Optimising whole-soil multiple substrate-induced respiration (MSIR) of soil microbiota for large scale surveillance and monitoring

Multiple substrate-induced respiration is a method for characterising and assessing the functional diversity of soil microbiota. In this procedure, an array of simple organic substrates is added to soil samples, and the resulting multiple respiration values are used to give a functional description of the microbial community. In this study, we tested 44 substrates and five substrate concentrations for their ability to discriminate land use types and individual sites, specifically in large scale surveillance and monitoring programs. We assessed the concentrations with the coefficient of variation and found only little differences (less than 0.8 units) in the discriminative power of sites. Therefore we recommend using the amount equivalent to the substrate-induced respiration. In practice, most substrates performed well with respect to number of re-measurements, linearity of measurement curves and retail price. A Principle Components Analysis of all 44 substrates successfully ordinated land use types in distinct clusters and identified sites of unusual soil condition (e.g. especially wet or freshly fertilised sites). The discriminative power of 26 substrates was high (> 60% contribution to total variance) and substrates were equally appropriate to differentiate land use. Four optimum substrates were identified (threonine, malonic acid, quinic acid and pantothenic acid) that together explained 86% of the empirical data variation and yielded an almost identical ordination of sites as the full substrate set. Thus, the number of substrates in future studies can be considerably reduced. A resemblance matrix based on root exudates was highly (76%) correlated to a non-exudate matrix, indicating that root exudates were not better suited for community-level profiling than others. We discuss current measurement systems and suggest using more than just several grams of whole soil samples per measurement to adequately represent field conditions.

► We discriminated land use types by profiling the functional diversity of microbiota.
► The dosages of the tested substrates did not influence the profiling considerably.
► Most substrates performed well and are practical for large scale studies.
► Only four substrates were sufficient to differentiate land use types.
► Root exudates are not better suited for the discrimination than other substrates.