Anaerobic Eury- and Crenarchaeota inhabit ectomycorrhizas of boreal forest Scots pine

European Journal of Soil Biology

Volumn 46, Issue 6, 2010, Pages 356-364

  Bomberg, Malin ^a,b   Montonen, Leone ^a   Timonen, Sari ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

Cultured soil archaea; Enrichment; Halobacterium; Methane; Methanogen; Rhizosphere

Indexed keywords

ARCHAEA; CRENARCHAEOTA; HALOBACTERIA; HALOBACTERIUM; METHANOLOBUS; PINUS SYLVESTRIS;

EID: 78149413231     PISSN: 11645563     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejsobi.2010.09.002     Document Type: Article

References (58)

1. Auguet J.C., Borrego C.M., Bañeras L., Casamayor E.O. Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ. Microbiol. 2008, 10:2527-2536.
2. Bassam B.J., Caetano-Anolles G., Gresshoff P.M. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 1991, 196:80-83.
3. Bomberg M., Jurgens G., Saano A., Sen R., Timonen S. Nested PCR detection of archaea in defined compartments of pine mycorrhizospheres developed in boreal forest humus microcosms. FEMS Microbiol. Ecol. 2003, 43:163-171.
4. Bomberg M., Timonen S. Distribution of Cren- and Euryarchaeota in Scots pine mycorrhizospheres and boreal forest humus. Microb. Ecol. 2007, 54:406-416.
5. Bomberg M., Timonen S. Effect of tree species and mycorrhizal colonisation on the archaeal population of boreal forest rhizospheres. Appl. Environ. Microbiol. 2009, 75:308-315.
6. Dixon R.K., Solomon A.M., Brown S., Houghton R.A., Trexier M.C., Wisniewski J. Carbon pools and flux of global forest ecosystems. Science 1994, 263:185-190.
7. Doddema H.J., Vogels G.D. Improved identification of methanogenic bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 1978, 36:752-754.
8. Erckel C., Kube M., Reinhardt R., Liesack W. Genome of rice cluster I archaea-the key methane producers in the rice rhizosphere. Science 2006, 313:370-372.
9. Francis C.A., Roberts K.J., Beman J.M., Santoro A.E., Oakley B.B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Nat. Acad. Sci. U S A 2005, 102:14683-14688.
10. Galand P.E., Fritze H., Yrjälä K. Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen. Environ. Microbiol. 2003, 5:1133-1143.
11. Grosskopf R., Stubner S., Liesack W. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 1998, 64:4983-4989.
12. Grosskopf R., Janssen P.H., Liesack W. 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. 1998, 64:960-969.
13. Hansel C.M., Fendorf S., Jardine P.M., Francis C.A. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 2008, 74:1620-1633.
14. Högberg P., Nordgren A., Buchmann N., Taylor A.F., Ekblad A., Högberg M.N., Nyberg G., Ottosson-Lofvenius M., Read D.J. Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 2001, 411:789-792.
15. Högberg P., Högberg M.N., Gottlicher S.G., Betson N.R., Keel S.G., Metcalfe D.B., Campbell C., Schindlbacher A., Hurry V., Lundmark T., Linder S., Näsholm T. High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms. New Phytol. 2008, 177:220-228.
16. 2 fixation pathways in archaea (Crenarchaeota). Arch. Microbiol. 2003, 179:160-173.
17. Jurgens G., Lindström K., Saano A. Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 1997, 63:803-805.
18. Jurgens G., Saano A. Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning. FEMS Microbiol. Ecol. 1999, 29:205-213.
19. Jurgens G., Glöckner F., Amann R., Saano A., Montonen L., Likolammi M., Münster U. Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol. Ecol. 2000, 34:45-56.
20. Kasimir Klemedtsson Å, Klemedtsson L. Methane uptake in Swedish forest soil in relation to liming and extra N-deposition. Biol. Fertil. Soils 1997, 25:296-301. (D.R. Boone).
21. Kemnitz D., Kolb S., Conrad R. High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol. Ecol. 2007, 60:442-448.
22. Kendall M.M., Boone D.R. The order Methanosarcinales. The Prokaryotes 2006, 244-256. Springer, New York. third ed. S. Falkow, E. Rosenberg, K.-H. Schleifer, E. Stackebrandt (Eds.).
23. Könneke M., Bernhard A.E., de la Torre J.R., Walker C.B., Waterbury J.B., Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437:543-546.
24. Küsel K., Wagner C., Drake H.L. Enumeration and metabolic product profiles of the anaerobic microflora in the mineral soil and litter of a beech forest. FEMS Microbiol. Ecol. 1999, 29:91-103.
25. Leininger S., Urich T., Schloter M., Schwark L., Qi J., Nicol G.W., Prosser J.I., Schuster S.C., Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442:806-809.
26. Lehtovirta L.E., Prosser J.I., Nicol G.W. Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol. Ecol. 2009, 70:367-376.
27. 2 affects soil microbial diversity associated with trembling aspen. Environ. Microbiol. 2008, 10:926-941.
28. Leyval C., Berthelin J. Rhizodeposition and net release of soluble organic compounds by pine and beech seedlings inoculated with rhizobacteria and ectomycorrhizal fungi. Biol. Fertil. Soils 1993, 15:259-267.
