ArticlePloS one2015
Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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.
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.
Who cites it
27 citing papers in PubMed, 61 citations in OpenAlex.
- Insights into the taxonomy and virulence-related genetic profiles in 97 Cupriavidus strains through comparative genomic analysis.BMC genomics · 2025Article
- Physiology, Heavy Metal Resistance, and Genome Analysis of TwoMicroorganisms · 2025Article
- Cupriavidus gilardii infection following heart failure: a case report and literature review.BMC infectious diseases · 2025Review
- Severe pneumonia due toFrontiers in medicine · 2025Article
- Article
- Dissecting the Simultaneous Extracellular/Intracellular Contributions to Cr(VI) Reduction under Aerobic and Anaerobic Conditions Using the Newly Isolating Cr(VI)-Reducing Bacterium ofMicroorganisms · 2024Article
- Genomic Sequencing of ClinicalInfection and drug resistance · 2024Article
- Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water.FEMS microbiology ecology · 2023Article
- Comparative Genomic Analysis and BTEX Degradation Pathways of a ThermotolerantJournal of microbiology and biotechnology · 2023Article
- Whole Genome Sequence Analysis ofMicroorganisms · 2023Article
- Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB.Environmental microbiology · 2022Article
- Transcriptome Analysis of EnvironmentalMicroorganisms · 2021Article
- Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5.MicrobiologyOpen · 2021Article
- Genomic and Physiological Investigation of Heavy Metal Resistance from Plant EndophyticInternational journal of environmental research and public health · 2021Article
- Mycotoxin Biodegradation Ability of the Cupriavidus Genus.Current microbiology · 2020Article
- Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria.MicrobiologyOpen · 2020Article
- Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium.Molecular biology reports · 2020Article
- Article
- The Microbiome of Leonardo da Vinci's Drawings: A Bio-Archive of Their History.Frontiers in microbiology · 2020Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.