Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Abstract

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

Diversity and abundance of comammox bacteria in the sediments of an urban lake

“…RDA analysis in this study showed that the abundance of the comammox amoA gene was positively correlated with the concentration of OM and TN in sediments, which was similar to the results in tidal sediments (Yu et al ). Studies have shown that comammox has a high affinity for NH 4 + ‐N and was suitable for growth at low NH 4 + ‐N concentrations (Kits et al ).…”

“…However, it was lower than the rice paddy soil and WWTPs (10 11 copies per gram dry sediment) (Pjevac et al ). The abundance of the comammox amoA gene in fertilized soils (Wang et al ) was close to that in the river and lake sediments (Yu et al ). However, it was lower than that in the acidic forest soils (Hu and He ), and the highest abundance value was found in groundwater wells (Pjevac et al ).…”

“…N. nitrosa was the dominant comammox bacterium in the sediment of Lake Donghu, followed by N. nitrificans , and then N. inopinata . These comammox bacteria was also widely found in other ecosystems, such as wastewater treatment systems (Wang et al ; Zheng et al ), drinking water treatment systems (Pinto et al ; Wang et al ) and tidal wetlands (Yu et al ). In a study of a sewage treatment plant, most of the samples were mainly composed of N. nitrosa (Keene‐Beach and Noguera ).…”

“…Although comammox bacteria were discovered just a few years ago, they have been found to coexist with AOA, and AOB, and widely distributed in different ecosystems using molecular biology techniques, such as in drinking water treatment plants (DWTPs), atmospheric particulate matter, soil, estuarine sediments and wastewater treatment plants (WWTPs) (Gao et al ; Wang et al ; Fowler et al ; Wang et al ; Yu et al ). AOA were previously thought to dominate in environments with low ammonium concentrations, such as oceans or oligotrophic lakes (Herrmann et al ; Hou et al ), and AOB had a higher abundance in nutrient‐rich waters and soils (Dang et al ; Prosser and Nicol ).…”

“…AOA were previously thought to dominate in environments with low ammonium concentrations, such as oceans or oligotrophic lakes (Herrmann et al ; Hou et al ), and AOB had a higher abundance in nutrient‐rich waters and soils (Dang et al ; Prosser and Nicol ). However, with further research on comammox community and its environments, it was shown that comammox bacteria may have advantages over AOA and AOB in low ammonium environments (Kits et al ), and ammonium concentrations could also affect the diversity of the commomox community (Yu et al ). In some drinking water influent, river, groundwater and urban waterway sediment samples, the proportion of comammox bacteria in the total number of ammonia‐oxidizing micro‐organisms was higher than 70% (Xia et al ), suggesting it may be an important functional community in the nitrification process in low dissolved oxygen (DO) environments (Roots et al ).…”