The overall and sequence-specific degradation of soil extracellular 16S rRNA genes across China: rates and influential factors

While extracellular DNA persistence substantially influences soil microbiome investigations, its degradation kinetics remain poorly quantified. Here, we developed a primer-labeled DNA approach coupled with microcosm incubation to determine the overall and sequence-specific degradation rates of extracellular 16S rRNA genes across China. We observed substantial variations in the overall degradation rates of extracellular 16S rRNA genes among the study sites, with degradation rate constants ranging from 0.05 to 0.16 day-1. The overall degradation rate constants showed significant correlations with soil moisture content, prokaryotic abundance, prokaryotic community profiles, and mean annual precipitation (MAP). The significant influences of moisture contents on the overall degradation rates were further verified by a moisture gradient microcosm experiment. The sequence-specific degradation rate constants were additionally correlated with pH, nitrogen content, and mean annual temperature (MAT). Furthermore, removing extracellular DNA significantly altered soil prokaryotic abundance, richness, and prokaryotic community profiles, and the sizes of sequence-specific extracellular 16S rRNA gene pools significant correlated with their respective degradation rates. This study developed a methodology for determining the overall and sequence-specific degradation rates of extracellular 16S rRNA genes, highlighting the profound influences of extracellular DNA on soil microbial research and informing the optimization of environmental DNA technologies.