Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater‐fed rapid sand filter communities

Abstract

The recent discovery of completely nitrifying Nitrospira demands a re-examination of nitrifying environments to evaluate their contribution to nitrogen cycling. To approach this challenge, tools are needed to detect and quantify comammox Nitrospira. We present primers for the simultaneous quantification and diversity assessement of both comammox Nitrospira clades. The primers cover a wide range of comammox diversity, spanning all available high quality sequences. We applied these primers to 12 groundwater-fed rapid sand filters, and found comammox Nitrospira to be abundant in all filters. Clade B comammox comprise the majority (∼75%) of comammox abundance in all filters. Nitrosomonadaceae were present in all filters, although at low abundance (mean = 1.8%). Ordination suggests that temperature impacts the structure of nitrifying communities, and in particular that increasing temperature favours Nitrospira. The nitrogen content of the filter material, sulfate concentration and surface ammonium loading rates shape the structure of the comammox guild in the filters. This work provides an assay for simultaneous detection and diversity assessment of clades A and B comammox Nitrospira, expands our current knowledge of comammox Nitrospira diversity and demonstrates a key role for comammox Nitrospira in nitrification in groundwater-fed biofilters.

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

“…For PCR-based approaches, a widely used functional marker of aerobic ammonia oxidation is the amoA gene. Recently, several different PCR assays and primer sets targeting comammox amoA genes were developed (Bartelme et al 2017; Fowler et al 2018; Pjevac et al 2017; Wang et al 2017). Although the two-step PCR approach of Wang and co-workers is a valuable tool to identify potential novel members of the copper containing membrane monooxygenase family (Wang et al 2017), other newly developed comammox amoA -targeting qPCR approaches with near-complete group coverages are more suitable to analyze comammox distribution and abundance in environmental samples (Fowler et al 2018; Pjevac et al 2017).…”

“…Recently, several different PCR assays and primer sets targeting comammox amoA genes were developed (Bartelme et al 2017; Fowler et al 2018; Pjevac et al 2017; Wang et al 2017). Although the two-step PCR approach of Wang and co-workers is a valuable tool to identify potential novel members of the copper containing membrane monooxygenase family (Wang et al 2017), other newly developed comammox amoA -targeting qPCR approaches with near-complete group coverages are more suitable to analyze comammox distribution and abundance in environmental samples (Fowler et al 2018; Pjevac et al 2017). By applying PCR assays that target comammox clade A and B amoA separately, complete nitrifiers could be detected in a wide range of environmental samples, including man-made systems like drinking and wastewater treatment plants, and several natural habitats, like forest and paddy field soils, rice rhizosphere, and lake sediments (Pjevac et al 2017).…”

“…In addition to environmental distribution studies, the relative abundance of comammox bacteria compared to canonical ammonia oxidizers has been explored in several ecosystems to elucidate their potential contribution to nitrification. Although large-scale surveys comparing the abundances of ammonia-oxidizing guilds are still missing, first quantitative studies showed co-occurrence of all three ammonia-oxidizing guilds with varying abundance patterns in different habitats (Bartelme et al 2017; Fowler et al 2018; Pjevac et al 2017; Orellana et al 2018). In engineered systems, like RAS biofilters and groundwater-fed rapid sand filters, comammox Nitrospira outnumbered AOB and AOA (Bartelme et al 2017; Fowler et al 2018).…”

“…In addition, analyzing metagenome-assembled genomes (MAGs) of clade B comammox Nitrospira gave first genomic insights into this group so far missing a cultured representative (Orellana et al 2018; Palomo et al 2018). Since the discovery of complete nitrifying Nitrospira , numerous studies have addressed their environmental distribution and abundance (e.g., Bartelme et al 2017; Fowler et al 2018; Hu and He 2017; Orellana et al 2018; Pjevac et al 2017) as well as their potential metabolic capabilities by (meta) genomic analyses (e.g., Camejo et al 2017; Orellana et al 2018; Palomo et al 2016; Palomo et al 2018; Wang et al 2017). Additionally, physiological investigations of the first comammox pure culture revealed vital insights into the nitrification kinetics of complete compared to canonical nitrifiers (Kits et al 2017).…”

Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes

“…Beside the proposed adaptation of comammox- Nitrospira to microaerophilic and low substrate fluxes (Lawson and Lücker 2018), Fowler et al . (2018) identified temperature to have a positive impact on Nitrospira in rapid sand filters. However, the authors could not distinguish if comammox and nitrite-oxidizing taxa were affected.…”