Molecular Identification and Determination of Antimicrobial Activity of Micromonospora and Nonomuraea Isolates

Abstract

Actinobacteria are the largest member of the Bacteria group, which can live in different ecosystems and create a rich source of secondary metabolites. Rare actinobacteria have become one of the important targets in terms of active metabolites. Micromonospora and Nonomuraea, which are rare Actinobacteria, are among the genera that have attracted the most attention recently. In the present study, it was aimed to isolate Micromonospora and Nonomuraea genus members from an endemic species. 16S rRNA gene region analyzes were used for molecular identification of isolates. As a result of the analysis, it was determined that 10 isolates were members of Micromonospora and 2 isolates were members of Nonomuraea. It has been determined that Nonomuraea sp. HCI 01 and HCI 02 strains and Micromonospora sp. HCI 04, HCI 23, HCI 39, HCI 44 and HCI 49 strains have the potential to become a possible new species. In biological activity studies, Micromonospora sp. HCI 45, HCI 47 and HCI 49 strains were found to be active against E. coli, HCI 20 and HSF 02 against S aureus, and HCI 04 and HSF 02 against S. cerevisiae. Nonomuraea sp. HCl 02 was found to have antimicrobial activity against S. cerevisiae. The results obtained have shown that there are possible new species and the existence of biologically active molecules with the potential to be antibiotics.

Keywords

• 16S rRNA
• antimicrobial activity
• Micromonospora
• Nonomuraea

Micromonospora ve Nonomuraea İzolatlarının Moleküler Tanımlamaları ve Antimikrobiyal Aktivitelerinin Belirlenmesi

Abstract

Aktinobakteriler farklı ekosistemlerde yaşayabilen ve sekonder metabolit açısından zengin kaynak oluşturan bakteri grubunun en büyük üyesini oluşturmaktadır. Nadir aktinobakteriler ise aktif metabolitler açısından önemli hedeflerden biri haline gelmiştir. Nadir aktinobakterilerden olan Micromonospora ve Nonomuraea son dönemde en çok ilgi çeken cinslerdendir. Sunulan çalışmada endemik bir türden Micromonospora ve Nonomuraea cins üyelerinin izolasyonu hedeflenmiştir. İzolatların moleküler tanımlamalarında 16S rRNA gen bölgesi analizleri kullanılmıştır. Analizler sonucunda 10 izolatın Micromonospora üyesi, 2 izolatın Nonomuraea üyesi olduğu belirlenmiştir. Nonomuraea sp. HCI 01 ve HCI 02 suşları Micromonospora sp. HCI 04, HCI 23, HCI 39, HCI 44 ve HCI 49 suşlarının olası yeni birer tür olma potansiyeline sahip olduğu tespit edilmiştir. Antimikrobiyal aktivite çalışmalarında Micromonospora sp. HCI 45, HCI 47 ve HCI 49 suşları E. coli’ye karşı, HCI 20 ve HSF 02 S. aureus’a karşı ve HCI 04 ve HSF 02 ise S. cerevisiae’a karşı etkinlik gösterdiği belirlenmiştir. Nonomuraea sp. ise HCI 02 S. cerevisiae’a karşı antimikrobiyal aktiviteye sahip olduğu görülmüştür. Elde edilen sonuçlarla, olası yeni türlerin olduğu ve antibiyotik olma potansiyeline sahip biyolojik aktif moleküllerin varlığı gösterilmiştir.

Keywords

• 16S rRNA
• antimikrobiyal aktivite
• Micromonospora
• Nonomuraea

References

1. Abdel-Mageed WM, Al-Wahaibi LH, Lehri B, Al-Saleem MS, Goodfellow M, KusumaAB, . . .Jaspars M, 2021. Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench. Marine Drugs, 19(5): 243.
2. Antal N, Fiedler HP, Stackebrandt E, Beil W, Ströch K, Zeeck A, 2005. Retymicin, Galtamycin B, Saquayamycin Z and Ribofuranosyllumichrome, novel secondary metabolites from Micromonospora sp. Tü 6368. The Journal of Antibiotics, 58(2): 95-102.
3. Ay H, Nouioui I, Klenk HP, Cetin D, Igual JM, Sahin N, Isik K, 2020. Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake. Antonie van Leeuwenhoek, 113(6): 791-801.
4. Back CR, Stennett H L, Williams SE, Wang L, Ojeda Gomez J, Abdulle OM, . . . Jepson MA, 2021. A new Micromonospora strain with antibiotic activity isolated from the microbiome of a mid-Atlantic deep-sea sponge. Marine Drugs, 19(2): 105.
5. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquar C, Klenk HP, . . . van Wezel GP, 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80(1): 1-43.
6. Benhadj M, Gacemi-Kirane D, Menasria T, Guebla K, Ahmane Z, 2019. Screening of rare actinomycetes isolated from natural wetland ecosystem (Fetzara Lake, northeastern Algeria) for hydrolytic enzymes and antimicrobial activities. Journal of King Saud University-Science, 31(4): 706-712.
7. Bérdy J, 2012. Thoughts and facts about antibiotics: where we are now and where we are heading. The Journal of Antibiotics, 65(8): 385-395.
8. Fei P, Chuan-Xi W, Yang X, Hong-Lei J, Lu-Jie C, Uribe P, . . Yun-Yang L, 2013. A new 20-membered macrolide produced by a marine-derived Micromonospora strain. Natural Product Research, 27(15): 1366-1371.

