Location: Crops Pathology and Genetics ResearchTitle: Microbial community structure and diversity as indicators for evaluating soil quality) Author
|Joshi, Om Prakash|
|Karlen, Douglas - Doug|
Submitted to: Sustainable Agriculture
Publication Type: Review Article
Publication Acceptance Date: 1/1/2010
Publication Date: 1/31/2010
Citation: Sharma, S.K., Aketi, R., Sharma, M.P., Joshi, O., Govaerts, B., Steenwerth, K.L., Karlen, D.L. 2010. Microbial community structure and diversity as indicators for evaluating soil quality. Sustainable Agriculture. 5:317-358. Interpretive Summary: We review the relationships between agricultural management practices, soil quality, and microbial diversity and function. Furthermore, we discuss tools for describing soil microbial communities and their associated strengths and shortcomings. We assert that a soil with increased microbial diversity will be associated with greater microbial diversity, and identify effects of agricultural management practices (e.g. crop rotation, tillage, organic amendments, etc.) on soil microorganisms. Pragmatically, we define the concept of the ‘minimum data set’ so as to develop a standard by which to evaluate agricultural practices, microbial diversity and associated soil quality parameters, and give suggestions regarding the application of our knowledge of these factors to improving agricultural sustainability.
Technical Abstract: This review addresses two critical questions regarding soil quality: (1) which soil microbial properties, in particular diversity and community structure, most effectively characterize soil quality and should be used as indicators, and (2) how can soil quality assessed by such indicators be improved or maintained? In particular, we provide an overview of techniques available to characterize microbial community structure and diversity for evaluating soil quality, and furnish information pertaining to strategies that can improve microbial diversity in relation to soil quality by adopting suitable agricultural practices to sustain soil and crop productivity. A healthy soil as part of the soil quality concept is defined as a stable soil system with high levels of biological diversity and activity, internal nutrient cycling and resilience to disturbance. Overall, soil quality is considered as an integrative indicator of environmental quality, food security and economic viability and therefore, it would serve as a good indicator for monitoring sustainable land management. We provide an overview of how soil diversity is linked to soil quality and agricultural practices and discuss methods for evaluating soil diversity: structural profiling (i.e., fatty acid methyl ester analysis), genetic profiling techniques (i.e., PCR-DGGE, SSCP, T-RFLP), catabolic profiling, and Gene Chip for profiling structural and functional communities of soil microorganisms. We also discuss arbuscular mycorrhizae fungi community diversity and structure as they relate to soil quality, and identify the importance of minimum data sets (MDS) of microbial indicators, such that they must be (i) compatible with basic ecosystem processes in soil as well as physical or chemical indicators of soil health, (ii) sensitive to management in acceptable time frames, (iii) easy to assess or measure, (iv) composed of robust methodology with standardized sampling techniques, (v) cost-effective, and (vi) relevant to human goals, food security, agricultural production, sustainability and economic efficiency. Finally, we focus on specific agricultural strategies (i.e., tillage, crop rotations, organic amendments and microbial inculation) to improve soil quality by managing microbial communities and diversity.