Folia Microbiologica

, Volume 61, Issue 2, pp 159–168 | Cite as

The isolation and characterization of actinobacteria from dominant benthic macroinvertebrates endemic to Lake Baikal

  • Denis Axenov-GribanovEmail author
  • Yuriy Rebets
  • Bogdan Tokovenko
  • Irina Voytsekhovskaya
  • Maxim Timofeyev
  • Andriy Luzhetskyy


The high demand for new antibacterials fosters the isolation of new biologically active compounds producing actinobacteria. Here, we report the isolation and initial characterization of cultured actinobacteria from dominant benthic organisms’ communities of Lake Baikal. Twenty-five distinct strains were obtained from 5 species of Baikal endemic macroinvertebrates of amphipods, freshwater sponges, turbellaria worms, and insects (caddisfly larvae). The 16S ribosomal RNA (rRNA)-based phylogenic analysis of obtained strains showed their affiliation to Streptomyces, Nocardia, Pseudonocardia, Micromonospora, Aeromicrobium, and Agromyces genera, revealing the diversity of actinobacteria associated with the benthic organisms of Lake Baikal. The biological activity assays showed that 24 out of 25 strains are producing compounds active against at least one of the test cultures used, including Gram-negative bacteria and Candida albicans. Complete dereplication of secondary metabolite profiles of two isolated strains led to identification of only few known compounds, while the majority of detected metabolites are not listed in existing antibiotic databases.


Streptomyces Agmatine Sulfamic Acid Freshwater Sponge Biomass Extract 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the Ministry of Education and Science of the Russian Federation as a part of Goszadanie projects (No. 6.382.2014/K), Russian Science Foundation (project N 14-14-00400), Russian Foundation for Basic Research (projects N 14-04-00501, 15-04-06685), US Civilian Research & Development Foundation (project N FSCX-15-61168-0), grants of Irkutsk State University for young researchers, and Deutscher Akademischer Austauschdienst.

Conflict of interest

The authors declare that they have no competing interests.

Statement of human rights

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Statement on the welfare of animals

This article does not contain any studies with human participants or vertebrate animals performed by any of the authors.

Mentioned in the article were Baikalian macroinvertebrate species not involved in endangered or protected species. No specific permissions were required for the sampling of invertebrate species.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

12223_2015_421_MOESM1_ESM.docx (8.4 mb)
ESM 1 (DOCX 8618 kb)


