Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire

ISME Journal

Volumn 2, Issue 11, 2008, Pages 1157-1168

  Juottonen, Heli ^a   Tuittila, Eeva Stiina ^a   Juutinen, Sari ^a   Fritze, Hannu ^b   Yrjälä, Kim ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Archaea; Methane; Peat; RNA; T RFLP; Winter

Indexed keywords

ARCHAEAL DNA; ARCHAEAL RNA; METHANE; RIBOSOME DNA; RNA 16S;

ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA GENE; SEASON; SEQUENCE HOMOLOGY;

ARCHAEA; BIODIVERSITY; DNA FINGERPRINTING; DNA, ARCHAEAL; DNA, RIBOSOMAL; ENVIRONMENTAL MICROBIOLOGY; GENES, RRNA; METHANE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S; SEASONS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARCHAEA; CRENARCHAEOTA; METHANOMICROBIALES; METHANOSAETACEAE; METHANOSARCINA; METHANOSARCINACEAE;

EID: 55549092047     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2008.66     Document Type: Article

References (73)

1. 2O fluxes on some natural and drained boreal peatlands. Biogeochemistry 44: 163-186.
2. 13C values of pore water methane in a Michigan peatland. Global Biogeochem Cycles 13: 475-484.
3. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE et al. (2006). Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314: 1933-1935.
4. Basiliko N, Yavitt JB, Dees PM, Merkel SM. (2003). Methane biogeochemistry and methanogen communities in two northern peatland ecosystems, New York State. Geomicrobiol J 20: 563-577.
5. Bergman I, Klarqvist M, Nilsson M. (2000). Seasonal variation in rates of methane production from peat of various botanical origins: effects of temperature and substrate quality. FEMS Microbiol Ecol 33: 181-189.
6. Bergman I, Svensson BH, Nilsson M. (1998). Regulation of methane production in a Swedish acid mire by pH, temperature and substrate. Soil Biol Biochem 30: 729-741.
7. Bräuer SL, Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH. (2006). Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442: 192-194.
8. Cadillo-Quiroz H, Bräuer SL, Yashiro E, Sun C, Yavitt JB, Zinder SH. (2006). Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ Microbiol 8: 1428-1440.
9. Chasar LS, Chanton JP, Glaser PH, Siegel DI. (2000). Methane concentration and stable isotope distribution as evidence of rhizospheric processes: comparison of a fen and bog in the glacial Lake Agassiz peatland complex. Ann Bot 86: 655-663.
10. Chin KJ, Lukow T, Conrad R. (1999). Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl Environ Microbiol 65: 2341-2349.
11. Delbes C, Moletta R, Godon JJ. (2001). Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem. FEMS Microbiol Ecol 35: 19-26.
12. Denman KL, Brasseur G, Chidthaisong A, Ciais P, Cox PM, Dickinson RE et al. (2007). Couplings between changes in the climate system and biogeochemistry. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB et al. (eds). Climate Change 2007: the Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press: Cambridge, United Kingdom and New York, NY, USA.
13. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al. (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-W399.
14. Dise NB. (1992). Winter fluxes of methane from Minnesota peatlands. Biogeochemistry 17: 71-83.
15. Duddleston KN, Kinney MA, Kiene RP, Hines ME. (2002). Anaerobic microbial biogeochemistry in a northern bog: acetate as a dominant metabolic end product. Global Biogeochem Cycles 16: 1063, doi:10.1029/2001GB001402.
16. Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA. (2001). Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67: 172-178.
17. Dunbar J, Ticknor LO, Kuske CR. (2001). Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67: 190-197.
18. Fey A, Conrad R. (2000). Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil. Appl Environ Microbiol 66: 4790-4797.
19. Friedrich MW. (2005). Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Methods Enzymol 397: 428-442.
20. Galand PE, Fritze H, Yrjälä K. (2003). Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen. Environ Microbiol 5: 1133-1143.
