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United States Department of Agriculture

Agricultural Research Service

Title: Molecular and Physiological Based Methods for the Characterization of Soil Microbial Communities

Author
item Mazzola, Mark

Submitted to: Proceedings of Management of Soilborne Plant Pathogens
Publication Type: Proceedings
Publication Acceptance Date: September 17, 2002
Publication Date: December 1, 2002
Citation: MAZZOLA, M. MOLECULAR AND PHYSIOLOGICAL BASED METHODS FOR THE CHARACTERIZATION OF SOIL MICROBIAL COMMUNITIES. PROCEEDINGS THIRTEENTH ANNUAL MEETING ON SOILBORNE PLANT DISEASES. AGRICULTURAL RESEARCH COUNCIL, PLANT PROTECTION RESEARCH INSTITUTE, STELLENBOSCH, SOUTH AFRICA. 2002. v. 13. p. 16-25.

Interpretive Summary: Soil ecosystmes possess a wealth of biological resources that can be harnessed for use in control of plant diseases. More recently, various elements of this community have been utilized for novel processes including the remediation of hazardous waste sites. However, our ability to use these microbial resources has been hindered by a lack of understating concerning the structure, function and diversity of microorganisms resident to soil habitats. Until recently our understanding of the species which comprise the microbial community resident to soils has been based on studies that have used culture-based methods. Unfortunately, a tiny fraction of the soil microbial community can be cultured on synthetic media, and thus, information concerning the vast majority of this biological resource has been limited or non-existent. More recently there has been an extensive effort to develop methods with the capacity to elucidate the composition and diversity of microorganisms in soil environments without need for cultivation during the processs of examination. Methods that rely on isolation of DNA directly from soil environmens have been developed which allow for an immensely broader evaluation of the microorganisms which reside in soil habitats. These techniques in concert with traditional methods will enable us to describe the vital roles that soil microorganisms have in shaping plant health.

Technical Abstract: Soil microorganisms play an important role in a number of processes important to soil quality and plant health. Optimum use of microbial resources requires a broad understanding of the composition and diversity of microorganisms resident to soil habitats. Traditional culture-based methods used in describing these populations has only allowed for examination of a fraction of the soil microbial community. There has been an extensive effort to develop methods with the capacity to elucidate the composition and diversity of microorganism in soil environments without need for cultivation during the process of examination. Certain physiological-based and molecular-based methods have been developed which partially fulfill this goal. Substrate utilization profiling allows for description of changes in the functional composition of microbial communities, but is hindered by the continued need for cultivation. Phospholipid fatty acid analysis circumvents some of the problems inherent with culture-based methods and is suitable for description of whole communities but is of little value for the identification of individual species. The primary advantage of nucleic acid-based methods is that individuals and microbial communities can be analyzed without need for culturing of the microorganism. Most methods currently employed are based on the polymerase chain reaction, with the small subunit rRNA as the target gene. Methods have been developed for analysis of the amplicons including sequence analysis, TGGE, DGGE and microarrays.

Last Modified: 10/21/2014
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