Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought

Abstract

Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO₂, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO₂ and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH₄⁺ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO₂ have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

Fig. 1. qPCR quantifications of amoA gene and transcript copy numbers per gram of dry soil from the ammonia-oxidizing microbial groups.

a Quantifications from plots affected by elevated temperature (eT) and atmospheric CO₂ concentrations (eCO₂). The dashed lines represent plots affected by elevated atmospheric CO₂ conditions (eCO₂). The colors represent plots affected by either ambient temperature (aT) or elevated temperature (eT). b Quantifications from plots affected by future climate (eT x eCO₂) and drought (D). The dashed lines separate plots affected by drought (D). The colors represent the drought treatment. The caption on the upper right corner of each subplot represents the ANOVA results. *p value <0.05; **p value <0.01. Whenever the ANOVA results showed a significant interaction term, lsmeans multiple comparison tests were ran. For details on the ANOVA and post-hoc tests, see Tables S2 and S3.

Fig. 2. Shannon diversity index based on amoA/nxrB gene and transcript sequences from all microbial groups.

a Quantifications from plots affected by elevated temperature (eT) and atmospheric CO₂ concentrations (eCO₂). The dashed lines represent plots affected by elevated atmospheric CO₂ conditions (eCO₂). The colors represent plots affected by either ambient temperature (aT) or elevated temperature (eT). b Quantifications from plots affected by future climate (eT x eCO₂) and drought (D). The dashed lines separate plots affected by drought (D). The colors represent the drought treatment. The caption on the upper right corner of each subplot represents the ANOVA results. *p value <0.05; **p value <0.01. Whenever the ANOVA results showed a significant interaction term, lsmeans multiple comparison tests were ran. For details on the ANOVA and post-hoc tests, see Tables S2 and S3.

Fig. 3. Relative abundance (%) of all nitrifying groups obtained by amoA and nxrB transcript sequences.

a Data for plots affected by single and interactive effects of elevated temperature (eT) and atmospheric CO₂ (eCO₂) concentrations. b Plots affected by single and interactive effects of future climate conditions (eT x eCO₂) and drought (D). The color code represents different genera/OTU/clades/lineages. “Amb” stands for “ambient conditions”. Multiple horizontal lines within the same color represent individual OTUs within a group. Taxa that comprised <0.1% of all reads per treatment are grouped as “Other”.