Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil

Microbial Ecology

Volumn 59, Issue 2, 2010, Pages 335-343

  Thomson, Bruce C ^a   Ostle, Nick ^a   McNamara, Niall ^a   Bailey, Mark J ^a   Whiteley, Andrew S ^a   Griffiths, Robert I ^a  

^a CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); PROTEOBACTERIA;

BACTERIAL DNA; CARBON; CARBON DIOXIDE; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; POACEAE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL; UNITED KINGDOM;

BACTERIA; BIODIVERSITY; CARBON; CARBON DIOXIDE; DNA, BACTERIAL; POACEAE; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SCOTLAND; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY;

EID: 77950560411     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-009-9575-z     Document Type: Article

References (41)

1. Anderson JPE, Domsch KH (1973) Quantification of bacterial and fungal contributions to soil respiration. Arch Mikrobiol 93: 113-127.
2. Axelrood PE, Chow ML, Radomski CC, McDermott JM, Davies J (2002) Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can J Microbiol 48: 655-674.
3. Bardgett RD (2005) Chapter 3: organism interactions and soil processes. In: Bardgett RD (ed) The biology of soil: a community and ecosystem approach. Oxford University Press, Oxford, pp 57-85.
4. Baudoin E, Benizri E, Guckert A (2002) Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting. App Soil Ecol 19: 135-145.
5. Clarke KR (1993) Nonparametric multivariate analyses of changes in community structure. Aust J Ecol 18: 117-143.
6. de Ridder-Duine AS, Kowalchuk GA, Klein Gunnewiek PJA, Smant W, van Veen JA, de Boer W (2005) Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition. Soil Biol Biochem 37: 349-357.
7. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
8. Dreyfus BL, Dommergues YR (1981) Nodulation of acacia species by fast-growing and slow-growing tropical strains of rhizobium. Appl Environ Microbiol 41: 97-99.
9. 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.
10. 2 effects on peatland plant community carbon dynamics and DOC production. Ecosystems 10: 635-647.
11. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
12. Floyd MM, Tang J, Kane M, Emerson D (2005) Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the American Type Culture Collection. Appl Environ Microbiol 71: 2813-2823.
13. Griffiths RI, Bailey MJ, McNamara NP, Whiteley AS (2006) The functions and components of the Sourhope soil microbiota. App Soil Ecol 33: 114-126.
14. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2003) Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 43: 35-43.
15. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
16. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuc Acid Sym Ser 41: 95-98.
17. Helal HM, Sauerbeck DR (1984) Influence of plant-roots on C and P metabolism in soil. Plant Soil 76: 175-182.
18. Hooper DU, Bignell DE, Brown VK, Brussaard L, Dangerfield JM, Wall DH, Wardle DA, Coleman DC, Giller KE, Lavelle P, van der Putten WH, De Ruiter PC, Rusek J, Silver WL, Tiedje JM, Wolters V (2000) Interactions between aboveground and belowground biodiversity in terrestrial ecosystems: patterns, mechanisms, and feedbacks. Bioscience 50: 1049-1061.
19. Hopkins DW, Gregorich EG (2005) Chapter four: carbon as a substrate for soil organisms. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils. Cambridge University Press, Cambridge, pp 57-82.
20. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72: 1719-1728.
21. Johnson D, Booth RE, Whiteley AS, Bailey MJ, Read DJ, Grime JP, Leake JR (2003) Plant community composition affects the biomass, activity and diversity of microorganisms in limestone grassland soil. Eur J Soil Sci 54: 671-677.
22. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Ant van Leeu Int J Gen and Mol Microbiol 81: 509-520.
23. Kuzyakov Y (2002) Separating microbial respiration of exudates from root respiration in non-sterile soils: a comparison of four methods. Soil Biol Biochem 34: 1621-1631.
24. Lane DJ (1991) Chapter 6. 16S/23S rRNA sequencing. In: Stackenbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115-175.
25. Ledgard SF, Steele KW (1992) Biological nitrogen fixation in mixed legume grass pastures. Plant Soil 141: 137-153.
26. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
27. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
28. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Dymock D, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 2333-2333.
29. Marilley L, Vogt G, Blanc M, Aragno M (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA. Plant Soil 198: 219-224.
30. Raich JW, Tufekcioglu A (2000) Vegetation and soil respiration: correlations and controls. Biogeochemistry 48: 71-90.
31. Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg A, Prosser JI (2005) Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environ Microbiol 7: 828-838.
32. Rodwell JS (1992) In: Rodwell JS (ed) British plant communities, vol 3. Cambridge University Press, Cambridge.
33. Sait M, Davis KER, Janssen PH (2006) Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Environ Microbiol 72: 1852-1857.
34. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742-4751.
35. Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67: 2284-2291.
36. Steer J, Harris JA (2000) Shifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth of Agrostis stolonifera. Soil Biol Biochem 32: 869-878.
37. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70: 4748-4755.
38. Treonis AM, Ostle NJ, Stott AW, Primrose R, Grayston SJ, Ineson P (2004) Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol Biochem 36: 533-537.
39. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
40. Wardle DA, Bardgett RD, Klironomos JN, Setala H, van der Putten WH, Wall DH (2004) Ecological linkages between aboveground and belowground biota. Science 304: 1629-1633.
41. Wood M, Cooper JE, Bjourson AJ (1988) Response of lotus rhizobia to acidity and aluminum in liquid culture and in soil. Plant Soil 107: 227-231.