Identification of putative methylotrophic and hydrogenotrophic methanogens within sedimenting material and copepod faecal pellets

Aquatic Microbial Ecology

Volumn 67, Issue 2, 2012, Pages 151-160

  Ditchfield, Arlene K ^a   Wilson, Samuel T ^a,c   Hart, Mark C ^a   Purdy, Kevin J ^b   Green, David H ^a   Hatton, Angela D ^a  

^a SCOTTISH MARINE INSTITUTE   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

^c UNIVERSITY OF HAWAII   (United States)

Author keywords

Copepod; Faecal pellets; Hydrogenotrophic methanogens; Methane production; Methyltrophic methanogens; Sedimenting particulate material

Indexed keywords

EID: 84867376464     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01585     Document Type: Article

References (56)

1. Alldredge AL, Cohen Y (1987) Can microscale chemical patches persist in the sea? Microelectrode study of marine snow and fecal pellets. Science 235: 689-691
2. Altschul SF, Madden TL, Schaffer AA, Zhang J and others (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search engines. Nucleic Acids Res 25: 3389-3402 (Pubitemid 27359211)
3. Angel R, Matthies D, Conrad R (2011) Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS ONE 6: 1-8
4. Benitez-Nelson CR, O'Neill L, Kolowith LC, Pellechia P, Thunell R (2004) Phosphonates and particulate organic phosphorus cycling in an anoxic marine basin. Limnol Oceanogr 49: 1593-1604 (Pubitemid 39320752)
5. Bianchi M, Marty D, Teyssie JL, Fowler SW (1992) Strictly aerobic and anaerobic bacteria associated with sinking particulate matter and zooplankton fecal pellets. Mar Ecol Prog Ser 88: 55-60 (Pubitemid 24406341)
6. Cynar FJ, Yayanos AA (1991) Enrichment and characterization of a methanogenic bacterium from the oxic upper layer of the ocean. Curr Microbiol 23: 89-96
7. Damm E, Kiene RP, Schwarz J, Falck E, Dieckmann G (2008) Methane cycling in arctic shelf water and its relationship with phytoplankton biomass and DMSP. Mar Chem 109: 45-59
8. Damm E, Helmke E, Thomas S, Schauer U, Nothig E, Bakker K, Kiene RP (2010) Methane production in aerobic oligotrophic surface waters in the central Arctic Ocean. Biogeosciences 7: 1099-1108
9. Daughton CG, Cook AM, Alexander M (1979) Bacterial conversion of alkylphosphonates to natural products via carbon-phosphorus bond cleavage. J Agric Food Chem 27: 1375-1382
10. de Angelis MA, Lee C (1994) Methane production during zooplankton grazing on marine phytoplankton. Limnol Oceanogr 39: 1298-1308 (Pubitemid 2148372)
11. Deevong P, Hattori S, Yamada A, Trakulnaleamsai S and others (2004) Isolation and detection of methanogens from the gut of higher termites. Microbes Environ 19: 221-226
12. Dyhrman ST, Benitez-Nelson CR, Orchard ED, Haley ST, Pellechia PJ (2009) A microbial source of phosphonates in oligotrophic marine systems. Nat Geosci 2: 696-699
13. Embley TM, Finlay BJ, Thomas RH, Dyal PL (1992) The use of ribosomal-RNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol 138: 1479-1487
14. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22: 521-565 (Pubitemid 19156673)
15. Gray ND, Miskin IP, Kornilova O, Curtis TP, Head IM (2002) Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants. Environ Microbiol 4: 158-168 (Pubitemid 34544041)
16. Grossart HP, Frindte K, Dziallas C, Eckert W, Tang KW (2011) Microbial methane production in oxygenated water column of an oligotrophic lake. Proc Natl Acad Sci USA 108: 19657-19661
17. Ingall ED (2008) Oceanography: making methane. Nat Geosci 1: 419-420
18. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, NY, p 21-132
19. Kampbell DH, Vandegrift SA (1998) Analysis of dissolved methane, ethane, and ethylene in ground water by a standard gas chromatographic technique. J Chromatogr Sci 36: 253-256 (Pubitemid 128478979)
20. Karl DM, Tilbrook BD (1994) Production and transport of methane in oceanic particulate organic matter. Nature 368: 732-734
21. Karl DM, Beversdorf L, Bjorkman KM, Church MJ, Martinez A, Delong EF (2008) Aerobic production of methane in the sea. Nat Geosci 1: 473-478
22. Kiene RP (1988) Dimethyl sulfide metabolism in salt marsh sediments. FEMS Microbiol Lett 53: 71-78
23. Kiene RP (1991) Production and consumption of methane in aquatic systems. In: Rogers JE, Whitman WB (eds) Microbial production and consumption of greenhouse gases: methane, nitrogen oxides and halomethanes. American Society for Microbiology, Washington, DC, p 111-146
24. Lamontagne RA, Swinnerton JW, Linnenboom VJ, Smith WD (1973) Methane concentration in various marine environments. J Geophys Res 78: 5317-5324
25. Leadbetter JR, Crosby LD, Berznak JA (1998) Methnobrevibacter filiformis sp. nov.: a filamentous methanogen from termite hindguts. Arch Microbiol 169: 287-292 (Pubitemid 28189532)
26. Leftley JW, MacDougall N (1991) The Dunstaffnage sediment trap and its moorings. In: DML Internal Report, No. 174. Dunstaffnage Marine Lab, Oban, p 8
27. LudwigW, Strunk O, Westram R, Richter L and others (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371 (Pubitemid 38854737)
28. Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Ann NY Acad Sci 1125: 171-189 (Pubitemid 351451164)
