Antifungal activity of endophytic Streptomyces strains from Dendrobium orchids and the secondary metabolites of strain DR7-3 with its genome analysis

Nisachon Tedsree Kittisak Likhitwitayawuid Boonchoo Sritularak Karaked Tedsree Somboon Tanasupawat   

Open Access   

Published:  Sep 15, 2022

DOI: 10.7324/JAPS.2022.121204

Chemical fungicides are widely used in the agriculture sector and cause severe environmental problems. Biological control, a method using antagonistic organisms, has been considered one of the most promising strategies to tackle this issue. Actinomycetes, particularly Streptomyces strains, produced diverse classes of bioactive secondary metabolites. In this study, four Streptomyces strains, DR5-1, DR7-3, DR8-5, and DR8-8, isolated from three Dendrobium species (Orchidaceae), exhibited significant antifungal activity against five phytopathogenic fungi, particularly with high potency against Curvularia oryzae. The bacterial identification was performed based on phenotypic and chemotaxonomic characteristics, including the 16S rRNA gene sequence. Strain DR7-3 from the roots of Dendrobium findlayanum exhibited high antifungal activity, and its culture filtrate caused damage to the cell structure of C. oryzae SA04. It was identified as Streptomyces solisilvae based on the average nucleotide identity, ANIb (98.49%), and DNA–DNA hybridization value (88.40%). The EtOAc extract from strain DR7-3 was analyzed by the gas chromatography-mass spectrometry method. Among the 15 identified compounds, eicosane, phenol-2,4-bis(1,1- dimethylethyl), hexadecane, and hexadecanoic acid-methyl ester showed significant antifungal activity. The draft genome sequence analysis of strain DR7-3 revealed 72 putative biosynthetic gene clusters of secondary metabolites. The genome alignment indicated that 13 gene clusters are involved in the biosynthesis of these antifungal metabolites. These results suggested that strain DR7-3 could be a promising candidate for developing new and safe microbial biological control agents for application in agricultural fields.

Keyword:     Antifungal activity Dendrobium GC-MS genome analysis secondary metabolites orchids Streptomyces


Tedsree N, Likhitwitayawuid K, Sritularak B, Tedsree K, Tanasupawat S. Antifungal activity of endophytic Streptomyces strains from Dendrobium orchids and the secondary metabolites of strain DR7-3 With its genome analysis. J Appl Pharm Sci, 2022;

Copyright: © The Author(s). This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

HTML Full Text


Ahsan T, Chen J, Zhao X, Irfan M, Wu Y. Extraction and identification of bioactive compounds (eicosane and dibutyl phthalate) produced by Streptomyces strain KX852460 for the biological control of Rhizoctonia solani AG-3 strain KX852461 to control target spot disease in tobacco leaf. AMB Express, 2017; 7(1):1-9.

Antoszczak M, Huczy?ski, A. Anticancer activity of polyether ionophore-salinomycin. Anti-Cancer Agents Med Chem, 2015; 15(5): 575-91.

Arai T. Culture media for actinomycetes. The Society for Actinomycetes Japan, Tokyo, Japan, 1975.

Atta H, El-Sayed A, El-Desoukey M, Hassan M, El-Gazar,M. Biochemical studies on the natamycin antibiotic produced by Streptomyces lydicus: fermentation, extraction and biological activities. J Saudi Chem Soc, 2015; 19(4):360-71.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol, 2012; 19(5):455-77.

Bellotti D, Remelli M. Deferoxamine B: a natural, excellent and versatile metal chelator. Molecules, 2021; 26(11):3255.

Benhadj M, Metrouh R, Menasria T, Gacemi-Kirane D, Slim FZ, Ranque S. Broad-spectrum antimicrobial activity of wetland-derived Streptomyces sp. ActiF450. EXCLI J, 2020; 19:360.

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res, 2019; 47(W1):W81-7.

Chen Y, Zhou D, Qi D, Gao Z, Xie J, Luo Y. Growth promotion and disease suppression ability of a Streptomyces sp. CB-75 from banana rhizosphere soil. Front Microbiol, 2018; 8:2704.

Chitraselvi R. Actinomycetes: dependable tool for sustainable agriculture. Curr Investig Agric Curr Res, 2018; 1:128-30.

Chutima R, Dell B, Vessabutr S, Bussaban B, Lumyong S. Endophytic fungi from Pecteilis susannae (L.) Rafin (Orchidaceae), a threatened terrestrial orchid in Thailand. Mycorrhiza, 2011; 21(3):221-9.

Corre J, Lucchini J, Mercier G, Cremieux A. Antibacterial activity of phenethyl alcohol and resulting membrane alterations. Res Microbiol, 1990; 141(4):483-97.

