The functions and components of the Sourhope soil microbiota

Applied Soil Ecology

Volumn 33, Issue 2, 2006, Pages 114-126

  Griffiths, Robert I ^a   Bailey, Mark J ^a   McNamara, Niall P ^a   Whiteley, Andrew S ^a  

^a CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

16S; Acidobacteria; Alphaproteobacteria; Bacteria; Soil; Sourhope; Stable isotope

Indexed keywords

EID: 33745759004     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2006.03.007     Document Type: Article

References (79)

1. Adams M.B. Ecological issues related to N deposition to natural ecosystems: research needs. Environ. Int. 29 (2003) 189-199
2. Amann R.I., Ludwig W., and Schleifer K.H. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol. Rev. 59 (1995) 143-169
3. Anderson I.C., and Cairney J.W.G. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ. Microbiol. 6 (2004) 769-779
4. Anderson J.P.E., and Domsch K.H. A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biol. Biochem. 10 (1978) 215-221
5. Barns S.M., Takala S.L., and Kuske C.R. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65 (1999) 1731-1737
6. Bligh E.G., and Dyer W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37 (1954) 911-917
7. Bonkowski M. Protozoa and plant growth: trophic links and mutualism. Eur. J. Protistol. 37 (2002) 363-365
8. Bradford M.A., Jones T.H., Bardgett R.D., Black H.I.J., Boag B., Bonkowski M., Cook R., Eggers T., Gange A.C., Grayston S.J., Kandeler E., McCaig A.E., Newington J.E., Prosser J.I., Setala H., Staddon P.L., Tordoff G.M., Tscherko D., and Lawton J.H. Impacts of soil faunal community composition on model grassland ecosystems. Science 298 (2002) 615-618
9. Bruneau P.M.C., Davidson D.A., Grieve I.C., Young I.M., and Nunan N. The effects of soil horizons and faunal excrement on bacterial distribution in an upland grassland soil. FEMS Microbiol. Ecol. 52 (2005) 139-144
10. Buckley D.H., and Schmidt T.M. Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ. Microbiol. 5 (2003) 441-452
11. Burt-Smith, G., 2002. Sourhope Field Experiment Report IV (1999-2002) http://soilbio.nerc.ac.uk/Download/ReportIV.pdf.
12. Cho J.-C., and Tiedje J.M. Biogeography and degree of endemicity of fluorescent pseudomonas strains in soil. Appl. Environ. Microbiol. 66 (2000) 5448-5456
13. Chow M.L., Radomski C.C., McDermott J.M., Davies J., and Axelrood P.E. Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol. Ecol. 42 (2002) 347-357
14. Cole L., Staddon P.L., Sleep D., and Bardgett R.D. Soil animals influence microbial abundance, but not plant-microbial competition for soil organic nitrogen. Funct. Ecol. 18 (2004) 631-640
15. Davidson D.A., Bruneau P.M.C., Grieve I.C., and Young I.M. Impacts of fauna on an upland grassland soil as determined by micromorphological analysis. Appl. Soil Ecol. 20 (2002) 133-143
16. Dawson L.A., Grayston S.J., Murray P.J., Ross J.M., Reid E.J., and Treonis A.M. Impact of Tipula paludosa larvae on plant growth and the soil microbial community. Appl. Soil Ecol. 25 (2004) 51-61
17. Dawson L.A., Grayston S.J., Murray P.J., Cook R., Gange A.C., Ross J.M., Pratt S.M., Duff E.I., and Treonis A. Influence of pasture management (nitrogen and lime addition and insecticide treatment) on soil organisms and pasture root system dynamics in the field. Plant Soil 255 (2003) 121-130
18. Dickens H.E., and Anderson J.M. Manipulation of soil microbial community structure in bog and forest soils using chloroform fumigation. Soil. Biol. Biochem. 31 (1999) 2049-2058
19. Felske A., Wolterink A., Van Lis R., De Vos W.M., and Akkermans A.D.L. Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl. Environ. Microbiol. 66 (2000) 3998-4003
20. Finlay B.J., Black H.I.J., Brown S., Clarke K.J., Esteban G.F., Hindle R.M., Olmo J.L., Rollett A., and Vickerman K. Estimating the growth potential of the soil protozoan community. Protist 151 (2000) 69-80
21. Gray N.D., Hastings R.C., Sheppard S.K., Loughnane P., Lloyd D., McCarthy A.J., and Head I.M. Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soil. FEMS Microbiol. Ecol. 46 (2003) 11-22
22. Griffiths B.S., Kuan H.L., Ritz K., Glover L.A., McCaig A.E., and Fenwick C. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microb. Ecol. 47 (2004) 104-113
23. Griffiths B.S., Ritz K., Wheatley R., Kuan H.L., Boag B., Christensen S., Ekelund F., Sorensen S.J., Muller S., and Bloem J. An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities. Soil. Biol. Biochem. 33 (2001) 1713-1722
