Abstract
Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 4.15 × 105 to 6.67 × 106 copies/g, 2.21- to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.
Highlights
Nitrification, a key process of the biogeochemical nitrogen cycle (Konneke et al, 2005), was for over a century considered to exclusively be a two-step microbial process: first, ammonia is oxidized to nitrite by ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB) (Purkhold et al, 2000; Konneke et al, 2005), with nitrite being further oxidized to nitrate by nitrite-oxidizing bacteria (NOB) (Winogradsky, 1890)
Among the sampling sites, located along the estuarine tidal flat wetlands of China, the latitude varied from 21◦34 to 40◦51 N, while longitude varied from 109◦05 to 121◦53 E (Figure 1)
Comammox Nitrospira was found widely distributed in the estuarine tidal flat wetland of China, but with lower abundances and diversity compared to canonical AOB and AOA
Summary
Nitrification, a key process of the biogeochemical nitrogen cycle (Konneke et al, 2005), was for over a century considered to exclusively be a two-step microbial process: first, ammonia is oxidized to nitrite by ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB) (Purkhold et al, 2000; Konneke et al, 2005), with nitrite being further oxidized to nitrate by nitrite-oxidizing bacteria (NOB) (Winogradsky, 1890). Based on kinetic theory of optimal metabolic processes, the hypothetical existence of complete ammonia-oxidizing (comammox) microorganisms had been proposed (Costa et al, 2006). Their discovery in 2015 (Daims et al, 2015; van Kessel et al, 2015) redefined this key process of the biogeochemical nitrogen cycle. Phylogenetic analysis based on either, the 16S rRNA or nxr genes, is not able to distinguish between comammox Nitrospira and classical NOB (Pjevac et al, 2017). According to similarity analysis of the amoA gene comammox Nitrospira were subdivided into clade A (including subclade A1 and A2) and clade B (Daims et al, 2015; Xia et al, 2018)
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