Screening the antagonistic ability to pathogenic microorganisms researching biochemical characteristics of streptomycetes sp vnuaa30

VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE FACULTY OF BIOTECHNOLOGY  GRADUATION THESIS TITTLE: SCREENING THE ANTAGONISTIC ABILITY TO PATHOGENIC MICROORGANISMS AND RESEARCHING BIOCHEMICAL CHARACTERISTICS OF STREPTOMYCETES SP VNUA30 Student name : PHAM QUANG TU Class : K62CNSHE Student’s code : 620552 Supervisor : Ph.D PHAM HONG HIEN : Ph.D NGUYEN XUAN CANH Department : MICROBIAL TECHNOLOGY Hanoi - 2022 COMMITMENT I hereby declare that the data and research results in this thesis are true and have never been used in any publication I hereby declare that any assistance in the preparation of this thesis has been received and that the sources cited have been acknowledged Hanoi, March 15, 2022 Student Phạm Quang Tú i ACKNOWLEDGEMENT During the process of completing my graduation thesis, I personally received a lot of encouragement and encouragement along with the enthusiastic and thoughtful guidance of teachers and teachers in the Department of Microbiology, of the Biotechnology Faculty, Vietnam National University of Agriculture On this day, I would also like to express my deep gratitude to Associate Professor Dr Nguyen Xuan Canh - Dean of Biotechnology Faculty, Vietnam National University of Agriculture and Dr Pham Hong Hien have wholeheartedly guided and helped me throughout the process of doing my graduation thesis I also sincerely thank the professional engineer Mrs Nguyen Thi Thu, M.s Tran Thi Dao and others at the Department of Microbiology, of the Biotechnology Faculty, Vietnam National University of Agriculture created favorable conditions for me to complete the report in the best way Finally, I would like to thank my family and friends who have always helped and encouraged me throughout the process Sincere thanks! Hanoi, March 15, 2022 Student Phạm Quang Tú ii INDEX COMMITMENT i ACKNOWLEDGEMENT ii INDEX iii LIST OF TABLES vii LIST OF FIGURES viii LIST OF ABBREVIATIONS ix ABSTRACT x PART I: INTRODUCTION 1.1 Problem 1.2 Research purpose and content PART II: LITERATURE REVIEW 2.1 Overview of Actinomycetes 2.1.1 Classification 2.1.2 Morphological characteristics 2.1.3 Significance of Actinomycetes 2.2 Introduction and classification of streptomycetes - VNUA30 2.2.1 Overview 2.2.2 Streptomycetes habitats 2.2.3 Morphology 2.2.4 Utilities 2.2.4.1 Streptomycetes and antibiotics 2.2.4.2 Plant - streptomyces interaction 11 2.2.4.3 What are the benefits of studying more? 13 iii 2.2.5 Related research 15 2.3 Literature of researched fungal 16 2.3.1 Fusarium solani 17 2.3.2 Collectotrium sp 18 2.4 Literature of researched bacterial 20 2.4.1 Ralstonia solanacearum 20 2.4.2 Clavibacter michiganesis 24 2.4.2.1 Clavibacter michiganensis subsp michiganensis (Cmm) 24 2.4.2.2 Clavibacter michiganensis subsp sepedonicus 26 2.5 Recent research on the antagonistic ability of Actinomycetes 29 PART III: MATERIALS AND METHODS 32 3.1 Materials 32 3.1.1 Research location and time of study 32 3.1.2 Material 32 3.1.3 Equiments 32 3.1.4 Medium 33 3.2 Methods 34 3.2.1 Screening the antagonistic ability to pathogenic microorganism of VNUA30 34 3.2.1.1 Antibacterial 34 3.2.1.2 Antifungal 34 3.2.2 Biochemical characteristics of streptomyces sp VNUA 30 35 3.2.2.1 Ability to produce extracellular enzymes 35 3.2.2.2 Ability to produce IAA 36 3.2.2.3 Ability to produce hydro sulfide (H₂S) 38 iv 3.2.2.4 Ability to produce indole 38 3.2.2.5 MR test 39 3.2.2.6 VP test 40 3.2.2.7 Ability to utilize citrate 40 3.2.2.8 Ability to hydrolyze gelatin 41 3.2.2.9 Ability to solubilize phosphate 42 3.2.2.10 Ability to decompose urea 43 3.2.2.11 Ability to produce siderophores 43 3.2.2.12 Ability to reduce nitrate 45 PART IV: RESULTS AND DISCUSSION 46 4.1 Antagonistic ability of streptomyces sp VNUA-30 46 4.1.1 Antibacterial 46 4.1.2 Antifungal 46 4.2 Biochemical characteristics of Streptomyces sp VNUA-30 48 4.2.1 Ability to produce extracellular enzymes 48 4.2.2 Ability to produce IAA 50 4.2.3 Ability to produce hydrosulfide (H₂S) 51 4.2.4 Ability to produce indole 52 4.2.5 MR test 52 4.2.6 VP test 53 4.2.7 Ability to utilize citrate 54 4.2.8 Ability to hydrolyze gelatin 55 4.2.9 Ability to solubilize phosphate 56 4.2.10 