Temporally resolved microbial community dynamics reveal the parallel proliferation of copiotrophic bacteria, fungi and protists after labile substrate addition irrespective of nitrogen availability

Microbial metabolism represents the major pathway for both the formation and the decomposition of soil organic matter, as carbon (C) consumed by microbes is either respired during catabolism and leaves the soil system as CO₂ or is incorporated into new biomass compounds during anabolism and eventually becomes stabilized as microbial necromass. The partitioning of C between these two metabolic branches, also known as the microbial carbon use efficiency (CUE), depends on the complex interplay of many factors such as the quality of the carbon substrate and the availability of nutrients such as nitrogen (N) and phosphorus (P).

In this contribution, we combined measurements of soil respiration, DNA and RNA content with highly temporally resolved metatranscriptomics and dynamic modeling to study microbial activity and community changes in an arable soil after batch input of glucose as a labile C source and further factorial addition of N and P sources in mineral form. While the respiration results indicated a strong N limitation in the studied soil, we observed similar short-term changes in the bacterial, fungal and protist communities regardless of nutrient addition, with an expansion of copiotrophic taxa in all three groups. Notably, while the resulting communities were comparable after two days, these shifts occurred at a faster rate in treatments that received additional N. These observations suggest that glucose stimulated the growth of the same species in the soil under both nutrient-rich and nutrient-poor conditions, with N availability modulating the kinetics and the efficiency of copiotroph growth instead of stimulating a distinct group of specialists adapted to nutrient limitation. This interpretation is also supported by the observed ratio of RNA to DNA as a metric of microbial activity status as well as by a simple dynamic model of microbial growth, both of which reveal a faster activation and more efficient growth in nutrient-rich treatments.

Overall, our findings demonstrate that the input of a labile C source determines a relatively small subset of actively growing copiotrophs in the bacterial, fungal and protist communities, whereas the stoichiometric availability of other nutrients such as N only controls the rate and efficiency with which
these species are able to grow.