Organic carbon transformations in high-Arctic peat soils: Key functions and microorganisms

ISME Journal

Volumn 7, Issue 2, 2013, Pages 299-311

  Tveit, Alexander ^a   Schwacke, Rainer ^a   Svenning, Mette M ^a   Urich, Tim ^b  

^a UNIVERSITY OF TROMSØ   (Norway)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

Arctic peat soils; metagenomics; metatranscriptomics; methane; microbial communities; soil organic carbon

Indexed keywords

CARBON; CARBON DIOXIDE; METHANE; TRANSCRIPTOME;

ACTIVE LAYER; ARCTIC ENVIRONMENT; BACTERIUM; CARBON DIOXIDE; DEGRADATION; GREENHOUSE GAS; GROWING SEASON; METABOLISM; METHANE; METHANOTROPHY; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; ORGANIC CARBON; PEAT SOIL; PERMAFROST; POLYMER; SOIL MICROORGANISM; SOIL ORGANIC MATTER; TRANSFORMATION; WARMING;

ARCHAEON; ARCTIC; ARTICLE; BACTERIUM; CHEMISTRY; DNA SEQUENCE; GENETICS; METABOLISM; METAGENOME; METAGENOMICS; MICROBIOLOGY; SOIL; SVALBARD AND JAN MAYEN;

ARCHAEA; ARCTIC REGIONS; BACTERIA; CARBON; CARBON DIOXIDE; METAGENOME; METAGENOMICS; METHANE; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; SVALBARD; TRANSCRIPTOME;

ARCTIC;

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; METHYLOBACTER TUNDRIPALUDUM; VERRUCOMICROBIA;

EID: 84872920243     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.99     Document Type: Article

References (62)

