Expressions of alkaline phosphatase genes during phosphate starvation are under positive influences of multiple cell wall hydrolase genes in &lt;i&gt;Bacillus subtilis&lt;/i&gt;

Shen, Yueh-Chi; Hu, Yi-Nei; Shaw, Gordon L.

doi:10.2323/jgam.62.106

Cited by 9 publications

(7 citation statements)

References 22 publications

(29 reference statements)

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“…Another characteristic of comammox Nitrospira is their genetic potential to compete under phosphorous and copper limiting conditions. Comammox Nitrospira genomes contain an alkaline phosphatase (phoD), which has been detected to be highly expressed under phosphorus limitation and starvation in other microorganisms [70,71]. This enzyme was not detected in AOA genomes and is not universal in AOB (putative homologs are present in Nitrosomonas sp.…”

Section: Comparison Between Comammox Nitrospira and Ammonia Oxidizingmentioning

confidence: 99%

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

et al. 2018

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The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss.

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Section: Comparison Between Comammox Nitrospira and Ammonia Oxidizingmentioning

confidence: 99%

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

et al. 2018

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“…Another 374 characteristic of comammox Nitrospira is its potential to compete under phosphorous and 375 copper limiting conditions. Comammox Nitrospira genomes contain an alkaline phosphatase 376 (phoD), which is highly expressed under phosphorus limitation and starvation (42,43). This 377 enzyme was not detected in AOA genomes and is not universal in AOB (putative homologs 378 are present in Nitrosomonas sp.…”

mentioning

confidence: 99%

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

Palomo

Pedersen

Fowler

et al. 2017

Preprint

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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.

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“…The comammox bacteria metabolism pathway is complex and can adapt to different nutrient substrates (Daims et al, 2015;Van Kessel et al, 2015;Shen et al, 2016;Kits et al, 2017;Han et al, 2019;Liu et al, 2020a;Wang et al, 2021;Zhao et al, 2021). Liu et al (2020a) found that comammox bacteria contribute 34%-87% of nitrification in a typical oligotrophic environment with high pH and low temperature along the Yangtze River.…”

Section: Enzymes and Metabolismmentioning

confidence: 99%

Research progress and prospects of complete ammonia oxidizing bacteria in wastewater treatment

Luo

Peng²,

Liu

et al. 2022

Front. Environ. Sci. Eng.

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Complete ammonia oxidizing bacteria, or comammox bacteria (CAOB), can oxidize ammonium to nitrate on its own. Its discovery revolutionized our understanding of biological nitrification, and its distribution in both natural and artificial systems has enabled a reevaluation of the relative contribution of microorganisms to the nitrogen cycle. Its wide distribution, adaptation to oligotrophic medium, and diverse metabolic pathways, means extensive research on CAOB and its application in water treatment can be promoted. Furthermore, the energy-saving characteristics of high oxygen affinity and low sludge production may also become frontier directions for wastewater treatment. This paper provides an overview of the discovery and environmental distribution of CAOB, as well as the physiological characteristics of the microorganisms, such as nutrient medium, environmental factors, enzymes, and metabolism, focusing on future research and the application of CAOB in wastewater treatment. Further research should be carried out on the physiological characteristics of CAOB, to analyze its ecological niche and impact factors, and explore its application potential in wastewater treatment nitrogen cycle improvement.

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Expressions of alkaline phosphatase genes during phosphate starvation are under positive influences of multiple cell wall hydrolase genes in <i>Bacillus subtilis</i>

Cited by 9 publications

References 22 publications

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

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

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

Research progress and prospects of complete ammonia oxidizing bacteria in wastewater treatment

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