ArticleThe ISME journal2015
Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand.
Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 40 citations in OpenAlex.
- Dysregulation of mRNA expression by hsa-miR-186 overexpression in arsenic-induced skin carcinogenesis.Toxicology and applied pharmacology · 2025Article
- Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill.Biotechnology reports (Amsterdam, Netherlands) · 2024Article
- Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders.The ISME journal · 2024Article
- From microbiome composition to functional engineering, one step at a time.Microbiology and molecular biology reviews : MMBR · 2023Review
- A nostoxanthin-producing bacterium,Frontiers in microbiology · 2023Article
- Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress.The ISME journal · 2021Article
- Microbial debromination of hexabromocyclododecanes.Applied microbiology and biotechnology · 2021Review
- Separate Upper Pathway Ring Cleavage Dioxygenases Are Required for Growth of Sphingomonas wittichii Strain RW1 on Dibenzofuran and Dibenzo-Applied and environmental microbiology · 2021Article
- Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils.Environmental microbiome · 2021Article
- Environmental connectivity controls diversity in soil microbial communities.Communications biology · 2021Article
- Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu "Sajino" Madre de Dios, Peru.Scientific reports · 2021Article
- Effect of Co-contamination by PAHs and Heavy Metals on Bacterial Communities of Diesel Contaminated Soils of South Shetland Islands, Antarctica.Microorganisms · 2020Article
- TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation.Microorganisms · 2020Review
- Soil Particles and Phenanthrene Interact in Defining the Metabolic Profile ofFrontiers in microbiology · 2018Article
- Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment.Scientific reports · 2016Article
- The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.PloS one · 2016Article
- Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay.PloS one · 2016Article
- Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery.Frontiers in microbiology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of genome-wide gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated non-sterile sand, compared with regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing dibenzodioxins and dibenzofurans. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well as during growth and stationary phase in sand. Cells during transition show stationary phase characteristics, evidence for stress and for nutrient scavenging, and adjust their primary metabolism if they were not precultured on the same contaminant as found in the soil. Cells growing and surviving in sand degrade dibenzofuran but display a very different transcriptome signature as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous 'soil-specific' expressed genes. Studies focusing on inoculation efficacy should test behaviour under conditions as closely as possible mimicking the intended microbiome conditions.
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.