Cui J, Wang Y, Xing Y, Guo S, Xiao P, Wang M. Antimicrobial activity of endophytic fungi isolated from Dendrobium species in southwestern China. China J Chin Mater Med, 2012; 37: 764-70.

Dehpour A, Yousefian M, Jafary Kelarijani S, Koshmoo M, Mirzanegad S, Mahdavi V, Javad Bayani M. Antibacterial activity and composition of essential oils of flower Allium rotundum. Adv Environ Biol, 2012; 6(3):1020-25.

Devi TS, Vijay K, Vidhyavathi R, Kumar P, Govarthanan M, Kavitha T. Antifungal activity and molecular docking of phenol, 2, 4-bis (1, 1-dimethylethyl) produced by plant growth-promoting actinobacterium Kutzneria sp. strain TSII from mangrove sediments. Arch Microbiol, 2021; 203(7):4051-64.

Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol, 1971; 20(4):406-16.

Francis M, Chacha M, Ndakidemi PA, Mbega E. Phytochemical analysis and in vitro antifungal evaluation of Jatropha curcas against late leaf spot disease on groundnut. J Anim Plant Sci, 2021; 47(1):8358-71

Fukuyo Y, Hunt CR, Horikoshi N. Geldanamycin and its anti-cancer activities. Cancer Lett, 2010; 290(1):24-35.

Girija S, Duraipandiyan V, Kuppusamy PS, Gajendran H, Rajagopal R. Chromatographic characterization and GC-MS evaluation of the bioactive constituents with antimicrobial potential from the pigmented ink of Loligo duvauceli. Int Sch Res Notices, 2014; 2014:820745.

Hanif A, Soekarno BPW, Munif A. Selection of endophytic bacteria producing metabolite compound to control seedborne fungal pathogen of maize. J Fitopatol Indones, 2017; 12(5):149.

Hashem M, Alamri SA, Alrumman SA, Moustafa MF. Suppression of phytopathogenic fungi by plant extract of some weeds and the possible mode of action. Br Microbiol Res J, 2016; 15:1-13.

Kadhim MJ, Al-Rubaye AF, Hameed IH. Determination of bioactive compounds of methanolic extract of Vitis Vinifera using GC-MS. Int J Toxicol Pharmacol, 2017; 9(2):113-26.

Karanja E, Boga H, Muigai A, Wamunyokoli F, Kinyua J, Nonoh J. Growth characteristics and production of secondary metabolites from selected novel Streptomyces species isolated from selected Kenyan national parks. In: Jkuat Annual Scientific Conference Proceedings, 2010.

Kawuri R, Darmayasa I. Bioactive compound of Streptomyces capoamus as biocontrol of bacterial wilt disease on banana plant. IOP Conf Ser: Earth Environ Sci, 2019; 347(1):012054..

Kelly K. Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors. US Government Printing Office, Washington, DC, 1964.

Kim YJ, Kim, Jh, Rho JY. Antifungal activities of Streptomyces blastmyceticus strain 12-6 against plant pathogenic fungi. Mycobiology, 2019; 47(3):329-34.

Kongtragoul P, Ishikawa K, Ishii H. Metalaxyl resistance of Phytophthora palmivora causing durian diseases in Thailand. Sci Hortic, 2021; 7(10):375.

Kudo T, Matsushima K, Itoh T, Sasaki J, Suzuki KI. Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia. Int J Syst Evol Microbiol, 1998; 48(4):1245-55.

Kuncharoen N, Fukasawa W, Mori M, Shiomi K, Tanasupawat S. Diversity and antimicrobial activity of endophytic actinomycetes isolated from plant roots in Thailand. Microbiology, 2019; 88(4):479-88.

Küster E, Williams S. Selection of media for isolation of Streptomycetes. Nature, 1964; 202(4935):928-29.

Li J, Duan M, Yao X, Tian D, Tang J. Prenylated benzenepropanoic acid analogues from the Citrus grandis (L.) Osbeck and their anti-neuroinflammatory activity. Fitoterapia, 2019; 139:104410.

Mearns-Spragg A, Bregu M, Boyd K, Burgess J. Cross-species induction and enhancement of antimicrobial activity produced by epibiotic bacteria from marine algae and invertebrates, after exposure to terrestrial bacteria. Lett Appl Microbiol, 1998; 27(3):142-46.

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics, 2013; 14(1):1-14.

Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun, 2019; 10(1):1-10.

Melinda YN, Widada J, Wahyuningsih TD, Febriansah R, Damayanti E, Mustofa M. Metabologenomics approach to the discovery of novel compounds from Streptomyces sp. GMR22 as anti-SARS-CoV-2 drugs. Heliyon, 2021; 7(11):e08308.

Nair DN, Padmavathy S. Impact of endophytic microorganisms on plants, environment and humans. Sci World J, 2014; 2014(2):250693.

