Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

Abstract

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Expansion and revision of the genus Xanthobacter and proposal of Roseixanthobacter gen. nov.

“…The majority of Xanthobacter strains currently available from cell culture repositories lack genome sequences and taxonomic validation. Additionally, despite their abundance worldwide and in the literature, there were only eight validly published species of Xanthobacter (1,5,7,(9)(10)(11)(12).…”

“…Other Xanthobacter (X. oligotrophicus, X. aminoxidans, X. autotrophicus) were described as non-motile, although occasionally slime-free mutants of the X. autotrophicus type strain 7C T (known as 7C SF) were inconsistently observed as motile (3,97). In their initial publications, X. tagetidis and X. dioxanivorans were also described to be motile (9,12); however, they are pictured with short projections unlike the long peritrichous flagella found in X. agilis and inducibly in X.…”

“…The genus Xanthobacter is known for its hydrogen-oxidizing, nitrogen-fixing, chemolithoautotrophic growth capabilities and yellow pigmentation from zeaxanthin dirhamnoside production (1)(2)(3). These strains are found worldwide across numerous diverse environments and are important members of ecosystems, including soil (2,(4)(5)(6), wastewater sludge (7)(8)(9)(10), sediment (3), water (11), root systems (12,13), and more. In ecosystems, Xanthobacter are fixers of carbon and nitrogen (3) and solubilize phosphate (14).…”

“…Despite the abundance, importance, and academic and industrial interest in Xanthobacter, the vast majority of repository strains lack a genome sequence and taxonomic validation. To date, only eight species have been validly published (1,5,7,(9)(10)(11)(12), although more have been described (39,(41)(42)(43), meaning we likely lack a great deal of knowledge on the diversity and evolutionary history of the genus. Previous taxonomic classification methods, such as 16S rRNA analyses, are notoriously inadequate for resolving genus and species boundaries between and within the genus Xanthobacter and the highly related genera Azorhizobium and Aquabacter due to high sequence similarity (44,45).…”

Draft Genome Sequence of Xanthobacter aminoxidans ATCC BAA-299 T

“…Additionally, X. aminoxidans , like other Xanthobacter species, is capable of fixing N 2 under low-oxygen conditions ( 10 , 12 ). While some Xanthobacter strains have been sequenced ( 12 , 15 – 17 ), X. aminoxidans was still not sequenced, which led to the sequencing effort described below.…”