Pedobacter anseongensis sp. nov., Pedobacter immunditicola sp. nov. and Pedobacter superstes sp. nov., three novel species isolated from hydrocarbon- and heavy metal-contaminated soils.

Abstract

Three novel, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated Du54ᵀ, Du274ᵀ and P351ᵀ, were isolated from contaminated environments in Anseong, South Korea. Strains Du54ᵀ and Du274ᵀ originated from landfill soil, whilst P351ᵀ was obtained from parking lot soil. These sites are frequently exposed to pollutants such as petroleum hydrocarbons, heavy metals and industrial runoff, which exert selective pressures on microbial communities. The taxonomic positions of the strains were determined using a polyphasic approach, including 16S rRNA gene sequencing, draft genome analysis and whole-genome-based phylogenetic reconstruction. Phylogenetic trees based on both 16S rRNA genes and core genome sequences (Type Genome Server and AutoMLST) showed that the three isolates belong to the genus Pedobacter. Du54ᵀ exhibited the highest 16S rRNA gene sequence similarity to Pedobacter insulae KCTC 12820ᵀ (98.40%), Du274ᵀ to Pedobacter bambusae KACC 17544ᵀ (98.31%) and P351ᵀ to Pedobacter mongoliensis KCTC 52859ᵀ (97.65%). The draft genomes of Du54ᵀ, Du274ᵀ and P351ᵀ were 4.43, 4.51 and 4.63 Mb in size, with G+C contents of 37.7, 40.6 and 39.2 %, respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and their closest relatives ranged from 73.76 to 76.36% and 18.8 to 22.6%, respectively, supporting their delineation as novel species. Genomic annotation revealed 294, 302 and 238 genes in Du54ᵀ, Du274ᵀ and P351ᵀ, respectively, associated with metal resistance, efflux transporters and stress response. All strains lacked flexirubin-type pigments, contained menaquinone-7 as the major respiratory quinone and possessed phosphatidylethanolamine as the dominant polar lipid. The predominant fatty acids included iso-_C16:0 and summed feature 3 (C_16:1  ω7c and/or C_16 : 1  ω6c). Based on these results, the names Pedobacter anseongensis sp. nov., Pedobacter immunditicola sp. nov. and Pedobacter superstes sp. nov. are proposed for strains Du54ᵀ (=KACC 23093ᵀ=LMG 32954ᵀ), Du274ᵀ (=KACC 23094ᵀ=LMG 32955ᵀ) and P351ᵀ (=KACC 23095ᵀ=LMG 32956ᵀ), respectively.