Nandhini SU, Sangareshwari S, Lata K. Gas chromatography-mass spectrometry analysis of bioactive constituents from the marine Streptomyces. J Pharm Clin Res, 2015; 8(2):244-46.

Narendhran S, Rajiv P, Vanathi P, Sivaraj R. Spectroscopic analysis of bioactive compounds from Streptomyces cavouresis kuv39: evaluation of antioxidant and cytotoxicity activity. Int J Pharm Pharm Sci, 2014; 6:319-22.

Office of Agricultural Economics (OAE). Summary of imported pesticides, 2021 [ONLINE]. Available via (Accessed 20 Jan 2022).

Padmavathi AR, Abinaya B, Pandian SK. Phenol, 2, 4-bis (1, 1-dimethylethyl) of marine bacterial origin inhibits quorum sensing mediated biofilm formation in the uropathogen Serratia marcescens. Biofouling, 2014; 30(9):1111-22.

Paramanantham M, Murugesan A. GC-MS analysis of Holarrhena antidysentrica Wall flower. Int J Sci Eng, 2014; 3(3):631-39.

Phuakjaiphaeo C, Chang C, Ruangwong O, Kunasakdakul K. Isolation and identification of an antifungal compound from endophytic Streptomyces sp. CEN 26 active against Alternaria brassicicola. Lett Appl Microbiol, 2016; 63(1):38-44.

Phuakjaiphaeo C, Kunasakdakul K. Isolation and screening for inhibitory activity on Alternaria brassicicola of endophytic actinomycetes from Centella asiatica (L.) Urban. Int J Agric Technol, 2015; 11(4):903-12.

Pithakkit S, Petcharat V, Chuenchit S, Pornsuriya C, Sunpapao A. Isolation of antagonistic actinomycetes species from rhizosphere as effective biocontrol against oil palm fungal diseases. Walailak J Sci Technol, 2015; 12(5):481-90.

Pokhrel AR, Dhakal D, Jha AK, Sohng JK. Herboxidiene biosynthesis, production, and structural modifications: prospect for hybrids with related polyketide. Appl Microbiol Biotechnol, 2015; 99(20):8351-62.

Prapagdee B, Akrapikulchart U, Mongkolsuk S, Prapagdee B, Mongkolsuk S. Potential of a soil-borne Streptomyces hygroscopicus for biocontrol of a anthracnose disease caused by Colletotrichum gloeosporioides in orchid. J Biol Sci, 2008; 8(7):1187-92.

Qi DF, Zou L, Zhou D, Zhang M, Wei Y, Zhang L, Xie J, Wang W. Identification and antifungal mechanism of a novel actinobacterium Streptomyces huiliensis sp. nov. against Fusarium oxysporum f. sp. cubense tropical race 4 of banana. Front Microbiol, 2021; 12:1-14.

Rahbar N, Shafaghat A, Salimi F. Antimicrobial activity and constituents of the hexane extracts from leaf and stem of Origanum vulgare L. ssp. viride (Boiss.) hayek growing wild in northwest Iran. J Med Plant Res, 2012; 6(13):2681-85.

Rangel-Sánchez G, Castro-Mercado E, García-Pineda E. Avocado roots treated with salicylic acid produce phenol-2,4-bis (1,1-dimethylethyl), a compound with antifungal activity. J Plant Physiol, 2013; 171:189-98.

Ren J, Wang J, Karthikeyan S, Liu H, Cai J. Natural anti-phytopathogenic fungi compound phenol, 2, 4-bis (1, 1-dimethylethyl) from Pseudomonas fluorescens TL-1. Indian J Biochem Biophys, 2019; 56(2):162-68.

Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics, 2016; 32(6):929-31.

Sakdapetsiri C, Ngaemthao W, Suriyachadkun C, Duangmal K, Kitpreechavanich V. Actinomycetospora endophytica sp. nov., isolated from wild orchid (Podochilus microphyllus Lindl.) in Thailand. Int J Syst Evol, 2018; 68(9): 3017-21.

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics, 2014; 30(14):2068-69.

Senthilmurugan G, Viji S, Sekar L, Suresh K. Enzyme analysis of endophytic new Streptomyces sp. viji10 isolated from velaman roots of orchid plant Vanda spathulata (L) spreng. Asian J Agri Biol, 2013; 1(13):149-54.

Shimizu M. Endophytic actinomycetes: biocontrol agents and growth promoters. In: Maheshwari DK (ed.). Bacteria in agrobiology: plant growth responses, Springer, Berlin, Heidelberg, pp 201-20, 2011.

Shirling ET, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Evol, 1966; 16(3):313-40.

Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol, 1974; 28:226-31.

Summerbell RC. The benomyl test as a fundamental diagnostic method for medical mycology. J Clin Microbiol, 1993; 31(3):572-7.

