The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. There is a necessity to identify the composition, diversity, and function of the soil microbiome to evaluate its properties and functioning and to assess ecotoxicological effects due to anthropogenic activities. Although numerous microbiological methods exist or are currently developed, only a limited number of methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the ecosystem service approach, new methods should focus on soil microbial functions (e.g. nutrient cycling, greenhouse gas emission, plant growth promotion, carbon cycling and sequestration, soil structure development and filter function). The few standardised methods focusing on function of the soil microbiome mostly include measurements like basal respiration, enzyme activities and biodegradation of organic matter under well-defined conditions. Of particular note is the current development of molecular methods using quantitative PCR for assessing the abundance of microbes that catalyse e.g. major transformation steps in nitrogen and phosphorus cycling or pesticide degradation. Most soil quality methods focus on bacteria and related endpoints, while methods for fungal communities and their functional traits are far less represented. Thus, techniques are proposed to analyse fungal enzyme activities. Additionally, methods for the determination of microbial growth rates and efficiencies are discussed. Field methods indicative of carbon turnover are presented, including the litter bag test and a modification of the tea bag test. With increasing development of high-throughput sequencing and big data analyses (including metagenomics), it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability and anthropogenic soil cultivation activities.
For further information, see the publication in Soil:
Thiele-Bruhn, S., Schloter, M., Wilke, B.-M., Beaudette, L. A., Martin-Laurent, F., Cheviron, N., Mougin, C., Römbke, J. (2020). Identification of new microbial functional standards for soil quality assessment. Soil 6, 17-34.
For additional new publications, see ECT’s publication list.