Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers
Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic d...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.01577/full |
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| author | Baoli Zhu Baoli Zhu Baoli Zhu Jiaqi Wang Lauren M. Bradford Katharina Ettwig Baolan Hu Tillmann Lueders Tillmann Lueders |
| author_facet | Baoli Zhu Baoli Zhu Baoli Zhu Jiaqi Wang Lauren M. Bradford Katharina Ettwig Baolan Hu Tillmann Lueders Tillmann Lueders |
| author_sort | Baoli Zhu |
| collection | DOAJ |
| description | Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal. |
| first_indexed | 2024-12-12T20:49:52Z |
| format | Article |
| id | doaj.art-525552ccdb204bfdbfd63db0ecbbf581 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-12T20:49:52Z |
| publishDate | 2019-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-525552ccdb204bfdbfd63db0ecbbf5812022-12-22T00:12:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-07-011010.3389/fmicb.2019.01577460339Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic DenitrifiersBaoli Zhu0Baoli Zhu1Baoli Zhu2Jiaqi Wang3Lauren M. Bradford4Katharina Ettwig5Baolan Hu6Tillmann Lueders7Tillmann Lueders8Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, GermanyDepartment of Microbiology, Radboud University Nijmegen, Nijmegen, NetherlandsChair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, GermanyDepartment of Environmental Engineering, Zhejiang University, Hangzhou, ChinaInstitute of Groundwater Ecology, Helmholtz Zentrum München, Munich, GermanyDepartment of Microbiology, Radboud University Nijmegen, Nijmegen, NetherlandsDepartment of Environmental Engineering, Zhejiang University, Hangzhou, ChinaInstitute of Groundwater Ecology, Helmholtz Zentrum München, Munich, GermanyChair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, GermanyOxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.https://www.frontiersin.org/article/10.3389/fmicb.2019.01577/fullnitric oxide dismutationoxygenic methanotrophsoxygenic denitrificationNC10nodpmoA |
| spellingShingle | Baoli Zhu Baoli Zhu Baoli Zhu Jiaqi Wang Lauren M. Bradford Katharina Ettwig Baolan Hu Tillmann Lueders Tillmann Lueders Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers Frontiers in Microbiology nitric oxide dismutation oxygenic methanotrophs oxygenic denitrification NC10 nod pmoA |
| title | Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers |
| title_full | Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers |
| title_fullStr | Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers |
| title_full_unstemmed | Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers |
| title_short | Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers |
| title_sort | nitric oxide dismutase nod genes as a functional marker for the diversity and phylogeny of methane driven oxygenic denitrifiers |
| topic | nitric oxide dismutation oxygenic methanotrophs oxygenic denitrification NC10 nod pmoA |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.01577/full |
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