A review of molecular methods to study the microbiota of soil and the mycosphere.

摘要

The availability of novel and advanced molecular methods based on soil nucleic acids has revolutionized our studies of the microbiota of soil. In particular, our understanding of the daunting diversity of soil microbes has grown to maturity, opening up a new box of challenging research questions about microbial functioning and interactions. We here review recent developments in, as well as the state-of-the-art of, the molecular methods applied to soil, and discuss a few salient cases in which they have enhanced our understanding of the soil microbiota and its functioning. In particular, we place a focus on the interface between soil fungal hyphae and the corresponding non-fungal-affected soil, i.e., the mycosphere. This selective environment may reduce the diversity of its inhabitants, allowing an improved picture of their ecology and functioning via molecular techniques. We present arguments for the contention that, to investigate testable hypotheses, a polyphasic approach is needed, in which work on the basis of molecular approaches such as metagenomics and metatranscriptomics is coupled to that based on culturable organisms. Thus, advances in our understanding of local functioning and adaptation of bacterial mycosphere inhabitants will be fostered by combined metagenomics/metatranscriptomics and cultivation-based approaches.Digital Object Identifier http://dx.doi.org/10.1016/j.ejsobi.2010.11.010