Evidence map›Paper›PMID 24795702›Full record

ArticleFrontiers in microbiology2014

Genetic basis for nitrate resistance in Desulfovibrio strains.

Hannah L Korte, Samuel R Fels, Geoff A Christensen, Morgan N Price, Jennifer V Kuehl, Grant M Zane, Adam M Deutschbauer, Adam P Arkin, Judy D Wall

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
17.2field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed, 253 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 1 country.

Hannah L KorteDepartment of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
Samuel R FelsEcosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA.
Geoff A ChristensenDepartment of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
Morgan N PriceEcosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Jennifer V KuehlEcosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Grant M ZaneDepartment of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
Adam M DeutschbauerEcosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Adam P ArkinEcosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Judy D WallDepartment of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA.
University of Missouri · USLawrence Berkeley National Laboratory · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.

Indexed as

Desulfovibriofitness profilingfunctional genomicsnitrate inhibitionnitritestress responsesulfate-reducing bacteriasulfide control

Identifiers

PMID24795702
PMCPMC4001038
OpenAlexW2105240801

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.