- Short genome report
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Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea
Standards in Genomic Sciences volume 10, Article number: 123 (2015)
Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type strain of L. dokdonensis. In this study, we determined the genome sequence to describe the genomic features including annotation information and COG functional categorization. The draft genome sequence consists of 25 contigs totaling 3,274,406 bp (67.24 % G + C) and contains 3,155 protein coding genes, 2 copies of ribosomal RNA operons, and 48 transfer RNA genes. Among the protein coding genes, 75.91 % of the genes were annotated with a putative function and 87.39 % of the genes were assigned to the COG category. In the genome of L. dokdonensis, a large number of genes associated with protein degradation and antibiotic resistance were detected.
The genus Lysobacter was firstly described by Christensen and Cook in 1979 as high G + C Gram-negative bacterium with gliding motility . In the past, Lysobacter species were classified as “unidentified myxobacters” due to their high G + C ratio and gliding motility. However, the genus Lysobacter has features distinctive from myxobacteria and had been proposed as a new genus of Gammaproteobacteria . Lysobacter species are ubiquitous and have been found in a variety of environments such as soil, water, and the rhizosphere. Currently, more than 30 Lysobacter species were registered in the GenBank taxonomy database and among them, 28 species have been validly published . Some of the Lysobacter species were known to produce several kinds of lytic enzymes and antibiotics  and have an antimicrobial activity against plant pathogens . Moreover, several Lysobacter species are known to produce bioactive natural products such as cyclodepsipeptide, cyclic lipodepsipeptide, cephem-type β-lactam, and polycyclic tetramate macrolactam . Despite their ubiquitous distribution, many identified species, and possible usefulness as a biocontrol agent, deciphered Lysobacter genomes are relatively limited. Here, we present the genome sequence and the genomic information of Lysobacter dokdonensis DS-58T (KCTC 12822 T = DSM1 7958 T), which is the type strain of the species.
Classification and features
L. dokdonensis DS-58T is a Gram-staining-negative, non-motile, and rod-shaped bacterium and was isolated from the soil sample in Dokdo, an island in the East Sea, Korea, in 2011 . L. dokdonensis DS-58 grows at the temperature range of 4 to 38 °C, the pH range of 6.0 to 8.0, and the NaCl concentration of 0 to 0.5 % (w/v) . Colony size of L. dokdonensis DS-58 is about 1.0 – 2.0 mm on nutrient agar medium and the cell size is 1.0–5.0 μm long and 0.4–0.8 μm wide  (Fig. 1). L. dokdonensis DS-58 can assimilate dextrin, Tween 40, maltose, α-ketobutyric acid, alaninamide, l-alanine, l-alanyl glycine, and l-glutamic acid as a carbon source . Minimum information about a genome sequence (MIGS) for L. dokdonensis DS-58 is described in Table 1. Phylogenetically, L. dokdonensis DS-58 belongs to the family Xanthomonadaceae of the class Gammaproteobacteria , and the 16S rRNA gene showed the highest sequence similarity (96.93 %) with L. niastensis GH41-7. However, a phylogenetic tree based on the 16S rRNA gene showed that the strain DS-58 is located in the deep branch of the genus Lysobacter (Fig. 2).
Genome sequencing information
Genome project history
The genome sequencing and analysis of L. dokdonensis DS-58 were performed by the Laboratory of Microbial Genomics and Systems/Synthetic Biology at Yonsei University using the next generation sequencing. The genomic information was deposited in the GenBank (Accession number is JRKJ00000000). Summary of the genome project is provided in Table 2.
Growth conditions and genomic DNA preparation
L. dokdonensis DS-58 (accession numbers of culture collection: KCTC 12822 = DSM1 7958) was routinely cultured on nutrient medium at 30 °C. Strain DS-58 forms light yellow colored colonies with average 1.0–2.0 mm of diameter in 5 days (Table 1) . For the genome sequencing, single colony of L. dokdonensis DS-58 was inoculated in nutrient medium and incubated in the shacking incubator at 30 °C. Genomic DNA was extracted using chemical and enzymatic method as described in Molecular Cloning, A Laboratory Manual . Cell lysis was conducted using sodium dodecyl sulfate and proteinase K. From the cell lysate, genomic DNA was purified using phenol:chloroform, precipitated using isopropanol, and finally eluted into Tris-EDTA buffer.
