Molecular approaches to the analysis of soil microbial community structure and function(Environment and Soil Microorganisms,Symposium)

抄録

Measurements of microbial community structure have historically been based upon isolation methods which rely on growth of microbes in culture media. Such methods do not provide a representative measure since only a small proportion of soil microbes are cultivable. Over the last decade or so, there has been a rapid acceleration in the development and application of molecular-based measures of microbial community structure, based on nucleic acids and "marker" compounds. Such measures do not require the cultivation of microbes since the compounds in question can be directly extracted from soil, and are therefore more representative of the indigenous communities. Molecular analyses may be based on genetic or phenotypic characteristics of the community. Genetic analyses first require the extraction and purification of nucleic acids from the soil communities. Community DNA can be analysed at a wide range of scales of resolution. Broad-scale analyses provide an overview of its composition and include measures such as % G+C profiling, community cross-hybridisation and reassociation kinetics. Application of the polymerase chain reaction (PCR) to community DNA using primer templates that are specific to phylogenetically wide or narrow groups allows analysis at a wide range of resolutions. Phenotypic methods rely on the extraction and quantification of marker compounds characteristic of particular microbial groups. For such compounds to be truly resolute, they should be restricted to the defined group for which they are putatively markers, and should be present in approximately constant concentration within such groups. For most compounds these criteria are not strictly met. There are also molecular- or chemical- based techniques which provide measures that lay somewhere between that of the compositional structure of soil microbial communities and their function. These include carbon utilisation profiling, as exemplified by the Biolog^[○!R] system, and volatile organic carbon (VOC) profiling. These approaches are reviewed in more detail, and examples of their contemporary application to soil microbial ecology discussed.