32. Lanoil BD, Sassen R, La Duc MT, Sweet ST & Nealson KH (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microb67: 5143-5153.
33. Lanzen A, Jorgensen SL, Bengtsson MM, Jonassen I, Overas L & Urich T (2011) Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol doi: DOI: 10.1111/j.1574-6941.2011.01138.x.
34. Leloup J, Loy A, Knab NJ, Borowski C, Wagner M & Jorgensen BB (2007) Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol9: 131-142.
35. Liao L, Xu XW, Wang CS, Zhang DS & Wu M (2009) Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea. J Zhejiang Univ Sci B10: 890-901.
36. Lloyd KG, Lapham L & Teske A (2006) An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microb72: 7218-7230.
37. Lloyd KG, Albert DB, Biddle JF, Chanton JP, Pizarro O & Teske A (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One5: e8738.
38. Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A & Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microb73: 3348-3362.
39. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer K-H & Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microb68: 5064-5081.
40. Meulepas RJ, Jagersma CG, Khadem AF, Buisman CJ, Stams AJ & Lens PN (2009) Effect of environmental conditions on sulfate reduction with methane as electron donor by an Eckemforde Bay enrichment. Environ Sci Technol43: 6553-6559.
41. Michaelis W, Seifert R, Nauhaus Ket al. (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science297: 1013-1015.
42. Morikawa K & Yanagida M (1981) Visualization of Individual DNA Molecules in Solution by Light Microscopy: DAPI Staining Method. J Biochem 89: 693-696.
43. Muyzer G, de Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb59: 695-700.
44. Muyzer G, Teske A, Wirsen CO & Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol164: 165-172.
45. Nauhaus K, Boetius A, Kruger M & Widdel F (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ Microbiol4: 296-305.
46. Niemann H, Lösekann T, de Beer Det al. (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature443: 854-858.
47. Orcutt B & Meile C (2008) Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions. Biogeosciences 5: 1587-1599.
48. Orphan VJ, Hinrichs KU, Ussler WIII, Paull CK, Taylor LT, Sylva SP, Hayes JM & Delong EF (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microb67: 1922-1934.
49. Orphan VJ, House CH, Hinrichs KU, McKeegan KD & DeLong EF (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. P Natl Acad Sci USA99: 7663-7668.
50. Ovreas L, Forney L, Daae FL & Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microb63: 3367-3373.
51. Pachiadaki MG, Lykousis V, Stefanou EG & Kormas KA (2010) Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol Ecol72: 429-444.
52. Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T & Orphan VJ (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. P Natl Acad Sci USA105: 7052-7057.
53. Quince C, Lanzen A, Davenport RJ & Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics12: 38.
54. Reeburgh WS (2007) Oceanic methane biogeochemistry. Chem Rev107: 486-513.
55. Reiche S, Hjelstuen BO & Haflidason H (2011) High-resolution seismic stratigraphy, sedimentary processes and the origin of seabed cracks and pockmarks at Nyegga, mid-Norwegian margin. Mar Geol284: 28-39.
56. Roesch LF, Fulthorpe RR, Riva Aet al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J1: 283-290.
57. Ronimus RS, Reysenbach A, Musgrave DR & Morgan HW (1997) The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: a proposal that AN1 represents a new species, Thermococcus zilligii sp. nov. Arch Microbiol 168: 245-248.
58. Sassen R, Roberts HH, Aharon P, Larkin J, Chinn EW & Carney R (1993) Chemosynthetic bacterial mats at cold hydrocarbon seeps, Gulf of Mexico continental-slope. Org Geochem20: 77-89.
59. Schreiber L, Holler T, Knittel K, Meyerdierks A & Amann R (2010) Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ Microbiol12: 2327-2340.
60. Steinsbu BO, Thorseth IH, Nakagawa S, Inagaki F, Lever MA, Engelen B, Ovreas L & Pedersen RB (2010) Archaeoglobus sulfaticallidus sp. nov., a novel thermophilic and facultatively lithoautotrophic sulfate-reducer isolated from black rust exposed to hot ridge flank crustal fluids. Int J Syst Evol Micr1: 1-2.
61. Stoecker K, Dorninger C, Daims H & Wagner M (2010) Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microb76: 922-926.
62. Takai K, Suzuki M, Nakagawa S, Miyazaki M, Suzuki Y, Inagaki F & Horikoshi K (2006) Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Micr56: 1725-1733.
63. Treude T, Kruger M, Boetius A & Jorgensen BB (2005) Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic). Limnol Oceanogr50: 1771-1786.
64. 2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl Environ Microb73: 2271-2283.
65. Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP & Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol7: 1985-1995.
66. Walker CB, de la Torre JR, Klotz MGet al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. P Natl Acad Sci USA107: 8818-8823.
67. Webster G, Parkes RJ, Cragg BA, Newberry CJ, Weightman AJ & Fry JC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol58: 65-85.
68. Webster G, Yarram L, Freese E, Koster J, Sass H, Parkes RJ & Weightman AJ (2007) Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS Microbiol Ecol62: 78-89.
69. Wegener G, Shovitri M, Knittel K, Niemann H, Hovland M & Boetius A (2008) Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosciences5: 1127-1144.
70. Whelan JA, Russell NB & Whelan MA (2003) A method for the absolute quantification of cDNA using real-time PCR. J Immunol Methods278: 261-269.
71. Zipper H, Buta C, Lammle K, Brunner H, Bernhagen J & Vitzthum F (2003) Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acids Res31: e39.