Dataset Information

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers.

ABSTRACT: 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.

SUBMITTER: Zhu B

PROVIDER: S-EPMC6636425 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers.

Zhu Baoli B Wang Jiaqi J Bradford Lauren M LM Ettwig Katharina K Hu Baolan B Lueders Tillmann T

Frontiers in microbiology 20190710

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, st ...[more]

PMID: 31354671

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Project description:Row crop production in the agricultural Midwest pollutes waterways with nitrate, and exacerbates climate change through increased emissions of nitrous oxide and methane. Oxygenic denitrification processes in agricultural soils mitigate nitrate and nitrous oxide pollution by short-circuiting the canonical pathway to avoid nitrous oxide formation. Furthermore, many oxygenic denitrifiers employ a nitric oxide dismutase (nod) to create molecular oxygen that is used by methane monooxygenase to oxidize methane in otherwise anoxic soils. The direct investigation of nod genes that could facilitate oxygenic denitrification processes in agricultural sites is limited, with no prior studies investigating nod genes at tile drainage sites. Thus, we performed a reconnaissance of nod genes at variably saturated surface sites, and within a variably to fully saturated soil core in Iowa to expand the known distribution of oxygenic denitrifiers. We identified new nod gene sequences from agricultural soil and freshwater sediments in addition to identifying nitric oxide reductase (qNor) related sequences. Surface and variably saturated core samples displayed a nod to 16S rRNA gene relative abundance of 0.004% to 0.1% and fully saturated core samples had relative nod gene abundance of 1.2%. The relative abundance of the phylum Methylomirabilota increased from 0.6% and 1% in the variably saturated core samples to 3.8% and 5.3% in the fully saturated core samples. The more than 10-fold increase in relative nod abundance and almost 9-fold increase in relative Methylomirabilota abundance in fully saturated soils suggests that potential oxygenic denitrifiers play a greater nitrogen cycling role under these conditions. IMPORTANCE The direct investigation of nod genes in agricultural sites is limited, with no prior studies investigating nod genes at tile drains. An improved understanding of nod gene diversity and distribution is significant to the field of bioremediation and ecosystem services. The expansion of the nod gene database will advance oxygenic denitrification as a potential strategy for sustainable nitrate and nitrous oxide mitigation, specifically for agricultural sites.

Project description:It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g-1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium "Ca Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.

Dataset Information

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers.

Publications

Nitric Oxide Dismutase (<i>nod</i>) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers.

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