Sphingobium lignivorans sp. nov., isolated from river sediment downstream of a paper mill

Abstract

A bacterial isolate, B1D3AT, was isolated from river sediment collected from the Hiwassee River near Calhoun, TN, by enrichment culturing with a model 5–5′ lignin dimer, dehydrodivanillate, as its sole carbon source. B1D3AT was also shown to utilize several model lignin-derived monomers and dimers as sole carbon sources in a variety of minimal media. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed yellow/cream-coloured colonies on rich agar. Optimal growth occurred at 30 °C, pH 7–8, and in the absence of NaCl. The major fatty acids of B1D3AT were C18 : 1 ω7c and C17 : 1 ω6c. The predominant hydroxy fatty acids were C14 : 0 2-OH and C15 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and sphingoglycolipid. B1D3AT contained spermidine as the only major polyamine. The major isoprenoid quinone was Q-10 with minor amounts of Q-9 and Q-11. The genomic DNA G+C content of B1D3AT was 65.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 49 core, universal genes defined by Clusters of Orthologous Groups gene families indicated that B1D3AT was a member of the genus Sphingobium . B1D3AT was most closely related to Sphingobium sp. SYK-6, with a 100 % 16S rRNA gene sequence similarity. B1D3AT showed 78.1–89.9 % average nucleotide identity and 19.5–22.2% digital DNA–DNA hybridization identity with other type strains from the genus Sphingobium . On the basis of phenotypic and genotypic properties and phylogenetic inference, strain B1D3AT should be classified as representing a novel species of the genus Sphingobium , for which the name Sphingobium lignivorans sp. nov. is proposed. The type strain is strain B1D3AT (ATCC TSD-279T=DSM 111877T).

Sphingobium cyanobacteriorum sp. nov., isolated from fresh water

“…The common characteristics of this genus are being Gram-negative, rod-shaped, motile or non-motile and strictly aerobic [1]. Chemotaxonomically, they contain Q-10 as the main respiratory quinone and summed feature 8 (C 18 : 1 ω7c and/or C 18 : 1 ω6c) and summed feature 3 (C 16 : 1 ω7c and/or C 16 : 1 ω6c) as primary fatty acids [1,5,6]. Members of the genus have been reported to degrade biphenyl, polychlorinated biphenyl [7], phenolic acid [8] and lignin-derived aromatic compounds [9], to produce antimicrobial compounds [10] and to promote the growth of plants [11].…”

Catabolic System of 5-Formylferulic Acid, a Downstream Metabolite of a β-5-Type Lignin-Derived Dimer, in Sphingobium lignivorans SYK-6

“…The catabolic system for lignin-derived aromatic compounds has been most thoroughly characterized for Sphingobium lignivorans SYK-6 (formerly Sphingobium sp. SYK-6), a Gram-negative bacterium belonging to the alphaproteobacteria. , SYK-6 can grow on various lignin-derived dimeric compounds with β- O -4 (β-aryl ether), β-1 (diarylpropane), 5-5 (biphenyl), and β-5 (phenylcoumaran) bonds as well as lignin-derived monomeric compounds, including vanillin, ferulic acid, and syringaldehyde, as the sole source of carbon and energy. Knowledge on the SYK-6 enzyme system, its substrate uptake system, and how these genes are regulated provides a practical foundation for biological funneling and helps clarify the processes by which lignin-derived aromatic compounds undergo bacterial catabolism. ,− …”

“…The catabolic system for lignin-derived aromatic compounds has been most thoroughly characterized for Sphingobium lignivorans SYK-6 (formerly Sphingobium sp. SYK-6), 5 a Gram-negative bacterium belonging to the alphaproteobacteria. 3,6 SYK-6 can grow on various ligninderived dimeric compounds with β-O-4 (β-aryl ether), β-1 (diarylpropane), 5-5 (biphenyl), and β-5 (phenylcoumaran) bonds as well as lignin-derived monomeric compounds, including vanillin, ferulic acid, and syringaldehyde, as the sole source of carbon and energy.…”