Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil

FEMS Microbiology Ecology

Volumn 42, Issue 1, 2002, Pages 89-98

  Pesaro, Manuel ^a   Widmer, Franco ^b  

^a ETH ZURICH   (Switzerland)

^b Eidg Forschungsanstalt fur Agrarokologie und Landbau   (Switzerland)

Author keywords

Archaea community changes; ARDRA; Phylogenetic analysis; Small subunit rDNA; Soil depth profile

Indexed keywords

BACTERIAL DNA; RESTRICTION ENDONUCLEASE; RIBOSOME DNA; SMALL SUBUNIT RIBOSOMAL RNA;

FOREST SOIL; MICROBIAL COMMUNITY; SOIL MICROORGANISM; SPECIES DIVERSITY; VERTICAL DISTRIBUTION;

ARTICLE; BACTERIAL FLORA; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; CRENARCHAEOTA; DNA EXTRACTION; DNA FINGERPRINTING; DNA SEQUENCE; EURYARCHAEOTA; FOREST SOIL; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA GENE; SOIL DEPTH; SOIL MICROFLORA; SURFACE SOIL; THERMOPLASMALES; UNINDEXED SEQUENCE;

SWITZERLAND;

ARCHAEA; CRENARCHAEOTA; EURYARCHAEOTA; THERMOPLASMATALES;

EID: 0036803181     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(02)00302-1     Document Type: Article

References (56)

