Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster

Cotto, Irmarie; Vilardi, Katherine J.; Huo, Linxuan; Fogarty, Emily C.; Khunjar, Wendell; Wilson, Christopher; Clippeleir, Haydée De; Gilmore, Kevin R.; Bailey, Erika; Lücker, Sebastian; Pinto, Ameet J.

doi:10.1016/j.watres.2022.119497

Cited by 14 publications

(26 citation statements)

References 88 publications

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“…However, these Nitrospira MAGs were at much lower abundances in this study (8.35 ± 1.91 RPKM) compared with the previous study (55.56 ± 14.71 RPKM). 9 The decrease in Nitrospira abundance could be the reason why several of the previously assembled MAGs could not be assembled in the current study, despite the fact that five out of seven of the previously assembled Nitrospira MAGs had a breadth of coverage of 90% using reads from this study (Figure 5A). Therefore, the relative abundance of all nitrifying groups was calculated from a set of dereplicated MAGs recovered from both studies (Table SI-3).…”

Section: Environmental Science and Technologymentioning

confidence: 65%

“…Our previous work demonstrated that comammox bacteria are most prevalent in nitrogen removal systems treating wastewater with an attached growth phase or long solids retention times, and they often cooccur with strict ammonia oxidizing bacteria (AOB) and Nitrospira-NOB. 8 Further, a large proportion of comammox bacteria detected in wastewater systems, including those in our past studies, 8,9 belong to clade A1 comammox bacteria and are affiliated with Ca. Nitrospira nitrosa-like populations.…”

Section: ■ Introductionmentioning

confidence: 66%

“…MAGs associated with Brocadia (n = 2) and Nitrospira (n = 3), were obtained from biomass attached to IFAS media, even though anammox bacteria were not found in our past study 8,9 (Table 1). Nitrospira and Brocadia MAGs represented 6.53 ± 0.34 and 6.25 ± 1.33% of total reads in the sample, respectively.…”

Section: Environmental Science and Technologymentioning

confidence: 82%

“…44 No comammox bacteria or AOB (e.g., Nitrosomonas) MAGs were assembled from this sample. Therefore, the amoA gene sequences found in the metagenomic assembly were aligned using BLAST with the comammox (n = 2) and Nitrosomonas (n = 9) MAGs previously obtained from the same IFAS system (Cotto 2023) to verify whether these populations were still present. A maximum likelihood phylogenetic tree of Nitrospiracomammox and Nitrosomonas, based on the amoA gene, was constructed by aligning them with MUSCLE v3.8.1551, followed by construction of the tree using IQ-TREE v2.0.3.…”

Section: ■ Introductionmentioning

confidence: 99%

“…A maximum likelihood phylogenetic tree of Nitrospiracomammox and Nitrosomonas, based on the amoA gene, was constructed by aligning them with MUSCLE v3.8.1551, followed by construction of the tree using IQ-TREE v2.0.3. 45 To calculate the relative abundances of the nitrifying bacteria, MAGs generated from this and the past study 9 were grouped and dereplicated using drep v2.5.4 46 at 95% ANI, with completeness and contamination thresholds set to 50 and 10%, respectively (Table SI-3). Only MAGs with breadth of coverage (proportion of the genome covered by at least one read) higher than 50% in each sample were used to calculate relative abundances (Table SI-5).…”

Section: ■ Introductionmentioning

confidence: 99%

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Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process

Vilardi

Cotto

Bachmann

et al. 2023

Environ. Sci. Technol.

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Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 – 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.

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Section: Environmental Science and Technologymentioning

confidence: 65%