Biogeographic distribution of comammox bacteria in diverse terrestrial habitats

Comammox, the microbial group capable of completely oxidizing ammonia to nitrate, challenged the traditional two-step nitrification process where ammonia is oxidized by ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite by nitrite-oxidizing bacteria (NOB). However, the distribution of comammox bacteria in various habitats and their potential environmental drivers remain poorly understood. Using qPCR and high-throughput sequencing approach, we analyzed the abundance and community patterns of comammox from 38 samples taken from five different habitat types including paddy fields in Shaoguan and Antu, the wheat fields, river, and grassland in the Qinghai-Tibet Plateau, and the fringe and central riparian zones of Chaohu Lake of China during winter and summer. Comammox bacteria were detected in all samples, with Ca. N. nitrificans dominating the community, followed by Ca. N. nitrosa. Generally, in paddy fields of Shaoguan and Antu, ammonia (NH₄⁺) was the key factor affecting comammox bacteria. However, in wheat fields, river and grassland of the Qinghai-Tibet Plateau, altitude was the strongest factor affecting comammox bacteria. In Chaohu Lake, comammox bacteria showed temporal heterogeneity, being higher in winter than summer, especially in the fringe riparian zone. Our results suggest that comammox is widespread in diverse habitats and exhibit niche partitioning, and can be affected by different environmental factors that may vary by habitat.