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New Zealand Plant Protection 63 (2010): 271

Microbial community profiling - applications in plant protection

E.M. Gerard, J. Monk, S.A. Wakelin and M. O’Callaghan

ABSTRACT

The function and diversity of microbial communities associated with plants, insects and soils directly impacts on plant health and production. Although community level investigations appear daunting, significant gains are being made through the application of molecular biology. An important technique involves polymerase chain reaction (PCR) amplification of genes from DNA/RNA isolated from the environment, removing limitations caused by microbial cultivation. PCR amplicons are then separated using denaturing gradient gel electrophoresis (DGGE) providing a 'fingerprint' of the diversity of that gene within the microbial community. This PCR-DGGE based method originally targeted the ribosomal RNA (rRNA) genes present in all microorganisms. Other genetic markers are now used, including general markers coding for conserved proteins involved in core cell functions, or genes essential to activities defining specific functional groups, such as ammonia oxidation, nitrogen fixation or antibiotic production. Reverse-transcription PCR-DGGE on community RNA can be used to profile metabolically active populations. PCR-DGGE allows for the rapid comparison of multiple samples and, when used in combination with other approaches, provides robust information of environmental microbial communities. Recent uses in plant protection research include examination of: effects of pesticides and biocontrol agents on microbial populations, soil disease suppression, plant rhizosphere communities, microbe-mineral interactions, microbe-insect interactions, insect microbiota, predator- prey studies and community responses to changing farming practices.

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