Use and abuse of potential rates in soil microbiology

Potential rate assays are used in soil microbial ecology to determine the rates of a functional process in environmental samples under a defined set of conditions. While they can be used appropriately to provide mechanistic insights, potential rates are also often used to estimate the abundance of specific taxonomic groups and their in situ activity. These estimates incorrectly assume that all contributing organisms in a community are active at a maximum rate under one set of 'optimal' incubation conditions and that potential rates reflect activity in the soil. While investigators now recognise that populations within communities are physiologically diverse, they often ignore the consequent suboptimal activity, or even inactivity, of the majority of community members performing that function. In this short perspective article, we discuss when potential assays can be informative and highlight the underlying conceptual problems under circumstances where potential assays are misused, using potential nitrification rate (PNR) as an example. PNR was originally developed to estimate the size of active ammonia oxidising communities in environmental samples. It is routinely determined in short-term shaken slurry incubations by measuring assumed maximum rates of nitrate or nitrite production under optimal, non-substrate-limiting conditions. As with other functional processes, it is now recognised that a broad diversity of organisms contribute to aerobic ammonia oxidation in terrestrial and other habitats, and this diversity represents a substantial range of physiologies, including variation in substrate affinity, ammonia tolerance, cell specific activity and substrate preference. Despite this, PNR, and other potential rate assays, are often inappropriately used in an attempt to determine an ecologically relevant measurement of activity in soil. As with any potential assay, PNR has inherent biases towards particular functional groups and its use in investigating the ecology of ammonia oxidisers in natural systems should be carefully considered.

Automated summary

Potential rate assays are used to determine functional process rates in environmental samples, but are often misused to estimate activity based on assumed maximum rates under optimal conditions. Despite recognizing the physiological diversity within communities, potential rate assays may overlook suboptimal or inactive community members. Hence, caution is needed when using potential rate assays to determine ecological relevance.