Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox)

Abstract

The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems. IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

“…The divergence of CAOB amoA hindered the development of the universal primer set covering both clades. The primer set targeting only clade A had been designed to quantify CAOB in wastewater treatment systems and other ecosystems (Wang et al, 2018; Xia et al, 2018). The sister primer sets target clade A and clade B were separately developed for identifying CAOB, although nonspecific amplifications were reported (Pjevacet al 2017; Keene-Beach and Noguera, 2018).…”

“…A newly designed primer set specifically targeting the clade A of CAOB amoA gene revealed high abundances of CAOB in full-scale WWTPs (Wang et al, 2018). Likewise, a clade A targeted primer set was designed to quantify the CAOB abundances in various environments (Xia et al, 2018).…”

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

“…By now, comammox Nitrospira were also detected in several natural environments, including lake sediment and forest and agricultural soils (Orellana et al ., ; Parks et al ., ; Pjevac et al ., ; Xia et al ., ). Notably, in fertilized soils (Orellana et al ., ) and acidic subtropical forest soils (Shi et al ., ), the increased abundances of comammox Nitrospira in response to human‐induced N loadings indicate that they can drive nitrification also under less oligotrophic conditions.…”

“…Notably, in fertilized soils (Orellana et al ., ) and acidic subtropical forest soils (Shi et al ., ), the increased abundances of comammox Nitrospira in response to human‐induced N loadings indicate that they can drive nitrification also under less oligotrophic conditions. The observed diversity together with the identification of comammox Nitrospira as the most abundant nitrifiers in acidic forest soil (Hu and He, ) as well as in estuary and coastal environments (Xia et al ., ) indicates their vital contribution to nitrification also in natural systems. However, comammox Nitrospira genomes from natural environments were rarely recovered and analysed so far, and thus the metabolic capabilities of complete nitrifiers in these ecosystems are poorly understood.…”

Distribution of comammox and canonical ammonia‐oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons

“…The three reported comammox species, Nitrospira inopinata , Candidatus Nitrospira nitrificans and Candidatus Nitrospira nitrosa, form a cluster (clade A) in a phylogenetic tree for the amino acid sequences of AmoA (Daims et al ; van Kessel et al ). Comammox clade A is further divided into two monophyletic groups, clades A.1 and A.2, and the identified comammox species are present in clade A.1 (Xia et al ). Another cluster (clade B) has been proposed based on amoA gene sequences from groundwater metagenome bins (Daims et al ); however, their complete nitrification activities have not yet been identified.…”