Journal of Microbiology and Biotechnology
The Korean Society for Microbiology and Biotechnology publishes the Journal of Microbiology and Biotechnology.

2019 ; Vol.29-7: 1144~1154

AuthorByeollee Kim, So-Ra Han, Janardan Lamichhane, Hyun Park, Tae-Jin Oh
Place of dutyDepartment of Life Science and Biochemical Engineering, SunMoon University, Asan, Korea
TitleDraft genome analysis of antimicrobial Streptomyces isolated from Himalayan lichen
PublicationInfo J. Microbiol. Biotechnol.2019 ; Vol.29-7
AbstractThere have been several studies regarding lichen-associated bacteria obtained from diverse environments. Our screening process identified 49 bacterial species in two lichens from the Himalayas: 17 species of Actinobacteria, 19 species of Firmicutes, and 13 species of Proteobacteria. We discovered five types of strong antimicrobial agent-producing bacteria. Although some strains exhibited weak antimicrobial activity, NP088, NP131, NP132, NP134, and NP160 exhibited strong antimicrobial activity against all multidrug-resistant strains. Polyketide synthase (PKS) fingerprinting revealed results for 69 of 148 strains; these had similar genes, such as fatty acid-related PKS, adenylation domain genes, PfaA, and PksD. Although the association between antimicrobial activity and the PKS fingerprinting results is poorly resolved, NP160 had six types of PKS fingerprinting genes, as well as strong antimicrobial activity. Therefore, we sequenced the draft genome of strain NP160, and predicted its secondary metabolism using antiSMASH version 4.2. NP160 had 46 clusters and was predicted to produce similar secondary metabolites with similarities of 5–100%. Although NP160 had 100% similarity with the alkylresorcinol biosynthetic gene cluster, our results showed low similarity with existing members of this biosynthetic gene cluster, and most have not yet been revealed. In conclusion, we expect that lichen-associated bacteria from the Himalayas can produce new secondary metabolites, and we found several secondary metabolite-related biosynthetic gene clusters to support this hypothesis.
Full-Text
Supplemental Data
Key_wordAntimicrobial activity, draft genome sequencing, fingerprinting, Himalayan lichen-associated bacteria, polyketide synthase, secondary metabolites
References
  1. White PA, Oliveira RC, Oliveira AP, Serafini MR, Araújo AA, Gelain DP, et al. 2014. Antioxidant activity and mechanisms of action of natural compounds, isolated from lichens: a systematic review. Molecules 19: 14496-14527.
    Pubmed CrossRef Pubmed Central
  2. He H, Bigelis R, Yang HY, Chang LP, Singh MP. 2005. Lichenicolins A and B, new bisnaphthopyrones from an unidentified lichenicolous fungus, strain LL-RB0668. J. Antibiot. Tokyo 58: 731-736.
    Pubmed CrossRef
  3. Oksanen I, Jokela J, Fewer DP, Wahlsten M, Rikkinen J, Sivonen K. 2004. Discovery of rare and highly toxic microcystins from lichen-associated cyanobacterium Nostoc sp. strain IO-102-I. Appl. Environ. Microbiol. 70: 5756-5763.
    Pubmed CrossRef Pubmed Central
  4. Mushegian AA, Peterson CN, Baker CC, Pringle A. 2011. Bacterial diversity across individual lichens. Appl. Environ. Microbiol. 77: 4249-4252.
    Pubmed CrossRef Pubmed Central
  5. Parrot D, Legrave N, Delmail D, Grube M, Suzuki M, Tomasi S. 2016. Review - lichen-associated bacteria as a hot spot of chemodiversity: focus on uncialamycin, a promising compound for future medicinal applications. Planta Med. 82:1143-1152.
    Pubmed CrossRef
  6. Parrot D, Intertaglia L, Jehan P, Grube M, Suzuki MT, Tomasi S. 2018. Chemical analysis of the alphaproteobacterium strain MOLA1416 associated with the marine lichen Lichina pygmaea. Phytochemistry 145: 57-67.
    Pubmed CrossRef
  7. Bertrand RL, Sorensen JL. 2018. A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J. Ind. Microbiol. Biotechnol. 45: 1067-1081.
    Pubmed CrossRef
  8. Miyanaga A, Kudo F, Eguchi T. 2018. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat. Prod. Rep. 35: 1185-1209.
    Pubmed CrossRef
  9. Zhang W, Zhang F, Li Z, Miao X, Meng Q, Zhang X. 2009. Investigation of bacteria with polyketide synthase genes and antimicrobial activity isolated from South China Sea sponges. J. Appl. Microbiol. 107: 567-575.
    Pubmed CrossRef
  10. Ayuso-Sacido A, Genilloud O. 2005. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes:detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb. Ecol. 49: 10 -24.
    Pubmed CrossRef
  11. Sigurbjörnsdóttir MA, Vilhelmsson O. 2016. Selective isolation of potentially phosphate-mobilizing, biosurfactantproducing and biodegradative bacteria associated with a sub-Artic, terricolous lichen, Peltigera membranacea. FEMS Microbiol. Ecol. 92(6): fiw090.
