Altering the mineral composition of soil causes a shift in microbial community structure

FEMS Microbiology Ecology

Volumn 61, Issue 3, 2007, Pages 414-423

  Carson, Jennifer K ^a   Rooney, Deirdre ^b   Gleeson, Deirdre B ^a   Clipson, Nicholas ^b  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

ARISA; Microbial community structure; Minerals; Soil

Indexed keywords

MICA; MINERAL; PHOSPHATE;

BACTERIUM; COMMUNITY STRUCTURE; FUNGUS; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MICROCOSM; MINERAL; SOIL NUTRIENT;

ARTICLE; BASALT; CLOVER; CONTROLLED STUDY; FUNGUS; LOLIUM; MICROCOSM; MICROFLORA; NONHUMAN; PLANT; PRIORITY JOURNAL; SOIL;

BACTERIA; BIOMASS; DNA, BACTERIAL; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; FUNGI; LOLIUM; MINERALS; SEQUENCE ANALYSIS, DNA; SILICATES; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); LOLIUM RIGIDUM; TRIFOLIUM SUBTERRANEUM;

EID: 34547830333     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2007.00361.x     Document Type: Article

References (55)

1. Alef K (1995) Dehydrogenase activity. Methods in Applied Soil Microbiology and Biochemistry (Alef K Nannipieri P, eds), pp. 228 231. Academic Press, London.
2. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26 : 32 46.
3. Bakken AK, Gautneb H, Sveistrup T Myhr K (2000) Crushed rocks and mine tailings applied as K fertilizers on grassland. Nutr Cycl Agroecosyst 56 : 53 57.
4. Banfield JF, Barker WW, Welch SA Taunton A (1999) Biological impact on mineral dissolution: application of the lichen model to understanding mineral weathering in the rhizosphere. Proc Natl Acad Sci USA 96 : 3404 3411.
5. Banning N, Brock F, Fry JC, Parkes RJ, Hornibrook ERC Weightman AJ (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Envir Microbiol 7 : 947 960.
6. Barker WW, Welch SA, Chu S Banfield JF (1998) Experimental observations of the effects of bacteria on aluminosilicate weathering. Am Min 83 : 1551 1563.
7. Bolland MDA Baker MJ (2000) Powdered granite is not an effective fertilizer for clover and wheat in sandy soils from Western Australia. Nutr Cycl Agroecosyst 56 : 59 68.
8. Bolland MDA, Clarke MF Yeates JS (1995) Effectiveness of rock phosphate, coastal superphosphate and single superphosphate for pasture on deep sandy soils. Nutr Cycl Agroecosyst 41 : 129 143.
9. Bolland MDA, Gilkes RJ Brennan RF (2001) The influence of soil properties on the effectiveness of phosphate rock fertilisers. Aust J Soil Res 39 : 773 798.
10. Brodie E, Edwards S Clipson N (2002) Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem. Microb Ecol 44 : 260 270.
11. Brookes PC, Kragt JF, Powlson DS Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: the effects of fumigation time and temperature. Soil Biol Biochem 17 : 831 835.
12. Certini G, Campbell CD Edwards AC (2004) Rock fragments in soil support a different microbial community from the fine earth. Soil Biol Biochem 36 : 1119 1128.
13. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Austral Ecol 18 : 117 143.
14. Clarke KR Ainsworth M (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol Prog Ser 92 : 205 219.
15. Clarke KR Warwick RM (2001) Change in Marine Communities: an Approach to Statistical Analysis and Interpretation. PRIMER-E, Plymouth.
16. Cookson WR, Marschner P, Clark IM et al 2006) The influence of season, agricultural management, and soil properties on gross nitrogen transformations and bacterial community structure. Aust J Soil Res 44 : 453 465.
17. Coroneos C, Hinsinger P Gilkes RJ (1996) Granite powder as a source of potassium for plants: a glasshouse bioassay comparing two pasture species. Fert Res 45 : 143 152.
18. Crosby LD Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. BioTechniques 34 : 790 802.
19. Dunbar J, Ticknor LO Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67 : 190 197.
20. Egert M Friedrich MW (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69 : 2555 2562.
21. FAO (1998) World Reference Base for Soil Resources. Food and Agriculture Organisation, Rome.
22. Gardes M Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes. Mol Ecol 2 : 113 118.
23. Gillman GP, Burkett DC Coventry RJ (2002) Amending highly weathered soils with finely ground basalt rock. Appl Geochem 17 : 987 1001.
24. Gleeson D, Clipson N, Melville K, Gadd G McDermott F (2005) Characterization of fungal community structure on a weathered pegmatitic granite. Microb Ecol 50 : 360 368.
25. Gleeson D, Kennedy N, Clipson N, Melville K, Gadd G McDermott F (2006) Characterization of bacterial community structure on a weathered pegmatitic granite. Microb Ecol 51 : 526 534.
26. Hazen TC, Jimenez L de Victoria GL (1991) Comparison of bacteria from deep subsurface sediment and adjacent groundwater. Microb Ecol 22 : 293 304.
