Methods for assessing the composition and diversity of soil microbial communities

Soil microorganisms play important roles in soil quality and plant productivity. The development of effective methods for studying the diversity, distribution, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil health. Traditionally, the analysis of soil microbial communities has relied on culturing techniques using a variety of culture media designed to maximize the recovery of diverse microbial populations. However, only a small fraction (<0.1%) of the soil microbial community has been accessible with this approach. To overcome these problems, other methods such as the analysis of phospholipid fatty acids and community-level physiological profiles have been utilized in an attempt to access a greater proportion of the soil microbial community. in recent years, molecular methods for soil microbial community analysis have provided a new understanding of the phylogenetic diversity of microbial communities in soil. Among the most useful of these methods are those in which small subunit rRNA genes are amplified from soil-extracted nucleic acids. Using these techniques, it is possible to characterize and study soil microbes that currently cannot be cultured. Microbial rRNA genes can be detected directly from soil samples and sequenced. These sequences can then be compared with those from other known microorganisms. Additionally, group- and taxon-specific oligonucleotide probes can be developed from these sequences making direct visualization of microorganisms in soil habitats possible. The use of these techniques provides new ways of assessing soil microbial diversity and ultimately, a more complete understanding of the potential impacts of environmental processes and human activities on responses of soil microorganisms. Information gained from such studies will have direct impacts on our understanding of the role of microbial processes in soil health. (C) 2000 Published by Elsevier Science B.V.