Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil

Environmental Microbiology

Volumn 6, Issue 8, 2004, Pages 861-867

  Nicol, Graeme W ^a   Webster, Gordon ^b   Glover, L Anne ^a   Prosser, James I ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIUM NITRATE; ARCHAEAL RNA; BACTERIAL RNA; NITRATE; RNA 16S;

ANIMAL; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CRENARCHAEOTA; DNA DENATURATION; DNA FINGERPRINTING; DNA SEQUENCE; DRUG EFFECT; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; PLANT ROOT; POLYACRYLAMIDE GEL ELECTROPHORESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SHEEP; URINE;

ANIMALS; ARCHAEA; BACTERIA; CRENARCHAEOTA; DNA FINGERPRINTING; ECOSYSTEM; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; NITRATES; NUCLEIC ACID DENATURATION; PLANT ROOTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SHEEP; SOIL MICROBIOLOGY;

ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; OVIS ARIES;

EID: 3543109163     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00627.x     Document Type: Article

References (27)

1. Alfreider, A., Pernthaler, J., Amann, R., Sattler, B., Glockner, F.-O., Wille, A., and Psenner, R. (1996) Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridisation. Appl Environ Microbiol 62: 2138-2144.
2. Bååth, E., and Anderson, T.-H. (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem 35: 955-963.
3. Buckley, D.H., Graber, J.R., and Schmidt, T.M. (1998) Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soil. Appl Environ Microbiol 64: 4333-4339.
4. Chelius, M.K., and Triplett, E.W. (2001) The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb Ecol 41: 252-263.
5. DeLong, E.F. (1998) Everything in moderation: Archaea as 'non-extremophiles.' Current Opin Genet Dev 8: 649-654.
6. DeLong, E.F., and Pace, N.R. (2001) Environmental diversity of Bacteria and Archaea. Syst Biol 50: 470-478.
7. Felske, A., and Akkermans, A.D.L. (1998) Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soil. Microb Ecol 36: 31-36.
8. Flardh, K., Cohen, P.S., and Kjelleberg, S. (1992) Ribosomes exist in large excess over the apparent demand for protein-synthesis during carbon starvation in marine Vibrio sp. strain-CCUG-15956. J Bacteriol 174: 6780-6788.
9. Giovannoni, S.J., DeLong, E.F., Olsen, G.J., and Pace, N.R. (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial-cells. J Bacteriol 170: 720-726.
10. Haynes, R.J., and Williams, P.H. (1993) Nutrient cycling and soil fertility in the grazed pasture ecosystem. In Advances in Agronomy, Vol. 49. Sparks, D.L. (ed.). San Diego, USA: Academic Press, pp. 119-199.
11. Jurgens, G., Lindstrom, K., and Saano, A. (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63: 803-805.
12. McCaig, A.E., Glover, L.A., and Prosser, J.I. (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65: 1721-1730.
13. Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
14. Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003a) The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ Microbiol 5: 152-162.
15. Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003b) Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils. Glob Change Biol 9: 1451-1457.
16. Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003c) Spatial analysis of archaeal community structure in grassland soil. Appl Environ Microbiol 69: 7420-7429.
17. Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L., and Schleper, C. (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5: 787-797.
18. Øvreås, L., Forney, L., Daae, F.L., and Torsvik, V.L. (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63: 3367-3373.
19. Peacock, A.D., Mullen, M.D., Ringelberg, D.B., Tyler, D.D., Hedrick, D.B., Gale, P.M., and White, D.C. (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33: 1011-1019.
20. Rodwell, J.S. (1992) British Plant Communities, Vol. 3. Cambridge, UK: Cambridge University Press.
21. Sherlock, R.R., and Goh, K.M. (1984) Dynamics of ammonia volatilization from urine patches and aqueous urea applied to pasture. I. Field experiments. Fert Res 5: 181-195.
22. Simon, H.M., Dodsworth, J.A., and Goodman, R.M. (2000) Crenarchaeota colonise terrestrial plant roots. Environ Microbiol 2: 495-505.
23. Wagner, M., Rath, G., Amann, R., Koops, H.-P., and Schleifer, K.-H. (1995) In-situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 18: 251-264.
24. Webster, G., Embley, T.M., and Prosser, J.I. (2002) Grassland management regimens reduce small-scale heterogeneity and species diversity of β-proteobacterial ammonia oxidizer populations. Appl Environ Microbiol 68: 20-30.
25. Williams, B.L., Shand, C.A., Sellers, S., and Young, M.E. (1999) Impact of synthetic sheep urine on N and P in two pastures in the Scottish uplands. Plant Soil 200: 1-11.
26. Williams, B.L., Grayston, S.J., and Reid, E.J. (2000) Influence of synthetic sheep urine on the microbial biomass, activity and community structure in two pastures in the Scottish uplands. Plant Soil 225: 175-185.
27. Woese, C.R., Kandler, O., and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-4579.