Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil

Nitrification, the oxidation of ammonia via nitrite to nitrate, contributes to nitrogen losses in agricultural soils. When nitrification is a two-step process, it depends on the successful metabolic interaction between ammonia oxidising archaea (AOA) and bacteria (AOB), and nitrite oxidising bacteria primarily within Nitrobacter (NIB) and Nitrospira (NIS). However, consequences of dry spells caused by climate change on the composition and co-associations of these microbial guilds and the fate of nitrogen remain unclear. Here we subject four distinct soils to either one long or two shorter drought periods (7–11 % water holding capacity) followed by rewetting in a microcosm experiment to evaluate the hypothesis that drying-rewetting stress triggers distinct responses in the functional guilds due to differences in environmental preferences and adaptation strategies. While AOB were highly resistant, AOA were the most sensitive to drying among the four guilds and decreased in relative abundance. This coincided with reduced ammonia oxidation rates in three soils by on average 27 % compared to the control. However, we observed almost full recovery of AOA one week after rewetting. NIS, but not NIB, were strongly affected by rewetting with no recovery during the experiment, showing shifts in community composition and relative abundance with up to 30 % affected ASVs. Network analysis revealed that drying-rewetting affected co-occurrences between ammonia and nitrite oxidisers in a soil-dependant manner, possibly indicating a destabilisation of their metabolic interaction. Overall, this study emphasises the importance to consider weather extremes like drought on soil nitrifier community dynamics and the fate of nitrogen in soils.