1. Allgaier M, Reddy A, Park JI, Ivanova N, D'Haeseleer P, Lowry S et al. (2010). Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5: 9.
2. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, MillerWet al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Alves RJE. (2011). Ammonia-oxidizing archaea from High Arctic soils. Master thesis, University of Lisbon: Lisbon, Portugal.
4. Berg MP, Bengtsson J. (2007). Temporal and spatial variability in soil food web structure. Oikos 116: 1789-1804.
5. Cao M, Marshall S, Gregson K. (1996). Global carbon exchange and methane emissions from natural wetlands: application of a process-based model. J Geophys Res 101: 399-414.
6. Chou HH, Holmes MH. (2001). DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
7. Chu HY, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. (2010). Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12: 2998-3006.
8. Conrad R. (1999). Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiol Ecol 28: 193-202.
9. Coolen MJL, van de Giessen J, Zhu EY, Wuchter C. (2011). Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw. Environ Microbiol 13: 2299-2314.
10. Dedysh SN, Pankratov TA, Belova SE, Kulichevskaya IS, Liesack W. (2006). Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 72: 2110-2117.
11. Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MMM et al. (2010). Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543-548.
12. Fenner N, Freeman C. (2011). Drought-induced carbon loss in peatlands. Nat Geosci 4: 895-900.
13. Forster P, Ramaswamy V, Artaxo P, Berntsen T, Betts R, Fahey DW et al. (2007). Changes in atmospheric constituents and in radiative forcing. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, Tignor M, Miller HL (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: UK.
14. Ganzert L, Jurgens G, Munster U, Wagner D. (2007). Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints. FEMS Microbiol Ecol 59: 476-488.
15. Gomez-Alvarez V, Teal TK, Schmidt TM. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J 3: 1314-1317.
16. Graef C, Hestnes AG, Svenning MM, Frenzel P. (2011). The active methanotrophic community in a wetland from the high Arctic. Environ Microbiol Rep 3: 466-472.
17. Hansen AA, Herbert RA, Mikkelsen K, Jensen LL, Kristoffersen T, Tiedje JM et al. (2007). Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway. Environ Microbiol 9: 2870-2884.
18. Harden JW, Mark RK, Sundquist ET, Stallard RF. (1992). Dynamics of soil carbon during deglaciation of the laurentide ice sheet. Science 258: 1921-1924.
19. Huang XQ, Madan A. (1999). CAP3: a DNA sequence assembly program. Genome Res 9: 868-877.
20. Huson DH, Auch AF, Qi J, Schuster SC. (2007). MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
21. Høj L, Olsen RA, Torsvik VL. (2005). Archaeal communities in high Arctic wetlands at Spitsbergen, Norway (78 degrees N) as characterized by 16S rRNA gene fingerprinting. FEMS Microbiol Ecol 53: 89-101.
22. 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.
23. 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.
24. IPCC (2007). Climate Change 2007-The Physical Science Basis Contribution of Working Group I to the Fourth Assessment Report of the IPCC (ISBN 978 0521 88009-1 Hardback; 978 0521 70596-7 Paperback).
25. Islam T, Jensen S, Reigstad LJ, Larsen Ø, Birkeland N-K. (2008). Methane oxidation at 55 1C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA 105: 300-304.
26. Kotsyurbenko OR. (2005). Trophic interactions in the methanogenic microbial community of low-temperature terrestrial ecosystems. FEMS Microbiol Ecol 53: 3-13.
27. Kotsyurbenko OR, Friedrich MW, Simankova MV, Nozhevnikova AN, Golyshin PN, Timmis KN et al. (2007). Shift from acetoclastic to H-2-dependent methanogenes is in a West Siberian peat bog at low pH values and isolation of an acidophilic Methanobactetium strain. Appl Environ Microbiol 73: 2344-2348.
28. Lanzen A, Jorgensen SL, Bengtsson MM, Jonassen I, Ovreas 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 77: 577-589.
29. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al. (2006). Archaea predominate among ammoniaoxidizing prokaryotes in soils. Nature 442: 806-809.
30. Liebner S, Harder J, Wagner D. (2008). Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia. Int Microbiol 11: 195-202.
31. Liebner S, Rublack K, Stuehrmann T, Wagner D. (2009). Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the lena delta, Siberia. Microb Ecol 57: 25-35.
32. Ligrone R, Carafa A, Duckett JG, Renzaglia KS, Ruel K. (2008). Immunocytochemical detection of ligninrelated epitopes in cell walls in bryophytes and the charalean alga Nitella. Plant Syst Evol 270: 257-272.
33. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ et al. (2011). Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480: 368-U120.
34. Martineau C, Whyte LG, Greer CW. (2010). Stable isotope probing analysis of the diversity and activity of methanotrophic bacteria in soils from the canadian high Arctic. Appl Environ Microbiol 76: 5773-5784.
35. 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.
36. Metje M, Frenzel P. (2007). Methanogenesis and methanogenic pathways in a peat from subarctic permafrost. Environ Microbiol 9: 954-964.
37. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M et al. (2008). The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 8.
38. Pankratov TA, Ivanova AO, Dedysh SN, Liesack W. (2011). Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environ Microbiol 13: 1800-1814.
39. Pena MJ, Darvill AG, Eberhard S, York WS, O'Neill MA. (2008). Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants. Glycobiology 18: 891-904.
40. Philippot L, Hallin S. (2005). Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Curr Opin Microbiol 8: 234-239.
41. Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA et al. (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci USA 107: 14793-14798.
42. Popper ZA, Michel G, Herve C, Domozych DS, Willats WGT, Tuohy MG et al. (2011). Evolution and diversity of plant cell walls: from algae to flowering plants. In: Merchant SS, Briggs WR, Ort D (eds). Annual Review of Plant Biology Vol 62. Annual Reviews: Palo Alto, pp 567-588.
43. Post WM, Emanuel WR, Zinke PJ, Stangenberger AG. (1982). Soil carbon pools and world life zones. Nature 298: 156-159.
44. R-Development-Core-Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical ComputingVienna. Austria.
45. Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T et al. (2012). Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol 14: 1308-1324.
46. Sarkar P, Bosneaga E, Auer M. (2009). Plant cell walls throughout evolution: towards a molecular understanding of their design principles. J Exp Bot 60: 3615-3635.
47. Schaefer M. (1990). The soil fauna of a beech forest on limestone: trophic structure and energy budget. Oecologia 82: 128-136.
48. Solheim B, Endal A, Vigstad H. (1996). Nitrogen fixation in Arctic vegetation and soils from Svalbard, Norway. Polar Biol 16: 35-40.
49. Stamatakis A, Ludwig T, Meier H. (2005). RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
50. Steven B, Pollard WH, Greer CW, Whyte LG. (2008). Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic. Environ Microbiol 10: 3388-3403.
51. Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG et al. (2011). Genome Sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol 193: 6418-6419.
52. Tarnocai C, Canadell JG, Schuur EAG, Kuhry P, Mazhitova G, Zimov S. (2009). Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles 23: GB2023, 11PP.
53. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al. (2005). Comparative metagenomics of microbial communities. Science 308: 554-557.
54. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC. (2008). Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3: 13.
55. Urich T, Schleper C. (2011). The 'double RNA' approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics. In: de Bruijn FJ (ed). Handbook of Molecular Microbial Ecology. Wiley-Blackwell: Hoboken, NJ, USA.
56. Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA et al. (2005). Functional marker genes for identification of sulfate-reducing prokaryotes. Methods Enzymol 397: 469-489.
57. Waldrop MP, Wickland KP, White R, Berhe AA, Harden JW, Romanovsky VE. (2010). Molecular investigations into a globally important carbon pool: permafrostprotected carbon in Alaskan soils. Glob Change Biol 16: 2543-2554.
58. Wartiainen I, Hestnes AG, McDonald IR, Svenning MM. (2006). Methylobacter tundripaludum sp nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 degrees N). Int J Syst Evol Microbiol 56: 109-113.
59. Wartiainen I, Hestnes AG, Svenning MM. (2003). Methanotrophic diversity in high arctic wetlands on the islands of svalbard (Norway)-denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures. Can J Microbiol 49: 602-612.
60. Wilhelm RC, Niederberger TD, Greer C, Whyte LG. (2011). Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Can J Microbiol 57: 303-315.
61. Yergeau E, Hogues H, Whyte LG, Greer CW. (2010). The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J 4: 1206-1214.
62. Zak DR, Kling GW. (2006). Microbial community composition and function across an arctic tundra landscape. Ecology 87: 1659-1670.