Flavobacterium potami sp. nov., a multi-metal resistance genes harbouring bacterium isolated from shallow river silt

Abstract

Environmental pollution by heavy metals is becoming an increasing problem and has become a matter of great concern due to the adverse effects worldwide. In this study, we report a novel strain of multi-metal resistant bacteria. A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped strain 17A^T, was isolated from the shallow silt of Fuyang River located in Longdian town, Hengshui city, Hebei province, China. Strain 17A^T grew at 20-35 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and 0-2% (w/v) NaCl (optimum, 1%). Phylogenetic analyses of 16S rRNA gene sequences showed that strain 17A^T was closely related to members of the genus Flavobacterium, and had the highest 16S rRNA gene sequence similarity with 'Flavobacterium panacis' DCY106^T (97.5%), followed by Flavobacterium johnsoniae subsp. johnsoniae UW101^T (97.3%), Flavobacterium cutihirudinis E89^T (97.2%), Flavobacterium limi THG-AG6.4^T (97.2%), Flavobacterium hibisci THG-HG1.4^T (97.2%) and Flavobacterium johnsoniae subsp. aurantiacum DSM 6792^T (97.1%). The genome size of strain 17A^T was 5.4 Mb and the DNA G + C content was 34.0%. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain 17A^T and reference strains were in the ranges of 79.8-86.1%, 24.1-31.4% and 80.5-88.6%, respectively, lower than the threshold values for species delineation. Strain 17A^T contained iso-C_15:0 and C_16:0 3-OH as the predominant fatty acids (≥ 10%). The main isoprenoid quinone of strain 17A^T was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, two unidentified aminophospholipids and six unidentified lipids. Comparative genomics analysis between strain 17A^T and its reference type strains revealed that there are a number of metal-resistant genes in strain 17A^T, which are located in 15 gene clusters responsible for the copper homeostasis, cobalt-zinc-cadmium resistance, copper resistance, and arsenic/antimony resistance, with the copper resistance protein NlpE being unique to 17A^T. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 17A^T is a representative of a novel species within the genus Flavobacterium, for which the name Flavobacterium potami sp. nov. is proposed. The type strain is 17A^T (= GDMCC 1.2723^T = JCM 34833^T).

Keywords: Flavobacterium potami sp. nov.; Genome; Multi-metal resistance genes; Phylogenomic tree.