Sun Y, Zhou X, Tu G, Deng Z. Identification of a gene cluster encoding meilingmycin biosynthesis among multiple polyketide synthase contigs isolated from Streptomyces nanchangensis NS3226. Arch Microbiol, 2003; 180(2):101-7.

Suriyachadkun C, Chunhametha S, Thawai C, Tamura T, Potacharoen W, Kirtikara K, Sanglier JJ. Planotetraspora thailandica sp. nov., isolated from soil in Thailand. Int J Syst Evol, 2009; 59(5):992-7.

Taechowisan T, Lumyong S. Activity of endophytic actimomycetes from roots of Zingiber officinale and Alpinia galanga against phytopathogenic fungi. Ann Microbiol, 2003; 53(3):291-8.

Tapadar SA, Jha DK. 2013. Disease management in staple crops: a bacteriological approach. In: Maheshwari DK (ed.). Bacteria in agrobiology: disease management, Springer, Berlin, Heidelberg, pp 111-52.

Tayade D, Jadhao N. Attempt in the synthesis of 2-[(2, 6 disubstitutedthiocarbamidophenyl) amino] benzeneacetic acid and their antimicrobial study. J Pure Appl Microbiol, 2012; 6:2025-8.

Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid K. Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl. Int J Syst Evol, 2021; 71(7):004902.

Tirado R, Englande AJ, Promakasikorn L, Novotny V.Use of agrochemicals in Thailand and its consequences for the environment. Greenpeace Research Laboratories Technical, Bangkok, Thailand, 2008.

Tobih F, Bosah B, Nweke F. Evaluation of the efficacy of radial growth, spore density of Curvularia lunata and Fusarium semitectum. Int J Agric Innov Res, 2015; 4(1):47-50.

Tsavkelova EA, Cherdyntseva TA, Botina SG, Netrusov AI. Bacteria associated with orchid roots and microbial production of auxin. Microbiol Res, 2007; 162(1):69-76.

Valsalam S, Agastian P, Arasu MV, Al-Dhabi NA, Ghilan AKM, Kaviyarasu K, Ravindran B, Chang SW, Arokiyaraj S. Rapid biosynthesis and characterization of silver nanoparticles from the leaf extract of Tropaeolum majus L. and its enhanced in-vitro antibacterial, antifungal, antioxidant and anticancer properties. J Photochem Photobiol B Biol, 2019; 191:65-74.

Wideman M. Herboxidiene, a new herbicidal substance from Streptomyces chromofuscus A7847. J Antibiotics, 1992; 45:914-21.

Williams ST, Cross T. Actinomycetes. In: Booth C (ed.). Methods in microbiology. Academic Press, London, UK, pp 295-334, 1771.

Wu LS, Jia M, Chen L, Zhu B, Dong HX, Si JP, Peng W, Han T. Cytotoxic and antifungal constituents isolated from the metabolites of endophytic fungus DO14 from Dendrobium officinale. Molecules, 2015; 21(1):0014.

Wu W, Chen W, Liu S, Wu J, Zhu Y, Qin L, Zhu B. Beneficial relationships between endophytic bacteria and medicinal plants. Front Plant Sci, 2021; 12:758.

Wu Y, Zhou J, Li C, Ma Y. Antifungal and plant growth promotion activity of volatile organic compounds produced by Bacillus amyloliquefaciens. Front Plant Sci, 2019; 8(8):e00813.

Xing YM, Chen J, Cui JL, Chen XM, Guo, SX. Antimicrobial activity and biodiversity of endophytic fungi in Dendrobium devonianum and Dendrobium thyrsiflorum from Vietman. Curr Microbiol, 2011; 62(4):1218-24.

Xu B, Chen W, Wu Zm, Long Y, Li K. A novel and effective Streptomyces sp. N2 against various phytopathogenic fungi. Appl Biochem Biotechnol, 2015; 177(6):1338-47.

Yin M, Jiang M, Ren Z, Dong Y, Lu T. The complete genome sequence of Streptomyces autolyticus CGMCC 0516, the producer of geldanamycin, autolytimycin, reblastatin and elaiophylin. J Biotechnol, 2017; 252:27-31.

Yogeswari S, Ramalakshmi S, Neelavathy R, Muthumary J. Identification and comparative studies of different volatile fractions from Monochaetia kansensis by GCMS. Glob J Pharmacol, 2012; 6(2):65-71.

Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol, 2017; 67(5):1613.

Zerikly M, Challis GL. Strategies for the discovery of new natural products by genome mining. ChemBioChem, 2009; 10(4):625-33.

Article Metrics

1 Absract views 1 PDF Downloads 2 Total views

   Abstract      Pdf Download

Related Search

By author names

Citiaion Alert By Google Scholar

Name Required
Email Required Invalid Email Address

Comment required