Hydrogenophaga soli sp. nov., isolated from rice field soil

Abstract

A novel Gram-stain-negative bacterial strain, designated strain S10, was isolated from soil collected in a rice field in Goyang, South Korea. Cells of strain S10 were strictly aerobic, motile and rod-shaped. Colonies were round, convex, smooth and white. The strain grew optimally at 37 °C, pH 7.0 and 0 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence of strain S10 revealed that the bacterium belongs to the family Comamonadaceae and is related to members of the genus Hydrogenophaga, with Hydrogenophaga caeni EMB71 being its closest relative (97.9 % sequence similarity). The DNA G+C content of strain S10 was 68.2 mol%. Strain S10 contained phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant respiratory quinone was ubiquinone Q-8. DNA-DNA hybridization values of strain S10 with Hydrogenophaga caeni KCTC 12613, Hydrogenophaga atypica DSM 15342 and Hydrogenophaga defluvii DSM 15341 were 16.1±4.8, 49.0±3.2 and 21.9±8.8 %, respectively. Based on phylogenetic distinctiveness, DNA-DNA hybridization and specific physiological and biochemical characteristics, strain S10 (=KCTC 52520=JCM 31711) is classified as a novel species of the genus Hydrogenophaga, for which the name Hydrogenophagasoli sp. nov. is proposed.

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

“…The DNA G+C content ranges from 61.3 to 69.9 mol% [5,6] and the predominant quinone system is ubiquinone-8 (Q-8) [1]. At the time of writing, 15 species of the genus Hydrogenophaga have been validly described, which were isolated from diverse habitats, such as wastewater [7][8][9], activated sludge [2][3][4][5][6][7][8][9], soil [1,10], freshwater ecosystems [3,4,11] or even pacific oyster [5]. Additionally, members of the genus Hydrogenophaga can be key benzene-degrading bacteria in petroleum hydrocarbon contaminated subsurface environments [12].…”

Nitrogen transformation processes catalyzed by manure microbiomes in earthen pit and concrete storages on commercial dairy farms

“…For example, Proteiniclasticum, Luteimonas, and Proteiniphilum are known to degrade and live on proteins using an inventory of proteases, peptidases and amino acid deaminases [44][45][46] (Additional file 2: Table S7-8). Similarly, Pseudomonas, Hydrogenophaga, Flavobacterium, and those from the Rhodobacteraceae family could obtain ammonia nitrogen from urea [47][48][49][50] (Additional file 2: Tables S6 and S7). As the pH for both storages ranged from 6.92 to 7.85 (Additional file 2: Table S2) and the pKa of ammonia is 9.2, not more than 4% of this compound will occur in the deprotonated or NH 3 form which could be released to the atmosphere (Additional file 2: Table S2).…”