Microbial nitrate respiration – Genes, enzymes and environmental distribution

Kraft, Beate; Strous, Marc; Tegetmeyer, Halina E.

doi:10.1016/j.jbiotec.2010.12.025

Cited by 355 publications

(274 citation statements)

References 237 publications

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“…Strains PV-1 and M34 were both isolated using medium in which ammonium was the sole nitrogen source, and genomic analysis indicates that they, as well as 13 SAGs, encode the genes necessary to utilize ammonium (Figure 7 and Supplementary Table S14). In addition, 11 SAGs have nitrate reductases, all of which show structural similarities to assimilatory nitrate reductases (Moreno-Vivián et al, 1999;Kraft et al, 2011). Nine SAGs contain nitrite reductases (both large and small subunits).…”

Section: Nitrogen Metabolismmentioning

confidence: 99%

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

et al. 2014

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The Zetaproteobacteria are a candidate class of marine iron-oxidizing bacteria that are typically found in high iron environments such as hydrothermal vent sites. As much remains unknown about these organisms due to difficulties in cultivation, single-cell genomics was used to learn more about this elusive group at Loihi Seamount. Comparative genomics of 23 phylogenetically diverse single amplified genomes (SAGs) and two isolates indicate niche specialization among the Zetaproteobacteria may be largely due to oxygen tolerance and nitrogen transformation capabilities. Only Form II ribulose 1,5-bisphosphate carboxylase (RubisCO) genes were found in the SAGs, suggesting that some of the uncultivated Zetaproteobacteria may be adapted to low oxygen and/or high carbon dioxide concentrations. There is also genomic evidence of oxygen-tolerant cytochrome c oxidases and oxidative stress-related genes, indicating that others may be exposed to higher oxygen conditions. The Zetaproteobacteria also have the genomic potential for acquiring nitrogen from numerous sources including ammonium, nitrate, organic compounds, and nitrogen gas. Two types of molybdopterin oxidoreductase genes were found in the SAGs, indicating that those found in the isolates, thought to be involved in iron oxidation, are not consistent among all the Zetaproteobacteria. However, a novel cluster of redox-related genes was found to be conserved in 10 SAGs as well as in the isolates warranting further investigation. These results were used to isolate a novel iron-oxidizing Zetaproteobacteria. Physiological studies and genomic analysis of this isolate were able to support many of the findings from SAG analyses demonstrating the value of these data for designing future enrichment strategies.

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Section: Nitrogen Metabolismmentioning

confidence: 99%

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

et al. 2014

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“…Other nitrogen respiration pathways such as anaerobic ammonium oxidation (anammox), which is the transformation of nitrite and ammonium into dinitrogen gas, and dissimilatory nitrate reduction to ammonium (DNRA), which is the reduction of nitrate to nitrite followed by the reduction of nitrite to ammonium, have also been proven to contribute a significant proportion to nitrate removal in various environments (Kartal et al, 2007;Smith et al, 2007;Dong et al, 2011). Favorable conditions for these pathways are hypothesized to depend mainly on the concentration and type of electron donor, the amount of inorganic nitrogen compounds present, along with the redox potential found in those systems (van Rijn et al, 2006;Kraft et al, 2011). To date, there had been several reports on the presence of anammox bacteria in aquaculture treatment systems that use degraded sludge as the substrates for denitrification (Tal et al, 2006;Lahav et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Denitrification and Dissimilatory Nitrate Reduction to Ammonium (DNRA) Activities in Freshwater Sludge and Biofloc from Nile Tilapia Aquaculture Systems

Chutivisut

Pungrasmi

Powtongsook

2014

J. of Wat. ^|^ Envir. Tech.

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Suspended organic sludge from freshwater and biofloc Nile tilapia systems were examined for the presence of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) activities under nitrate and sulfide stimulation. Initial nitrate concentrations at 25 and 100 mg NO 3 --N/L were added to the freshwater sludge and biofloc samples to simulate low and high nitrate levels that are normally found in aquaculture systems. The results showed that freshwater sludge and biofloc both had denitrifying activity immediately after nitrate addition. However, ammonium accumulated in the biofloc reactors but not in the freshwater reactors, indicating the activity of DNRA in the high C/N biofloc particles. The influence of sulfide on nitrate reduction was also studied by adding different concentrations of sulfide along with 100 mg NO 3 --N/L. The results showed that elevated sulfide concentrations partially inhibited denitrification in the freshwater sludge and caused nitrite and ammonium accumulation, in which ammonium formation was probably responsible by DNRA activity. In sulfide-added biofloc reactors, ammonium accumulated at the same level as found in the biofloc reactors without sulfide. Therefore, DNRA bacteria residing in the biofloc aquaculture system were more likely to be heterotrophs that did not use sulfide as their electron donor.

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“…4 Indeed, even if it is not exhaustive yet, the large panel of enzymatic activity they catalyze make them key players in fundamental geochemical cycles and efficient tools for bioremediation and depollution. [8][9][10][11] In bacteria, among the 3 families of molybdoenzymes (the xanthine oxidase (XO) family, the sulfite oxidase (SO) family and the dimethyl sulfoxide (DMSO) reductase family) only members of the SO family can be matured without the support of auxiliary proteins while molybdoenzymes of the 2 others have been described to require specific accessory proteins dedicated to their biogenesis. 12,13 To study the maturation of molybdoenzymes of the DMSO reductase family, we have chosen to dissect the maturation process of TorA.…”

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confidence: 99%

Chaperones in maturation of molybdoenzymes: Why specific is better than general?

et al. 2016

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Molybdoenzymes play essential functions in living organisms and, as a result, in various geochemical cycles. It is thus crucial to understand how these complex proteins become highly efficient enzymes able to perform a wide range of catalytic activities. It has been established that specific chaperones are involved during their maturation process. Here, we raise the question of the involvement of general chaperones acting in concert with dedicated chaperones or not.

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Microbial nitrate respiration – Genes, enzymes and environmental distribution

Cited by 355 publications

References 237 publications

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

Denitrification and Dissimilatory Nitrate Reduction to Ammonium (DNRA) Activities in Freshwater Sludge and Biofloc from Nile Tilapia Aquaculture Systems

Chaperones in maturation of molybdoenzymes: Why specific is better than general?

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