Genomic Characterization of Micromonospora Sp. B9E7 Isolated from a Rice Field in the Bafra Plain: Taxonomic Position and Secondary Metabolite Potential

Yıl 2025, Cilt: 8 Sayı: 6, 1831 - 1840, 15.11.2025

Ali Tokatlı , Kamil Işık

https://doi.org/10.34248/bsengineering.1768698

Öz

This study comprehensively examined the genetic, metabolic, and biotechnological potential of the Micromonospora sp. B9E7 isolate. Whole-genome sequencing and digital DNA-DNA hybridization (dDDH) analyses revealed that the isolate is genetically distinct from known species, suggesting it represents a novel species. Genome annotation identified 6,826 protein-coding genes and 297 functional subsystems; however, only 18% of the genome matched known functional categories, indicating many genes remain uncharacterized. Nineteen biosynthetic gene clusters associated with secondary metabolite production were detected, some showing similarity to known antibiotic and anticancer compounds. The isolate exhibited key plant growth-promoting traits, including phosphate solubilization, siderophore production, and high indole-3-acetic acid (IAA) synthesis. Conversely, it did not produce ammonia, fix nitrogen, or show antimicrobial activity against tested pathogens. These results suggest that B9E7 promotes plant growth primarily through direct mechanisms, such as nutrient solubilization and siderophore-mediated micronutrient acquisition, rather than indirect pathogen suppression. Overall, Micromonospora sp. B9E7 emerges as a promising candidate both as a taxonomically novel species and for biotechnological applications. Future research should focus on detailed phenotypic and biochemical characterization, and functional studies of its secondary metabolites. Additionally, combining B9E7 with other beneficial microorganisms or optimizing environmental conditions may enhance its efficacy in agricultural settings.

Anahtar Kelimeler

Bafra plain , Micromonospora , Biotechnology , Whole-genome , Plant growth-promoting

Etik Beyan

Ethics committee approval was not required for this study because there was no study on animals or humans.

Destekleyen Kurum

Ondokuz Mayıs University, TÜBİTAK

Proje Numarası

PYO.FEN.1904.22.005, 123Z804

Teşekkür

This study was supported by the Scientific Research Projects Coordination Unit (BAPKOB) of Ondokuz Mayıs University under project number PYO.FEN.1904.22.005 and also by The Scientific and Technological Research Council of Türkiye (TÜBİTAK) under the 1002-B Rapid Support Program (Project No: 123Z804).