24. Griffiths B.S., Ritz K., Bardgett R.D., Cook R., Christensen S., Ekelund F., Sorensen S.J., Baath E., Bloem J., de Ruiter P.C., Dolfing J., and Nicolardot B. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90 (2000) 279-294
25. Griffiths R.I., Whiteley A.S., O'Donnell A.G., and Bailey M.J. 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 (2000) 5488-5491
26. Griffiths R.I., Whiteley A.S., O'Donnell A.G., and Bailey M.J. Physiological and community responses of established grassland bacterial populations to water stress. Appl. Environ. Microbiol. 69 (2003) 6961-6968
27. Griffiths R.I., Whiteley A.S., O'Donnell A.G., and Bailey M.J. Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol. Ecol. 43 (2003) 35-43
28. 2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere. J. Microbiol. Meth. 58 (2004) 119-129
29. Hoitink H., and Boehm M. Biocontrol within the context of soil microbial communities: a substrate-dependent phenomenon. Annu. Rev. Phytopathol. 37 (1999) 427-446
30. Hooper D.U., Chapin F.S., Ewel J.J., Hector A., Inchausti P., Lavorel S., Lawton J.H., Lodge D.M., Loreau M., Naeem S., Schmid B., Setala H., Symstad A.J., Vandermeer J., and Wardle D.A. Effects of biodiversity on ecosystem functioning: A consensus of current knowledge. Ecol. Monogr. 75 (2005) 3-35
31. Horner-Devine M.C., Leibold M.A., Smith V.H., and Bohannan B.J.M. Bacterial diversity patterns along a gradient of primary productivity. Ecol. Lett. 6 (2003) 613-622
32. Hugenholtz P., Goebel B.M., and Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180 (1998) 4765-4774
33. Hunt H.W., Coleman D.C., Ingham E.R., Ingham R.E., Elliott E.T., Moore J.C., Rose S.L., Reid C.P.P., and Morley C.R. The detrital food web in a shortgrass prairie. Biol. Fertil. Soils 3 (1987) 57-68
34. Janssen P.H., Yates P.S., Grinton B.E., Taylor P.M., and Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria, proteobacteria, and verrucomicrobia. Appl. Environ. Microbiol. 68 (2002) 2391-2396
35. 2)-C-13 pulse-labelling of upland grassland demonstrates a rapid pathway of carbon flux from arbuscular mycorrhizal mycelia to the soil. N. Phytol. 153 (2002) 327-334
36. Johnston C.A., Groffman P., Breshears D.D., Cardon Z.G., Currie W., Emanuel W., Gaudinski J., Jackson R.B., Lajtha K., Nadelhoffer K., Nelson D., Post W.M., Retallack G., and Wielopolski L. Carbon cycling in soil. Front. Ecol. Environ. 2 (2004) 522-528
37. Kennedy N., Brodie E., Connolly J., and Clipson N. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms. Environ. Microbiol. 6 (2004) 1070-1080
38. Kirk J.L., Beaudette L.A., Hart M., Moutoglis P., Klironomos J.N., Lee H., and Trevors J.T. Methods of studying soil microbial diversity. J. Microbiol. Meth. 58 (2004) 169-188
39. Krsek M., and Wellington E.M.H. Assessment of chitin decomposer diversity within an upland grassland. Antonie Van Leeuwenhoek 79 (2001) 261-267
40. Kuzyakov Y., and Domanski G. Carbon input by plants into the soil. Z. Pflanzenernahr. Bodenkd. 163 (2000) 421-431 (Review: J. Plant Nutr. Soil Sci.)
41. Lipson D.A., and Schmidt S.K. Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl. Environ. Microbiol. 70 (2004) 2867-2879
42. Lynch J.M. Products of soil microorganisms in relation to plant growth. C.R.C. Crit. Rev. Microbiol. 5 (1976) 67-107
43. Macrae A., Rimmer D.L., and O'Donnell A.G. Novel bacterial diversity recovered from the rhizosphere of oilseed rape (Brassica napus) determined by the analysis of 16S ribosomal DNA. Antonie Van Leeuwenhoek 78 (2000) 13-21
44. Manz W., Amann R., Ludwig W., Wagner M., and Schleifer K.H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria-problems and solutions. Syst. Appl. Microbiol. 15 (1992) 593-600
45. Marchesi J.R., Sato T., Weightman A.J., Martin T.A., Fry J.C., Hiom S.J., and Wade W.G. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64 (1998) 795-799
46. Marilley L., and Aragno M. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl. Soil Ecol. 13 (1999) 127-136
47. McCaig A.E., Glover L.A., and Prosser J.I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65 (1999) 1721-1730
48. McCaig A.E., Glover L.A., and Prosser J.I. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 67 (2001) 4554-4559
49. Muyzer G., Dewaal E.C., and Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rRNA. Appl. Environ. Microbiol. 59 (1993) 695-700