Ability to decompose ureases 57 v 4.2.11 Ability to produce siderophores 58 4.2.12 Ability to reduce nitrate 60 PART V: CONCLUSION AND PROPOSAL 61 5.1 Conclusion 63 5.2 Proposal 64 REFERENCE 63 vi LIST OF TABLES Table List of some antibiotics produced by Streptomyces sp VNUA30 11 Table Ingredients for medium 35 Table Chemical composition of standard IAA solution 36 Table 3 Ingredients of indole test 38 Table MR Broth medium for reaction test 39 Table VP Broth medium for reaction test 40 Table Citrate utilization medium 40 Table Gelatin hydrolysis medium 41 Table Phosphate solubilization medium 42 Table Stuart’s Urea Broth medium 43 vii LIST OF FIGURES Figure Streptomyces sp VNUA30 co-culture with bacterials 46 Figure Streptomyces sp VNUA-30 against fungus 48 Figure Extracellular enzymes result 49 Figure 4 IAA production result 50 Figure The amount of IAA produced 51 Figure Produce hydrosulfide result 51 Figure Produce Indole result 52 Figure MR reaction result 53 Figure VP Reaction result 54 Figure 10 Citrate utilization result 55 Figure 11 Gelatin hydrolysis result 56 Figure 12 Phosphate solubilization result 57 Figure 13 Urea decomposition result 58 Figure 14 Siderophores production result 59 Figure 15 Nitrate redution test 60 viii LIST OF ABBREVIATIONS PGP Plant growth promoting IAA Indole-3-acetic acid DNA Deoxyribonucleic acid PDA Potato dextrose agar PIRG Percentage inhibition of radial growth IMS Integrated management system BGCs Biosynthetic gene clusters L-DAP Lightweight directory access protocol ix - XK30 Figure 11 Gelatin hydrolysis result (- is the control tube; xk30 is the experiment tube) Gelatinase can hydrolyze gelatine into peptides and amino acids which is called hydrolyzed gelatin and this is used in industries (Islam et al., 2009) and (Shrivastava et al., 2017) have reported a similar subject to my thesis that Streptomyces producing antifungal and antibacteria agents (Rhizoctonia solani and Macrophomina phaseolina) but all of these showed negative Gelatin hydrolysis test Thus VNUA-30 might has exciting expectation 4.2.9 Ability to solubilize phosphate Soil contains a wide range of organic substrates, which are the source of P for the growth of plants But it must 61 be hydrolyzed to inorganic P before its assimilation by the plants The predominant form of organic P in soil is phytate nearly 60% Many of the plants cannot uptake the phytate-P and organic phosphorous, because the lack of sufficient level of phosphatase So in order to reduce the depletion of global P reserves, research should 64 be oriented towards more effective utilization of phosphates Problem of decreasing resources of phosphate rock for P fertilizers production can be mitigated by searching microbes producing phytase and plant biostimulant Streptomyces sp They are also known 56 for the production of various types of secondary metabolites, antibiotics, and pharmaceutically important compounds They have important role in organic material conversion (Seipke et al , 2012) Figure 12 Phosphate solubilization result The Streptomyces sp VNUA30 forming the clear zone of hydrolysis on Pikovskaya agar plates indicating the solubilization of phosphate present in media This result is similar with a report of (Puppala et al., 2019) The Streptomyces sp strain (NCIM 5533) displayed additional PGP traits such as phosphate solubilization activity So its application as bioinoculant will increase the available P in soil along with reduced requirement of P-fertilizers, will decrease environmental pollution and promote sustainabl 4.2.10 Ability to decompose urea The change in the color of the medium is because streptomyces sp VNUA30 is able to produce urease enzyme to break down urea into CO and NH3 An increase in pH due to the production of ammonia results in a color change from yellow (pH 6.8) to bright pink (pH 8.2) 57 Figure 13 Ureases decomposition result (DC is the control tube; XK30 is the experiment tube) Urea broth (Stuart’s urea broth) is a highly buffered medium requiring large quantities of ammonia to raise the pH above 8.0 resulting in a color change From the above results based on the biochemical characterisation, my research has similar result with (Taddei et al., 2006) has published the biochemical characteristics of 71 Streptomyces sp isolated