Eight new genomes of organohalide-respiring <i>Dehalococcoides mccartyi</i> reveal evolutionary trends in reductive dehalogenase enzymes
Bibliographic record
Abstract
ABSTRACT Background Bioaugmentation is now a well-established approach for attenuating toxic groundwater and soil contaminants, particularly for chlorinated ethenes and ethanes. The KB-1 and WBC-2 consortia are cultures used for this purpose. These consortia contain organisms belonging to the Dehalococcoidia, including strains of Dehalococcoides mccartyi in KB-1 and of both D. mccartyi and Dehalogenimonas in WBC-2. These tiny anaerobic bacteria couple respiratory reductive dechlorination to growth and harbour multiple reductive dehalogenase genes ( rdhA ) in their genomes, the majority of which have yet to be characterized. Results Using a combination of Illumina mate-pair and paired-end sequencing we closed the genomes of eight new strains of Dehalococcoides mccartyi found in three related KB-1 sub-cultures that were enriched on trichloroethene (TCE), 1,2-dichloroethane (1,2-DCA) and vinyl chloride (VC), bringing the total number of genomes available in NCBI to 24. A pangenome analysis was conducted on 24 Dehalococcoides genomes and five Dehalogenimonas genomes (2 in draft) currently available in NCBI. This Dehalococcoidia pangenome generated 2875 protein families comprising of 623 core, 2203 accessory, and 49 unique protein families. In Dehalococcoides mccartyi the complement of reductive dehalogenase genes varies by strain, but what was most surprising was how the majority of rdhA sequences actually exhibit a remarkable degree of synteny across all D. mccartyi genomes. Several homologous sequences are also shared with Dehalogenimonas genomes. Nucleotide and predicted protein sequences for all reductive dehalogenases were aligned to begin to decode the evolutionary history of reductive dehalogenases in the Dehalococcoidia. Conclusions The conserved synteny of the rdhA genes observed across Dehalococcoides genomes indicates that the major differences between strain rdhA gene complement has resulted from gene loss rather than recombination. These rdhA have a long evolutionary history and trace their origin in the Dehalococcoidia prior to the speciation of Dehalococcoides and Dehalogenimonas. The only rdhA genes suspected to have been acquired by lateral gene transfer are protein-coding rdhA that have been identified to catalyze dehalogenation of industrial pollutants. Sequence analysis suggests that evolutionary pressures resulting in new rdhA genes involve adaptation of existing dehalogenases to new substrates, mobilization of rdhA between genomes or within a genome, and to a lesser degree manipulation of regulatory regions to alter expression.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".