Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “
            <i>Candidatus</i>
            Nitrospira nitrosa”

Camejo, Pamela Y.; Domingo, Jorge Santo; McMahon, Katherine D.; Noguera, Daniel R.

doi:10.1128/msystems.00059-17

Cited by 118 publications

(94 citation statements)

References 92 publications

(97 reference statements)

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“…In this search, we found 33 nearly full-length sequences that clustered with the comammox sequences and contained the target sites for both primers (Figure 3), including amoA sequences from comammox metagenomes that have been recently described in the literature. 1–3, 16, 17, 24…”

Section: Resultsmentioning

confidence: 99%

“…An in silico primer-target analysis (Figure 4) shows that N. sp. UW-LDO-01 16 , originally described as a strain of Ca. N. nitrosa, has perfect matches to the newly designed primers targeting this species.…”

Section: Resultsmentioning

confidence: 99%

“…12–15 The amoA of comammox is distinguishable from amoA sequences of AOB and AOA, and thus, it can be used to detect the presence of comammox in environmental samples. 1–3, 16 Recent descriptions of PCR primers targeting the amoA gene of commamox include a primer pair designed specifically for Candidatus ( Ca. ) Nitrospira inopinata, 1 a primer pair designed specifically for a comammox-like clone within a freshwater aquaculture system, 5 a primer collection that differentiates two broad clades of comammox within the Nitrospira genus, 17 and a highly degenerate primer pair attempting to encompass all comammox within Nitrospira .…”

Section: Introductionmentioning

confidence: 99%

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Design and assessment of species-level qPCR primers targeting comammox

Beach

Noguera

2018

Preprint

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14Published PCR primers targeting the ammonia monooxygenase gene (amoA) were applied to 15 samples from activated sludge systems operated with low dissolved oxygen (DO) to quantify total 16 and clade-level Nitrospira that perform complete ammonium oxidation (comammox); however, 17 we found these existing primers resulted in significant artifact-associated non-target amplification. 18This not only overestimated comammox amoA copies but also resulted in numerous false positive 19detections in the environmental samples tested, as confirmed by gel electrophoresis. Therefore, to 20 more accurately quantify known comammox, we designed specific and sensitive primers targeting 21 three candidate species: Candidatus (Ca.) Nitrospira nitrosa, Ca. N. inopinata, and Ca. N. 22nitrificans. The primers were tested with amoA templates of these candidate species, and used to 23 quantify comammox at the species level in low DO activated sludge systems. We found that 24 comammox related to Ca. N. nitrosa were present and abundant in the majority of samples from 25 low DO bioreactors and were not detected in samples from a high DO system. In addition, the 26 greatest abundance of Ca. N. nitrosa was found in bioreactors operated with a long solids retention 27 time. Ca. N. inopinata and Ca. N. nitrificans were only detected sporadically in these samples, 28 indicating a minor role of these comammox in nitrification under low DO conditions. 29 Keywords 30Comammox, Nitrospira, Nitrification, Low dissolved oxygen, Biological nutrient removal, qPCR, 31 Real-time PCR, PCR primers 32All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/348664 doi: bioRxiv preprint first posted online Jun. 15, 2018; 3 Abstract art 33 34 35All rights reserved. No reuse allowed without permission.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Design and assessment of species-level qPCR primers targeting comammox

Beach

Noguera

2018

Preprint

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“…433 amoA qPCR primers revealed comammox at the same plant as comprising 14 to 35% of total amoA 466 via qPCR (Pjevac et al, 2017), still a minority of the overall NH4 + oxidizing community. In a 467 separate study, while developing a bench-scale biological nutrient removal reactor with synthetic 468 feed, researchers at the University of Wisconsin-Madison serendipitously enriched comammox to 469 38% of total Nitrospira, or 5.4% of total normalized metagenomic reads during the first stage of 470 operation (Camejo et al, 2017). Comammox were far more abundant than AOA and AOB in this 471 stage (which together comprised just 0.23% of total reads), suggesting that comammox was the 472 dominant NH4 + oxidizer.…”

Section: Bioreactor Performance 229mentioning

confidence: 99%

ComammoxNitrospiraare the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

Roots¹,

Wang²,

Rosenthal³

et al. 2018

Preprint

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Recent findings show that a subset of bacteria affiliated with Nitrospira, a genus known for its importance in nitrite oxidation for biological nutrient removal applications, are capable of complete ammonia oxidation (comammox) to nitrate. Early reports suggested that they were absent or present in low abundance in most activated sludge processes, and thus likely functionally irrelevant. Here we show the accumulation of comammox Nitrospira in a nitrifying sequencing batch reactor operated at low dissolved oxygen (DO) concentrations. Actual mainstream wastewater was used as influent after primary settling and an upstream pre-treatment process for carbon and phosphorus removal. The ammonia removal rate was stable and exceeded that of the treatment plant’s parallel full-scale high DO nitrifying activated sludge reactor. 16S rRNA sequencing showed a steady accumulation of Nitrospira to 53% total abundance and a decline in conventional ammonia oxidizing bacteria to <1% total abundance over 400+ days of operation. After ruling out other known ammonia oxidizers, qPCR confirmed the accumulation of comammox Nitrospira beginning around day 200, to eventually comprise 94% of all detected amoA and 4% of total bacteria by day 407. Quantitative fluorescence in-situ hybridization confirmed the increasing trend and high relative abundance of Nitrospira. These results demonstrate that comammox can be metabolically relevant to nitrogen transformation in wastewater treatment, and can even dominate the ammonia oxidizing community. Our results suggest that comammox may be an important functional group in energy efficient nitrification systems designed to operate at low DO levels.

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“…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).…”

Section: Introductionmentioning

confidence: 99%

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Koch

Kessel

Lücker

2018

Appl Microbiol Biotechnol

261

148

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Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.Electronic supplementary materialThe online version of this article (10.1007/s00253-018-9486-3) contains supplementary material, which is available to authorized users.

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Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

Cited by 118 publications

References 92 publications

Design and assessment of species-level qPCR primers targeting comammox

Design and assessment of species-level qPCR primers targeting comammox

ComammoxNitrospiraare the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

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