Linking microbial growth in soil to changes in ecosystem function using heavy water stable isotope probing

Background/Question/Methods

Microbial growth in soil is a rudimentary characteristic that directly impacts ecosystem processes, yet remains difficult to characterize even with the ever-expanding suite of available culture independent molecular approaches. Several approaches have been developed for measuring growth, but generally involve the addition of a substrate that can act as an energy or nutrient source which is often not useable by all organisms. The development of heavy water (H₂¹⁸O) stable isotope probing provides an ideal approach for investigating microbial growth in soil since the uptake of water is universal and does not suffer from C or N addition fertilization artifacts. We hypothesized that heavy water SIP would be suitable for characterizing new growth under both dynamic and static environmental conditions, and knowledge of growth dynamics would lead to greater understanding of connections between microbial activities and ecosystem functions. Here we applied DNA stable isotope probing with H₂¹⁸O coupled with quantitative PCR and high throughput sequencing of bacterial 16S rRNA genes to characterize new microbial growth in soil following a rapid environmental change (rewetting of seasonally dried soil) and in soil under static conditions (maintained at -1.5 °C under anaerobic conditions).

Results/Conclusions

Bacterial growth response to a rapid change in water potential in Mediterranean grassland soil was observable within 3 hours and followed a sequential growth pattern over time. This pattern was observable at a high taxonomic level suggesting ecological coherence in growth response at the phylum and order level. Total community abundance correlated poorly with CO₂ production, but new growth was highly correlated with cumulative CO₂ production for the total soil community. Approximately 50% of the C that was mineralized during the 7 d incubation occurred within the first 24 h, and during this first day growth was only observed in 2 out of 260 detected bacterial taxa (at the order level), suggesting that select few bacterial taxa were responsible for a large portion of the bacterial C mineralization.  Bacterial growth was also observed in frozen anaerobic boreal soil and corresponded with continuous production of CO₂. Growth was only observed in two bacterial phyla, Firmicutes and Bacteroidetes, suggesting that fermentation was likely the major carbon mineralization pathway. Results demonstrate that heavy water SIP is suitable for studying growth dynamics across a large range of growth rates, and knowledge of new growth does indeed lead to stronger mechanistic linkages between the soil microbial community and ecosystem processes.