Cropping system modulates the effect of drought on ammonia-oxidizing communities

The severity of drought is predicted to increase across Europe due to climate change. Droughts can substantially impact terrestrial nitrogen (N) cycling and the corresponding microbial communities. Here, we investigated how ammonia-oxidizing bacteria (AOB), archaea (AOA), and comammox (complete ammonia oxidizers) respond to simulated drought in a rain-out shelter experiment in the DOK long-term field trial comparing different organic and conventional agricultural practices since 1978. This study is part of the MICROSERVICES (BiodivERsA) project aiming to understand and predict the effects of climate change on crop-associated microbiomes and their ecosystem functions. We monitored the diversity, the composition, and the abundance of ammonia-oxidizers for five months by Illumina-based amplicon sequencing and quantitative real-time PCR using the amoA gene as molecular marker.

We found that the effect of drought varied depending on the ammonia-oxidizing community and also on the agricultural practices. The community structures of AOA and comammox were more strongly affected by drought than the AOB community structure. Drought also had a stronger impact on the community structure in the biodynamic (organic) cropping system than in both the mixed and mineral-fertilized conventional systems. The abundance of ammonia oxidizers was also influenced by drought, with comammox clade B exhibiting the strongest sensitivity to drought. The drought effect on the community abundance was more prominent in the biodynamic and mixed-conventional systems than in the mineral-fertilized conventional system. We further found a significant interaction between drought and agricultural practices on the abundance of all groups of ammonia-oxidizers except AOB. Overall, our study showed that the impact of drought on ammonia oxidizers was modulated by agricultural practices and varied with time as well as among members of ammonia-oxidizers. These results underscore the significance of agricultural management practices in influencing the response of nitrogen cycling and the corresponding communities to drought.