Introduction
Crude oil-contaminated soils harbor bacteria with specialized hydrocarbon-degrading capabilities, yet the
Stenotrophomonas
genus remains incompletely characterized at the species level. Strain ASS1, a motile Gram-negative rod, was isolated from crude oil-contaminated soil in Tabasco, Mexico, and initial 16S rRNA gene sequencing indicated affiliation with
Stenotrophomonas
, warranting full polyphasic characterization.
Methods
The complete genome was sequenced using Illumina MiSeq and assembled into a single closed contig (4,564,481 bp; G+C content 66.59%; GenBank: CP031167). Genome quality was assessed with BUSCO v6.0.0 and CheckM2. Species boundaries were evaluated using average nucleotide identity (ANIb via JSpeciesWS) and digital DNA–DNA hybridization (dDDH via GGDC Formula 2) against 38 representative
Stenotrophomonas genomes
. Taxonomic placement was further resolved by TYGS, MLST, and core genome phylogenomics. PAH catabolic capacity was assessed through genome annotation and in vitro growth assays on four PAHs as sole carbon sources, analyzed by Kruskal–Wallis test.
Results
BUSCO completeness was 99.7% and CheckM2 confirmed 100.0% completeness with 0.0% contamination. Despite 99.86% 16S rRNA gene identity to
Stenotrophomonas geniculata
ATCC 19374T, ANIb against the closest neighbor Stenotrophomonas
riyadhensis
CFS3442T was 93.30%, and dDDH was 50.4% (95% CI: 47.8–53.1%), both below established species thresholds. No pairwise comparison across the 38 genomes exceeded 54.3% dDDH. TYGS, MLST, and core genome phylogenomics consistently resolved ASS1 as a distinct lineage. Pan genome analysis confirmed an open pan genome (alpha = 0.485). A complete upper pathway PAH catabolic gene cassette was identified, and in vitro growth was statistically equivalent across all four PAH substrates (Kruskal–Wallis H(3) = 2.403,
p
= 0.493).
Discussion
Collectively, the genomic, phylogenomic, and phenotypic evidence supports ASS1 as the type strain of a novel species,
Stenotrophomonas oleivorans
sp. nov. (= WFCC 1006/CM-CNRG 934T), with demonstrated broad spectrum PAH degradation capacity relevant to bioremediation.