[Effect of pH on the Abundance and Community Structure of Comammox in Paddy Soils].

Soil pH is recognized as an important environmental factor in determining the niche differentiation for ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Species of comammox, a single microorganism capable of the complete oxidation of ammonia to nitrate, have recently been discovered. Metagenomic analysis and quantitative PCR showed that Comammox were found in a wide range of environments, including soil. Comammox bacteria are differentiated into one of two clades (A and B) based on the phylogeny of genes encoding the α-subunit of ammonia monooxygenase genes (). However, all discovered Comammox strains have been isolated and cultured in aquatic ecosystems, including and , all belonging to clade A. Currently, Comammox has not been obtained from soil environments, which limits our understanding of soil Comammox . Here we hypothesized that, as AOA and AOB, the ecological site of Comammox may also be affected by pH. Therefore, soil samples with differing pH were collected, and the abundances and community structures were studied to elucidate the mechanism of pH effect on the distributions and community compositions of Comammox in soil. Quantitative PCR of comammox clade A and clade B genes in DNA extracts were performed using QuantStudio 6 Flex Real-Time PCR Systems. The community compositions for Comammox were studied by the cloning libraries of genes method. The results showed that the abundance of Comammox clade A gene in acidic paddy soil was two orders of magnitude higher than that in neutral paddy soil (<0.05), and the abundance of Comammox clade B in acidic paddy soil was significantly higher than that in neutral paddy soil (<0.05); the abundance of Comammox clade A gene in acidic paddy soil was 60 times higher than that of clade B, whereas the abundance ratio of Comammox clade A and clade B genes in neutral paddy soil was about two times higher. These results indicated that soil pH significantly affected the abundance of Comammox . The results of cloning and sequencing showed that the Comammox in neutral paddy soil was mainly , which belonged to clade A; no strain belonging to clade B was annotated. Comammox clade A in acidic paddy soil was mainly Composed of and , and clade B was mainly uncultured bacterium (FN395328). The results indicated that soil pH was an important factor in shaping Comammox community structure. Comammox were detected in all soil samples, and Comammox clade A had a preference for acidic environments. It seemed that species from possessed the ecological niche of low pH environments, whereas species from preferred to live in neutral environments. In conclusion, pH had a significant effect on the abundance and community structure of Comammox , which was one of the important factors affecting the niche differentiation of Comammox .