Genome sequencing and assembly
For the whole genome shotgun sequencing, a library with 500-bp insert size was prepared and paired-end genome sequencing was performed with HiSeq2000 of the Illumina/Solexa platform (Macrogen, Inc., South Korea). Sequence trimming was conducted using CLC Genomics Workbench 5.1 (CLC bio, Qiagen, Netherlands) with parameters of 0.01 quality score and none of the ambiguous nucleotide. Sequence reads below 60 bp in length were discarded. After trimming, a total of 28,810,330 reads with an average read length of 95.8 bp were generated. De novo assembly was performed with CLC Genomics Workbench with parameters of automatic word and bubble size, deletion and insertion cost of 3, mismatch cost of 2, similarity fraction of 1.0, length fraction of 0.5, and minimum contig length of 500 bp. After the de novo assembly, scaffolding was performed using SSPACE  and automatic gap filling was carried out with IMAGE . Following the automatic gap filling, manual gap filling was conducted using CLC Genomics Workbench with the function of Find Broken Pair Mates in the end of the contigs. Basic information of the genome sequencing project is described in Table 2.
Structural gene prediction was conducted using Glimmer 3  in RAST server  with automatic fixation of errors and frame shifts. Functional assignment of the predicted protein coding sequences (CDSs) was performed using AutoFact  with the results of BLASTP or RPS-BLAST with Uniref100, NR, COG, and Pfam databases. For the accurate annotation, the functional assignment results from the RAST server and BLAST were compared each other. When assignment of the gene function was not the same between the results from RAST and BLAST, an additional BLASTP search was performed with NR database at NCBI and the top-hit result was selected for the annotation.
The draft genome sequence of the strain DS-58 consists of 25 contigs and the sum of the contigs is 3,274,406 bp (G + C content 67.24 %) (Table 3 and Fig. 3). From the genome of the strain DS-58, 3,155 CDSs, 2 copies of ribosomal RNA operons, and 48 transfer RNAs were detected. Among the predicted CDSs, 2,436 CDSs were annotated with a putative function and 2,757 CDSs were assigned to a COG category. The numbers and percentages of COG assigned genes are shown in Table 4.
Insights from the genome sequence
Some Lysobacter species are known to produce the secondary metabolite with antimicrobial activities [13, 14]. In the genome of L. dokdonensis DS-58, biosynthetic gene clusters for a bacteriocin and an arylpolyene were detected. The structure of bacteriocin-biosynthetic gene cluster of DS-58 was similar to the one in L. arseniciresistens ZS79 and the structure of arylpolyene-biosynthetic gene cluster was similar to the one in Xanthomonas campestris NCPPB 4392 (Fig. 4).
In the genome of L. dokdonensis DS-58, a number of genes associated with proteolysis were detected that include 63 genes encoding peptidases and 33 genes encoding proteases. Microbial proteases are among the most important industrial enzymes due to their diverse activities and the genus Bacillus is major source of protease in the market [15, 16]. Results from the text mining of annotated gene products indicated that L. dokdonensis DS-58 has more genes encoding proteases and peptidases than other genome-sequenced Lysobacter species except for L. antibioticus ASM73109v1 and L. capsici AZ78. Moreover, in the genome of the strain DS-58, genes encoding 17 β-lactamases for degrading chemicals such as β-lactam antibiotics, biotin-biosynthetic proteins, and type IV fimbrial biogenesis proteins that could be involved in gliding motility were detected.
