Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

FEMS Microbiology Ecology

Volumn 77, Issue 3, 2011, Pages 518-532

  Hamdan, Leila J ^a   Gillevet, Patrick M ^b   Pohlman, John W ^c   Sikaroodi, Masoumeh ^b   Greinert, Jens ^d   Coffin, Richard B ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

^b GEORGE MASON UNIVERSITY   (United States)

^c U S GEOLOGICAL SURVEY   (United States)

^d ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

454 pyrosequencing; AOM; Bacteria; Marine sediment; Methane; Sulfate

Indexed keywords

BACTERIAL DNA; METHANE; RNA 16S; SULFATE;

ACCRETIONARY PRISM; BACTERIUM; BIOGEOCHEMISTRY; COMMUNITY STRUCTURE; MARINE SEDIMENT; METHANE; MICROBIAL COMMUNITY; ORGANIC MATTER; SPECIES DIVERSITY; SULFATE;

ARTICLE; BACTERIUM; BIODIVERSITY; BIOTA; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NEW ZEALAND; PHYLOGENY; SEDIMENT;

BACTERIA; BIODIVERSITY; BIOTA; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; METHANE; MOLECULAR SEQUENCE DATA; NEW ZEALAND; PHYLOGENY; RNA, RIBOSOMAL, 16S; SULFATES;

BACTERIA (MICROORGANISMS); BURKHOLDERIALES; DELTAPROTEOBACTERIA; RHODOBACTERALES;

EID: 79961166442     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01133.x     Document Type: Article

References (73)

