A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Yang, Jixian; Feng, Liang; Pi, Shanshan; Cui, Di; Ma, Fang; Zhao, He-Ping; Li, Ang

doi:10.1016/j.scitotenv.2020.139080

Cited by 181 publications

(48 citation statements)

References 139 publications

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“…The ability of aerobic denitrification is widely distributed among prokaryotic taxa such as Paracoccus, Pseudomonas, Marinobacter, and Achromobacter, as well as 1 https://lpsn.dsmz.de/genus/halomonas some eukaryotes in various natural and engineered ecosystems (Ji et al, 2015;He et al, 2016;Liu et al, 2016bLiu et al, , 2018Luque-Almagro et al, 2017). Most of our current knowledge about aerobic denitrification is related to the nitrogen removal characteristics of single strains, the expression patterns of functional genes, and practical applications, as well as electron transfer (Yang et al, 2020). Denitrification has been recognized as an important functional trait of the genus Halomonas, as many species have been described as denitrifiers, and some even as aerobic denitrifiers (González-Domenech et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Wang

Shao

2021

Front. Microbiol.

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Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the “H. desiderata group.” To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the “H. desiderata group,” in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the “H. desiderata group,” while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

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Section: Introductionmentioning

confidence: 99%

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Wang

Shao

2021

Front. Microbiol.

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“…Among these categories, cellular function of electron transport and consumption through the electron transfer chains (ETC) are considered to be essential for aerobic denitrification [ 34 ]. The canonical ETC system consists of NADH dehydrogenase (complex I), succinic dehydrogenase (complex II), quinone pool, the bc 1 complex (complex III), cytochrome c, and terminal oxidase (complex IV) [ 35 , 36 ]. It was found that there were complete components of ETC systems in the chromosome of JD-014, and most of the key DEGs related to electron transport were up-regulated in YE50 and YE300 ( Table S1 ).…”

Section: Resultsmentioning

confidence: 99%

A Novel Regulator Participating in Nitrogen Removal Process of Bacillus subtilis JD-014

Yang

Shi

Yang

et al. 2021

IJMS

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Aerobic denitrification is considered as a promising biological method to eliminate the nitrate contaminants in waterbodies. However, the molecular mechanism of this process varies in different functional bacteria. In this study, the nitrogen removal characteristics for a newly isolated aerobic denitrifier Bacillus subtilis JD-014 were investigated, and the potential functional genes involved in the aerobic denitrification process were further screened through transcriptome analysis. JD-014 exhibited efficient denitrification performance when having sodium succinate as the carbon source with the range of nitrate concentration between 50 and 300 mg/L. Following the transcriptome data, most of the up-regulated differentially expressed genes (DEGs) were associated with cell motility, carbohydrate metabolism, and energy metabolism. Moreover, gene nirsir annotated as sulfite reductase was screened out and further identified as a regulator participating in the nitrogen removal process within JD-014. The findings in present study provide meaningful information in terms of a comprehensive understanding of genetic regulation of nitrogen metabolism, especially for Bacillus strains.

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“…3 ) as an electron acceptor in a four-step reductase-dependent process composed of the sequential formation of NO À 2 , NO and N 2 O and the final release of N 2 (Yang et al, 2020). CuNiRs are periplasmic enzymes that catalyze the reduction of NO À 2 by copper(I) with the subsequent addition of two protons to form water and NO as follows (Eady & Hasnain, 2003):…”

Section: Copper Nitrite Reductasementioning

confidence: 99%

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Schröder

Meilleur

2021

Acta Cryst Sect D Struct Biol

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Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

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A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Cited by 181 publications

References 139 publications

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

A Novel Regulator Participating in Nitrogen Removal Process of Bacillus subtilis JD-014

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

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