Acidovorax bellezanensis sp. nov., a novel bacterium from uranium mill tailings repository sites with selenium bioremediation capabilities

Abstract

A Gram-stain-negative bacterial strain designated Be4^T, belonging to the genus Acidovorax, was isolated from mining porewaters sampled in uranium mill tailings repository sites, located in Bellezane, near Bessines-sur-Gartempe (Limousin, France). Cells were facultative anaerobic, rod-shaped, non-endospore-forming and motile with flagella. The mean cell size was 1.25-1.31 μm long and 0.70-0.73 μm wide. Colonies were light yellow, opaque, circular, convex with smooth margins, and 1-2 mm in diameter. Growth occurs at 4-37 °C and between pH 5.5-9.0. It differed from its phylogenetically related strains by phenotypic and physiological characteristics such as growth at 4 °C, presence of acid phosphatase, naphthol-AS-BI-phosphohydrolase and β-glucosidase enzymatic activities, and fermentation of l-xylose and esculin. The major fatty acids were C_16:0, C_16:1 ω7c/C_16:1 ω6c, C_17:0 cyclo and C_18:1 ω7c. Phylogenetic analysis based on 16S rRNA and 938 core genes, confirmed its placement within the genus Acidovorax as a novel species. Strain Be4^T showed highest 16S rRNA sequence similarity to Acidovorax antarcticus (98.2 %), Acidovorax radicis (97.9 %), Acidovorax temperans (97.8 %) and Acidovorax facilis (97.7 %). The genome of strain Be4^T is 5,041,667 bp size with a DNA G + C content of 65.15 %. By automatic annotation numerous sequences involved in the interaction with metals/metalloids including some genes related to Se uptake and selenite resistance were detected in its genome. The average nucleotide identity (ANI) values calculated from whole genome sequences between strain Be4^T and the most closely related strains A. radicis and A. facilis were below the threshold value of 95 %. Thus, the data from the phylogenetic, physiological, biochemical, and genomic analyses clearly indicates that strain Be4^T represents a novel species with the suggested name Acidovorax bellezanensis sp. nov. The type strain is Acidovorax bellezanensis Be4^T (=DSM116209^T = CECT30865^T). This novel species, due to its unique isolation source, genomic analysis, and preliminary laboratory tests where it was able to reduce toxic Se(IV) to less harmful Se(0) in the form of nanoparticles, holds great potential for further investigation in bioremediation, particularly concerning Se.

Keywords: Acidovorax bellezanensis; Average nucleotide identity; Bioremediation; Genome; Selenium.

Fig. 1

Scanning electron microscopy image of Be4 cells cultured in R2A medium for 48 h at a temperature of 28 °C.

Fig. 2

Phylogenetic reconstruction based on 16S rRNA genes of strains of members of the genus Acidovorax, Simplicispira, Comamonas and Delftia available in the LTP_01_2022. This is a consensus tree between the neighbor-joining and RaxML reconstructed trees using the termini filter and taking into account all variable positions. Bar, 0.01 substitutions per nucleotide position.

Fig. 3

Phylogenetic tree reconstruction based on neighbor-joining calculation for the 938 single copy core genes shared between the genomes affiliated to Acidovorax, Simplicispira, Comamonas, Delftia and Polaromonas. Genome sequence accession numbers are given in parentheses. Bar, 0.1 substitutions per amino-acid position.

Fig. 4

Cell cultures on liquid and solid R2A medium of the strain Acidovorax sp. Be4^T in the absence (A and C) and presence of Se(IV) (B and D) after incubation at 28 °C.

Fig. 5

HAADF-STEM micrographs of Se nanoparticles produced by Acidovorax sp. Be4^T intra- and extracellularly (A–D). EDX-element mapping and spectra derived from a single nanoparticle are displayed in D and E, respectively.