Culture-independent molecular techniques for soil microbial ecology

A - Papers appearing in refereed journals

Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2010. Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry. 42 (6), pp. 878-887.

AuthorsHirsch, P. R., Mauchline, T. H. and Clark, I. M.

The advent of nucleic acid-based molecular methods, in particular the polymerase chain reaction (PCR), has revolutionised the study of soil microbial ecology, previously constrained by an inability to culture the majority of cells detected by direct microscopic observation. Extraction of DNA and RNA directly from cells in soil circumvents the requirement to grow microorganisms in laboratory culture, avoiding problems associated with the differential growth rates of the estimated 1% that can be grown routinely. However, not all cells that contain DNA are capable of growth, and in some conditions such as air-dried soil, DNA can be extracted from non-viable microorganisms after 140 years of storage. To investigate the active microbial community, RNA can also be isolated directly from soil. Analysis of ribosomal RNA (rRNA) indicates the dominant active population in any particular set of conditions and the large, constantly increasing electronic database of gene sequences for the small subunit of rRNA (16S for prokaryotes, 18S for eukaryotes) provides identification of many soil bacteria, archaea and fungi with varying degrees of certainty to the genus, species or sub-species level. More precise information on which functional genes are active can be obtained from messenger RNA (mRNA). Newer methods including high-throughput (massively parallel) sequencing and microarrays offer further advances. We describe a range of molecular techniques used to investigate soil microbial communities, discuss how they relate to other methods for investigating bacterial and fungal activity, and explore their drawbacks and limitations.

KeywordsMicrobial communities; Molecular diagnostics; Genetic diversity; DNA; RNA; Microarrays; High-throughput sequencing; Metagenomics
Year of Publication2010
JournalSoil Biology and Biochemistry
Journal citation42 (6), pp. 878-887
Digital Object Identifier (DOI)
Open accessPublished as non-open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeSEF
Soil microbial community function and diversity
The diversity, biology and dynamics of microbial agents that regulate nematode populations in the rhizosphere
Publisher's version
Copyright license
Publisher copyright
Output statusPublished
Publication dates
Online17 Mar 2010
Publication process dates
Accepted19 Feb 2010

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