Microbial growth in intact soil cores assessed by deuterium isotope probing

A key parameter to understand microbial activity in soil is growth. However, our approaches to measure microbial growth fail to integrate a potential key element for microbial functioning: the spatial structure of soil. In this study we used soil cores together with deuterium-labelling of soil water via vapor exchange to identify growing microbial groups in undisturbed soil compared to sieved soil via the production of (labelled) phospholipid fatty acids (PLFAs). Our results showed comparable measurements of community-level microbial respiration, mass-specific growth rates, and carbon use efficiency in intact and sieved soil. Although soil cores exhibited a larger variability of PLFA biomarker production rates, a high level of overlap was observed among the growing community members in intact and sieved soils. Contrary to our assumption, we conclude that sieving does not necessarily affect quantification of soil microbial growth rates. Importantly, the presented approach enables to identify and to quantify the growing soil microbial subpopulation in experimental conditions close to the field, which opens new avenues for spatial detection of soil microbial growth in situ.