The study of microbial diversity in soil requires a wide variety of methods.  We have developed refined and applied relevant techniques to a wide range of organisms and problems in soil.  This included developing methods for extracting DNA from soil suitable for PCR amplification (Cullen & Hirsch, 1998) to monitor GM rhizobia (Cullen et al., 1998) and extracting mRNA directly from soil to use in gene expression studies (Mendum et al., 1998).  Recent studies have included the impact of heavy metal contamination on rhizobia (Hirsch et al., 1993) and other soil bacteria (O'Flaherty et al., 2001; Lawlor et al., 1999, 2000); effects of pesticide use on culturable rhizosphere bacteria (Nicholson & Hirsch, 1998); interactions between take-all fungus, rhizobacteria, plant and soil (Rengel et al., 1996; 1998); the diversity of mycobacteria in different soils (Mendum et al., 2000); and the distribution of rhizobial bacteriophages and plasmids (Mendum et al., 2001; Clark et al., 2002). (Penny Hirsch and Ian Clark)

References:

Clark, I. M., Mendum, T. A. & Hirsch, P. R. (2002). The influence of the symbiotic plasmid pRL1J1 on the distribution of GM rhizobia in soil and crop rhizospheres, and implications for gene flow. Antonie van Leeuwenhoek 81, 607-616.

Cullen,D.W. & Hirsch, P.R,. (1998) A simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biology and Biochemistry 30: 983-993.

Cullen, D.W., Nicholson, P.S., Mendum, T.A. & Hirsch, P.R. (1998) Monitoring genetically-modified rhizobia in field soils using the polymerase chain reaction. Journal of Applied Microbiology 84:1025-1034.

Hirsch, P.R,., Jones, M.J., Mcgrath, S.P. & Giller, K.E. (1993) Heavy metals from past applications of sewage sludge decrease the genetic diversity of Rhizobium leguminosarum biovar trifolii populations. Soil Biology. Biochemistry 25, 1485-1490.

Lawlor, K., Chaudri, A.M., McGrath, S.P. & Hirsch, P.R. (1999) Gene transfer in bacteria from soils contaminated with heavy metals.  Letters in Applied Microbiology 28: 317-320.

Lawlor, K., Knight, B.P., Barbosa-Jefferson, V.L., Lane, P.W., Lilley, A.K., Paton, G.I., McGrath, S.P., O'Flaherty, S.M. & Hirsch, P.R,. (2000) Comparison of methods to investigate microbial populations in soils under different agricultural management. FEMS Microbiology Ecology 33, 129-137.

Mendum, T.A., Sockett, R.E. & Hirsch, P.R,. (1998) The detection of Gram-negative bacterial mRNA from soil by RT-PCR FEMS Microbiology Letters 164: 369-373.

Mendum, T.A., Chilima, B.Z. & Hirsch, P.R,. (2000) The PCR amplification of non-tuberculous mycobacterial 16S rRNA sequences from soil. FEMS Microbiological Letters. 185: 189-192.

Mendum, T.A., Clark, I.M & Hirsch, P.R,. (2001) Characterization of two novel Rhizobium leguminosarum bacteriophages from a field release site of genetically-modified rhizobia.  Antonie van Leeuwenhoek 79: 189-197.

Nicholson, P.S. & Hirsch, P.R,. (1998) The effects of pesticides on the diversity of culturable soil bacteria.  Journal of Applied Microbiology 84: 551-558.

O'Flaherty, S., McGrath, S. & Hirsch, P. (2001)  Comparison of phenotypic, functional and genetic diversity of bacterial communities in soils. In: Sustainable Management of Soil Organic Matter.  Eds. R.M. Rees, B.C. Ball, C.D. Campbell and C.A. Watson.  CAB International.

Rengel, Z., Gutteridge, R., Hirsch, P., & Hornby, D. (1996)  Plant genotype, micronutrient fertilization and take-all infection influence bacterial populations in the rhizosphere of wheat.  Plant & Soil 183: 269-277.

Rengel, Z., Ross, G. & Hirsch, P. (1998) Colonisation of wheat roots by soil bacteria depends on the plant genotype and micronutrient nutrition. Journal of Plant Nutrition 21: 99-113.

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