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J Microbiol Methods. 2012 Nov;91(2):246-51. doi: 10.1016/j.mimet.2012.08.011. Epub 2012 Aug 29.

Application of metatranscriptomics to soil environments.

Author information

1
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia. l.carvalhais@uq.edu.au

Abstract

The activities of soil microbial communities are of critical importance to terrestrial ecosystem functioning. The mechanisms that determine the interactions between soil microorganisms, their environment and neighbouring organisms, however, are poorly understood. Due to advances in sequencing technologies, an increasing number of metagenomics studies are being conducted on samples from diverse environments including soils. This information has not only increased our awareness of the functional potential of soil microbial communities, but also constitutes powerful reference material for soil metatranscriptomics studies. Metatranscriptomics provides a snapshot of transcriptional profiles that correspond to discrete populations within a microbial community at the time of sampling. This information can indicate the potential activities of complex microbial communities and the mechanisms that regulate them. Here we summarise the technical challenges for metatranscriptomics applied to soil environments and discuss approaches for gaining biologically meaningful insight into these datasets.

PMID:
22963791
DOI:
10.1016/j.mimet.2012.08.011
[Indexed for MEDLINE]

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