Genome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations

Abstract

The complete genome sequence of Brevundimonas diminuta represented a chromosome (∼4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908 and 30,654 bp, respectively. The sequence of the genome showed no significant similarity with the known bacterial genome sequences, instead showed weak similarity with the members of different genera of family, Sphingomonadaceae. Contradicting existing taxonomic position, the core genome-guided phylogenetic tree placed B. diminuta in the genus Sphingopyxis and showed sufficient genome-to-genome distance warranting a new species name. Reflecting the strains ability to grow in harsh environments, the genome-contained genetic repertoire required for mineralization of several recalcitrant man-made aromatic compounds.

Fig. 1.—

The circular maps of the S. wildii genome and plasmids: (A) Circles 1 and 2 (from exterior to interior) represent CDS on forward (green-annotated, red-hypothetical) and reverse strands (blue annotated, red hypothetical); circles 3 and 4 show RNA genes (orange for tRNA, pink for rRNA, and purple for tmRNA); and VNTRS (turquoise). The GC content (olive for positive and purple for negative) and GC skew (green for positive and red for negative) are shown in 5 and 6. The maroon blocks shown above circle 1 represent genomic islands. CDS on the forward (green for annotated, red for hypothetical) and reverse strands (blue for annotated, red for hypothetical) of plasmids pCMS1 and pCMS2 in (B, C).

Fig. 2.—

Phylogenetic tree: In the radial cladogram, the branches of each genus are colored uniquely. The branch length is not proportional to time. The scale bar indicates the number of substitutions per site. Each node of the tree is supported by a bootstrap value of 100. The tree in the inset depicts the relationship of S. wildii with other members of Sphingopyxis.

Fig. 3.—

Degradation pathways: The pathways (A) and the genomic location of degradative traits are shown (B).