9. Hu X, Wang Y, Zhao C, Li S, Hu X, You X, . . . Jiang B, 2022. Mintaimycins, a Group of Novel Peptide Metabolites from Micromonospora sp. C-3509. Molecules, 27(4): 1150.
10. Igarashi M, Sawa R, Umekita M, Hatano M,Arisaka R, Hayashi C, . . . Kato C, 2021. Sealutomicins, new enediyne antibiotics from the deep-sea actinomycete Nonomuraea sp. MM565M-173N2. The Journal of Antibiotics, 74(5): 291-299.
11. Jones KL, 1949. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. Journal of Bacteriology, 57(2): 141-145.
12. Jukes TH, Cantor CR, 1969. Evolution of protein molecules. Mammalian Protein Metabolism, 3: 21-132.
13. Kim M, Chun J, 2014. 16S rRNA gene-based identification of bacteria and archaea using the EzTaxon server Methods in Microbiology (Vol. 41: 61-74): Elsevier.
14. Kim TK, Hewavitharana AK, Shaw PN, Fuerst JA, 2006. Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction. Applied and Environmental Microbiology, 72(3): 2118-2125.
15. Kumar S, Stecher G, Li M, Knyaz C, Tamura K, 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547.
16. Lancini G, Lorenzetti R, 1993. Biosynthesis of secondary metabolites Biotechnology of Antibiotics and Other Bioactive Microbial Metabolites (ss. 95-132): Springer.
17. Malisorn K, Embaen S, Sribun A, Saeng-in P, Phongsopitanun W,Tanasupawat S, 2020. Identification and antimicrobial activities of Streptomyces, Micromonospora, and Kitasatospora strains from rhizosphere soils. Journal of Applied Pharmaceutical Science, 10(02): 123-112.
18. Martínez-Hidalgo P, Flores-Félix JD, Velázquez E, Brau L, Trujillo ME, Martínez-Molina E, 2020. High taxonomic diversity of Micromonospora strains isolated from Medicago sativa nodules in Western Spain and Australia. Systematic and Applied Microbiology, 43(1): 126043.
19. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, . . . Göker M, 2018. Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology, 2007.
20. Ouhdouch Y, Barakate M, Finance C, 2001. Actinomycetes of Moroccan habitats: isolation and screening for antifungal activities. European Journal of Soil Biology, 37(2): 69-74.
21. Ozdemir-Kocak F, Isik K, Veyisoglu A, Tatar D, Sahin N, 2014. Nonomuraea muscovyensis sp. nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 64(7): 2467-2472.
22. Primahana G, Risdian C, Mozef T, Sudarman E, Köck M, Wink J, Stadler M, 2020. Nonocarbolines A–E, β-carboline antibiotics produced by the rare actinobacterium Nonomuraea sp. from Indonesia. Antibiotics, 9(3): 126.
23. Sembiring L, 2000. Selective isolation and characterisation of streptomycetes associated with the rhizosphere of the tropical legume, Paraserianthes falcataria (L) Nielsen. University of Newcastle upon Tyne.
24. Sun X, Qiu S, Luo X, Jin P, Zhao J, Wu X, . . . Xiang W, 2021. Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin. Antonie van Leeuwenhoek, 114(6): 697-708.
25. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W,Kämpfer P, 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. International Journal of Systematic and Evolutionary Microbiology, 60(1): 249-266.
26. Veyisoglu A, Carro L, Cetin D, Igual JM, Klenk HP, Sahin N, 2020. Micromonospora orduensis sp. nov., isolated from deep marine sediment. Antonie van Leeuwenhoek, 113(3): 397-405.
27. Vickers NJ, 2017. Animal communication: when i’m calling you, will you answer too? Current Biology, 27(14): 713-715.
28. Williams S, Goodfellow M, Alderson G, Wellington E, Sneath P, Sackin M, 1983. Numerical classification of Streptomyces and related genera. Microbiology, 129(6): 1743-1813.
29. Yamamura H, Hayakawa M, Iimura Y, 2003. Application of sucrose‐gradient centrifugation for selective isolation of Nocardia spp. from soil. Journal of Applied Microbiology, 95(4): 677-685.
30. Yang T, Yamada K, Zhou T, Harunari E, Igarashi Y, Terahara T, . . . Imada C, 2019. Akazamicin, a cytotoxic aromatic polyketide from marine-derived Nonomuraea sp. The Journal of Antibiotics, 72(4): 202-209.