Isolation of actinomycetes from maize rhizosphere from Kupang, East Nusa Tenggara Province, and evaluation of their antibacterial, antifungal, and extracellular enzyme activity

Umi Fatmawati; Yulin Lestari; Anja Meryandini; Abdjad Asih Nawangsih; Aris Tri Wahyudi

doi:10.22146/ijbiotech.33064

Isolation of actinomycetes from maize rhizosphere from Kupang, East Nusa Tenggara Province, and evaluation of their antibacterial, antifungal, and extracellular enzyme activity

https://doi.org/10.22146/ijbiotech.33064

Umi Fatmawati^(1*), Yulin Lestari⁽²⁾, Anja Meryandini⁽³⁾, Abdjad Asih Nawangsih⁽⁴⁾, Aris Tri Wahyudi⁽⁵⁾

(1) Graduate School of Bogor Agricultural University, Microbiology Study Program, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor
(2) Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Indonesia
(3) Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Indonesia
(4) Department of Plant Protection, Faculty of Agricultural Technology, Bogor Agricultural University, Indonesia
(5) Department of Plant Protection, Faculty of Agricultural Technology, Bogor Agricultural University, Indonesia
(*) Corresponding Author

Abstract

Actinomycetes are the one of the components of the rhizospheric microbial population and useful for producing secondary metabolites such as lytic enzymes, antibiotics, and antifungal. The aim of the study was to isolate the actinomycetes from maize rhizosphere collected from Kupang, East Nusa Tenggara. The screening was focused on the actinomycetes that showed the ability to produce antibacterial, antifungal, and extracellular enzymes such as amylase, cellulase, and protease. The actinomycetes were isolated using Humic-Acid Vitamin B (HV) agar media. The antagonistic assay was tested against Escherichia coli, Staphylococcus aureus, Sclerotium rolfsii and Fusarium oxysporum. Isolate JKP-8 was an isolate that showed the highest activity in inhibiting the growth of E. coli and S. aureus bacteria. Isolate JKP-5 showed the highest activity in inhibiting the growth of F.oxysporum. There were no actinomycetes isolates that showed an ability to inhibit the growth of S. rolfsii fungus based on dual culture assay. JKP-3 and JKP-4 isolates exhibited the highest ability to hydrolyze amylum, while JKP-5 and JKP-8 isolates exhibited the highest ability to hydrolyze CMC. The results of the amplification of 16S rRNA gene in selected potential isolates JKP 5 and JKP 8 indicated that both isolates belong to the genus Streptomyces.

Keywords

actinomycetes; antibacterial; antifungal; hydrolytic enzyme; rhizosphere

Full Text:

Fatmawati et al.

References

Alimuddin A, Widada J, Asmara W, Mustofa M. 2011. Antifungal production of a strain of Actinomycetes spp. isolated from the rhizosphere of cajuput plant: selection and detection of exhibiting activity against tested fungi. Indonesian Journal of Biotechnology 16(1):1–10. doi:10.22146/ijbiotech.7829.

Ashokvardhan T, Rajithasri A, Prathyusha P, Satyaprasad K. 2014. Actinomycetes from Capsicum annuum L. rhizosphere soil have the biocontrol potential against pathogenic fungi. International Journal of Current Microbiology and Applied Sciences 3:894–903.

Barakate M, Ouhdouch Y, Oufdou K, Beaulieu C. 2002. Characterization of rhizospheric soil streptomycetes from Moroccan habitats and their antimicrobial activities. World Journal of Microbiology and Biotechnology 18:49–54. doi:10.1023/A:1013966407890.

Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58:3413–3416.

Chet I, Henis Y, Mitchell R. 1967. Chemical composition of hyphal and sclerotial walls of Sclerotium rolfsii Sacc. Canadian Journal of Microbiology 13:137–141. doi:10.1139/m67-019.

Dikin A, Sijam K, Kadir J, Seman IA. 2006. Antagonistic bacteria against Schizophyllum commune Fr. in Peninsular Malaysia. Biotropia 13:111–121. doi:10.11598/btb.2006.13.2.221.

Gopalakrishnan S, Pande S, Sharma M, Humayun P, Kiran BK, Sandeep D, Vidya MS, Deepthi K, Rupela O. 2011. Evaluation of actinomycete isolates obtained from herbal vermicompost for the biological control of Fusarium wilt of chickpea. Crop Protection 30:1070–1078. doi:10.1016/j.cropro.2011.03.006.

Hamdali H, Hafidi M, Virolle MJ, Ouhdouch Y. 2008. Growth promotion and protection against damping-off of wheat by two rock phosphate solubilizing actinomycetes in a P-deficient soil under greenhouse conditions. Applied Soil Ecology 40:510–517. doi:10.1016/j.apsoil.2008.08.001.

Hayakawa M, Nonomura H. 1987. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. Journal of Fermentation Technology 65:501–509. doi:10.1016/0385-6380(87)90108-7.

Huang X-F, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM. 2014. Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275. doi:10.1139/cjb-2013-0225.

