Evidence map›Paper›PMID 29540736›Full record

ArticleScientific reports2018

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways.

Siavash Atashgahi, Bastian Hornung, Marcelle J van der Waals, Ulisses Nunes da Rocha, Floor Hugenholtz, Bart Nijsse, Douwe Molenaar, Rob van Spanning, Alfons J M Stams, Jan Gerritse and 1 more

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing papers in PubMed
31.3field-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

32 citing papers in PubMed, 449 citations in OpenAlex.

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  10. Anaerobic benzene oxidation inApplied and environmental microbiology · 2024
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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

11 authors at 4 institutions in 3 countries.

Siavash AtashgahiWageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands. siavash.atashgahi@wur.nl.ORCID 0000-0002-2793-2321
Bastian HornungWageningen University & Research, Laboratory of Systems and Synthetic Biology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Marcelle J van der WaalsWageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Ulisses Nunes da RochaVrije Universiteit Amsterdam, Department of Molecular Cell Biology, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
Floor HugenholtzWageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Bart NijsseWageningen University & Research, Laboratory of Systems and Synthetic Biology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Douwe MolenaarVrije Universiteit Amsterdam, Department of Molecular Cell Biology, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
Rob van SpanningVrije Universiteit Amsterdam, Department of Molecular Cell Biology, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
Alfons J M StamsWageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Jan GerritseDeltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, The Netherlands.
Hauke SmidtWageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
Wageningen University & Research · NLDeltares · NLVrije Universiteit Amsterdam · NLHelmholtz Centre for Environmental Research · DE

Funding

European Research Council 323009
6 · The paper itself

Abstract

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.

Indexed as

AnaerobiosisMetabolic Networks and PathwaysMicrobial ConsortiaBenzeneBiodegradation, EnvironmentalBiofilmsGene Expression ProfilingGene Expression Regulation, BacterialNitratesOxidation-ReductionOxygenPeptococcaceaeTranscriptomeBenzeneNitratesOxygen

Identifiers

PMID29540736
PMCPMC5852087
OpenAlexW2792873451

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.