Deuterium stable isotope probing of fatty acids reveals climate change effects on soil microbial physiology.

The raise of atmospheric CO₂ concentrations, with consequent increase in global warming and the likelihood of severe droughts, is altering the terrestrial biogeochemical carbon (C) cycle, with potential feedback to climate change.  Microbial physiology, i.e. growth, turnover and carbon use efficiency, control soil carbon fluxes to the atmosphere. Thus, improving our ability to accurately quantify microbial physiology, and how it is affected by climate change, is essential. Recent advances in the field have allowed the quantification of community-level microbial growth and carbon use efficiency in dry conditions via an ¹⁸O water vapor equilibration technique, allowing for the first time to evaluate microbial growth rates under drought conditions.

We modified the water vapor equilibration method using ²H-labelled water to estimate microbial community growth via deuterium incorporation into fatty acids. First, we verified that a rapid equilibration of ²H with soil water is possible. Then, we applied this approach to soil samples collected from a long-term climate change experiment (https://www.climgrass.at/) where warming, elevated atmospheric CO₂ (eCO₂) and drought are manipulated in a full factorial combination. Samples were taken in the field during peak drought and one week after rewetting. We used a high-throughput method to extract phospho- and neutral- lipid fatty acids (PLFA and NLFA) and we measured ²H enrichment in these compounds via GC-IRMS.

Our results show that within 48 h, ²H in water vapor was in equilibrium with soil water and was detectable in microbial PLFA and NLFAs. We were able to quantify growth rates for different groups of microorganisms (Gram-positive, Gram-negative, Fungi and Actinobacteria) and calculate community level carbon use efficiency. We showed that a reduction of carbon use efficiency in the combined warming + eCO₂ treatment was caused by a reduced growth of fungi and overall higher respiration rates. During drought, all groups showed a reduction in growth rates, albeit the reduction was stronger in bacteria than in fungi. Moreover, fungi accumulated high amounts of ²H into NLFAs, representing up to one third of the amount in PLFAs and indicating enhanced investment into storage compounds. This investment was still higher than in control plots two days after rewetting and returned to control levels within a week.

Our study demonstrates that climate change can have strong effects on microbial physiology, with group-specific responses to different climate change factors. Our approach has the benefit of using fatty acid biomarkers to improve resolution into community level growth responses to climate change. This allowed a quantification of group-specific growth rates and concomitantly a measurement of investment into reserve compounds.