Microbial Community Structure and Diversity as Indicators for Evaluating Soil Quality

The living soil system is of primary importance in sustainable agricultural production. Soil quality is considered as an integrative indicator of environmental quality, food security and economic viability. Therefore, soil itself serves as a potential indicator for monitoring sustainable land management. As part of the soil quality concept, a healthy soil supports high levels of biological diversity, activity, internal nutrient cycling and resilience to disturbance. The use of microbial community structure and diversity as an indicator to monitor soil quality is challenging due to little understanding of the relationship between community structure and soil function. This review addresses two critical questions regarding soil quality: (1) which soil microbial properties, particularly diversity and community structure, most effectively characterize soil quality and can be used as indicators, and (2) how can soil quality assessed by such indicators be improved or maintained? We provide an overview of available techniques to characterize microbial community structure and diversity, and furnish information pertaining to strategies that can improve microbial diversity, including mycorrhizae, in relation to soil quality by adopting suitable agricultural practices to sustain soil and crop productivity. These techniques include those for structural profiling, i.e. fatty acid methyl ester analysis, genetic profiling, i.e. PCR-DGGE, SSCP, T-RFLP, functional profiling, i.e. catabolic profiling, diversity of enzyme activity, and to profile both structural and functional communities comprehensively, i.e. gene chip. We 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. We focus on specific agricultural strategies such as tillage, crop rotations, organic amendments and microbial inoculation to improve soil quality by managing microbial communities and diversity. Overall, we provide techniques to assess microbial communities and diversity, and their management through agricultural practices to improve quality of soil.