Diversity distribution and characteristics of comammox in different ecosystems

The discovery of complete ammonia oxidizers (comammox), which can oxidize ammonia into nitrate, has recently changed the concept of traditional nitrification. However, comparative studies on the analysis of comammox microbial community in different ecosystems are still scarce. In this study, the distribution and diversity of the comammox microbial community in farmlands, riparian zones, and river sediments in summer and winter were investigated by high-throughput sequencing. And the relative abundance of ammonia-oxidizing microorganisms was measured via their amoA genes of real-time quantitative polymerase chain reaction (qPCR). The relationships between ammonia oxidation microorganisms and the environmental factors were further analyzed. The abundance of comammox clade A was one order of magnitude lower than that of ammonia-oxidizing archaea (AOA) but higher than that of ammonia-oxidizing bacteria (AOB). The abundance of comammox was higher in summer than in winter and higher in farmland soils (1.81 ± 0.95 × 107 copies g−1) than in riparian zones and river sediments. Meanwhile, Candidatus Nitrospira nitrosa were the most widespread comammox in most samples (up to 86.31%), followed by Candidatus Nitrospira nitrificans, with a low abundance of Candidatus Nitrospira inopinata (lower than 0.61%). Furthermore, the abundance of comammox clade A had a significantly negative correlation with pH and NH4+ concentration (P < 0.05). The study revealed the potential advantages of comammox in farmlands and may be conducive to further research on comammox in microbial nitrogen cycling.