Crystal E. Young, Harrison O’Sullivan, Hussain Alattas, Ravi Tiwari, Andrew Macrae, et al. (2026).
Refining Salinivibrio pangenome dynamics and biotechnological potential through comparative analysis.
Microbial Genomics. 10.1099/mgen.0.001786
Read on Microbial Genomics · 
OpenAlex
Refining Salinivibrio Pangenome Dynamics and Biotechnological Potential
Standardized homology-based re-analysis reveals that the halophilic genus Salinivibrio is more genomically dynamic than previously thought and likely harbors overlooked PHA depolymerases relevant to bioplastic bioprocessing.
Background
Salinivibrio is a halophilic genus of interest for polyhydroxyalkanoate (PHA) bioplastic production. Genomic understanding has been limited: of 62 public genomes, only 7 were complete. Prior pangenome work described a closed genome and concluded that Salinivibrio possesses PHA biosynthesis genes but lacks depolymerases for degradation — an odd asymmetry the authors set out to test.
Methods
- Sequenced 8 new complete genomes from Pearse Lakes (Rottnest Island, Western Australia) using Oxford Nanopore long reads.
- Combined with 38 high-quality public genomes (≥90% completeness, ≤5% contamination), for a total of 46.
- Ran pangenome analysis and Panstripe to test gene gain/loss dynamics against phylogenetic branch lengths.
- Tested selection on PHA biosynthesis genes.
- Critically, searched for depolymerases via HMM-based homology rather than relying on standard annotation pipelines.
Key Findings
A more open pangenome than reported. Core genome = 25% of gene clusters; accessory = 71%. Panstripe detected significant temporal signal in gene gain/loss on both core (P = 1.72×10⁻⁴) and tip branches (P = 2.64×10⁻¹⁴), indicating ongoing genomic turnover.
PHA biosynthesis is conserved and under selection. All 46 genomes carry the complete phaB-phaA-phaP-phaC operon, with strong purifying selection (Z = 30.30, P < 0.001). This conservation in an otherwise dynamic genome is hard to square with prior claims of no degradation capacity.
Putative depolymerases recovered by HMM search. Seven candidate depolymerases were identified, forming a single accessory cluster present in 15% of strains. All had been mis-annotated as 3-oxoadipate enol-lactonase-2. They retain catalytic residues characteristic of active PHA depolymerases but are divergent from reference sequences — plausibly explaining why standard annotation missed them.
Limitations and Open Questions
- The seven depolymerase candidates are putative; biochemical confirmation of activity is still needed.
- Only 15% of strains carry the candidate cluster, leaving open how the remaining strains handle (or fail to handle) PHA turnover.
- The broader message — that annotation-dependent workflows can systematically miss divergent enzyme families in non-model organisms — is supported here but warrants testing across other taxa.
Original abstract
Current understanding of genomic diversity within the halophilic genus Salinivibrio relies predominantly on draft genomes, with only seven complete genomes among the 62 publicly available. Previous pangenome analysis suggested a closed genomic structure while concluding that Salinivibrio lacks polyhydroxyalkanoate (PHA) degradation capacity despite possessing biosynthesis genes. Here, we present eight complete Salinivibrio genomes from Pearse Lakes (Rottnest Island, Western Australia) generated using Oxford Nanopore long-read sequencing, alongside re-analysis of 38 high-quality public genomes (≥90% completeness and ≤5% contamination cut-off). Pangenome analysis revealed a more open structure than previously reported, with a core genome comprising 25% of total gene clusters and an accessory genome accounting for 71%. Panstripe analysis demonstrated significant temporal signal in gene gain and loss events associated with phylogenetic branch length (core: P =1.72×10⁻⁴; tip: P =2.64×10⁻¹⁴). All 46 genomes contained complete PHA biosynthesis operons ( phaB-phaA-phaP-phaC ) with high sequence conservation under strong purifying selection (Z=30.30, P <0.001). In a genome that readily gains and loses genes, this conservation indicates that PHA synthesis is a maintained pathway, which is difficult to reconcile with a previous report that Salinivibrio lacks PHA degradation capacity. We therefore searched the genomes by Hidden Markov Model-based homology rather than standard annotation and identified seven putative depolymerases that form a single accessory cluster in 15% of strains, all previously annotated as 3-oxoadipate enol-lactonase-2. These candidates retained all catalytic residues characteristic of active depolymerases but are divergent from reference PHA depolymerases which could explain why annotation missed them. They remain putative and require biochemical confirmation. Both the expanded pangenome and these candidates emerged from standardized homology-based re-analysis, showing that annotation-dependent approaches can overlook genomic diversity and divergent enzyme families in non-model organisms. Together, these results establish Salinivibrio as a genomically dynamic genus with potential for halophilic bioplastic production.
—
Posted automatically by paper-surveyor.