A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria

Pinchbeck, Benjamin J.; Soriano-Laguna, Manuel J.; Sullivan, Matthew J.; Luque-Almagro, Víctor M.; Rowley, Gary; Ferguson, Stuart J.; Roldán, María Dolores; Richardson, David J.; Gates, Andrew J.

doi:10.1111/mmi.14239

Cited by 20 publications

(9 citation statements)

References 23 publications

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“…S29-S31 ). The early onset of NO 3 − reduction, before depletion of oxygen, suggesting that NasC was active under oxic conditions in this isolate, which was also reported for Paracoccus denitrificans (Pinchbeck et al 2019). Of the two isolates, CB-01 makes for a particularly promising N 2 O-reducing soil inoculant.…”

Section: Resultssupporting

confidence: 83%

A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture

Ormaasen

Duffner

et al. 2021

Preprint

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Manipulating soil metabolism by heavy inoculation with microbes is deemed realistic if waste from anaerobic digestion (digestate) is utilized as substrate and vector, but requires organisms that can grow both in digestate and soil (=generalist). We designed a strategy to enrich and isolate such generalist N2O-respiring bacteria (NRB) in soil and digestate, to provide inoculum for reducing N2O-emissions from agricultural soil. Sequential anaerobic enrichment cultures were provided with a small dose of O2 and unlimited N2O, alternating between sterilized digestate and soil as substrates. The cultures were monitored for gas kinetics and community composition (16SrDNA), and cluster-analysis identified generalist-OTUs which became dominant, digestate/soil-specialists which did not, and a majority that were diluted out. Several NRBs circumscribed by generalist-OTU’s were isolated, genome sequenced to screen for catabolic capacity, and phenotyped, to assess their capacity as N2O-sinks in soil. The two isolates Cloacibacterium sp., carrying only N2O-reductase (Clade-II) and Pseudomonas sp., with full-fledged denitrification-pathway, were both very effective N2O-sinks in soil, with Pseudomonas sp., showing a long-lasting sink effect, suggesting better survival in soil. This avenue for utilizing waste to bioengineer the soil microbiota holds promise to effectively combat N2O-emissions but could also be utilized for enhancing other metabolic functions in soil.Graphical abstract

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Section: Resultssupporting

confidence: 83%

A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture

Ormaasen

Duffner

et al. 2021

Preprint

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“…together through a corporate chaperone encoded by narJ in the Paracoccus denitrification strain [46]. However, though this study proved the aerobic nitrate removal was caused by the respiratory nitrate reductases under transcriptional results, the nitrate distribution mechanism in assimilation is still unclear.…”

Section: Single Factor Experimentsmentioning

confidence: 73%

Nitrogen Removal Performance and Metabolic Pathways Analysis of a Novel Aerobic Denitrifying Halotolerant Pseudomonas balearica Strain RAD-17

et al. 2020

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An aerobic denitrification strain, Pseudomonas balearica RAD-17, was identified and showed efficient inorganic nitrogen removal ability. The average NO3−-N, NO2−-N, and total ammonium nitrogen (TAN) removal rate (>95% removal efficiency) in a batch test was 6.22 mg/(L∙h), 6.30 mg/(L∙h), and 1.56 mg/(L∙h), respectively. Meanwhile, optimal incubate conditions were obtained through single factor experiments. For nitrogen removal pathways, the transcriptional results proved that respiratory nitrate reductases encoded by napA, which was primarily performed in aerobic denitrification and cell assimilation, were conducted by gluS and gluD genes for ammonium metabolism. In addition, adding the strain RAD-17 into actual wastewater showed obvious higher denitrification performance than in the no inoculum group (84.22% vs. 22.54%), and the maximum cell abundance achieved 28.5 ± 4.5% in a ratio of total cell numbers. Overall, the efficient nitrogen removal performance plus strong environmental fitness makes the strain RAD-17 a potential alternative for RAS (recirculating aquaculture system) effluent treatment.

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“…There is increasing evidence that these types of structures provide opportunities to regulate DNA metabolism in bacteria [51,[75][76][77]. The genome of the bacterium Paracoccus denitrificans PD1222 has a relatively high G + C content (∼67%) and a range of biophysical, molecular, and microbiological studies show that targeting of four-stranded structures can be controlled under cellular conditions, allowing regulation of expression of some genes [48,[78][79][80][81].…”

Section: Biochemical and Cellular Impacts Of Simple Repeat Sequences mentioning

confidence: 99%

Structures and stability of simple DNA repeats from bacteria

Brázda

Fojta

Bowater

2020

Biochemical Journal

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DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

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A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria

Cited by 20 publications

References 23 publications

A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture

A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture

Nitrogen Removal Performance and Metabolic Pathways Analysis of a Novel Aerobic Denitrifying Halotolerant Pseudomonas balearica Strain RAD-17

Structures and stability of simple DNA repeats from bacteria

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A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria

Cited by 20 publications

References 23 publications

A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture

A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture

Nitrogen Removal Performance and Metabolic Pathways Analysis of a Novel Aerobic Denitrifying Halotolerant Pseudomonas balearica Strain RAD-17

Structures and stability of simple DNA repeats from bacteria

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A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture

A novel dual enrichment strategy provides soil- and digestate-competent N₂O-respiring bacteria for mitigating climate forcing in agriculture