29. Li C., Massicote H., Moore L.V.H. Nitrogen-fixing Bacillus sp. associated with Douglas-fir tuberculate ectomycorrhizae. Plant Soil 1992, 140:35-40.
30. Lueders T., Friedrich M. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 2000, 66:2732-2742.
31. Maljanen M., Jokinen H., Saari A., Strommer R., Martikainen P.J. Methane and nitrous oxide fluxes, and carbon dioxide production in boreal forest soil fertilized with wood ash and nitrogen. Soil Use Manag. 2006, 22:151-157.
32. Maljanen M., Nykänen H., Moilanen M., Martikainen P.J. Greenhouse gas fluxes of coniferous forest floors as affected by wood ash addition. For. Ecol. Manag. 2006, 237:143-149.
33. Muhkin V.A., Voronin P.Yu. A new source for methane in boreal forests. Appl. Biochem. Microbiol. 2008, 44:297-299.
34. üller J.A.M., DasSarma S. Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors. J. Bacteriol. 2005, 187:1659-1667.
35. Nicol G.W., Campbell C.D., Chapman S.J., Prosser J.I. Afforestation of moorland leads to changes in crenarchaeal community structure. FEMS Microbiol. Ecol. 2007, 60:51-59.
36. Nicol G.W., Tscherko D., Embley T.M., Prosser J.I. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ. Microbiol. 2005, 7:337-347.
37. Oline D.K., Schmidt S.K., Grant M.C. Biogeography and landscape-scale diversity of the dominant Crenarchaeota of soil. Microb. Ecol. 2006, 52:480-490.
38. Orphan V.J., House C.H., Hinrichs K.U., McKeegan K.D., DeLong E.F. Direct phylogenetic and isotopic evidence for multiple groups of archaea involved in the anaerobic oxidation of methane. Geochim. Cosmochim. Acta 2002, 66. A571-A571.
39. R.K. Pachauri, A. Reisinger (Eds.), IPCC, 2007: Climate Change 2007: Synthesis Report. Contribution of Working Groups I, II and III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, IPCC, Geneva, Switzerland, 2007, pp.104.
40. Paul E.A., Clarck F.E. Soil Microbiology and Biochemistry 1996, Academic Press, London, pp. 340. second ed.
41. Pesaro M., Widmer F. Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil. FEMS Microbiol. Ecol. 2002, 42:89-98.
42. Peters S., Koschinsky S., Schwieger F., Tebbe C.C. Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl. Environ. Microbiol. 2002, 66:930-936.
43. Rincon B., Raposo F., Borja R., Gonzalez J.M., Portillo M.C., Saiz-Jimenez C. Performance and microbial communities of a continuous stirred tank anaerobic reactor treating two-phases olive mill solid wastes at low organic loading rates. J. Biotechnol. 2006, 121:534-543.
44. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25:39-67.
45. Simankova M.V., Kotsyurbenko O.R., Lueders T., Nozhevnikova A.N., Wagner B., Conrad R., Friedrich M.W. Isolation and characterization of new strains of methanogens from cold terrestrial habitats. Syst. Appl. Microbiol. 2003, 26:312-318.
46. Simon H.M., Jahn C.E., Bergerud L.T., Sliwinski M.K., Weimer P.J., Willis D.K., Goodman R.M. Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl. Environ. Microbiol. 2005, 71:4751-4760.
47. Sinha V., Williams J., Crutzen P., Lelieveld J. Methane emissions from boreal and tropical forest ecosystems derived from in-situ measurements. Atmos. Chem. Phys. Discuss. 2007, 7:14011-14039.
48. Sizova M.V., Panikov N.S., Tourova T.P., Flanagan P.W. Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol. Ecol. 2003, 45:301-315.
49. Sliwinski M.K., Goodman R.M. Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl. Environ. Microbiol. 2004, 70:1821-1826.
50. Smith K.S., Ingram-Smith C. Methanosaeta, the forgotten methanogen?. Trends Microbiol. 2007, 15:150-155.
51. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) 2003, Sinauer Associates, Sunderland, MA, USA, 4.10b.
52. Söderström B. Ecological potential of ectomycorrhizal mycelium. Mycorrhizas in Ecosystems 1992, 77-83. Cambridge University Press, Cambridge. J.D. Read, D.H. Lewis, A.H. Fitter, I.J. Alexander (Eds.).
53. Timonen S., Jorgensen K.S., Haahtela K., Sen R. Bacterial community structure at defined locations of Pinus sylvestris Suillus bovinus and Pinus sylvestris Paxillus involutus mycorrhizospheres in dry pine forest humus and nursery peat. Can. J. Microbiol. 1998, 44:499-513.
54. Torsvik V., Øvreås L. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 2002, 5:240-245.
55. Tourna M., Freitag T.E., Nicol G.W., Prosser J.I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 2008, 10:1357-1364.
56. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 1991, 173:697-703.
57. Whalen S.C., Reeburgh W.S., Barber V.A. Oxidation of methane in boreal forest soils: a comparison of seven measures. Biogeochemistry 1992, 16:181-211.
58. Yrjälä K., Katainen R., Jurgens G., Saarela U., Saano A., Romantchuk M., Fritze H. Wood ash fertilization alters the forest humus Archaea community. Soil Biol. Biochem. 2004, 36:199-201.