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. Soil pH is considered one of the main determinants of theassembly of globally distributed microorganisms that catalyze thebiogeochemical cycles of carbon (C) and nitrogen (N). However, directevidence for niche specialization of microorganisms in association with soilpH is still lacking. Using methane-oxidizing bacteria (methanotrophs) as amodel system of C cycling, we show that pH is potentially the key drivingforce selecting for canonical γ (type I) and α (type II)methanotrophs in rice paddy soils. DNA-based stable isotope probing(DNA-SIP) was combined with high-throughput sequencing to reveal thetaxonomic identities of active methanotrophs in physiochemically contrastingsoils from six different paddy fields across China. Following microcosmincubation amended with 13CH4 , methane was primarily consumed by Methylocystis-affiliatedtype II methanotrophs in soils with a relatively low pH (5.44–6.10), whereasMethylobacter- or Methylosarcina-affiliated type I methanotrophs dominated methane consumption in soilswith a high pH (7.02–8.02). Consumption of 13CH4 contributed0.203 % to 1.25 % of soil organic C, but no significant difference wasobserved between high-pH and low-pH soils. The fertilization of ammoniumnitrate resulted in no significant changes in the compositions of 13C -labeled methanotrophs in the soils, although significant inhibitionof methane oxidation activity was consistently observed in low-pH soils.Mantel analysis further validated that soil pH, rather than other parameterstested, had significant correlation to the variation in activemethanotrophic compositions across different rice paddy soils. These resultssuggest that soil pH might have played a pivotal role in mediating the nichedifferentiation of ecologically important aerobic methanotrophs interrestrial ecosystems and imply the importance of such niche specializationin regulating methane emissions in paddy fields following increasinglyintensified input of anthropogenic N fertilizers.

The pH-based ecological coherence of active canonical methanotrophs in paddy soils