Distinct from other genera in the Xanthomonadaceae , Lysobacter spp. exhibit gliding motility . Type IV pili-associated bacterial motility is widespread in members of diverse taxa such as Proteobacteria , Bacteroidetes , and Fibrobacteres  and known to be responsible for S-motility in Myxococcus and twitching motility in Lysobacter  as well as Pseudomonas and Neisseria . Thus, there is a possibility that the gliding motility of Lysobacter is associated with type IV fimbriae. On the other hand, GltA, which is involved in A-motility of Myxococcus xanthus that best fits the definition of gliding motility , was detected in the genome of DS-58 (56 % identity with 88 % coverage).
Lysobacter species typically have been isolated from soil and water, but several studies indicated that Lysobacter species may survive in more diverse habitats of anaerobic or extreme-cold [21, 22]. A great diversity of secreted degrading enzymes such as proteases and ß-lactamases may contribute to the adaptation of Lysobacter species to such diverse environments. Abundant genes encoding proteases and peptidases in the genome of DS-58 may contribute to the discovery of effective and commercially useful proteolytic enzymes. Moreover, in the genome of DS-58, dozens of genes involved in the biosynthesis of type IV fimbriae were detected. The mechanism of gliding motility has not yet been clearly revealed, and we expect that the genome information of DS-58 may contribute to the genetic analysis of bacterial gliding motility.
L. dokdonensis DS-58, the type strain of the species, is a soil bacterium isolated from Dokdo in Korea. Through a phylogenetic analysis of the 16S rRNA gene, L. dokdonensis is located in a deep branch of the genus Lysobacter . The genome sequence of L. dokdonensis DS-58 is comprised of 25 contigs of 3,274,406 bp with G + C content of 67.24 %. In the genome of DS-58, a total of 3,155 CDSs were predicted and 87.39 % of the CDSs were functionally assigned to COG categories. Dozens of genes associated with protein degradation and resistance to antibiotics were detected. Through the genome analysis of L. dokdonensis DS-58, we report that this soil bacterium harbors a large number of peptidases and proteases, which may represent a rich source of protein-degrading enzymes.
Clusters of Orthologous Groups
UniProt Reference Clusters
SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension
Iterative Mapping and Assembly for Gap Elimination
Rapid Annotation using Subsystem Technology
Automatic Functional Annotation and Classification Tool
Basic Local Alignment Search Tool
Reversed Position Specific-BLAST
Molecular Evolutionary Genetics Analysis
Minimum Information about a Genome Sequence
Clustered Regularly Interspaced Short Palindromic Repeat.
Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol. 1978;28:367–93.
Garrity GM, Lyons C. Future-proofing biological nomenclature. OMICS. 2003;7:31–3.
Puopolo G, Raio A, Zoina A. Identification and charactherization of Lysobacter Capsici strain PG4: a new plant health-promoting rhizobacterium. J Plant Pathol. 2010;92:157–64.
Qian GL, Hu BS, Jiang YH, Liu FQ. Identification and characterization of Lysobacter enzymogenes as a biological control agent against some fungal pathogens. Agr Sci China. 2009;8:68–75.
Xie Y, Wright S, Shen Y, Du L. Bioactive natural products from Lysobacter. Nat Prod Rep. 2012;29:1277–87.
Oh KH, Kang SJ, Jung YT, Oh TK, Yoon JH. Lysobacter dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol. 2011;61:1089–93.
Green Michael R, Sambrook J. MOLECULAR CLONING A Laboratory Manual. fourthth ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2012.
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27:578–9.
Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2010;11:R41.
Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998;26:544–8.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: Rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Koski LB, Gray MW, Lang BF, Burger G. AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics. 2005;6:151.
Zhang J, Du LC, Liu FQ, Xu FF, Hu BS, Venturi V, et al. Involvement of both PKS and NRPS in antibacterial activity in Lysobacter enzymogenes OH11. Fems Microbiol Lett. 2014;355:170–6.
Puopolo G, Cimmino A, Palmieri MC, Giovannini O, Evidente A, Pertot I. Lysobacter capsici AZ78 produces cyclo(L-Pro-L-Tyr), a 2,5-diketopiperazine with toxic activity against sporangia of Phytophthora infestans and Plasmopara viticola. J Appl Microbiol. 2014;117:1168–80.
