Use and abuse of potential rates in soil microbiology
Résumé
Potential rate assays are used in soil microbial ecology to determine the maximum rate of a functional process in environmental samples. They assume that all contributing organisms in a community are active at a maximum rate under one set of ‘optimal’ incubation conditions. Potential rates are then often compared to the abundance of specific taxonomic groups to infer their relative contribution in situ . However, 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 highlight the underlying conceptual problems associated with potential assays and use potential nitrification rate (PNR) as an example. PNR was originally developed to estimate the size of active ammonia oxidising communities in environmental samples. They are routinely performed 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 is routinely used in an attempt to determine an ecologically relevant measurement of nitrification activity in soil. As with other potential assays, PNR has inherent biases towards particular functional groups and its use in investigating the ecology of ammonia oxidisers in natural systems is severely restricted.
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