Quantitative stable isotope probing with H₂ ¹⁸O reveals that most bacterial taxa in soil synthesize new ribosomal RNA

Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed ¹⁸O composition of RNA extracted from soil incubated with H₂ ¹⁸O and used quantitative stable isotope probing to characterize rRNA synthesis among microbial taxa. RNA was not fully labeled with ¹⁸O, peaking at a mean of 23.6 ± 6.8 atom percent excess (APE) ¹⁸O after eight days of incubation, suggesting some ribonucleotides in soil were more than eight days old. Microbial taxa varied in the degree they incorporated ¹⁸O into their rRNA over time and there was no correlation between the APE¹⁸O of bacterial rRNA and their rRNA to DNA ratios, suggesting that the ratios were not appropriate to measure ribonucleotide synthesis. Our study indicates that, on average, 94% of soil taxa produced new rRNA and therefore were metabolically active.