1. Arakawa S, Sato T, Sato R et al. (2006) Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea. Extremophiles 10: 311-319.
2. Azam F (1998) Microbial control of oceanic carbon flux: the plot thickens. Science 280: 694-696.
3. Baco AR, Rowden AA, Levin LA, Smith CR & Bowden DA (2010) Initial characterization of cold seep faunal communities on the New Zealand Hikurangi margin. Mar Geol 272: 251-259.
4. Barnes PM, Lamarche G, Bialas J, Henrys S, Pecher I, Netzeband GL, Greinert J, Mountjoy JJ, Pedley K & Crutchley G (2010) Tectonic and geological framework for gas hydrates and cold seeps on the Hikurangi subduction margin, New Zealand. Mar Geol 272: 26-48.
5. Barnette KG, Glover DD, Boyd CB, Lalka D & Sarkar MA (1993) Polycyclic aromatic hydrocarbon (Pah) inducible P450 isozymes (1a1 and 1a2) and glutathione-S-transferase (Gst) activity in human uterine tissues. Clin Res 41: A127.
6. 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. P Natl Acad Sci USA 105: 10583-10588.
7. Birnbaum SJ & Wireman JW (1984) Bacterial sulfate reduction and pH - implications for early diagenesis. Chem Geol 43: 143-149.
8. Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gleseke A, Amann R, Jørgensen BB, Witte U & Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation methane. Nature 407: 623-626.
9. Borowski WS (2004) A review of methane and gas hydrates in the dynamic, stratified system of the Blake Ridge region, offshore southeastern North America. Chem Geol 205: 311-346.
10. Borowski WS, Paull CK & Ussler W (1996) Marine pore-water sulfate profiles indicate in situ methane flux from underlying gas hydrate. Geology 24: 655-658.
11. Burns SJ (1998) Carbon isotopic evidence for coupled sulfate reduction methane oxidation in Amazon Fan sediments. Geochim Cosmochim Ac 62: 797-804.
12. Carter L & Manighetti B (2006) Glacial/interglacial control of terrigenous and biogenic fluxes in the deep ocean off a high input, collisional margin: a 139 kyr-record from New Zealand. Mar Geol 226: 307-322.
13. Clarke KR & Ainsworth M (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol-Prog Ser 92: 205-219.
14. Clarke KR & Warwick RM (2006) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation. Plymouth Marine Laboratory, Plymouth, UK.
15. Claypool GE & Kaplan IR (1974) The origin and distribution of methane in marine sediments. Natural Gases in Marine Sediments (Kaplan IR, ed), pp. 99-139. Plenum, New York.
16. Cline J (1969) Spectrophotometric determination of hydrogen sulphide in natural waters. Limnol Oceanogr 14: 454-458.
17. Crutchley GJ, Pecher IA, Gorman AR, Henrys SA & Greinert J (2010) Seismic imaging of gas conduits beneath seafloor seep sites in a shallow marine gas hydrate province, Hikurangi Margin, New Zealand. Mar Geol 272: 114-126.
18. Dang H & Lovell CR (2000) Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microb 66: 467-475.
19. Dekas AE, Poretsky RS & Orphan VJ (2009) Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326: 422-426.
20. Demaster DJ (1981) The supply and accumulation of silica in the marine-environment. Geochim Cosmochim Ac 45: 1715-1732.
21. Dickens GR (2001) Sulfate profiles and barium fronts in sediment on the Blake Ridge: present and past methane fluxes through a large gas hydrate reservoir. Geochim Cosmochim Ac 65: 529-543.
22. Edlund A, Hårdeman F, Jansson JK & Sjöling S (2008) Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environ Microbiol 10: 2051-2063.
23. Faure K, Greinert J, Pecher IA, Graham IJ, Massoth GJ, De Ronde CEJ, Wright IC, Baker ET & Olson EJ (2006) Methane seepage and its relation to slumping and gas hydrate at the Hikurangi margin, New Zealand. New Zeal J Geol Geop 49: 503-516.
24. Fredrickson JK & Balkwill DL (2006) Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiol J 23: 345-356.
25. Galand PE, Potvin M, Casamayor EO & Lovejoy C (2010) Hydrography shapes bacterial biogeography of the deep Arctic Ocean. ISME J 4: 564-576.
26. Gilhooly W, Macko SA & Flemings PB (2008) Data report: isotope compositions of sedimentary organic carbon and total nitrogen from Brazos-Trinity Basin IV (Sites U1319 and U1320) and Ursa Basin (Sites U1322 and U1324), deepwater Gulf of Mexico. Proceedings of the Integrated Ocean Drilling Program, DOI: DOI: 10.2204/iodp.proc.308.208.2008.
27. Grasshoff K, Ehrhardt M, Kremling K & Almgren T (1983) Methods of Seawater Analysis. Verlag Chemie, Weinheim.
28. Haese RR, Meile C, Van Cappellen P & De Lange GJ (2003) Carbon geochemistry of cold seeps: methane fluxes and transformation in sediments from Kazan mud volcano, eastern Mediterranean Sea. Earth Planet Sc Lett 212: 361-375.
29. Hamdan LJ, Gillevet PM, Sikaroodi M, Pohlman JW, Plummer RE & Coffin RB (2008) Geomicrobial characterization of gas hydrate-bearing sediments along the mid-Chilean margin. FEMS Microbiol Ecol 65: 15-30.
30. 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 Microb 75: 1487-1499.
31. Heijs S, Haese R, van der Wielen P, Forney L & van Elsas J (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 Ecol 53: 384-398.
32. Henrys SA, Ellis S & Uruski C (2003) Conductive heat flow variations from bottom-simulating reflectors on the Hikurangi margin, New Zealand. Geophys Res Lett 30: 1-4.
33. Hoehler TM, Borowski WS, Alperin MJ, Rodriguez NM & Paull CK (2000) Model, stable isotope, and radiotracer characterization of anaerobic methane oxidation in gas hydrate-bearing sediments of the Blake Ridge. Proceedings of the Ocean Drilling Program: Scientific Results, Vol. 164, DOI: DOI: 10.2973/odp.proc.sr.164.242.2000.
34. 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. Appl Environ Microb 69: 7224-7235.
35. Inagaki F, Nunoura T, Nakagawa S et al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin. P Natl Acad Sci USA 103: 2815-2820.
36. Jones AT, Greinert J, Bowden DA, Klaucke I, Petersen CJ, Netzeband GL & Weinrebe W (2010) Acoustic and visual characterisation of methane-rich seabed seeps at Omakere Ridge on the Hikurangi Margin, New Zealand. Mar Geol 272: 154-169.
37. Jørgensen BB & Boetius A (2007) Feast and famine - microbial life in the deep-sea bed. Nat Rev Microbiol 5: 770-781.
