ArticleThe ISME journal2014
Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.
Article in The ISME journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 55 citations in OpenAlex.
- Novel Genomes ofMicroorganisms · 2026Article
- Comparative genomics reveal unique markers to monitor by routine PCR assay bioinoculant ofIndian journal of microbiology · 2024Article
- Comprehensive review on Haloalkane dehalogenase (LinB): a β-hexachlorocyclohexane (HCH) degrading enzyme.Archives of microbiology · 2024Review
- Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation.Environmental science and pollution research international · 2022Review
- Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade.Indian journal of microbiology · 2020Review
- Microbiology of the built environment.Nature reviews. Microbiology · 2018Review
- Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element.Scientific reports · 2018Article
- Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype.Genome biology and evolution · 2017Article
- Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq.Scientific reports · 2017Article
- The hidden life of integrative and conjugative elements.FEMS microbiology reviews · 2017Review
- Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics.Indian journal of microbiology · 2017Review
- Metagenomic Analysis of a Complex Community Present in Pond Sediment.Journal of genomics · 2017Article
- Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants.Environmental science and pollution research international · 2016Review
- Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.BMC genomics · 2015Article
- Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains.G3 (Bethesda, Md.) · 2015Article
- Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic Hydrocarbon-Degrading Strain.Genome announcements · 2015Article
- Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics.Microbial ecology · 2015Article
- Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways.BMC genomics · 2014Article
- Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite.Genome announcements · 2014Article
- Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.mBio · 2014Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.
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