Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity

FEMS Microbiology Ecology

Volumn 68, Issue 2, 2009, Pages 142-151

  Wasmund, Kenneth ^a,b   Kurtböke, D Ipek ^b   Burns, Kathryn A ^a   Bourne, David G ^a  

^a AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^b UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

Clone libraries; Methane seep; Methanotrophs; PmoA; Real time PCR; Timor Sea

Indexed keywords

CARBONIC ACID; HYDROCARBON; METHANE; METHANE MONOOXYGENASE; PARTICULATE METHANE MONOOXYGENASE; PETROLEUM; RNA 16S; UNCLASSIFIED DRUG;

BENTHOS; CORAL; DIVERGENCE; HYDROCARBON SEEP; METHANOTROPHY; MICROBIAL COMMUNITY; OXIC CONDITIONS; PHYLOGENETICS; POLYMERASE CHAIN REACTION; RNA; SEEPAGE; SPECIES DIVERSITY;

AEROBIC BACTERIUM; ARCHAEBACTERIUM; ARTICLE; AUSTRALIA; CONTROLLED STUDY; CORAL; GENETIC ANALYSIS; METHANOBACTERIUM; METHYLOCALDUM; METHYLOCOCCUS; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEDIMENT; SEQUENCE ANALYSIS; TIMOR SEA; UNINDEXED SEQUENCE;

ARCHAEA; AUSTRALIA; BIODIVERSITY; ECOSYSTEM; GENES, RRNA; GEOLOGIC SEDIMENTS; METHANE; METHYLOCOCCACEAE; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEAWATER;

INDIAN OCEAN; TIMOR SEA;

ANTHOZOA; ARCHAEA; BACTERIA (MICROORGANISMS); METHYLOCALDUM; METHYLOCOCCUS;

EID: 64149099408     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2009.00667.x     Document Type: Article

References (51)