38. Joye SB, Boetius A, Orcutt BN, Montoya JP, Schulz HN, Erickson MJ & Lugo SK (2004) The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chem Geol 205: 219-238.
39. Kastner M, Kvenvolden KA & Lorenson TD (1998) Chemistry, isotopic composition, and origin of a methane-hydrogen sulfide hydrate at the Cascadia subduction zone. Earth Planet Sc Lett 156: 173-183.
40. King D & Nedwell DB (1985) The influence of nitrate concentration upon the end-products of nitrate dissimilation by bacteria in anaerobic salt marsh sediment. FEMS Microbiol Lett 31: 23-28.
41. Klaucke I, Weinrebe W, Petersen CJ & Bowden D (2010) Temporal variability of gas seeps offshore New Zealand: multi-frequency geoacoustic imaging of the Wairarapa area, Hikurangi margin. Mar Geol 272: 49-58.
42. Knittel K, Lösekann T, Boetius A, Amann R & Kort R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microb 71: 467-479.
43. Kormas KA, Smith DC, 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.
44. Kuehl SA, Nittrouer CA, Allison MA, Ercilio L, Faria C, Dukat DA, Jaeger JM, Pacioni TD, Figueiredo AG & Underkoffler EC (1996) Sediment deposition, accumulation, and seabed dynamics in an energetic fine-grained coastal environment. Cont Shelf Res 16: 787-815.
45. 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 Microb 67: 5143-5153.
46. Martin RA, Nesbitt EA & Campbell KA (2010) The effects of anaerobic methane oxidation on benthic foraminiferal assemblages and stable isotopes on the Hikurangi Margin of eastern New Zealand. Mar Geol 272: 270-284.
47. Milkov AV, Vogt PR, Crane K, Lein AY, Sassen R & Cherkashev GA (2004) Geological, geochemical, and microbial processes at the hydrate-bearing Haakon Mosby mud volcano: a review. Chem Geol 205: 347-366.
48. Mills HJ, Hodges C, Wilson K, MacDonald IR & Sobecky PA (2003) Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol Ecol 46: 39-52.
49. Mills HJ, Hunter E, Humphrys M, Kerkhof L, McGuinness L, Huettel M & Kostka JE (2008) Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the Northeastern Gulf of Mexico. Appl Environ Microb 74: 4440-4453.
50. Naqvi A, Rangwala H, Spear G & Gillevet P (2010) Analysis of multitag pyrosequence data from human cervical lavage samples. Chem Biodivers 7: 1076-1085.
51. Naudts L, Greinert J, Poort J, Belza J, Vangampelaere E, Boone D, Linke P, Henriet J-P & De Batist M (2010) Active venting sites on the gas-hydrate-bearing Hikurangi Margin, off New Zealand: diffusive- versus bubble-released methane. Mar Geol 272: 233-250.
52. Niggemann J & Schubert CJ (2006) Fatty acid biogeochemistry of sediments from the Chilean coastal upwelling region: sources and diagenetic changes. Org Geochem 37: 626-647.
53. Nunoura T, Soffientino B, Blazejak A, Kakuta J, Oida H, Schippers A & Takai K (2009) Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308). FEMS Microbiol Ecol 69: 410-424.
54. Orphan VJ, Hinrichs KU, Ussler W III, 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 Microb 67: 1922-1934.
55. Osburn CL & St-Jean G (2007) The use of wet chemical oxidation with high-amplification isotope ratio mass spectrometry (WCO-IRMS) to measure stable isotope values of dissolved organic carbon in seawater. Limnol Oceanogr-Meth 5: 296-308.
56. Parkes RJ, Cragg BA, Banning N et al. (2007) Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ Microbiol 9: 1146-1161.
57. Paull CK, Ussler W III, Lorenson T, Winters W & Dougherty J (2005) Geochemical constraints on the distribution of gas hydrates in the Gulf of Mexico. Clim Dynam 25: 273-280.
58. Pecher IA, Henrys SA, Wood WT et al. (2010) Focussed fluid flow on the Hikurangi Margin, New Zealand - Evidence from possible local upwarping of the base of gas hydrate stability. Mar Geol 272: 99-113.
59. 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 USA 105: 7052-7057.
60. Peterson B, Fry B, Hullar M, Saupe S & Wright R (1994) The distribution and stable carbon isotopic composition of dissolved organic-carbon in estuaries. Estuaries 17: 111-121.
61. Pierre C & Fouquet Y (2007) Authigenic carbonates from methane seeps of the Congo deep-sea fan. Geo-Mar Lett 27: 249-257.
62. Pohlman JW, Ruppel C, Hutchinson DR, Downer R & Coffin RB (2008) Assessing sulfate reduction and methane cycling in a high salinity pore water system in the northern Gulf of Mexico. Mar Petrol Geol 25: 942-951.
63. Reed A, Lutz R & Vetriani C (2006) Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10: 199-211.
64. Sala VMR, Cardoso EJBN, Garboggini FF, Nogueira ND & da Silveira APD (2008) Achromobacter insolitus and Zoogloea ramigera associated with wheat plants (Triticum aestivum). Biol Fert Soils 44: 1107-1112.
65. Schink DR, Fanning KA & Pilson MEQ (1974) Dissolved silica in upper pore waters of Atlantic ocean-floor. J Geophys Res 79: 2243-2250.
66. Schink DR, Guinasso NL & Fanning KA (1975) Processes affecting concentration of silica at sediment-water interface of Atlantic ocean. J Geophys Res-Oc Atm 80: 3013-3031.
67. Schwalenberg K, Wood W, Pecher I, Hamdan L, Henrys S, Jegen M & Coffin R (2010) Preliminary interpretation of electromagnetic, heat flow, seismic, and geochemical data for gas hydrate distribution across the Porangahau Ridge, New Zealand. Mar Geol 272: 89-98.
68. Sekiguchi Y (2006) Yet-to-be cultured microorganisms relevant to methane fermentation processes. Microbes Environ 21: 1-15.
69. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM & Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. P Natl Acad Sci USA 103: 12115-12120.
70. Sommer S, Linke P, Pfannkuche O, Niemann H & Treude T (2010) Benthic respiration in a seep habitat dominated by dense beds of ampharetid polychaetes at the Hikurangi Margin (New Zealand). Mar Geol 272: 223-232.
71. Thomsen TR, Finster K & Ramsing NB (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in marine sediment. Appl Environ Microb 67: 1646-1656.
72. Thurber AR, Kröger K, Neira C, Wiklund H & Levin LA (2010) Stable isotope signatures and methane use by New Zealand cold seep benthos. Mar Geol 272: 260-269.
73. 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 Ecol 58: 65-85.