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Draft Genome Sequence of Newly Isolated Agarolytic Bacteria Cellulophaga omnivescoria sp. nov. W5C Carrying Several Gene Loci for Marine Polysaccharide Degradation

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Abstract

The continued research in the isolation of novel bacterial strains is inspired by the fact that native microorganisms possess certain desired phenotypes necessary for recombinant microorganisms in the biotech industry. Most studies have focused on the isolation and characterization of strains from marine ecosystems as they present a higher microbial diversity than other sources. In this study, a marine bacterium, W5C, was isolated from red seaweed collected from Yeosu, South Korea. The isolate can utilize several natural polysaccharides such as agar, alginate, carrageenan, and chitin. Genome sequence and comparative genomics analyses suggest that strain W5C belongs to a novel species of the Cellulophaga genus, from which the name Cellulophaga omnivescoria sp. nov. is proposed. Its genome harbors 3,083 coding sequences and 146 carbohydrate-active enzymes (CAZymes). Compared to other reported Cellulophaga species, the genome of W5C contained a higher proportion of CAZymes (4.7%). Polysaccharide utilization loci (PUL) for agar, alginate, and carrageenan were identified in the genome, along with other several putative PULs. These PULs are excellent sources for discovering novel hydrolytic enzymes and pathways with unique characteristics required for biorefinery applications, particularly in the utilization of marine renewable biomass. The type strain is JCM 32108T (= KCTC 13157BPT).

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References

  1. Abt B, Lu M, Misra M et al (2011) Complete genome sequence of Cellulophaga algicola type strain (IC166). Stand Genom Sci 4:72–80. https://doi.org/10.4056/sigs.1543845

    Article  CAS  Google Scholar 

  2. Alper H, Stephanopoulos G (2009) Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 7:715–723. https://doi.org/10.1038/nrmicro2186

    Article  PubMed  CAS  Google Scholar 

  3. Auch AF, Jan von M, Klenk H-P, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci 2:117–134. https://doi.org/10.4056/sigs.531120

    Article  Google Scholar 

  4. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry, 5th Edn. W. H. Freeman, New York

    Google Scholar 

  5. Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50(Pt 5):1861–1868. https://doi.org/10.1099/00207713-50-5-1861

    Article  PubMed  CAS  Google Scholar 

  6. Fang G, Rocha EPC, Danchin A (2008) Persistence drives gene clustering in bacterial genomes. BMC Genom 9:4. https://doi.org/10.1186/1471-2164-9-4

    Article  CAS  Google Scholar 

  7. Johansen JE, Nielsen P, Sjøholm C (1999) Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. Int J Syst Bacteriol 49 Pt 3:1231–1240. https://doi.org/10.1099/00207713-49-3-1231

  8. Kahng H-Y, Chung BS, Lee D-H et al (2009) Cellulophaga tyrosinoxydans sp. nov., a tyrosinase-producing bacterium isolated from seawater. Int J Syst Evol Microbiol 59:654–657. https://doi.org/10.1099/ijs.0.003210-0

    Article  PubMed  CAS  Google Scholar 

  9. Lahaye M, Robic A (2007) Structure and functional properties of ulvan, a polysaccharide from green seaweeds. Biomacromol 8:1765–1774. https://doi.org/10.1021/bm061185q

    Article  CAS  Google Scholar 

  10. Lee I, Kim YO, Park S-C, Chun J (2015) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760

    Article  PubMed  CAS  Google Scholar 

  11. Lee SB, Cho SJ, Kim JA et al (2014) Metabolic pathway of 3,6-anhydro-L-galactose in agar-degrading microorganisms. Biotechnol Bioproc Eng 19:866–878. https://doi.org/10.1007/s12257-014-0622-3

    Article  CAS  Google Scholar 

  12. Lee SB, Kim JA, Lim HS (2016) Metabolic pathway of 3,6-anhydro-D-galactose in carrageenan-degrading microorganisms. Appl Microbiol Biotechnol 100:4109–4121. https://doi.org/10.1007/s00253-016-7346-6

    Article  PubMed  CAS  Google Scholar 

  13. Liu G, Wu S, Jin W, Sun C (2016) Amy63, a novel type of marine bacterial multifunctional enzyme possessing amylase, agarase and carrageenase activities. Sci Rep 6:415. https://doi.org/10.1038/srep18726

    Article  CAS  Google Scholar 

  14. Lombard V, Golaconda Ramulu H, Drula E et al (2013) The carbohydrate-active enzymes database (CAZy) in 2013. Nucl Acids Res 42:D490–D495. https://doi.org/10.1093/nar/gkt1178

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Ma S, Tan Y-L, Yu W-G, Han F (2013) Cloning, expression and characterization of a new ι-carrageenase from marine bacterium, Cellulophaga sp. Biotechnol Lett 35:1617–1622. https://doi.org/10.1007/s10529-013-1244-0

