Microbial communities and their interactions in soil and rhizosphere ecosystems

Annu Rev Microbiol. 2002;56:211-36. doi: 10.1146/annurev.micro.56.012302.161120. Epub 2002 Jan 30.


Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Archaea / growth & development
  • Archaea / metabolism
  • Bacteria / classification
  • Bacteria / growth & development*
  • Bacteria / metabolism
  • Environmental Microbiology*
  • Environmental Pollutants / adverse effects
  • Mutation
  • Plant Roots / metabolism
  • Plant Roots / microbiology*
  • Polymerase Chain Reaction / methods
  • Soil Microbiology*


  • Environmental Pollutants