1. Woese C.R., Magrum L.J., Fox G.E. Archaebacteria. J. Mol. Evol. 11:1978;245-252.
2. Woese C.R., Kandler O., Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl. Acad. Sci. USA. 87:1990;4576-4579.
3. Maidak B.L., Cole J.R., Lilburn T.G., Parker C.D. Jr., Saxman P.R., Stredwick J.M., Garrity G.M., Li B., Olsen G.J., Pramanik S., Schmidt T.M., Tiedje J.M. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:2000;173-174.
4. DeLong E.F. Everything in moderation: Archaea as 'non-extremophiles'. Curr. Opin. Genet. Dev. 8:1998;649-654.
5. DeLong E.F., Wu K.Y., Prezelin B.B., Jovine R.V.M. High abundance of Archaea in antarctic marine picoplankton. Nature. 371:1994;695-697.
6. Fuhrman J.A., Davis A.A. Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar. Ecol.-Prog. Ser. 150:1997;275-285.
7. Munson M.A., Nedwell D.B., Embley T.M. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63:1997;4729-4733.
8. Hinrichs K.-U., Hayes J.M., Sylva S.P., Brewer P.G., DeLong E.F. Methane-consuming Archaebacteria in marine sediments. Nature. 398:1999;802-805.
9. Cytryn E., Minz D., Oremland R.S., Cohen Y. Distribution and diversity of Archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl. Environ. Microbiol. 66:2000;3269-3276.
10. Jurgens G., Glöckner F.O., Amann R., Saano A., Montonen L., Likolammi M., Münster U. Identification of novel Archaea in bacterioplancton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol. Ecol. 34:2000;45-56.
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. 64:1998;4983-4989.
12. Lueders T., Friedrich M. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 66:2000;2732-2742.
13. Friedrich M.W., Schmitt-Wagner D., Lueders T., Brune A. Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartimentalized gut of the soil feeding termite Cubitermes orthognathus. Appl. Environ. Microbiol. 67:2001;4880-4890.
14. Fuhrman J.A., McCallum K., Davis A.A. Novel major archaebacterial group from marine plankton. Nature. 356:1992;148-149.
15. DeLong E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA. 89:1992;5685-5689.
16. Vetriani C., Jannasch H.W., MacGregor B.J., Stahl D.A., Reysenbach A.-L. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65:1999;4375-4384.
17. McInerney J.O., Wilkinson M., Patching J.W., Embley T.M., Powell R. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl. Environ. Microbiol. 61:1995;1646-1648.
18. MacGregor B.J., Moser D.P., Alm E.W., Nealson K.H., Stahl D.A. Crenarchaeota in Lake Michigan sediment. Appl. Environ. Microbiol. 63:1997;1178-1181.
19. Ueda T., Suga Y., Matsuguchi T. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:1995;415-421.
20. Bintrim S.B., Donohue T.J., Handelsman J., Roberts G.P., Goodman R.M. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA. 94:1997;277-282.
21. Bornemann J., Triplett E.W. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:1997;2647-2653.
22. Jurgens G., Lindstrom K., Saano A. Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63:1997;803-805.
23. Buckley D.H., Graber J.R., Schmidt T.M. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64:1998;4333-4339.
24. Jurgens G., Saano A. Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning. FEMS Microbiol. Ecol. 29:1999;205-213.
25. Sandaa R.A., Enger O., Torsvik V. Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65:1999;3293-3297.
26. Hershberger K.L., Barns S.M., Reysenbach A.L., Dawson S.C., Pace N.R. Wide diversity of Crenarchaeota. Nature. 384:1996;420.
27. Schleper C., Holben W., Klenk H.P. Recovery of crenarchaeotal rDNA sequences from freshwater lake sediments. Appl. Environ. Microbiol. 63:1997;321-323.
28. Chandler D.P., Brockmann F.J., Bailey T.J., Fredrickson J.K. Phylogenetic diversity of Archaea and Bacteria in deep sea subsurface paleosol. Microb. Ecol. 36:1998;37-50.
29. Simon H.M., Dodsworth J.A., Goodman R.M. Crenarchaeota colonize terrestrial plant roots. Environ. Microbiol. 2:2000;495-505.
30. Chelius M.K., Triplett E.W. The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb. Ecol. 41:2001;252-263.
31. Bundt M., Widmer F., Pesaro M., Zeyer J., Blaser P. Preferential flow paths: biological 'hot spots' in soils. Soil Biol. Biochem. 33:2001;729-738.
32. United States Department of Agriculture (1994) Keys to soil taxonomy, 6th edn., 524 pp. Pocahontas Press, Blacksburg, Virginia.
33. Flury M., Flühler H. Brilliant Blue FCF as a dye tracer for solute transport studies - a toxicological overview. J. Environ. Qual. 23:1994;1108-1112.
34. Chatzinotas A., Sandaa R.-A., Schönhuber W., Amann R., Daae F.L., Torsvik V., Zeyer J., Hahn D. Analysis of broad-scale differences in microbial community composition of two pristine forest soils. Syst. Appl. Microbiol. 21:1998;579-587.
35. Widmer F., Seidler R.J., Watrud L.S. Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol. Ecol. 5:1996;603-613.
36. Sandaa R.-A., Enger Ø., Torsvik V. Rapid method for fluorometric quantification of DNA in soil. Soil Biol. Biochem. 30:1998;265-268.
37. Widmer F., Seidler R.J., Gillevet P.M., Watrud L.S., Di Giovanni G.D. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl. Environ. Microbiol. 64:1998;2545-2553.
38. Amann R.I., Ludwig W., Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
39. Widmer F., Shaffer B.T., Porteous L.A., Seidler R.J. Analysis of nifH gene pool complexity in soil and litter at a douglas fir forest site in the Oregon cascade mountain range. Appl. Environ. Microbiol. 65:1999;374-380.
40. Widmer F., Fliessbach A., Lackó E., Schulze-Aurich J., Zeyer J. Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and Biolog™-analyses. Soil Biol. Biochem. 33:2001;1029-1036.
41. Raaijmakers J.G.W. Statistical analysis of the Michaelis-Menten equation. Biometrics. 43:1987;793-803.
42. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:1999;95-98.
43. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics. 5:1989;164-166.
44. Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In: Mammalian Protein Metabolism (Munro, H.N. Eds.), pp. 21-132. Academic Press, New York.
45. Saitou N., Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
46. Olsen G.J., Matsuda H., Hagstrom R., Overbeel R. FastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:1994;41-48.
47. Kumar, S., Tamura, K., Jakobsen, I., Nei, M. (2001) MEGA2: Molecular Evolutionary Genetics Analysis Software 17, pp. 1244-1245.
48. Takai K., Moser D.P., DeFlaun M., Onstott T.C., Fredrickson J.K. Archaeal diversity in waters from deep South African gold mines. Appl. Environ. Microbiol. 67:2001;5750-5760.
49. Dojka M.A., Hugenholtz P., Haack S.K., Pace N.R. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:1998;3869-3877.
50. Kudo Y., Shibata S., Miyaki T., Aono T., Oyaizu H. Peculiar Archaea found in Japanese paddy soils. Biosci. Biotechnol. Biochem. 61:1997;917-920.
51. Chin K.J., Lukow T., Conrad R. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65:1999;2341-2349.
52. Zepp-Falz K., Holliger C., Grosskopf R., Liesack W., Nozhevnikova A.N., Muller B., Wehrli B., Hahn D. Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl. Environ. Microbiol. 65:1999;2402-2408.
53. Wachinger G., Fiedler S., Zepp K., Gattinger A., Sommer M., Roth K. Variability of soil methane production on the micro-scale: spatial association with hot spots of organic material and archaeal populations. Soil Biol. Biochem. 32:2000;1121-1130.
54. Stein J.L., Marsh T.L., Wu K.Y., Shizuya H., DeLong E.F. Characterization of uncultivared prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine Archaeon. J. Bacteriol. 178:1996;591-599.
55. Schleper C., DeLong E.F., Preston C.M., Feldman R.A., Wu K.Y., Swanson R.V. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic Archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:1998;5003-5009.
56. Schleper C., Swanson R.V., Mathur E.J., DeLong E.F. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 179:1997;7803-7811.