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:10.1101/144600

Cited by 11 publications

(24 citation statements)

References 86 publications

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“…It has been found that AOA, AOB and anammox bacteria can coexist in habitats, such as soils, rivers, lake sediments and marine sediments (Kuypers et al ; Chen and Gu ; Wang et al ). Some studies indicated that anammox bacteria can also coexist with comammox bacteria (Annavajhala et al ), and these four types of micro‐organisms were all detected in a sequencing batch reactor (SBR) (Camejo et al ). However, these micro‐organisms all require ammonium as a substrate for their reaction, and thus there may be a complex competition–collaboration relationship between them.…”

Section: Introductionmentioning

confidence: 99%

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Xu¹,

Lü

Liu³

et al. 2020

J Appl Microbiol

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Aims Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia‐oxidizing microbe exists in urban lakes and to determine the factors influencing its existence. Methods and Results This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia‐oxidizing micro‐organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co‐existed with ammonia‐oxidizing archaea (AOA), ammonia‐oxidizing bacteria (AOB) and anaerobic ammonia‐oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 108, 1·07 × 108, 3·24 × 107 and 3·21 × 1011 copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria. Conclusions Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments. Significance and Impact of the Study Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

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Section: Introductionmentioning

confidence: 99%

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Xu¹,

Lü

Liu³

et al. 2020

J Appl Microbiol

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“…Intriguingly, based on 16S rRNA gene all the three CAOB strains were phylogenetically affiliated with genus Nitrospira , which was the most abundant and widespread genus of NOB (Daims et al, 2016; Koch et al, 2015). However, CAOB were confirmed to possess a whole set of nitrifying genes encoding for ammonia monooxygenase (AMO), hydroxylamine dehydrogenase (HAO) and nitrite oxidoreductase (NXR), providing strong evidences for the capability of performing complete ammonia oxidation to nitrate via nitrite (Daims et al 2015; van Kessel et al 2015; Camejo et al 2017). CAOB amoA gene formed a distinct phylogenetic cluster with a low similarity to the canonical AOB amoA , suggesting it was an ideal phylogenetic biomarker to identify and quantify CAOB in complex microbial communities.…”

Section: Introductionmentioning

confidence: 99%

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

Zhao

Huang

Wang

et al. 2018

Preprint

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1were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal 3 2 zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that 3 3 clade A existed in all the five types of ecosystems, while clade B were only detected in soil and 3 4 sediment samples. Four sub-clusters were further classified within clade A, in which N. 3 5 nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized 3 6 soil cluster was the primary constitute in soils. Moreover, the niche specialization between 3 7 different CAOB species and the environmental conditions were supposed to be the primary 3 8 driven force to shape the diversity and community of CAOB. This study provided a strong 3 9 evidence in support of the ubiquities and high abundances of CAOB in various environmental 4 0 ecosystems and highlighted the significance of including CAOB as the new member of AOMs 4 1 to re-evaluate the biogeochemical nitrogen cycle. 4 2 4 3

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“…Due to different nitrogen sources, nxr in reactor SA (TPM = 5099) outnumbered that in reactor SB (TPM = 4071) during the nitrification process, and the amo (TPM = 3915) ( Fig. 6), ure (TPM = 3638) and urt (TPM = 4106) (Table S2) [14]. In this study, the regulation of different nitrogen sources on the enrichment of comammox was shown.…”

Section: Structural Differences In Microbial Communitiesmentioning

confidence: 57%

“…Pinto et al detected urt and ure on the comammox genome from a biological filter [10]. Metagenomic data showed that three typical comammox enrichments (pure cultures) contained amo, nxr, urt and ure [13,14]. urt and ure were only observed in several AOA and AOB [15][16][17], so fewer number of AOA and AOB could hydrolyze urea in the cell [18,19].…”

Section: Introductionmentioning

confidence: 99%

“…urt and ure were only observed in several AOA and AOB [15][16][17], so fewer number of AOA and AOB could hydrolyze urea in the cell [18,19]. In addition, comammox contained urtABCDE, a high-affinity urea transporter, which indicated that it can grow at low urea concentration [14,20]. The urtABCDE may also cause the niche differentiation of comammox, AOA, and AOB, which indicated that urea could be used as a nitrogen source to regulate the ammonia-oxidizing community.…”

Section: Introductionmentioning

confidence: 99%

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Multidimensional Reveal of Nitrogen Regulation on Comammox

Zhao

Yang

et al. 2020

Preprint

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Background The discovery of complete ammonia oxidizer (comammox) was groundbreaking. Comammox can use ammonia as the sole nitrogen source and turn it to nitrate. Moreover, genomic data indicated that comammox contained genes which can metabolize urea and nitrite. However, the feasibility of enriching comammox with urea and nitrite in long term has not been proved. This study enriched comammox’s culture by using nitrite in reactor SA and urea in reactor SB. Results The nitrification rate of reactor SB (1.29 mg N·g -1 biofilm · d -1 ) was higher than that in reactor SA (0.6 mg N · g -1 biofilm · d -1 ) at the 390 th day. Comammox outnumbered ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in both reactor SA (9.04 × 10 9 copies / g biofilm) and reactor SB (5.34×10 10 copies/ g biofilm). In reactor SA, comammox’s amoA accounted for 92% of the total amoA, which was higher than that in reactor SB (85%). However, the percentage of comammox (4%) in total bacteria was much lower than reactor SB (14%). The results of metagenomic sequencing showed that all the pathways of nitrogen cycle including nitrification, nitrogen fixation, denitrification, assimilation nitrate reduction, and dissimilation nitrate reduction can be detected in both reactor SA and reactor SB except the anammox pathway. The genes related to nitrite oxidation and nitrate reduction in reactor SA (TPM = 5099; TPM = 3329) was higher than that of in reactor SB (TPM = 4071; TPM = 2984), presumably due to the demand of turning nitrite to nitrate and turning nitrate to ammonia. While genes related to ammonia oxidation and urea metabolism in reactor SB (TPM = 3915; TPM = 3638) was higher than that in reactor SA (TPM = 2708; TPM = 3002). Conclusion Nitrite and urea can regulate the enrichment culture of comammox by converting its metabolic pathway. Using nitrite as sole nitrogen source can improve the proportion comammox’s amoA in total amoA while using urea as the sole nitrogen source may increase comammox’s proportion in total bacteria. These results can accelerate the enrichment of comammox and facilitate the promotion of comammox’s engineering operation.

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Genome-enabled insights into the ecophysiology of the comammox bacteriumCandidatusNitrospira nitrosa

Cited by 11 publications

References 86 publications

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Diversity and abundance of comammox bacteria in the sediments of an urban lake

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

Multidimensional Reveal of Nitrogen Regulation on Comammox

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