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

Species clustering within <i>Dickeya zeae</i> has been recently identified as complex, encompassing validly published names, including <i>Dickeya oryzae</i> and <i>Dickeya parazeae</i>, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (<i>Ananas comosus</i> var. <i>comosus</i>) 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 <i>D. zeae</i>, <i>D. parazeae</i> and <i>D. oryzae</i> 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, <i>gapA</i>, 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 <i>D. zeae</i> complex, with <i>D. oryzae</i> as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the <i>Klebsiella</i> 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 <i>D. zeae</i>. We propose the name <i>Dickeya ananatis</i> sp. nov. for this taxon, represented by the type strain A5410^T (=ICMP 25020^T=LMG 33197^T).