Characterization of three strains isolated from different ecosystems and proposal of sp. nov. and sp. nov.

Unlabelled: spp. have primarily been reported as non-pathogenic, plant-probiotic bacteria, despite the presence of some opportunistic human pathogens in the genus. Here, three Gram-stain negative, rod-shaped, non-spore-forming bacteria, designated as strains CPCC 101365, CPCC 101269, and CPCC 101426 were isolated from surface-sterilized medicinal plant roots of a mulberry plant in Chuxiong of the Yunnan Province, freshwater from Erhai Lake in the Yunnan Province, and sandy soils in the Badain Jaran desert in Inner Mongolia Autonomous Region, China, respectively. The 16S rRNA gene sequences analysis of these isolates in comparison with sequences from the GenBank database indicated that they belong to the genus , with nucleotide similarities of 96.52-99.92% to identified members. Phylogenetic analysis based on 16S rRNA gene and genome sequences confirmed that the isolates are members of the genus . Values for genomic average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; < 70%) indicated that strains CPCC 101365 and CPCC 101269 were well-differentiated from validly described species, while strain CPCC 101426 shared high ANI (97.7%) and dDDH (78.3%) identity with its closest phylogenetic neighbor, JCM 13256. The three genomes were approximately 3.1-4.0 Mbp in size and their G + C content ranged in 66.2-70.2%, with values slightly differing between CPCC 101365 (3.4 Mbp; 70.2%), CPCC 101269 (4.0 Mbp; 66.4%), and CPCC 101426 (3.1 Mbp; 66.2%). Genes encoding enzymes involved in the biosynthesis of (IAA) and siderophores were identified in the genomes of the three isolates, suggesting that these strains might serve roles as plant-growth promoting microorganisms. The polar lipid fractions of the three isolates primarily comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The predominant cellular fatty acid was iso-C: , with moderate amounts of antesio-C, iso-C, iso C 9c/C 10-methyl, iso-C, and C 7/C 6. These results indicated that polyphasic characteristics of strains CPCC 101365 and CPCC 101269 differed from other identified species and that strain CPCC 101426 was affiliated with the species . Accordingly, two novel species of the genus were consequently proposed, corresponding to sp. nov. (type strain CPCC 101365 = DY006 = KCTC 82900) and sp. nov. (type strain CPCC 101269 = K32 = KCTC 82901).

Highlights: Members of the genus , and particularly , are opportunistic human pathogens, but not enough research has evaluated the identification of environmental spp. However, most spp. serves as plant-probiotic bacteria.In this study, we obtained and characterized three strains from different ecosystems. Based on phenotypic differences, chemotaxonomic properties, ANI and dDDH identity values, and phylogenetic analyses, two novel species are proposed for the strains identified here. The encoding genes related to plant-growth promotion in the genomes of the newly recovered spp. were retrieved. Follow-on experiments confirmed that these strains produced the important plant hormone IAA. Thus, these spp. could considerably contribute to shaping and maintaining ecological stability in plant-associated environments, particularly while acting as plant-probiotic microorganisms.