Abebe B, Abrham S, Genet A, Hiwot G, Paulos K, Melese A. Isolation, optimization and characterization of protease producing bacteria from soil and water in Gondar town, North West Ethiopia. IJBVI. 2014;1:20–4.
Soundra JF, S Ramya V, Neelam D, Suresh Babu G, G Siddalingeshwara K, Venugopal N, et al. Isolation, production and characterization of protease from Bacillus sp. isolated from soil sample. J Microbiol Biotech Res. 2012;2:163–8.
Agrebi R, Wartel M, Brochier-Armanet C, Mignot T. An evolutionary link between capsular biogenesis and surface motility in bacteria. Nat Rev Microbiol. 2015;13:318–26.
Zhou X, Qian GL, Chen Y, Du LC, Liu FQ, Yuen GY. PilG is Involved in the Regulation of Twitching Motility and Antifungal Antibiotic Biosynthesis in the Biological Control Agent Lysobacter enzymogenes. Phytopathology. 2015;105:1318–24.
Shi W, Sun H. Type IV pilus-dependent motility and its possible role in bacterial pathogenesis. Infection and Immunity. 2002;70:1–4.
Mauriello EMF, Mignot T, Yang ZM, Zusman DR. Gliding Motility Revisited: How Do the Myxobacteria Move without Flagella? Microbiol Mol Biol R. 2010;74:229−+.
Bae HS, Im WT, Lee ST. Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int J Syst Evol Micr. 2005;55:1155–61.
Kimura T, Fukuda W, Sanada T, Imanaka T. Characterization of water-soluble dark-brown pigment from Antarctic bacterium, Lysobacter oligotrophicus. J Biosci Bioeng. 2014;14:S1389–1723.
Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, et al. AntiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 2013;41:W204–212.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.
Woese CR, Kandler O, Wheelis ML. Towards a Natural System of Organisms - Proposal for the Domains Archaea, Bacteria, and Eucarya. P Natl Acad Sci USA. 1990;87:4576–9.
Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, vol. 2. 2nd ed. New York: Springer; 2005. p. 1.
Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, vol. 2. 2nd ed. New York: Springer; 2005. p. 1.
Saddler GS, Bradbury JF. Order III. Xanthomonadales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, editors. Bergey’s Manual of Systematic Bacteriology, vol. 2. 2nd ed. New York: Springer; 2005. p. 63.
Saddler GS, Bradbury JF. Family I. Xanthomonadaceae. In: Garrity GM, editor. Bergey’s Manual of Systematic Bacteriology, vol. 2. 2nd ed. New York: Springer; 2005. p. 63.
Saddler GS, Bradbury JF. Lysobacter Christensen and Cook 1978, 372AL. In: Garrity GM, editor. Bergey’s Manual of Systematic Bacteriology, vol. 2. New York: Springer; 2005. p. 95–101.
Christensen P, Cook FD. Lysobacter, a New Genus of Nonfruiting, Gliding Bacteria with a High Base Ratio. Int J Syst Evol Microbiol. 1978;28:367–93.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.
This work was financially supported by the National Research Foundation (NRF-2011-0017670) of the Ministry of Science, ICT and Future Planning, Republic of Korea.
The authors declare that they have no competing interests.
JFK conceived, organized and supervised the project, interpreted the results, and edited the manuscript. SKK prepared the high-quality genomic DNA and arranged the acquisition of sequence data. MJK performed the sequence assembly, gene prediction, gene annotation, analyzed the genome information, and drafted the manuscript. JHY provided the bacterium and its microscopic image. All of the authors read and approved the final version of the manuscript before submission.
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Kwak, M., Kwon, S., Yoon, J. et al. Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea. Stand in Genomic Sci 10, 123 (2015) doi:10.1186/s40793-015-0116-8
- Soil bacterium