Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov.

Abstract

The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.

Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov.

“…Furthermore, strains SYSU D00823 T , SYSU D00873 T and P. xinjiangensis CCTCC AB 208092 T showed 56.7-57.3 % POCP values with P. mongoliensis KCTC 52859 T . Although a 50 % POCP cut-off value was proposed for defining bacterial genera [23], it has been shown that this universal cut-off is too conservative to be appropriate for circumscribing many bacterial genera [31][32][33]. The detailed paired overall genome relatedness indices (OGRIs) are shown in Table 2.…”

Alcanivorax borkumensis and Bioremediation: The Actual Perspective of a Vintage Bacteria

“…A. borkumensis [27] is classified within the order Oceanospirillales of the class of the Gammaproteobacteria. Recent phylotaxogenomic analysis [16S rDNA sequencing, DNA-DNA Hybridization (dDDH), Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), Percentage of Conserved Proteins (POCP) and comparative genomic studies [20,28] showed that Alcanivorax species formed three clades named Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto (Table 1).…”