BackgroundLignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments.ResultsTo investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC–MS analysis was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis was carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least twofold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis, assembly, etc.ConclusionsGC–MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0735-y) contains supplementary material, which is available to authorized users.

An alkaliphilic and halotolerant Gram-stain-positive bacterium, which was isolated from sediment samples from the South China Sea, was subjected to a taxonomic study. The isolate, strain L1 T , grew well at a wide range of temperatures and pH values, 10.0-45.0 6C and pH 6-11, with optima at 30 6C and pH 9.0, respectively. The growth of strain L1 T occurred at total salt concentrations of 0-10 % (w/v) with an optimum at 2 % (w/v). Phylogenetic analysis based on 16S rRNA sequence comparison indicated that the isolate represented a member of the genus Bacillus. The strains most closely related to strain L1 T were Bacillus nanhaiisediminis JCM 16507 T , Bacillus halodurans DSM 497 T and Bacillus pseudofirmus DSM 8715 T , with 16S rRNA similarities of 96.5 %, 95.9 % and 95.7 %, respectively. DNA-DNA hybridization of strain L1 T with the type strains of the most closely related species, B. nanhaiisediminis JCM 16507 T , B. halodurans DSM 497 T and B. pseudofirmus DSM 8715 T , showed reassociation values of about 21.7 %, 14.3 % and 13.9 %, respectively. The DNA G+C content of strain L1 T was 40.76 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain L1 T were iso-C 14 : 0 and anteiso-C 15 : 0 . The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain L1 T (5JCM 18543 T 5DSM 26145 T ) should be classified as the type strain of Bacillus ligniniphilus sp. nov.The genus Bacillus, which already contains more than 200 species, is one of the largest genera in the bacterial kingdom (http://www.bacterio.net/b/bacillus.html). Members of this genus live in a wide range of habitats, such as desert sands, hot spring vents and polar regions (Amoozegar et al., 2009;Gugliandolo et al., 2003; Shi et al., 2011;Sorokin et al., 2008; Zhang et al., 2011a, b). Generally, cells of members of the genus Bacillus are aerobic or facultatively anaerobic, sporeforming, alkaliphilic, halophilic or halotolerant and Gramstain-positive rods. During an investigation of the culturable bacterial community from sediments of the South China Sea from a depth of 100-4000 m, a large number of bacterial strains were isolated. In the present study, a halotolerant alkaliphilic bacterium that was able to utilize lignin as a sole carbon source was isolated, with the aim of studying its degradation mechanisms for the depolymerization of lignin. Based on the results of phenotypic and chemotaxonomic studies and a phylogenetic analysis of 16S rRNA gene sequences, the novel isolate L1 T should be classified as representing a novel species of the genus Bacillus. The reference strains used in this study were type strains belonging to the genus Bacillus including Bacillus nanhaiisediminis JCM 16507 T , Bacillus halodurans DSM 497 T and Bacillus pseudofirmus DSM 8715 T , obtained from the G...

A Gram-stain-negative bacterium, designated SP-35T, was isolated from compost and was subjected to a taxonomic study. This isolate was short-rod-shaped and non-spore-forming. Phylogenetic analysis based on 16S rRNA sequence comparison indicated the isolate was related to the genus Comamonas . 16S rRNA gene sequence analysis showed that its closest neighbours were the type strains Comamonas odontotermitis Dant 3-8T (96.8 % similarity), Comamonas testosteroni DSM 50244T (96.5 %), Comamonas guangdongensis CY01T (95.9 %) and Comamonas composti YY287T (95.6 %). Using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics we could clearly distinguish strain SP-35T from type strains of the genus Comamonas . The genomic DNA G+C content of strain SP-35T was 63.1 mol%. The predominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidlyglycerol. Differences in phenotypic and phylogenetic characteristics support the classification of strain SP-35T as a representative of a novel species in the genus Comamonas , for which the name Comamonas serinivorans sp. nov. is proposed. The type strain is SP-35T ( = DSM 26136T = JCM 18194T).

A Gram-stain-positive bacterium, designated T14T , was isolated from the gut of Holotrichia oblita larvae and was subjected to a taxonomic study.

A halotolerant, Gram-positive bacterium (strain NE-14 T ), which was isolated from sediment samples of the South China Sea, was subjected to a taxonomic study. Strain NE-14 T grew well at wide temperature and pH ranges, 10.0-45.0 8C and pH 6-10, with an optimum at 30 8C and pH 8.0, respectively. Growth of strain NE-14 T was observed at total salt concentrations of 0-10 % (w/v) with optimum at 2 % (w/v