Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the Rhizosphere of Seagrass
            <i>Enhalus acodoides</i>

Ling, Juan; Lin, Liyun; Zhang, Yanying; Lin, Xiancheng; Ahamad, Manzoor; Zhou, Wan; Dong, Junde

doi:10.1128/genomea.01412-16

Cited by 7 publications

(2 citation statements)

References 8 publications

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“…Marinobacter spp. are ubiquitous in marine environments, being found in different depths in the oceans and marine ecosystems ( Kaye & Baross, 2000 ; Yoon et al, 2003 ) and so far, three strains of M. hydrocarbonoclasticus had its genome sequenced ( Grimaud et al, 2012 ; Ling et al, 2017 ; Singer et al, 2011 ) (note that Marinobacter aquaeolei is a M. hydrocarbonoclasticus strain Marquez & Ventosa, 2005 ). This microorganism is proposed to have a high impact on the different biogeochemical cycles ( Singer et al, 2011 ), including the N-cycle, and have a versatile metabolism in terms of carbon source and can use either nitrate/nitrite and/or oxygen as electron acceptors.…”

Section: Introductionmentioning

confidence: 99%

Genomic organization, gene expression and activity profile ofMarinobacter hydrocarbonoclasticusdenitrification enzymes

Carreira

Mestre

Nunes

et al. 2018

PeerJ

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BackgroundDenitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab.MethodsBioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5.ResultsThe bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h).DiscussionM. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.

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Section: Introductionmentioning

confidence: 99%

Genomic organization, gene expression and activity profile ofMarinobacter hydrocarbonoclasticusdenitrification enzymes

Carreira

Mestre

Nunes

et al. 2018

PeerJ

View full text Add to dashboard Cite

show abstract

“…Marinobacter spp. are ubiquitous in marine environments, being found in different depths in the oceans and marine ecosystems (Kaye & Baross 2000;Yoon et al 2003) and so far, three strains of M. hydrocarbonoclasticus had its genome sequenced (Grimaud et al 2012;Ling et al 2017;Singer et al 2011) (note that Marinobacter aquaeolei is a M. hydrocarbonoclasticus strain (Marquez & Ventosa 2005)). This microorganism is proposed to have a high impact on the different biogeochemical cycles (Singer et al 2011), including the N-cycle, and have a versatile metabolism in terms of carbon source and can use either nitrate/nitrite and/or oxygen as electron acceptors.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes (v0.2)"

Villemur¹

2018

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Background. Denitrificationis one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab.Methods. Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results. The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the coexistence of genes encoding a q-and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch-or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion . M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.

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Genomic approaches for the investigation of seagrass rhizosphere microbiome and bioprospecting potential: a field study from Chilika Lagoon, Odisha, India

Mohapatra,

Dash,

Rastogi

2024

Applications of Metagenomics

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Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the Rhizosphere of Seagrass Enhalus acodoides

Cited by 7 publications

References 8 publications

Genomic organization, gene expression and activity profile ofMarinobacter hydrocarbonoclasticusdenitrification enzymes

Genomic organization, gene expression and activity profile ofMarinobacter hydrocarbonoclasticusdenitrification enzymes

Peer Review #1 of "Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes (v0.2)"

Genomic approaches for the investigation of seagrass rhizosphere microbiome and bioprospecting potential: a field study from Chilika Lagoon, Odisha, India

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