1. Aharon P Fu B (2000) Microbial sulfate reduction rates and sulfur and oxygen isotope fractionations at oil and gas seeps in deepwater Gulf of Mexico. Geochim Cosmochim Ac 64 : 233 246.
2. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
3. Bauer JE, Spies RB, Vogel JS, Nelson DE Southon JR (1990) Radiocarbon evidence of fossil-carbon cycling in sediments of a nearshore hydrocarbon seep. Nature 348 : 230 232.
4. Bourne DG, McDonald IR Murrell JC (2001) Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl Environ Microb 67 : 3802 3809.
5. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11 : 265 270.
6. Chen Y, Dumont MG, Cébron A Murrell JC (2007) Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environ Microbiol 9 : 2855 2869.
7. Costello AM Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microb 65 : 5066 5074.
8. DeSantis TZ, Hugenholtz P, Larsen N et al 2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb 72 : 5069 5072.
9. Dumont MG Murrell JC (2005) Community-level analysis: key genes of aerobic methane oxidation. Method Enzymol 397 : 413 427.
10. Elsaied HE, Hayashi T Naganuma T (2005) Molecular analysis of deep-sea hydrothermal vent aerobic methanotrophs by targeting genes of 16S rRNA and particulate methane monooxygenase. Mar Biotechnol 7 : 503 509.
11. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package), Version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle.
12. Formolo MJ, Lyons TW, Zhang CL, Kelley C, Sassen R, Horita J Cole DR (2004) Quantifying carbon sources in the formation of authigenic carbonates at gas hydrate sites in the Gulf of Mexico. Chem Geol 205 : 253 264.
13. Hallam SJ, Girguis PR, Preston CM, Richardson PM DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microb 69 : 5483 5491.
14. Hayashi T, Kaneko R, Tanahashi M Naganuma T (2007a) Molecular diversity of the genes encoding ammonia monooxygenase and particulate methane monooxygenase from deep-sea sediments. Res J Microbiol 2 : 530 537.
15. Hayashi T, Obata H, Gamo T, Sano Y Naganuma T (2007b) Distribution and characteristics of genes encoding enzymes relevant to methane oxidation in oxygen minimum zones of the eastern Pacific Ocean. Res J Environ Sci 1 : 275 284.
16. Heck KL, Belle GV Simberloff D (1975) Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56 : 1459 1461.
17. Heyer J, Galchenko VF Dunfield PF (2002) Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology 148 : 2831 2846.
18. Hinrichs K-U, Summons RE, Orphan VJ, Sylva SP Hayes JM (2000) Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments. Org Geochem 31 : 1685 1701.
19. Huber T, Faulkner G Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 : 2317 2319.
20. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K Nealson KH (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Ohkotsk. Appl Environ Microb 69 : 7224 7235.
21. Inagaki F, Tsunogai U, Suzuki M et al 2004) Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microb 70 : 7445 7455.
22. 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.
23. Judd AG (2004) Natural seabed gas seeps as sources of atmospheric methane. Environ Geol 46 : 988 996.
24. Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
25. Knittel K, Losekann T, Boetius A, Kort R Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microb 71 : 467 479.
26. Kolb S, Knief C, Stubner S Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microb 69 : 2423 2429.
27. Kruger M, Treude T, Wolters H, Nauhaus K Boetius A (2005) Microbial methane turnover in different marine habitats. Palaeogeogr Palaeocl 227 : 6 17.
28. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E Goodfellow M, eds), pp. 115 175. John Wiley and Sons, Chichester, UK.
29. Levin L (2005) Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes. Oceanogr Mar Biol 43 : 1 46.
30. Losekann 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 Microb 73 : 3348 3362.
31. Ludwig W, Strunk O, Westram R et al 2004) ARB: a software package environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
32. Luff R Wallmann K (2003) Fluid flow, methane fluxes, carbonate precipitation and biogeochemical turnover in gas hydrate-bearing sediments at Hydrate Ridge, Cascadia Margin: numerical modeling and mass balances. Geochim Cosmochim Ac 67 : 3403 3421.
33. Luff R, Wallmann K Aloisi G (2004) Numerical modelling of carbonate crust formation at cold vent sites: significance for fluid and methane budgets and chemosynthetic biological communities. Earth Planet Sc Lett 221 : 337 353.
34. Magurran AE (1988) Ecological Diversity and its Measurement. Princeton University Press, Princeton, NJ.
35. McDonald IR, Smith K Lidstrom ME (2005) Methanotrophic populations in estuarine sediments from Newport Bay, California. FEMS Microbiol Lett 250 : 287 293.
36. 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.
37. Niemann H, Losekann T, de Beer D et al 2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443 : 854 858.
38. O'Brien GW, Lawrence G, Williams A, Webster M, Wilson D Burns S (2000) Using integrated remote sensing technologies to evaluate and characterise hydrocarbon migration and charge characteristics on the Yampi Shelf, northwestern Australia: a methodological study. APPEA J 40 : 203 255.
39. Rollet N, Logan GA, Kennard JM, O'Brien P, Jones A Sexton M (2006) Characterisation and correlation of active hydrocarbon seepage using geophysical data sets: an example from the tropical, carbonate Yampi Shelf, Northwest Australia. Mar Petrol Geol 23 : 145 165.
40. Saitou N Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
41. Schloss PD Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microb 71 : 1501 1506.
42. Sommer S, Pfannkuche O, Linke P et al 2006) Efficiency of the benthic filter: biological control of the emission of dissolved methane from sediments containing shallow gas hydrates at Hydrate Ridge. Global Biochem Cy 20 : GB2019.
43. Stackebrandt E Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Micr 44 : 846 849.
44. Stolyar S, Costello AM, Peeples TL Lidstrom ME (1999) Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145 : 1235 1244.
45. Stolyar S, Franke M Lidstrom ME (2001) Expression of individual copies of Methylococcus capsulatus Bath particulate methane monooxygenase genes. J Bacteriol 183 : 1810 1812.
46. Tavormina PL, Ussler W III. Orphan VJ (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American Margin. Appl Environ Microb 74 : 3985 3995.
47. Teske A, Hinrichs K-U, Edgcomb V et al 2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microb 68 : 1994 2007.
48. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F Higgins DG (1994) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 22 : 4673 4680.
49. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA Reysenbach A-L (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microb 65 : 4375 4384.
50. Yan T, Ye Q, Zhou Z Zhang CL (2006) Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol Ecol 57 : 251 259.
51. Zimmermann S, Hughes RG Flugeb HJ (1997) The effect of methane seepage on the spatial distribution of oxygen and dissolved sulfide within a muddy sediment. Mar Geol 137 : 149 157.