Novosphingobium humi sp. nov., isolated from soil of a military shooting range

Abstract

A Gram-stain-negative, strictly aerobic bacterium, designated R1-4T, was isolated from soil from a military shooting range in the Republic of Korea. Cells were non-motile short rods, oxidase-positive and catalase-negative. Growth of R1-4T was observed at 15-45 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, pH 7.0). R1-4T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), cyclo-C19 : 0ω8c and C16 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, an unknown glycolipid and four unknown lipids were detected as polar lipids. The major polyamine was spermidine. The G+C content of the genomic DNA was 64.4 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that R1-4T formed a tight phylogenetic lineage with Novosphingobium sediminicola HU1-AH51T within the genus Novosphingobium. R1-4T was most closely related to N. sediminicola HU1-AH51T with a 98.8 % 16S rRNA gene sequence similarity. The DNA-DNA relatedness between R1-4T and the type strain of N. sediminicola was 37.8±4.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that R1-4T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium humi sp. nov. is proposed. The type strain is R1-4T (=KACC 19094T=JCM 31879T).

Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1

“…Novosphingobium bacteria are widely distributed and can degrade a wide range of xenobiotic compounds (Tiirola et al, 2005 ; Hegedus et al, 2017 ; Kampfer et al, 2018 ; Sheu et al, 2018 ). They have been detected in rhizosphere soil (Krishnan et al, 2017 ), wood (Ohta et al, 2015 ), contaminated environments (Saxena et al, 2013 ; Hyeon et al, 2017 ; Singh et al, 2017 ), and marine and freshwater environments (Chen et al, 2017 ; Sheu et al, 2017 ; Zhang et al, 2017 ). Novosphingobium isolates display a wide variety of metabolic features.…”

Phosphate (Bio)mineralization Remediation of 90Sr-Contaminated Groundwaters

“… − The relative enrichment in citrate-degrading bacteria was consistent with the decrease in citrate seen within the citrate amended system and suggests microbial degradation of citrate is occurring in addition to sorption to sediment. For the CR glycerol phosphate experiment, there was enrichment in species from the genus Novosphingobium, Azospirillum, and Curvibacter, which contain aerobic and anaerobic species that have phosphatase activity. − Enrichment of these species was consistent with the increase in aqueous phosphate as the bacteria capable of cleaving the C–PO 4 bond in glycerol phosphate became enriched.…”

Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production

“…5 , Doğanbey hot spring hosts dominantly Novospingobium species belonging in Proteobacteria genus, which is frequently encountered in thermal water resources 18 . Novospingobium sp., which live in milder temperature conditions (30–45 °C), also dominate the Çeşme hot spring community 19 . This was an expected finding considering the temperature of the hot spring was measured as 38–43 °C.…”