Sanchez-Varela, Alejandro

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.

Background: Stenotrophomonas species are multi-resistant bacteria with ability to cause opportunistic infections. Objective: We isolated 45 Stenotrophomonas species from soil, sewage and the clinic with the aim of investigating their susceptibility to commonly used antimicrobial agents. Methodology: The identities of isolates were confirmed with 16S rRNA gene sequence and MALDI-TOF analysis. Anti-mi- crobial resistance, biofilm production and clonal diversity were also evaluated. The minimum inhibitory concentration technique as described by Clinical & Laboratory Standards Institute: CLSI Guidelines (CLSI) was employed for the evaluation of isolate susceptibility to antibiotics. Result: Forty-five Stenotrophomonas species which include 36 environmental strains and 9 clinical strains of S. maltophilia were considered in this study. 32 (88.9 %) environmental strains were identified to be S. maltophilia, 2 (5.6 %) were Stenotrophomonas nitritireducens, and 2 (5.6 %) cluster as Stenotrophomonas spp. Stenotrophomonas isolates were resistant to at least six of the antibiotics tested, including Trimethoprim/Sulfamethoxazole (SXT). Conclusion: Environmental isolates from this study were resistant to SXT which is commonly used for the treatment of S. maltophilia infections. This informs the need for good public hygiene as the environment could be a reservoir of multi-resistant bacteria. It also buttresses the importance of surveillance study in the management of bacterial resistance. Keywords: Stenotrophomonas; environmental; biochemical characterization; clonal diversity; anti-microbial susceptibility.