Kaynakça

• Alexander DB, Zuberer DA. 1991. Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fertil Soils, 12(1): 39-45.
• Ali B, Sabri AN, Ljung K, Hasnain S. 2009. Auxin production by plant associated bacteria: impact on endogenous IAA content and growth of Triticum aestivum L. Lett Appl Microbiol, 48(5): 542-547.
• Asolkar RN, Kirkland TN, Jensen PR, Fenical W. 2010. Arenimycin, an antibiotic effective against rifampin-and methicillin-resistant Staphylococcus aureus from the marine actinomycete Salinispora arenicola. J Antibiot, 63(1): 37-39.
• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol, 19(5): 455-477.
• Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee S, Weber T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res, 47(W1): W81-W87.
• Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Xia F. 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep, 5(1): 8365.
• Cappuccino JG, Sherman N. 2002. Microbiology: A laboratory manual. San Francisco, CA: Pearson Education, Inc. 6th ed., pp: 15-224.
• Carro L, Pukall R, Spröer C, Kroppenstedt RM, Trujillo ME. 2012. Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum. Int J Syst Evol Microbiol, 62 (12): 2971-2977.
• Carro L, Riesco R, Spröer C, Trujillo ME. 2016. Micromonospora luteifusca sp. nov. isolated from cultivated Pisum sativum. Syst Appl Microbiol, 39(4): 237-242.
• Carro L, Veyisoglu A, Riesco R, Spröer C, Klenk HP, Sahin N, Trujillo ME. 2018. Micromonospora phytophila sp. nov. And Micromonospora luteiviridis sp. nov., isolated as natural inhabitants of plant nodules. Int J Syst Evol Microbiol, 68(1): 248-253.
• Cassinelli G, Di Matteo FR, Forenza S, Ripamonti MC, Rivola G, Arcamone, F, Pratesi G. 1980. New Anthracycline Glycosides from Micromonospora Ii. Isolation, Characterization and Biological Properties. J Antibiot, 33(12): 1468-1473.
• Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa M, Trujillo ME. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol, 68(1): 461-466.
• Compant S, Duffy B, Nowak J, Clément C, Barka EA. 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: Principles, mechanisms of action, and future prospects. Appl Environ Microbiol, 71(9): 4951-4959.
• Coronelli C, Bardone MR, Depaoli A, Ferrari P, Tuan G, Gallo GG. 1984. Teicoplanin, antibiotics from Actinoplanes teichomyceticus sp. nov. J Antibiot, 37(6): 621-626.
• Debono M, Merkel KE, Molloy RM, Barnhart M, Presti E, Hunt AH, Hamill RL. 1984. Actaplanin, new glycopeptide antibiotics produced by Actinoplanes missouriensis. J Antibiot 37(1): 85-95.
• Garcia LC, Martínez ME, Trujillo ME. 2010. Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. Int J Syst Evol Microbiol 60(2): 331-337.
• Gaur AC. 1990. Phosphate solubilizing microorganisms as biofertilizers. Omega Scientific, New Delhi, India
• Genilloud O. 2012. Genus micromonospora. The actinobacteria. In: Goodfellow M et al (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp: 1039-1057.
• Genilloud O. 2017. Actinomycetes: still a source of novel antibiotics. Nat Prod Rep, 34(10): 1203-1232.
• Hayakawa M, Nonomura H. 1987. Humic acid-vitamin agar, a new medium for the selective isolation of soil Actinomycetes. J Ferment Technol, 65(5): 501-509.
• Huang H, Wu X, Yi S, Zhou Z, Zhu J, Fang Z, Bao S. 2009. Rifamycin S and its geometric isomer produced by a newly found Actinomycete, Micromonospora rifamycinica. Antonie Van Leeuwenhoek, 95(2):143-148.
• Katz L, Baltz RH. 2016. Natural product discovery: past, present, and future. J Ind Microbiol Biotechnol, 43(2-3): 155-176.
• Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Chun J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J Syst Evol Microbiol, 62(Pt 3): 716-721.
• Kim TK, Hewavitharana AK, Shaw PN, Fuerst JA. 2006. Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction. Appl Environ Microb, 72(3): 2118-2125.
• Lancini G, Lorenzetti R. 1993. Biosynthesis of secondary metabolites. Biotechnology of antibiotics and other bioactive microbial metabolites. Springer, Berlin, pp 95-132.
• Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14(1): 60.
• Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker, M. 2022. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res, 50(D1): D801-D807.
• Meier-Kolthoff JP, Göker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun, 10(1): 2182.
• Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res, 42(D1): D206-D214.
• Parte AC, Sardà CJ, Meier-Kolthoff JP, Reimer LC, Göker M 2020. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol, 70(11): 5607-5612.
• Rajkumar M, Ae N, Prasad MNV, Freitas H. 2010. Potential of siderophore-producing bacteria for improving heavy metal phytoextraction. Trends Biotechnol, 28(3): 142-149.
• Riedlinger J. 2004. Abyssomicins, inhibitors of the paraaminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032. J Antibiot, 57(3): 271-279.
• Rodríguez H, Fraga R. 1999. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv, 17(4-5): 319-339.
• Rosselló-Móra R, Amann R. 2015. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol, 38(4): 209-216.
• Shirling ET, Gottlieb D. 1966. Methods for characterization of Streptomyces species. Int J Syst Bacteriol, 16(3): 313-340.
• Spaepen S, Vanderleyden J. 2011. Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol, 3(4): a001438.
• Subramani R, Aalbersberg W. 2012. Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res, 167(10): 571-580.
• Talukdar M, Bora TC, Jha DK. 2016. Micromonospora: a potential source of antibiotic. In Bioprospecting of Indigenous Bioresources of North-East India. Singapore, Springer Singapore, pp. 195-213.
• Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Rev Microbiol, 3(9): 711-721.
• Trujillo ME, Kroppenstedt RM, Fernádez-Molinero C, Schumann P, Martínez Molina E. 2007. Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. Nov., isolated from root nodules of Lupinus angustifolius. Int J Syst Evol Microbiol, 57(12): 2799-2804.
• Trujillo ME, Kroppenstedt RM, Schumann P, Carro L, Martínez-Molina E. 2006. Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia. Int J Syst Evol Microbiol, 56(10): 2381-2385.
• Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev, 71(3): 495-548.
• Veyisoğlu A, Tatar D. 2021. Screening of acidophilic actinobacteria that show activity against paddy pest fungi. Int J Agric Environ Food Sci, 5(3): 425-432.
• Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Stevens RL. 2017. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res, 45(D1): D535-D542.
• Williams ST, Goodfellow M, Wellington EMH, Vickers JC, Alderson G, Sneath PHA, Mortimer AM. 1983. A probability matrix for identification of some streptomycetes. Microbiology, 129(6): 1815-1830.