  1. Abdelmohsen UR, Bayer K, Hentschel U (2014) Diversity, abundance and natural products of marine sponge-associated actinomycetes. Nat Prod Rep 31:381–399. doi: 10.1039/C3np70111e CrossRefPubMedGoogle Scholar
  2. Alvin A, Miller KI, Neilan BA (2014) Exploring the potential of endophytes from medicinal plants as sources of antimycobacterial compounds. Microbiol Res 169:483–495. doi: 10.1016/j.micres.2013.12.009 CrossRefPubMedGoogle Scholar
  3. Bagwell CE, Bhat S, Hawkins GM, Smith BW, Biswas T, Hoover TR, Shimkets LJ (2008) Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. PLoS One 3:e3878. doi: 10.1371/journal.pone.0003878 PubMedCentralCrossRefPubMedGoogle Scholar
  4. Costa R, Keller-Costa T, Gomes NCM, da Rocha UN, van Overbeek L, van Elsas JD (2013) Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis. Microb Ecol 65:232–244. doi: 10.1007/s00248-012-0102-2 CrossRefPubMedGoogle Scholar
  5. Currie CR, Scott JA, Summerbell RC, Malloch D (2003) Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature 423:461–461. doi: 10.1038/Nature01563 CrossRefGoogle Scholar
  6. Demain AL, Adrio JL (2008) Contributions of microorganisms to industrial biology. Mol Biotechnol 38:41–55. doi: 10.1007/s12033-007-0035-z CrossRefPubMedGoogle Scholar
  7. Duncan SJ, Grüschow S, Williams DH, McNicholas C, Purewal R, Hajek M, Moore M (2002) Isolation and structure elucidation of chlorofusin, a novel p53-MDM2 antagonist from a Fusarium sp. J Am Chem Soc 124:14503–14503. doi: 10.1021/Ja025114k CrossRefGoogle Scholar
  8. Exposito MA, López B, Fernández R, Vázquez M, Debitus C, Iglesias T, Riguera R (1998) Minalemines A-F: sulfamic acid peptide guanidine derivatives isolated from the marine tunicate Didemnun rodriguesi. Tetrahedron Lett 54:7539–7550. doi: 10.1016/S0040-4020(98)00388-3 CrossRefGoogle Scholar
  9. Exposito A, Fernandez-Suarez M, Iglesias T, Munoz L, Riguera R (2001) Total synthesis and absolute configuration of minalemine A, a guanidine peptide from the marine tunicate Didemnum rodriguesi. J Org Chem 66:4206–4213. doi: 10.1021/Jo010076t CrossRefPubMedGoogle Scholar
  10. Faghri J, Bourbour S, Moghim S, Meidani M, Safaei HG, Hosseini N, Sedighi M (2014) Comparison of three phenotypic and deoxyribonucleic acid extraction methods for isolation and Identification of Nocardia spp. Adv Biomed Res 3:151. doi: 10.4103/2277-9175.137839 PubMedCentralCrossRefPubMedGoogle Scholar
  11. Gladkikh AS, Kalyuzhnaya OV, Belykh OI, Ahn TS, Parfenova VV (2014) Analysis of bacterial communities of two Lake Baikal endemic sponge species. Microbiology 83:787–797. doi: 10.1134/S002626171406006x CrossRefGoogle Scholar
  12. Gledhill WE, Casida LE (1969) Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 18:340–349PubMedCentralPubMedGoogle Scholar
  13. Hale KJ, Cai JQ (1996) Synthetic studies on the azinothricin family of antitumour antibiotics. 5. Asymmetric synthesis of two activated esters for the northern sector of A83586C. Tetrahedron Lett 37:4233–4236. doi: 10.1016/0040-4039(96)00804-0 CrossRefGoogle Scholar
  14. Hentschel U, Piel J, Degnan SM, Taylor MW (2012) Genomic insights into the marine sponge microbiome. Nat Rev Microbiol 10:641–675. doi: 10.1038/Nrmicro2839 CrossRefPubMedGoogle Scholar
  15. Jenke-Kodama H, Dittmann E (2009) Evolution of metabolic diversity: insights from microbial polyketide synthases. Phytochemistry 70:1858–1866. doi: 10.1016/j.phytochem.2009.05.021 CrossRefPubMedGoogle Scholar
  16. Jin JM, Lee S, Lee J, Baek SR, Kim JC, Yun SH, Lee YW (2010) Functional characterization and manipulation of the apicidin biosynthetic pathway in Fusarium semitectum. Mol Microbiol 76:456–466. doi: 10.1111/j.1365-2958.2010.07109.x CrossRefPubMedGoogle Scholar
  17. Jung D, Seo EY, Epstein SS, Joung Y, Han J, Parfenova VV, Ahn TS (2014) Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia. FEMS Microbiol Ecol 90:417–423. doi: 10.1111/1574-6941.12399 PubMedGoogle Scholar
  18. Kaluzhnaya OV, Itskovich VB (2014) Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia. Rus J Genet 50:667–676. doi: 10.1134/S1022795414060052 CrossRefGoogle Scholar
  19. Kaluzhnaya OV, Itskovich VB, McCormack GP (2011) Phylogenetic diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis. World J Microbiol Biotechnol 27:1955–1959. doi: 10.1007/s11274-011-0654-1 CrossRefGoogle Scholar
  20. Kaluzhnaya OV, Krivich AA, Itskovich VB (2012) Diversity of 16S rRNA genes in metagenomic community of the freshwater sponge Lubomirskia baicalensis. Rus J Genet 48:855–858. doi: 10.1134/S1022795412070058 CrossRefGoogle Scholar
  21. Katoh S (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780PubMedCentralCrossRefPubMedGoogle Scholar
  22. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199 PubMedCentralCrossRefPubMedGoogle Scholar
  23. Kieser BM, Buttner MJ, Charter KF, Hopwood D (2000) Practical streptomyces genetics. John Innes Foundation, NorwichGoogle Scholar
  24. Kozhova O, Izmest’eva L (1998) Lake Baikal. Evolution and biodiversity. Backhuys Publ, LeidenGoogle Scholar