from soil samples collected at different places of Venezuela The majority of the strains (62 out of 71) could degrade urea 4.2.11 Ability to produce siderophores Siderophore productions from streptomyces sp VNUA30 of endophytic The clear zone around the Streptomyces colonies indicates the secretion of siderophores, as they utilized the iron sources and clear it 58 Figure 14 Siderophores resolution result Siderophore is a compound secreted by Actinomycetes into the environment to collect low-molecular-weight iron ions from the surrounding environment when they live in iron-deficient conditions, thus helping plants to resist iron-deficiency stress Candlestick Pathogenic microorganisms need iron for growth, thus leading to iron competition, however, the affinity for iron of beneficial Actinomycetes is higher than that of harmful plant pathogens and fungi organisms, resulting in the limitation of pathogens in the environment., (Chung et al., 2005) That might related to antifungal ability of VNUA-30 to Collectotrium Sp and Fusarium Solani sp that the thesis has shown above Similar with the report of (Verma et al., 2011) Siderophore productions from two strains of endophytic Streptomyces sp AzR-049 and AzR-051, isolated from Azadirachta, India that produces siderophores are also having very significant antagonistic activity against the pathogen Alternaria, this suggests that siderophores of these endophytic Streptomyces species due to having high Fe3+ complexing capacity may be responsible for depriving the pathogen for iron for its metabolic activity and thus reduce their growth and survival (Verma et al , 2011) 59 4.2.12 Ability to reduce nitrate XK30 Figure 15 Nitrate redution test (- is the control tube; xk30 is the experiment tube) After adding sulfanilic acid, acetic acid, sulfanilic acid becomes diazotized form of sulfanilic acid Then, adding alpha naphthylelediamine will give pSulfobenzene-azo- alpha naphthylelediamine which is red But because the diazotized Sulfanilicacid can be broken down to the Hydroxyl-azo derivative or the nitrate is reduced to N2, a colorless phenomenon can occur Therefore, this reaction can be checked by the addition of zinc powder Observing the results in 30 seconds, we see that the test tube does give red color It shows that Nitrate has been reduced by Zn to Nitrite, the culture solution did change the color Thus, strain VNUA-30 tested gave positive results 60 PART V: CONCLUSION AND PROPOSAL 5.1 Conclusion From the actinomycete samples isolated and the study of actinomycete strains isolated from ground banana samples collected in the mainland of Ha Tinh province, the initial experiments were conducted at the Department of Biotechnology I continue to study the antagonistic properties and biochemical characteristics of Streptomyces sp VNUA30 - Streptomyces sp VNUA30 capable of antagonizing two fungal strains was isolated and studied at the Department of Biotechnology (F.solani HT39 and C Gloeosporioides) with the results of 55.51% and 33.95%, respectively The pathogenic fungus Fusarium oxysporum on bananas was found to be hostile to the streptomyces strain utilized in the investigation However, in addition to wilt disease, bananas and other plants are susceptible to a variety of illnesses caused by various biological agents The antagonistic activity of this actinomycete strain against certain common plant pathogens in Vietnam was investigated, as well as the biochemical features and some associated traits on the efficacy of strain VNUA30 to boost plant growth - Streptomyces sp VNUA30 is capable of producing 06 enzymes: amylase, cellulase, pectinase, protease, catalase Through observation, the ability to produce chitinase enzyme is the largest and the protease is the smallest - In additionally organisms also possess other plant growth promoting activities (PGP) like phosphate solubilization, indole acetic acid (IAA), ammonia and siderophore production its application as bioinoculant in soil will be promising Streptomyces sp VNUA30 strains also gave positive results for biochemical experiments such as: Hydrogen sulfide, hydrolysis gelatin and nitrate redution 61 5.2 Proposal The results are positive, so I recommend to continue the research on the 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