27. Hildebrand EE Schack-Kirchner H (2000) Initial effects of lime and rock powder application on soil solution chemistry in a dystric cambisol: results of model experiments. Nutr Cycl Agroecosyst 56 : 69 78.
28. Hinsinger P Gilkes RJ (1997) Dissolution of phosphate rock in the rhizosphere of five plant species grown in an acid, P-fixing mineral substrate. Geoderma 75 : 231 249.
29. Hinsinger P, Jaillard B Dufey JE (1992) Rapid weathering of a trioctahedral mica by the roots of ryegrass. Soil Sci Soc Am 56 : 977 982.
30. Hinsinger P, Bolland MDA Gilkes RJ (1996) Silicate rock powder: effect on selected chemical properties of a range of soils from Western Australia and on plant growth as assessed in a glasshouse experiment. Fert Res 45 : 69 79.
31. Holm PE, Nielsen PH, Albrechtsen H-J Christensen TA (1992) Importance of unattached bacteria and bacteria attached to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer. Appl Environ Microbiol 58 : 3020 3026.
32. Hughes JC Gilkes RJ (1994) Rock phosphate dissolution and bicarbonate-soluble P in some soils from South-Western Australia. Aust J Soil Res 32 : 767 779.
33. Ibekwe AM Kennedy AC (1998) Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils. Plant and Soil 206 : 151 161.
34. Joergensen RG (1996) The fumigation-extraction method to estimate soil microbial biomass: calibration of the kEC value. Soil Biol Biochem 28 : 25 31.
35. Kennedy N, Brodie E, Connolly J Clipson N (2004) Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms. Environ Microbiol 6 : 1070 1080.
36. Kennedy NM, Connolly J Clipson NJW (2005a) Impact of lime, nitrogen and plant species on fungal community structure in grassland microcosms. Environ Microbiol 7 : 780 788.
37. Kennedy NM, Gleeson DE, Connolly J Clipson NJW (2005b) Seasonal and management influences on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 53 : 329 337.
38. Lejon DPH, Chaussod R, Ranger J Ranjard L (2005) Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb Ecol 50 : 614 625.
39. Longanathan P, Hedley MJ, Bolan NS Currie LD (2002) Field evaluation of the liming value of two phosphate rocks and their partially acidulated products after 16 years of annual application to grazed pasture. Nutr Cycl Agroecosyst 72 : 287 297.
40. Lueders T Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69 : 320 326.
41. McArthur WM (2004) Reference Soils of South-Western Australia. Department of Agriculture Western Australia, Perth.
42. Normand P, Ponsonnet C, Nesme X, Neyra M Simonet P (1996) ITS analysis of prokaryotes. Molecular Microbial Ecology Manual (Akkermans DL, van Elsas JD De Bruijn EL, eds), pp. 1 12. Kluwer Academic Publishers, Amsterdam.
43. Priyono J Gilkes RJ (2004) Dissolution of milled-silicate rock fertilisers in the soil. Aust J Soil Res 42 : 441 448.
44. Ranjard L, Poly F, Combrisson J, Richaume A, Gourbière F, Thioulouse J Nazaret S (2000) Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb Ecol 39 : 263 272.
45. Ranjard L, Poly F, Lata JC, Thiolouse J Nazaret S (2001) Characterisation of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67 : 4479 4487.
46. Rayment GE Higginson FR (1992) Soil pH. Australian Laboratory Handbook of Soil and Water Chemical Methods, pp. 15 16. Inkata Press, Melbourne.
47. Rogers JR Bennett PC (2004) Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates. Chem Geol 203 : 91 108.
48. Sanz Scovino JI Rowell DL (1988) The use of feldspars as potassium fertilizers in the savannah of Colombia. Fert Res 17 : 71 84.
49. Sparling G Zhu C (1993) Evaluation and calibration of biochemical methods to measure microbial biomass C and N in soils from Western Australia. Soil Biol Biochem 25 : 1793 1801.
50. Thorseth IH, Furnes H Tumyr O (1995) Textural and chemical effects of bacterial activity on basaltic glass: an experimental approach. Chem Geol 119 : 139 160.
51. Ullman WJ, Kirchman DL, Welch SA Vandevivere P (1996) Laboratory evidence for microbiologically mediated silicate mineral dissolution in nature. Chem Geol 132 : 11 17.
52. Vale M, Nguyen C, Dambrine E Dupouey JL (2005) Microbial activity in the rhizosphere soil of six herbaceous species cultivated in a greenhouse is correlated with shoot biomass and root C concentrations. Soil Biol Biochem 37 : 2329 2333.
53. Wang JG, Zhang FS, Cao YP Zhang XL (2000) Effect of plant types on release of mineral potassium from gneiss. Nutr Cycl Agroecosyst 56 : 37 44.
54. Welch SA, Barker WW Banfield JF (1999) Microbial extracellular polysaccharides and plagioclase dissolution. Geo Cosmo Acta 63 : 1405 1419.
55. White TJ, Bruns T, Lee S Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ White TJ, eds), pp. 315 322. Academic Press, New York.