Refined NrfA Phylogeny Improves PCR-Based
            <i>nrfA</i>
            Gene Detection

Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils.

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“…4), as noted before (36). However, the dominant soil taxa were restricted to two phyla, the Deltaproteobacteria and Verrucomicrobia (Fig.…”

Section: Resultssupporting

confidence: 73%

Global biogeography of microbial nitrogen-cycling traits in soil

Nelson

Martiny

2016

Proc. Natl. Acad. Sci. U.S.A.

400

232

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“…NrfA is widely present across the Gamma-, Delta-, and Epsilonproteobacteria (16) and in other phyla, such as Firmicutes and Bacteroidetes (18,19), and has been well studied in nitrate-respiring organisms, such as Desulfovibrio desulfuricans (20), Escherichia coli (21), and Wolinella succinogenes (22). The nrfA gene is associated with either nrfH, as seen in Delta-and Epsilonproteobacteria, or nrfBCD, as seen in the Gammaproteobacteria, and these accessory genes help in the transfer of electrons to NrfA (23).…”

mentioning

confidence: 99%

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

et al. 2015

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Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. IMPORTANCEThe NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB. Sulfate-reducing bacteria (SRB) are important members of syntrophic anaerobic microbial communities. While SRB are useful in remediation of contaminated groundwater by reduction of toxic heavy metals (1), they are also a major problem in offshore oil industries, where they cause biofouling due to corrosive sulfide production (2). Additions of nitrate and nitrite have been used to control SRB growth and the resulting biofouling sulfide (3, 4). Nitrite is more effective for inhibition of SRB than nitrate (3), and most SRB are sensitive to low concentrations of nitrite (5, 6). Nitrite is toxic because it inhibits sulfite reduction by competing for the sulfite reductase enzyme (7,8). Also, the reaction of nitrite with sulfide to form polysulfide results in the release of reactive nitrogen species (9).The sensitivity to nitrite varies among SRB. Some SRB, such as Desulfovibrio alaskensis G20, lack any means for reducing the nitrite and are highly sensitive to small amounts of nitrite (10, 11). However, other SRB can reduce nitrite via a cytochrome c-type nitrite reductase, NrfA, and are able to tolerate low millimolar amounts of nitrite (7, 12). NrfA-carrying SRB also can utilize nitrite as the sole terminal electron acceptor (TEA), provided the nitrite is at subinhibitory concentrations (12-14). Some nitritereducing SRB also have the ability to utilize nitrate as the TEA via dissimilatory nitrate/nitrite reduction (15).NrfA is ...

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“…A broad diversity of microorganisms is capable of DNRA, mainly prokaryotic organisms belonging to Proteobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Acidobacteria, Chloroflexi, and Chlorobia (Tiedje, 1988;Welsh et al, 2014). 20…”

Section: Dissimilatory Nitrate Reduction To Ammonia (Dnra)mentioning

confidence: 99%

Reviews and syntheses: Processes and functional genes involved in nitrogen cycling in marine environments

Ramos

Pajares

2018

Preprint

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Abstract. Nitrogen is a key element for life in the oceans. It controls primary productivity in many parts of the global ocean, consequently playing a crucial role in the uptake of atmospheric carbon dioxide. The nitrogen cycle is driven by complex biogeochemical transformations mediated by microorganisms, including classical processes such as nitrogen fixation, 10 assimilation, nitrification, denitrification, and dissimilarity nitrate reduction to ammonia, as well as novel processes such as anaerobic ammonium oxidation, comammox and nitrite-driven anaerobic methane oxidation. The nitrogen cycle maintains the functioning of marine ecosystems and will be a crucial component in how the ocean responds to global environmental change. In this review, we summarize the current understanding of the marine microbial nitrogen cycle, its underlying biochemical and enzymatic reactions, the ecology and distribution of the microorganisms involved, and the main impacts of 15 anthropogenic activities.

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Refined NrfA Phylogeny Improves PCR-Based nrfA Gene Detection

Cited by 187 publications

References 75 publications

Global biogeography of microbial nitrogen-cycling traits in soil

Global biogeography of microbial nitrogen-cycling traits in soil

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

Reviews and syntheses: Processes and functional genes involved in nitrogen cycling in marine environments

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