Abstract
Bacillus ligninesis strain L1, isolated from seafloor sediment, was able to grow on medium with lignin as its sole carbon source. Here, we report a 3.8-Mbp high-quality genome sequence for this bacterium. The genes involving ectoine and glycine betaine synthesis, as well as those involved in the degradation of lignin, were identified.
GENOME ANNOUNCEMENT
An alkaliphilic and halotolerant Gram-positive bacterium strain, Bacillus ligninesis L1, was isolated from sediment samples at a benthal depth of 3,000 m in the South China Sea. The strain L1 grew and adapted well at a wide range of temperatures (10.0 to 50.0°C) and pH levels (6 to 11.5), with the optimal growing conditions being 30°C and pH 9.0. Strain L1 is able to utilize lignin as its sole carbon source, which presents its potential value in the cellulosic biofuels industry.
The whole genome sequence of B. ligninesis L1 was obtained using the Illumina/Solexa HiSeq 2000 sequencing system at Majorbio BioTech (China) with a paired-end library. A total of ~833 Mb of paired reads with about 213-fold coverage of the genome was generated, which was then trimmed to ~439 Mb of paired reads and assembled into 241 contigs and 72 scaffolds using the Short Oligonucleotide Alignment Program (SOAP)denovo software (1). The open reading frames (ORFs) were identified with the GeneMark gene prediction tool (http://exon.gatech.edu/GeneMark) and further analyzed using BLAST to screen the nonredundant protein database, and the relevant gene functions were determined with the help of the Clusters of Orthologous Genes (COGs) (2) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Following these data analyses, the genes encoding tRNA and rRNA were eventually obtained using the RNAmmer software.
The genome of strain L1 is 3,862,148 bp long with a G+C content of 40.76% and contains 4,101 open reading frames, of which 2,847 ORFs have positive biological functions. In addition, a total of 4,101 coding sequences (CDSs) were identified (of which 2,505 CDSs were for putative biological functions), including 72 tRNA genes and 7 rRNA operons in the genome.
The strain L1 genome contains four gene clusters involved in compatible solute synthesis, including two ectoine synthesis gene clusters and two glycine betaine synthesis genes, which potentially enhance cell survival in high salinity or other extreme environments (3, 4). The relevant genes associated with lignin degradation were also identified in the strain L1 genome, including two aryl-alcohol dehydrogenase genes, 19 NADH dehydrogenase genes (5), two glycolate oxidase genes (6), and one Mn-superoxide dismutase gene (7).
This genome information suggests that L1 has a function in degrading lignin substrates that might offer a unique value for the cellulosic biofuels industry.
Nucleotide sequence accession number.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ANNK00000000.
ACKNOWLEDGMENTS
This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions, China, a grant (no. BK2012695) by the Natural Science Foundation of Jiangsu Province, China, a project (no. 10JDG084) by the Startup Foundation for Distinguished Scholars of Jiangsu University, China, and a project by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, China.
Footnotes
Citation Zhu D, Li P, Tanabe S-H, Sun J. 2013. Genome sequence of the alkaliphilic bacterial strain Bacillus ligninesis L1, a novel degrader of lignin. Genome Announc. 1(2):e00042-13. doi:10.1128/genomeA.00042-13.
REFERENCES
- 1. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Calderón MI, Vargas C, Rojo F, Iglesias-Guerra F, Csonka LN, Ventosa A, Nieto JJ. 2004. Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043T. Microbiology 150:3051–3063 [DOI] [PubMed] [Google Scholar]
- 4. Boch J, Nau-Wagner G, Kneip S, Bremer E. 1997. Glycine betaine aldehyde dehydrogenase from Bacillus subtilis: characterization of an enzyme required for the synthesis of the osmoprotectant glycine betaine. Arch. Microbiol. 168:282–289 [DOI] [PubMed] [Google Scholar]
- 5. Pelmont J, Tournesac C, Mliki A, Barrelle M, Beguin C. 1989. A new bacterial alcohol dehydrogenase active on degraded lignin and several low molecular weight aromatic compounds. FEMS Microbiol. Lett. 48:109–113 [DOI] [PubMed] [Google Scholar]
- 6. Hammel KE, Mozuch MD, Jensen KA, Jr, Kersten PJ. 1994. H2O2 recycling during oxidation of the arylglycerol beta-aryl ether lignin structure by lignin peroxidase and glyoxal oxidase. Biochemistry 33:13349–13354 [DOI] [PubMed] [Google Scholar]
- 7. Barr DP, Aust SD. 1994. Effect of superoxide and superoxide dismutase on lignin peroxidase-catalyzed veratryl alcohol oxidation. Arch. Biochem. Biophys. 311:378–382 [DOI] [PubMed] [Google Scholar]