    Article  PubMed  CAS  Google Scholar 

  16. Mann AJ, Hahnke RL, Huang S et al (2013) The genome of the alga-associated marine Flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. Appl Environ Microbiol 79:6813–6822. https://doi.org/10.1128/AEM.01937-13

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60

    Article  Google Scholar 

  18. Mergaert J, Verdonck L, Kersters K (1993) Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend. as Pantoea ananas (Serrano 1928) comb. nov., respectively, and description of Pantoea stewartii subsp. indologenes subsp. nov. Int J Syst Bacteriol 43:162–173. https://doi.org/10.1111/j.1574-6968.199.tb08826.x

    Article  Google Scholar 

  19. Mori T, Takahashi M, Tanaka R et al (2014) Draft genome sequence of Falsirhodobacter sp. strain Alg1, an alginate-degrading bacterium isolated from fermented brown algae. Genome Announc 2:e00826–e00814. https://doi.org/10.1128/genomeA.00826-14

    Article  PubMed  PubMed Central  Google Scholar 

  20. Park S, Oh K-H, Lee S-Y et al (2012) Cellulophaga geojensis sp. nov., a member of the family Flavobacteriaceae isolated from marine sand. Int J Syst Evol Microbiol 62:1354–1358. https://doi.org/10.1099/ijs.0.033340-0

    Article  PubMed  CAS  Google Scholar 

  21. Parte S, Sirisha VL, D’Souza JS (2017) Biotechnological applications of marine enzymes from algae, bacteria, fungi, and sponges. Adv Food Nutr Res 80:75–106. https://doi.org/10.1016/bs.afnr.2016.10.005

    Article  PubMed  CAS  Google Scholar 

  22. Pati A, Abt B, Teshima H et al (2011) Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Stand Genom Sci 4:221–232. https://doi.org/10.4056/sigs.1774329

    Article  CAS  Google Scholar 

  23. Ramos KRM, Valdehuesa KNG, Liu H et al (2014) Combining De Ley–Doudoroff and methylerythritol phosphate pathways for enhanced isoprene biosynthesis from D-galactose. Bioproc Biosyst Eng 37:2505–2513. https://doi.org/10.1007/s00449-014-1228-z

    Article  CAS  Google Scholar 

  24. Sun C, Fu G-Y, Zhang C-Y et al (2016) Isolation and complete genome sequence of Algibacter alginolytica sp. nov., a novel seaweed-degrading bacteroidetes bacterium with diverse putative polysaccharide utilization loci. Appl Environ Microbiol 82:2975–2987. https://doi.org/10.1128/AEM.00204-16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Tamura J-I, Hasegawa K, Kadowaki K et al (1995) Molecular cloning and sequence analysis of the gene encoding an endo α-1,4 polygalactosaminidase of Pseudomonas sp. 881. J Ferment Bioeng 80:305–310. https://doi.org/10.1016/0922-338X(95)94196-X

    Article  CAS  Google Scholar 

  26. Whitman WB (2015) Bergey’s manual of systematics of archaea and bacteria. https://doi.org/10.1002/9781118960608

  27. Yin Y, Mao X, Yang J et al (2012) dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucl Acids Res 40:W445–W451. https://doi.org/10.1093/nar/gks479

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Yun EJ, Lee S, Kim HT et al (2014) The novel catabolic pathway of 3,6-anhydro-L-galactose, the main component of red macroalgae, in a marine bacterium. Environ Microbiol 17:1677–1688. https://doi.org/10.1111/1462-2920.12607

    Article  PubMed  CAS  Google Scholar 

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Funding

This work was supported by the Basic Science Research Program and Korea Research Fellowship Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (Nos. 2015H1D3A1062172 and 2016R1C1B1013252), and the Ministry of Education (No. 2009-0093816).

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Author notes

  1. Llewelyn S. Moron

    Present address: Biology Department, College of Science, De La Salle University, Manila, Philippines

  2. Kris Niño G. Valdehuesa and Kristine Rose M. Ramos have contributed equally to this work.

Authors and Affiliations

  1. Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea

    Kris Niño G. Valdehuesa, Kristine Rose M. Ramos, Llewelyn S. Moron, Grace M. Nisola & Wook-jin Chung

  2. School of Biological Sciences, Seoul National University, Seoul, South Korea

    Imchang Lee

  3. Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, South Korea

    Won-keun Lee

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  1. Kris Niño G. Valdehuesa
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Correspondence to Wook-jin Chung.

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Valdehuesa, K.N.G., Ramos, K.R.M., Moron, L.S. et al. Draft Genome Sequence of Newly Isolated Agarolytic Bacteria Cellulophaga omnivescoria sp. nov. W5C Carrying Several Gene Loci for Marine Polysaccharide Degradation. Curr Microbiol 75, 925–933 (2018). https://doi.org/10.1007/s00284-018-1467-3

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