Dickeya ananatis sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus)

Species clustering within Dickeya zeae has been recently identified as complex, encompassing validly published names, including Dickeya oryzae and Dickeya parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93 to 99.9% and 91.8 to 99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae and D. oryzae ranged from 94.4-95.9% to 57.2-66.5%, respectively. These values fall below the proposed boundaries for species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis of ten housekeeping genes, whole genome and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the 7 pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological and phylogenomic analyses, we propose the reclassification into a new species of the five pineapple strains from Hawaii A5391, A5410^T, A5611, A6136 and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananatis sp. nov. for this taxon, represented by the type strain A5410^T (=ICMP 25020^T=LMG 33197^T).