21. Galand PE, Saarnio S, Fritze H, Yrjälä K. (2002). Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol Ecol 42: 441-449.
22. Garcia JL, Patel BKC, Ollivier B. (2000). Taxonomic, phylogenetic and ecological diversity of methanogenic Archaea. Anaerobe 6: 205-226.
23. Gentile G, Giuliano L, D'Auria G, Smedile F, Azzaro M, De Domenico M et al. (2006). Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environ Microbiol 8: 2150-2161.
24. Glissman K, Chin KJ, Casper P, Conrad R. (2004). Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature. Microb Ecol 48: 389-399.
25. Grosskopf R, Janssen PH, Liesack W. (1998a). Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64: 960-969.
26. Grosskopf R, Stubner S, Liesack W. (1998b). Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64: 4983-4989.
27. Guindon S, Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
28. Høj L, Olsen RA, Torsvik VL. (2005). Archaeal communities in High Arctic wetlands at Spitsbergen, Norway (78°N) as characterized by 16S rRNA gene fingerprinting. FEMS Microbiol Ecol 53: 89-101.
29. Høj L, Olsen RA, Torsvik VL. (2008). Effects of temperature on the diversity and community structure of known methanogenic groups and other Archaea in high Arctic peat. ISME J 2: 37-48.
30. Høj L, Rusten M, Haugen LE, Olsen RA, Torsvik VL. (2006). Effects of water regime on archaeal community composition in Arctic soils. Environ Microbiol 8: 984-996.
31. Horn MA, Matthies C, Kusel K, Schramm A, Drake HL. (2003). Hydrogenotrophic methanogenesis by moderately acid-tolerant methanogens of a methane-emitting acidic peat. Appl Environ Microbiol 69: 74-83.
32. Hornibrook ERC, Longstaffe FJ, Fyfe WS. (1997). Spatial distribution of microbial methane production pathways in temperate zone wetland soils: stable carbon and hydrogen isotope evidence. Geochim Cosmochim Acta 61: 745-753.
33. Huber T, Faulkner G, Hugenholtz P. (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
34. Jaatinen K, Tuittila ES, Laine J, Yrjälä K, Fritze H. (2005). Methane-oxidizing bacteria in a Finnish raised mire complex: effects of site fertility and drainage. Microb Ecol 50: 429-439.
35. Jetten MSM, Stams AJM, Zehnder AJB. (1992). Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol Rev 88: 181-198.
36. Juottonen H, Galand PE, Tuittila ES, Laine J, Fritze H, Yrjälä K. (2005). Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex. Environ Microbiol 7: 1547-1557.
37. Jurgens G, Lindström K, Saano A. (1997). Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63: 803-805.
38. Kemnitz D, Kolb S, Conrad R. (2007). High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol Ecol 60: 442-448.
39. Kerkhof L, Kemp P. (1999). Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth. FEMS Microbiol Ecol 30: 253-260.
40. Kerkhof L, Ward BB. (1993). Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl Environ Microbiol 59: 1303-1309.
41. Kettunen A, Kaitala V, Lehtinen A, Lohila A, Alm J, Silvola J et al. (1999). Methane production and oxidation potentials in relation to water table fluctuations in two boreal mires. Soil Biol Biochem 31: 1741-1749.
42. Korkama-Rajala T, Mü ller MM, Pennanen T. (2007). Decomposition and fungi of needle litter from slow-and fast-growing Norway spruce (Picea abies) clones. Microb Ecol, advance online publication 18 October 2007; doi: 10.1007/s00248-007-9326-y.
43. Kotsyurbenko OR. (2005). Trophic interactions in the methanogenic microbial community of low-temperature terrestrial ecosystems. FEMS Microbiol Ecol 53: 3-13.
44. Kotsyurbenko OR, Chin KJ, Glagolev MV, Stubner S, Simankova MV, Nozhevnikova AN et al. (2004). Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog. Environ Microbiol 6: 1159-1173.
45. Lipson DA, Schadt CW, Schmidt SK. (2002). Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt. Microb Ecol 43: 307-314.
46. Lu Y, Lueders T, Friedrich MW, Conrad R. (2005). Detecting active methanogenic populations on rice roots using stable isotope probing. Environ Microbiol 7: 326-336.
