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<p>Soil pH is considered one of the main determinants of the assembly of globally distributed microorganisms that catalyze the biogeochemical cycles of carbon (C) and nitrogen (N). However, direct evidence for niche specialization of microorganisms in association with soil pH is still lacking. Using methane-oxidizing bacteria (methanotrophs) as a model system of C cycling, we show that pH is potentially the key driving force selecting for canonical <span class="inline-formula"><i>γ</i></span> (type I) and <span class="inline-formula"><i>α</i></span> (type II) methanotrophs in rice paddy soils. DNA-based stable isotope probing (DNA-SIP) was combined with high-throughput sequencing to reveal the taxonomic identities of active methanotrophs in physiochemically contrasting soils from six different paddy fields across China. Following microcosm incubation amended with <span class="inline-formula">¹³CH₄</span>, methane was primarily consumed by <i>Methylocystis</i>-affiliated type II methanotrophs in soils with a relatively low pH (5.44–6.10), whereas <i>Methylobacter</i>- or <i>Methylosarcina</i>-affiliated type I methanotrophs dominated methane consumption in soils with a high pH (7.02–8.02). Consumption of <span class="inline-formula">¹³CH₄</span> contributed 0.203&thinsp;% to 1.25&thinsp;% of soil organic C, but no significant difference was observed between high-pH and low-pH soils. The fertilization of ammonium nitrate resulted in no significant changes in the compositions of <span class="inline-formula">¹³C</span>-labeled methanotrophs in the soils, although significant inhibition of methane oxidation activity was consistently observed in low-pH soils. Mantel analysis further validated that soil pH, rather than other parameters tested, had significant correlation to the variation in active methanotrophic compositions across different rice paddy soils. These results suggest that soil pH might have played a pivotal role in mediating the niche differentiation of ecologically important aerobic methanotrophs in terrestrial ecosystems and imply the importance of such niche specialization in regulating methane emissions in paddy fields following increasingly intensified input of anthropogenic N fertilizers.</p>