50. Naeem S. Disentangling the impacts of diversity on ecosystem functioning in combinatorial experiments. Ecology 83 (2002) 2925-2935
51. Nicol G.W., Glover L.A., and Prosser J.I. Spatial analysis of archaeal community structure in grassland soil. Appl. Environ. Microbiol. 69 (2003) 7420-7429
52. Nicol G.W., Glover L.A., and Prosser J.I. The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ. Microbiol. 5 (2003) 152-162
53. Nicol G.W., Webster G., Glover L.A., and Prosser J.I. Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environ. Microbiol. 6 (2004) 861-867
54. Nogales B., Moore E.R.B., Abraham W.R., and Timmis K.N. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl polluted moorland soil. Environ. Microbiol. 1 (1999) 199-212
55. O'Donnell A.G., and Gorres H.E. 16S rDNA methods in soil microbiology. Curr. Opin. Biotechnol. 10 (1999) 225-229
56. 2 pulse labelling system. Rapid Commun. Mass Spectrom. 14 (2000) 1345-1350
57. 2 spike. Soil. Biol. Biochem. 35 (2003) 877-885
58. Øvreås L., and Torsvik V. Microbial diversity and community structure in two different agricultural soil communities. Microb. Ecol. 36 (1998) 303-315
59. Quaiser A., Ochsenreiter T., Lanz C., Schuster S.C., Treusch A.H., Eck J., and Schleper C. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50 (2003) 563-575
60. Radajewski S., Ineson P., Parekh N.R., and Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature 403 (2000) 646-649
61. Rangel-Castro J.I., Killham K., Ostle N., Nicol G.W., Anderson I.C., Scrimgeour C.M., Ineson P., Meharg A., and Prosser J.I. Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environ. Microbiol. 7 (2005) 828-838
62. Rosch C., Mergel A., and Bothe H. Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Environ. Microbiol. 68 (2002) 3818-3829
63. Saito A., Mitsui H., Hattori R., Minamisawa K., and Hattori T. Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum. FEMS Microbiol. Ecol. 25 (1998) 277-286
64. Sessitsch A., Weilharter A., Gerzabek M.H., Kirchmann H., and Kandeler E. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67 (2001) 4215-4224
65. Sheppard S.K., and Lloyd D. Direct mass spectrometric measurement of gases in soil monoliths. J. Microbiol. Meth. 50 (2002) 175-188
66. Sinsabaugh R.S. Enzymic analysis of microbial pattern and process. Biol. Fertil. Soils (Historical Arch.) 17 (1994) 69-74
67. Smit E., Leeflang P., Gommans S., van den Broek J., van Mil S., and Wernars K. 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 (2001) 2284-2291
68. Staddon P.L., Ostle N., Dawson L.A., and Fitter A.H. The speed of soil carbon throughput in an upland grassland is increased by liming. J. Exp. Bot. 54 (2003) 1461-1469
69. Sugden A., Stone R., and Ash C. Ecology in the Underworld. Science 304 (2004) 1613
70. Sun H.Y., Deng S.P., and Raun W.R. Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl. Environ. Microbiol. 70 (2004) 5868-5874
71. Tiedje J.M., Asuming-Brempong S., Nusslein K., Marsh T.L., and Flynn S.J. Opening the black box of soil microbial diversity. Appl. Soil Ecol. 13 (1999) 109-122
72. Vandenkoornhuyse P., Husband R., Daniell T.J., Watson I.J., Duck J.M., Fitter A.H., and Young J.P.W. Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Mol. Ecol. 11 (2002) 1555-1564
73. van der Gast C.J., Knowles C.J., Starkey M., and Thompson I.P. Selection of microbial consortia for treating metal-working fluids. J. Ind. Microbiol. Biotechnol. 29 (2002) 20-27
74. van Elsas J.D., Duarte G.F., Rosado A.S., and Smalla K. Microbiological and molecular biological methods for monitoring microbial inoculants and their effects in the soil environment. J. Microbiol. Meth. 32 (1998) 133-154
75. Wardle D.A. Communities and Ecosystems: Linking the Aboveground and Belowground Components (2002), Princeton University Press, Princeton, NJ
76. Wilson K.H., Wilson W.J., Radosevich J.L., DeSantis T.Z., Viswanathan V.S., Kuczmarski T.A., and Andersen G.L. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68 (2002) 2535-2541
77. Zhou J., Xia B., Treves D.S., Wu L.-Y., Marsh T.L., O'Neill R.V., Palumbo A.V., and Tiedje J.M. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68 (2002) 326-334
78. Zhou J.Z., Xia B.C., Huang H., Palumbo A.V., and Tiedje J.M. Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microbiol. 70 (2004) 1723-1734
79. Zhou J.Z., Xia B.C., Huang H.S., Treves D.S., Hauser L.J., Mural R.J., Palumbo A.V., and Tiedje J.M. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil. Biol. Biochem. 35 (2003) 915-924