Intra B, Mungsuntisuk I, Nihira T, Igarashi Y, Panbangred W. 2011. Identification of actinomycetes from plant rhizospheric soils with inhibitory activity against Colletotrichum spp., the causative agent of anthracnose disease. BMC Research Notes 4:98. doi:10.1186/1756-0500-4-98.

Jain R, Agrawal SC, Jain PC. 2009. Proteolytic actinomycetes from Indian habitats. Journal of Culture Collections 6:28–37.

Kanti A. 2005. Cellulolytic Actinomycetes isolated from soil in Bukit Duabelas National Park, Jambi. Biodiversitas 6:85–89. doi:10.13057/biodiv/d060203.

Khamna S, Yokota A, Peberdy JF, Lumyong S. 2010. Indole-3-acetic acid production by Streptomyces sp. isolated from some Thai medicinal plant rhizosphere soils. EurAsian Journal of Biosciences 4:23–32. doi:10.5053/ejobios.2010.4.0.4.

Kyselková M, Kopecký J, Felföldi T, Cermák L, Omelka M, Grundmann GL, Moënne-Loccoz Y, Ságová-Marecková M. 2008. Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera. Antonie Van Leeuwenhoek 94:439–453. doi:10.1007/s10482-008-9261-z.

Lahdenperä M-L, Simon E, Uoti J. 1991. Mycostop - a novel biofungicide based on Streptomyces bacteria. In: Beemster ABR, Bollen GJ, Gerlagh M, Ruissen MA, Schippers B, Tempel A, editors. Developments in agricultural and managed forest ecology. Vol. 23. Elsevier. (Biotic interactions and soil-borne diseases). p. 258–263.

Li Q, Chen X, Jiang Y, Jiang C. 2016. Morphological identification of actinobacteria. In: Dhanasekaran D, Jiang Y, editors. Actinobacteria - basics and biotechnological applications. InTech.

Macagnan D, Romeiro R da S, Pomella AWV, deSouza JT. 2008. Production of lytic enzymes and siderophores, and inhibition of germination of basidiospores of Moniliophthora (ex Crinipellis) perniciosa by phylloplane actinomycetes. Biological Control 47:309–314. doi:10.1016/j.biocontrol.2008.08.016.

Merckx R, Dijkstra A, Hartog A den, Veen JA van. 1987. Production of root-derived material and associated microbial growth in soil at different nutrient levels. Biology and Fertility of Soils 5:126–132. doi:10.1007/BF00257647.

Meschke H, Schrempf H. 2010. Streptomyces lividans inhibits the proliferation of the fungus Verticillium dahliae on seeds and roots of Arabidopsis thaliana. Microbial Biotechnology 3:428–443. doi:10.1111/j.1751-7915.2010.00165.x.

Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences 110:6548–6553. doi:10.1073/pnas.1302837110.

Rovira AD. 1969. Plant root exudates. The Botanical Review 35:35–57. doi:10.1007/BF02859887.

Sadeghi A, Hessan AR, Askari H, Aghighi S, Shahidi Bonjar GH. 2006. Biological control potential of two Streptomyces isolates on Rhizoctonia solani, the causal agent of damping-off of sugar beet. Pakistan Journal of Biological Sciences 9:904–910. doi:10.3923/pjbs.2006.904.910.

Shimizu M. 2011. Endophytic actinomycetes: biocontrol agents and growth promoters. In: Maheshwari DK, editor. Bacteria in agrobiology: plant growth responses. Berlin, Heidelberg: Springer. p. 201–220.

Shirling EB, Gottlieb D. 1966. Methods for characterization of Streptomyces species. International Journal of Systematic Bacteriology 16:313–340. doi:10.1099/00207713-16-3-313.

Singh BK, Millard P, Whiteley AS, Murrell JC. 2004. Unravelling rhizosphere–microbial interactions: opportunities and limitations. Trends in Microbiology 12:386–393. doi:10.1016/j.tim.2004.06.008.

Solans M, Vobis G. 2003. Saprophytic actinomycetes associated to the rhizosphere and rhizoplane of Discaria trinervis. Ecologia Australian 13:97–107.

Sreevidya M, Gopalakrishnan S, Kudapa H, Varshney RK. 2016. Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea. Brazilian Journal of Microbiology 47:85–95. doi:10.1016/j.bjm.2015.11.030.

Sukamto, Wahyuno D. 2016. Identifikasi dan karakterisasi Sclerotium rolfsii Sacc. penyebab penyakit busuk batang nilam (Pogostemon cablin Benth) [Identification and characterization of Sclerotium rolfsii Sacc. the cause of stem rot disease on Pogostemon cablin Benth]. Buletin Penelitian Tanaman Rempah dan Obat 24:35–41. doi:10.21082/bullittro.v24n1.2013.%p.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28:2731–2739. doi:10.1093/molbev/msr121.

Ting ASY, Hermanto A, Peh KL. 2014. Indigenous actinomycetes from empty fruit bunch compost of oil palm: evaluation on enzymatic and antagonistic properties. Biocatalysis and Agricultural Biotechnology 3:310–315. doi:10.1016/j.bcab.2014.03.004.

DOI: https://doi.org/10.22146/ijbiotech.33064