47. Lueders T, Friedrich MW. (2002). Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil. Appl Environ Microbiol 68: 2484-2494.
48. Luton PE, Wayne JM, Sharp RJ, Riley PW. (2002). The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530.
49. Marchesi JR, Weightman AJ, Cragg BA, Parkes RJ, Fry JC. (2001). Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol 34: 221-228.
50. Melloh RA, Crill PM. (1996). Winter methane dynamics in a temperate peatland. Global Biogeochem Cycles 10: 247-254.
51. Mengoni A, Tatti E, Decorosi F, Viti C, Bazzicalupo M, Giovannetti L. (2005). Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent. Microb Ecol 50: 375-384.
52. Metje M, Frenzel P. (2005). Effect of temperature on anaerobic ethanol oxidation and methanogenesis in acidic peat from a northern wetland. Appl Environ Microbiol 71: 8191-8200.
53. Metje M, Frenzel P. (2007). Methanogenesis and methanogenic pathways in a peat from subarctic permafrost. Environ Microbiol 9: 954-964.
54. Nicol GW, Campbell CD, Chapman SJ, Prosser JI. (2007). Afforestation of moorland leads to changes in crenarchaeal community structure. FEMS Microbiol Ecol 60: 51-59.
55. 2 emission from boreal peat bogs (West Siberia): winter fluxes and thaw activation dynamics. Global Biogeochem Cycles 14: 1071-1080.
56. Rinne J, Riutta T, Pihlatie M, Aurela M, Haapanala S, Tuovinen JP et al. (2007). Annual cycle of methane emission from a boreal fen measured by the eddy covariance technique. Tellus B 59: 449-457.
57. Riutta T, Laine J, Aurela M, Rinne J, Vesala T, Laurila T et al. (2007). Spatial variation in plant community functions regulates carbon gas dynamics in a boreal fen ecosystem. Tellus B 59: 838-852.
58. Röling WFM. (2007). Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity. FEMS Microbiol Ecol 62: 202-210.
59. Rooney-Varga JN, Giewat MW, Duddleston KN, Chanton JP, Hines ME. (2007). Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands. FEMS Microbiol Ecol 60: 240-251.
60. 4 emissions and production and oxidation potentials at microsites on an oligotrophic pine fen. Oecologia 110: 414-422.
61. Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H, Kamagata Y. (2007). Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. Appl Environ Microbiol 73: 4326-4331.
62. Schulz S, Matsuyama H, Conrad R. (1997). Temperature dependence of methane production from different precursors in a profundal sediment (Lake Constance). FEMS Microbiol Ecol 22: 207-213.
63. Simankova MV, Kotsyurbenko OR, Lueders T, Nozhevnikova AN, Wagner B, Conrad R et al. (2003). Isolation and characterization of new strains of methanogens from cold terrestrial habitats. Syst Appl Microbiol 26: 312-318.
64. Simon HM, Dodsworth JA, Goodman RM. (2000). Crenarchaeota colonize terrestrial plant roots. Environ Microbiol 2: 495-505.
65. Svensson BH, Sundh I. (1992). Factors affecting methane production in peat soils. Suo 43: 183-190.
66. ter Braak CJF, Prentice IC. (1988). A theory of gradient analysis. Adv Ecol Res 18: 271-317.
67. ter Braak CJF, Šmilauer P. (2002). CANOCO Reference Manual and CanoDraw for Windows user's Guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power: Ithaca, NY, USA.
68. Turunen J, Tomppo E, Tolonen K, Reinikainen A. (2002). Estimating carbon accumulation rates of undrained mires in Finland - application to boreal and subarctic regions. Holocene 12: 69-80.
69. Utsumi M, Belova SE, King GM, Uchiyama H. (2003). Phylogenetic comparison of methanogen diversity in different wetland soils. J Gen Appl Microbiol 49: 75-83.
70. Valentine DW, Holland EA, Schimel DS. (1994). Ecosystem and physiological controls over methane production in northern wetlands. J Geophys Res 99: 1563-1571.
71. Wagner D, Gattinger A, Embacher A, Pfeiffer E, Schloter M, Lipski A. (2007). Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget. Global Change Biol 13: 1089-1099.
72. Whalen SC. (2005). Biogeochemistry of methane exchange between natural wetlands and the atmosphere. Environ Eng Sci 22: 73-94.
73. 2 in anaerobic, Sphagnum-derived peat from Big Run Bog, West Virginia. Biogeochemistry 4: 141-157.