Phylogenetics of Halomonadaceae strain JSM 104105 based on multilocus sequence analysis and comparative genomics analysis

Abstract:

[Objective] To investigate the phylogenetic position of the siderophore-producing halophilic bacterium JSM 104105 in the family Halomonadaceae. [Methods] Molecular phylogenetic analysis of strain JSM 104105 was performed by means of multilocus sequence analysis (MLSA) based on 3 housekeeping genes, i.e., 16S rRNA gene, DNA gyrase B subunit gene (gyrB) and RNA polymerase sigma factor RpoD gene (rpoD), and then its exact systematic position was investigated by comparative genomics analysis based on whole-genome sequences, including comparisons of G+C content, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values, and phylogenomic analysis. [Results] The MLSA results showed that the data both from single-gene (16S rRNA, gyrB, or rpoD) sequence comparisons and concatenated 16S rRNA-gyrB-rpoD sequence comparisons were consistent, and could indicate the phylogeny of strain JSM 104105 and related taxa of Halomonadaceae, and that strain JSM 104105 belonged to the genus Halomonas, being in closestly genetic relationship with Halomonas gudaonensis CGMCC 1.16133^T (16S rRNA gene similarity, 98.9%), Halomonas azerbaijanica TBZ202^T (98.6%) and Halomonas lysinitropha 3(2)^T (97.3%), and strain JSM 104105 formed a coherent branch in the phylogenetic trees which were generated based on either single-gene sequence or concatenated-gene sequence comparisons. MLSA data also suggested that strain JSM 104105 could represent a different phylogenic subline separated from recognized Halomonas species. The results of comparative genomics analysis supported the conclusion from MLSA data. Either ANI (78.9%-91.6%) or dDDH values (22.1%-43.7%) were all well below the standard criteria (ANI, 95%-96%; dDDH≥70%) for delineation of prokaryotic species. The results of phylogenomic analysis also showed that strain JSM 104105 clearly represented an independent subclade in Halomonas. [Conclusion] From the perspective of molecular phylogeny, the combination of MLSA and comparative genomics analysis demonstrated definitely that strain JSM 104105 belongs to Halomonas, being phylogenetically closely related to H. gudaonensis, H. azerbaijanica and H. lysinitropha, and that strain JSM 104105 cannot be assigned to any recognized species but represents a novel genospecies of the genus Halomonas.