CCRA-4: Soil Metagenomics to Construct Indicators of Soil Degradation

Prinicipal Investigator:

Karen Garrett
Associate Professor, Department of Plant Pathology, Kansas State University 


Soil degradation is one of the most important problems for sustainable agriculture worldwide.  Because tropical soils have been studied less than temperate soils, understanding and developing methods for stopping tropical soil degradation is an important topic for the SANREM CRSP. SANREM also provides a unique social science context for studying human impacts on soil degradation. The program’s External Evaluation Panel in 2007 recommended applying soil metagenomic approaches to tropical soils to identify indicators of soil degradation. Ultimately, more complete profiles of soil communities will also contribute to the development of methods to foster disease-suppressive soils and soil communities that optimize other microbes’ contributions to plant health and productivity.

One of the most exciting outcomes of the biotechnology revolution in genomics is researchers’ ability to characterize soil microbial communities with much greater coverage. New technologies such as 454 sequencing allow evaluation of DNA from millions of microbes in soil samples, including species previously overlooked because they could not be cultured using standard techniques. While the first studies in soil metagenomics emphasized extensive analysis of a small number of samples, a research group at Kansas State University has developed techniques to add molecular tags and simultaneously process many tagged replicate soil samples. This allows comparisons of soil microbial communities in carefully designed replicated experiments.

Objectives of this research include:

  • Characterize soil microbial communities from soils representing a range of levels of degradation
  • Identify microbial taxa that are indicators for levels of degradation, especially those that may indicate the process of degradation has begun but is still reversible, and
  • Link soil community structure to both the general soil biophysical context and the social science context to understand human impacts and drivers of human decision-making for soil management.