  25. Kroiss J, Kaltenpoth M, Schneider B, Schwinger MG, Hertweck C, Maddula RK, Svatoš A (2010) Symbiotic streptomycetes provide antibiotic combination prophylaxis for wasp offspring. Nat Chem Biol 6:261–263. doi: 10.1038/Nchembio.331 CrossRefPubMedGoogle Scholar
  26. Madden AA, Grassetti A, Soriano JAN, Starks PT (2013) Actinomycetes with antimicrobial activity isolated from paper wasp (Hymenoptera: Vespidae: Polistinae) nests. Environ Entomol 42:703–710. doi: 10.1603/En12159 CrossRefPubMedGoogle Scholar
  27. Mao J, Tang Q, Zhang Z, Wang W, Wei D, Huang Y, Goodfellow M (2007) Streptomyces radiopugnans sp. nov. a radiation-resistant actinomycete isolated from radiation-polluted soil in China. Int J Syst Evol Microbiol 57:2578–2582. doi: 10.1099/ijs.0.65027-0
  28. Monciardini P, Iorio M, Maffioli S, Sosio M, Donadio S (2014) Discovering new bioactive molecules from microbial sources. Microb Biotechnol 7:209–220. doi: 10.1111/1751-7915.12123 PubMedCentralCrossRefPubMedGoogle Scholar
  29. Mushegian AA, Peterson CN, Baker CCM, Pringle A (2011) Bacterial diversity across individual lichens. Appl Environ Microbiol 77:4249–4252. doi: 10.1128/Aem.02850-10 PubMedCentralCrossRefPubMedGoogle Scholar
  30. Nakagawa M, Hayakawa Y, Adachi K, Seto H (1990a) A new depsipeptide antibiotic, variapeptin. Agric Biol Chem 54:791–794CrossRefPubMedGoogle Scholar
  31. Nakagawa M, Hayakawa Y, Furihata K, Seto H (1990b) Structural studies on new depsipeptide antibiotics, variapeptin and citropeptin. J Antibiot 43:477–484CrossRefPubMedGoogle Scholar
  32. Nikapitiya C (2012) Bioactive secondary metabolites from marine microbes for drug discovery. Adv Food Nutr Res 65:363–387. doi: 10.1016/B978-0-12-416003-3.00024-X CrossRefPubMedGoogle Scholar
  33. Ruangpan L, Tendencia EA (2004) Disk diffusion method. Laboratory manual of standardized methods for antimicrobial sensitivity tests for bacteria isolated from aquatic animals and environment. SEAFDEC, Aquaculture Department, Tigbauan, pp 13–29Google Scholar
  34. Russinek OT, Takhteev VV, Gladkochub DP, Khodzher TV, Budnev NM (2012) Baikalogy. Nauka, NowosibirskGoogle Scholar
  35. Strohl WR (1997) Industrial antibiotics: today and the future. In: Strohl WR (ed) Biotechnology of antibiotics, 2nd edn. Marcel Dekker, New York, pp 1–47CrossRefGoogle Scholar
  36. Sujada N, Sungthong R, Lumyong S (2014) Termite nests as an abundant source of cultivable actinobacteria for biotechnological purposes. Microbes Environ 29:211–219. doi: 10.1264/jsme2.ME13183 PubMedCentralCrossRefPubMedGoogle Scholar
  37. Tang Y, Zhou G, Zhang L, Mao J, Luo X, Wang M, Fang C (2008) Aeromicrobium flavum sp. nov. isolated from air. Int J Syst Evol Microbiol 58:1860–1863. doi: 10.1099/ijs.0.65443-0
  38. Terkina IA, Drukker VV, Parfenova VV, Kostornova TY (2002) The biodiversity of actinomycetes in Lake Baikal. Microbiology 71:346–349. doi: 10.1023/A:1015871115187 CrossRefGoogle Scholar
  39. Terkina IA, Parfenova VV, Ahn TS (2006) Antagonistic activity of actinomycetes of Lake Baikal. Appl Biochem Microbiol 42:173–176. doi: 10.1134/S0003683806020104 CrossRefGoogle Scholar
  40. Timoshkin OA, Sitnikova TY, Rusinek OT, Pronin NM, Proviz VI, Melnik NG, Kamaltynov RM, Mazepova DF, Shoshnin AV (2001) Index of animal species inhabiting Lake Baikal and its catchment area. Nauka, NovosibirskGoogle Scholar
  41. Valverde A, Tuffin M, Cowan DA (2012) Biogeography of bacterial communities in hot springs: a focus on the actinobacteria. Extremophiles 16:669–679. doi: 10.1007/s00792-012-0465-9 CrossRefPubMedGoogle Scholar
  42. Vicente J, Stewart A, Song B, Hill RT, Wright JL (2013) Biodiversity of actinomycetes associated with Caribbean sponges and their potential for natural product discovery. Mar Biotechnol 15:413–424. doi: 10.1007/s10126-013-9493-4 CrossRefPubMedGoogle Scholar
  43. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi: 10.1128/Aem.00062-07 PubMedCentralCrossRefPubMedGoogle Scholar
  44. Whittle M, Willett P, Klaffke W, van Noort P (2003) Evaluation of similarity measures for searching the dictionary of natural products database. J Chem Inf Comput Sci 43:449–457. doi: 10.1021/Ci025591m CrossRefPubMedGoogle Scholar
  45. Zakharova YR, Galachyants YP, Kurilkina MI, Likhoshvay AV, Petrova DP, Shishlyannikov SM, Likhoshway YV (2013) The structure of microbial community and degradation of diatoms in the deep near-bottom layer of Lake Baikal. Plos One 8:1–12 8. doi: 10.1371/journal.pone.0059977 ARTN e59977

Copyright information

© Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2015

Authors and Affiliations

  • Denis Axenov-Gribanov
    • 1
    Email author
  • Yuriy Rebets
    • 2
  • Bogdan Tokovenko
    • 2
  • Irina Voytsekhovskaya
    • 1
  • Maxim Timofeyev
    • 1
  • Andriy Luzhetskyy
    • 2
  1. 1.Institute of Biology at Irkutsk State UniversityIrkutskRussia
  2. 2.Helmholtz Institute for Pharmaceutical Research SaarlandSaarbruckenGermany

Personalised recommendations