    Pubmed CrossRef
  12. Sigurbjörnsdóttir MA, Heiðmarsson S, Jónsdóttir AR, Vilhelmsson O. 2014. Novel bacteria associated with Arctic seashore lichens have potential roles in nutrient scavenging. Can. J. Microbiol. 60: 307-317.
    Pubmed CrossRef
  13. Baniya CB, Solhøy T, Gauslaa Y, Palmer MW. 2010. The elevation gradient of lichen species richness in Nepal. Lichenologist 42: 83-96.
    CrossRef
  14. Devkota S, Chaudhary RP, Werth S, Scheidegger C. 2017. Indigenous knowledge and use of lichens by the lichenophilic communities of the Nepal Himalaya. J. Ethnobiol. Ethnomed. 13: 1-10.
    Pubmed CrossRef Pubmed Central
  15. Jha BN, Shrestha M, Pandey DP, Bhattarai T, Bhattarai HD, Paudel B. 2017. Investigation of antioxidant, antimicrobial and toxicity activities of lichens from high altitude regions of Nepal. BMC Complement Altern. Med. 17(1): 282 doi:10.1186/s12906-017-1797-x.
    Pubmed CrossRef Pubmed Central
  16. Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. 2011. Bacterial communities associated with the lichen symbiosis. Appl. Environ. Microbiol. 77: 1309-1314.
    Pubmed CrossRef Pubmed Central
  17. Han S R, Y u SC, Ahn DH, P ark H , O h TJ. 20 16. C omplete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen. J. Biotechnol. 226: 16-17.
    Pubmed CrossRef
  18. Kim MK, Park H, Oh TJ. 2014. Antibacterial and antioxidant capacity of polar microorganisms isolated from Arctic lichen Ochrolechia sp. Pol. J. Microbiol. 63: 317-322.
  19. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
    Pubmed CrossRef
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549.
    Pubmed CrossRef Pubmed Central
  21. Bauer AW, Kirby MM, Sherris JC, Truck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clinic. Pathol. 45: 493-496.
    Pubmed CrossRef
  22. Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J, et al. 2011. The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi plateau, China. Curr. Microbiol. 62: 182-190.
    Pubmed CrossRef
  23. Gaber A A, B adr O M, E mara S A, I brahim A M. 2 0 15. Antitumor activity of two Streptomyces extracts (Ag18 & Ag20) on Ehrlich ascites tumor in mice: in vitro and in vivo studies. J. Biosci. Appl. Res. 1: 20-29.
  24. Wawrik B, Kerkhof L, Zylstra GJ, Kukor JJ. 2005. Identification of unique type II polyketide synthase genes in soil. Appl. Environ. Microbiol. 71: 2232-2238.
    Pubmed CrossRef Pubmed Central
  25. Han SR, Lee JH, Kang S, Park H, Oh TJ. 2016. Complete genome sequence of opine-utilizing Variovorax sp. strain PAMC28711 isolated from an Antarctic lichen. J. Biotechnol. 25: 46-47.
    Pubmed CrossRef
  26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
    Pubmed CrossRef Pubmed Central
  27. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, et al. 2017. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45: W36-W41.
    Pubmed CrossRef Pubmed Central
  28. Ayuso A, Clark D, González I, Salazar O, Anderson A, Genilloud O. 2005. A novel actinomycete strain de-replication approach based on the diversity of polyketide synthase and nonribosomal peptide synthetase biosynthetic pathways. Appl. Microbiol. Biotechnol. 67: 795-806.
    Pubmed CrossRef
  29. Zheng KX, Jiang Y, Jiang JX, Huang R, He J, Wu SH. 2019. A new phthalazinone derivative and a new isoflavonid glycoside from lichen-associated Amycolatopsis sp. Fitoterapia 35: 85-89.
    Pubmed CrossRef
  30. Sigurbjörnsdóttir MA, Andrésson ÓS, Vilhelmsson O. 2016. Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review. World J. Microbiol. Biotechnol. 32: 68.
    Pubmed CrossRef
  31. Butcher RA, Schroeder FC, Fischbach MA, Straight PD, Kolter R, Walsh CT, Clardy J. 2007. The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 104: 1506-1509.
    Pubmed CrossRef Pubmed Central
  32. Schneider O, Simic N, Aachmann FL, Rückert C, Kristiansen KA, Kalinowski J, et al. 2018. Genome mining of Streptomyces sp. YIM 130001 isolated from lichen affords new thiopeptide antibiotic. Front Microbiol. 9: 3139.
    Pubmed CrossRef Pubmed Central
  33. Jeon BJ, Kim JD, Han JW, Kim BS. 2016. Antifungal activity of rimocidin and a new rimocidin derivative BU16 produced by Streptomyces mauvecolor BU16 and their effects on pepper anthracnose. J. Appl. Microbiol. 120: 1219-1228.
    Pubmed CrossRef
  34. Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. 2018. Secondary metabolism in the lichen symbiosis. Chem. Soc. Rev. 47: 1730-1760.
    Pubmed CrossRef



Copyright © 2009 by the Korean Society for Microbiology and Biotechnology.
All right reserved. Mail to jmb@jmb.or.kr
Online ISSN: 1738-8872    Print ISSN: 1017-7825    Powered by INFOrang Co., Ltd