Gene-copy normalized heterotrophic soil respiration as a field proxy for the soil microbiomes' dormancy and carbon use efficiency – A proof-of-concept

Soil respiration (SR) represents a major carbon flux from terrestrial ecosystems, yet the physiological mechanisms underlying the microbiome-driven heterotrophic SR (SR H ) remain poorly understood. Here, we present a proof-of-concept evaluation of the gene-copy normalized respiration rate (SR GC ), a field-applicable metric that normalizes SR H by rRNA-based microbial gene copy numbers derived from intracellular DNA (iDNA). Because dormant cells retain intact DNA and often perform basal respiration, while active cells differ in carbon use efficiency (CUE), SR GC may reflect community-level physiological patterns, including potential variation in dormancy and carbon allocation strategies, without the need of directly assessing dormancy or CUE. We quantified SR GC across montane and alpine grasslands in the European Alps and assessed its environmental and biological drivers. SR GC increased at lower elevations with steeper slopes, higher pH, and elevated C:N ratios, indicating enhanced microbial activity and reduced dormancy under favorable conditions. Soil faunal richness was negatively associated with SR GC , suggesting a regulatory role of faunal biodiversity on microbial carbon losses. Importantly, SR GC was positively correlated with the temperature sensitivity (Q10) of SR H , although each parameter was linked to distinct metabolic pathways, implying that communities with lower CUE are also more temperature sensitive. While rRNA gene copy variation among taxa and kingdoms may influence absolute values, SR GC captures microbiome-scale physiological trends rather than taxon-specific respiration rates. Our findings demonstrate that SR GC has the potential to be used as a comparative indicator for a microbiomes' physiological state and carbon allocation strategies, complementing laboratory-based approaches and offering new opportunities to improve predictions of soil carbon dynamics under environmental change.