Comparative genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira

Abstract

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.Comammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to β-AOB.β-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from β-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from β-AOB to comammox Nitrospira is predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.SignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

“…), which can hamper the identification of novel comammox organisms when they cluster close to but not within the known comammox clades. An additional group containing canonical Nitrospira clustering in between the comammox clades further suggests a complex evolutionary history of the ammonia oxidation pathway within Nitrospira , as already discussed in the former studies (Palomo et al ., ).…”

“…The genus Nitrospira , which prior to the discovery of comammox had been regarded to comprise specialized nitrite oxidizers only, represents the most diverse NOB clade, harbouring at least six phylogenetic sublineages observed in a wide range of natural aquatic and terrestrial habitats, and engineered environments like drinking and wastewater treatment plants (Daims et al ., ; Lebedeva et al ., ; Daebeler et al ., ; Daims et al ., ; Gülay et al ., ). All complete nitrifiers known to date are affiliated with Nitrospira sublineage II (Daims et al ., ; van Kessel et al ., ; Pinto et al ., ; Palomo et al ., ). Furthermore, comammox Nitrospira form two divergent clades, referred to as comammox clades A and B, based on phylogenetic analysis of the ammonia monooxygenase (AMO), the enzyme catalysing ammonia oxidation (Daims et al ., ).…”

“…So far, most comammox Nitrospira genomes were obtained from engineered systems (Daims et al ., ; van Kessel et al ., ; Pinto et al ., ; Wang et al ., ; Palomo et al ., ), some of which are characterized by low concentrations of ammonium. Especially in these, comammox Nitrospira appeared to dominate the nitrifying community (Bartelme et al ., ; Pjevac et al ., ; Koch et al ., ), which is in line with the hypothesis that the comammox process is beneficial under substrate‐limited conditions selecting for high growth yields (Costa et al ., ).…”

Long‐term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing

“…One reason for this inconsistent result may be explained by our focus on the active nitrifiers, rather than the composition of the overall community, which exhibited functional redundancy to some extent (Schauss et al, 2009). Unlike canonical Nitrospira, comammox Nitrospira have lost the potential to use external NO 2 − -N (Palomo et al, 2017). S6).…”

A fight for scraps of ammonia

“…That horizontal gene transfer does occur has been shown by analyses 4,14 of the genomes of comammox Nitrospira suggesting that the microbes' ammonia-oxidizing pathway was either transferred to or obtained from betaproteobacterial AOB (β-AOB). Cultured β-AOB have a lower ammonia affinity than N. inopinata, making this a puzzling observation at first sight.…”