29. Marty DG (1993) Methanogenic bacteria in seawater. Limnol Oceanogr 38: 452-456 (Pubitemid 24429277)
30. Marty DG, Nival P, Yoon WD (1997) MethanoArchaea associated with sinking particles and zooplankton collected in the northeastern tropical Atlantic. Oceanol Acta 20: 863-869 (Pubitemid 27515280)
31. Morales CE (1987) Carbon and nitrogen content of copepod faecal pellets: effect of food concentration and feeding behavior. Mar Ecol Prog Ser 36: 107-114
32. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63: 4729-4733 (Pubitemid 27524204)
33. Oremland RS (1979) Methanogenic activity in plankton samples and fish intestines: a mechanism for in situ methanogenesis in oceanic surface waters. Limnol Oceanogr 24: 1136-1141
34. Paytan A, Cade-Menun B, McLaughlin K, Faul K (2003) Selective phosphorus regeneration of sinking marine particles: evidence from 31P-NMR. Mar Chem 82: 55-70 (Pubitemid 36715006)
35. Ploug H, Jørgensen BB (1999) A net-jet flow system for mass transfer and microsensor studies of sinking aggregates. Mar Ecol Prog Ser 176: 279-290 (Pubitemid 29107464)
36. Ploug H, Kühl M, Buchholz-Cleven B, Jørgensen BB (1997) Anoxic aggregates - an ephemeral phenomenon in the pelagic environment? Aquat Microb Ecol 13: 285-294 (Pubitemid 127471736)
37. Purdy KJ, Nedwell DB, Embley TM (2003) Analysis of the sulfate-reducing bacterial and methanogenic Archaeal populations in contrasting Antarctica sediments. Appl Environ Microbiol 69: 3181-3191 (Pubitemid 36693321)
38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
39. Scranton M, Brewer P (1977) Occurrence of methane in the near-surface waters of the western subtropical North Atlantic. Deep-Sea Res 24: 127-138
40. Shanks AL, Reeder ML (1993) Reducing microzones and sulfide production in marine snow. Mar Ecol Prog Ser 96: 43-47 (Pubitemid 24392211)
41. Sieburth JM (1987) Contrary habitats for redox-specific processes: methanogenesis in oxic waters and oxidation in anoxic waters. In: Sliegh MA (ed) Microbes in the sea. Series in Marine Sciences, Ellis Horwood, Chichester, p 11-38
42. Sieburth JM, Donaghay PL (1993) Planktonic methane production and oxidation within the algal maximum of the pycnocline: seasonal fine-scale observations in an anoxic estuarine basin. Mar Ecol Prog Ser 100: 3-15 (Pubitemid 24416301)
43. Sieburth JM, Johnson PW, Macario AJL, Demacario EC (1993) C1 bacteria in the water column of Chesapeake Bay, USA. II. The dominant O2- and H2S-tolerant methylo trophic methanogens, coenriched with their oxidative and sulphate reducing bacterial consorts, are all new immunotypes and probably include new taxa. Mar Ecol Prog Ser 95: 81-89 (Pubitemid 24411448)
44. Simon M, Grossart HP, Schweitzer B, Ploug H (2002) Microbial ecology of organic aggregates in aquatic ecosystems. Aquat Microb Ecol 28: 175-211 (Pubitemid 34780562)
45. SprengerWW, Hackstein HP, Keltjens JT (2007) The competition success of Methanomicrococcus blatticola, a dominant methylotrophic methanogen in the cockroach hindgut, is supported by high substrate affinities and favorable thermodynamics. FEMS Microbiol Ecol 60: 266-275 (Pubitemid 46597314)
46. Tang KW, Glud RN, Glud A, Rysgaard S, Nielsen TG (2011) Copepod guts as biogeochemical hotspots in the sea: evidence from microelectrode profiling of Calanus spp. Limnol Oceanogr 56: 666-672
47. Tholen A, Pester M, Brune A (2007) Simultaneous methanogenesis and oxygen reduction by Methanobrevibacter cuticularis at low oxygen fluxes. FEMS Microbiol Ecol 62: 303-312 (Pubitemid 350076058)
48. Tilbrook BD, Karl DM (1995) Methane sources, distributions and sinks from California coastal waters to the oligo - trophic North Pacific gyre. Mar Chem 49: 51-64
49. Traganza ED, Swinnerton JW, Cheek CH (1979) Methane supersaturation and ATP-zooplankton blooms in nearsurface waters of the Western Mediterranean and the subtropical North Atlantic Ocean. Deep-Sea Res Part A 26: 1237-1245 (Pubitemid 10448511)
50. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57: 1070-1074
51. van der Maarel MJ, Artz RR, Haanstra R, Forney LJ (1998) Association of marine Archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol 64: 2894-2898 (Pubitemid 28363158)
52. van der Maarel M, Sprenger W, Haanstra R, Forney LJ (1999) Detection of methanogenic Archaea in seawater particles and the digestive tract of a marine fish species. FEMS Microbiol Lett 173: 189-194 (Pubitemid 29132790)
53. Wagner A, Blackstone N, Cartwright P, Dick M and others (1994) Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst Biol 43: 250-261 (Pubitemid 24977978)
54. Ward BB, Kilpatrick KA, Novelli PC, Scranton MI (1987) Methane oxidation and methane fluxes in the ocean surface layer and deep anoxic waters. Nature 327: 226-229
55. Whitman WT, Bowen T, Boone D (2006) The methanogenic bacteria. In: Dworkin W, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, Vol 3, 3rd edn. Springer, New York, NY, p 1165-1207
56. Wilson S (2007) The production of biogenic gases in the marine environment. PhD thesis, Scottish Association for Marine Science, UHI Millennium Institute, Scotland