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Gajera HP, Hirpara DG, Savaliya DD, Parakhia MV. Biochemical and molecular depictions to develop ech42 gene-specific SCAR markers for recognition of chitinolytic Trichoderma inhibiting Macrophomina phaseolina (Maubl.) Ashby. Arch Microbiol 2023; 205:242. [PMID: 37204527 DOI: 10.1007/s00203-023-03582-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Trichoderma isolates were inhibited variably in-vitro growth of soil-borne phytopathogen Macrophomina phaseolina (Maubl.) Ashby causes root rot in cotton. The growth inhibition of test-pathogen was found to be higher (90.36%) in T. viride NBAIITv23 followed by T. koningii MTCC796 (85.77%) under dual culture antagonism. The microscopic examination suggested that the antagonists Tv23 and MTCC796 adopted mycoparasitism as a strong mode of action to restrain pathogen growth. However, antagonists T. harzianum NBAIITh1 (77.89%) and T. virens NBAIITvs12 (61.74%) demonstrated strong antibiosis action for growth inhibition of the test pathogen. A significant positive correlation was established between the growth inhibition of M. phaseolina and the release of cell wall degrading enzymes- chitinase (p = 0.001), β-1,3, glucanase (p = 0.01), and protease (p = 0.05) under the influence of pathogen cell wall. The chitinase and β-1,3, glucanase activities were elevated 2.09 and 1.75 folds, respectively, in potent mycoparasitic Tv23 strain influenced by a pathogen cell wall compared to glucose as a carbon source. The three unique DNA-RAPD fragments OPA-07(1033), OPA-16(983), and OPO-15(239), amplified by potent mycoparasitic Tv23 strain, were subjected to DNA sequencing and derived functional 864 bp from OPA-16(983) and have sequence homology to ech42 gene with partial CDs of 262 amino acids (nucleotide accession No. KF723016.1 and protein accession No.AHF57046.1). Novel SCAR markers were developed from a functional sequence of OPA-16 fragments and validated across the genomic DNA of eleven Trichoderma antagonists. The novel SCAR markers evolved from the RAPD-SCAR interface to authenticate chitinolytic Trichoderma associated with mycoparasitic action for eco-friendly biocontrol activity.
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Affiliation(s)
- H P Gajera
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, 362 001, India.
| | - Darshna G Hirpara
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, 362 001, India
| | - Disha D Savaliya
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, 362 001, India
| | - M V Parakhia
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, 362 001, India
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Ambreetha S, Balachandar D. SCAR marker: A potential tool for authentication of agriculturally important microorganisms. J Basic Microbiol 2023; 63:4-16. [PMID: 35916264 DOI: 10.1002/jobm.202200419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/23/2022] [Indexed: 01/04/2023]
Abstract
Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Hernández I, Sant C, Martínez R, Fernández C. Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains. Front Microbiol 2020; 11:208. [PMID: 32210925 PMCID: PMC7077341 DOI: 10.3389/fmicb.2020.00208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/29/2020] [Indexed: 11/29/2022] Open
Abstract
Biological control is emerging as a feasible alternative to chemical pesticides in agriculture. Measuring the microbial biocontrol agent (mBCA) populations in the environment is essential for an accurate environmental and health risk assessment and for optimizing the usage of an mBCA-based plant protection product. We hereby show a workflow to obtain a large number of qPCR markers suitable for robust strain-specific quantification. The workflow starts from whole genome sequencing data and consists of four stages: (i) identifying the strain-specific sequences, (ii) designing specific primer/probe sets for qPCR, and (iii) empirically verifying the performance of the assays. The first two stages involve exclusively computer work, but they are intended for researchers with little or no bioinformatic background: Only a knowledge of the BLAST suite tools and work with spreadsheets are required; a familiarity with the Galaxy environment and next-generation sequencing concepts are strongly advised. All bioinformatic work can be implemented using publicly available resources and a regular desktop computer (no matter the operating system) connected to the Internet. The workflow was tested with five bacterial strains from four different genera under development as mBCAs and yielded thousands of candidate markers and a triplex qPCR assay for each candidate mBCA. The qPCR assays were successfully tested in soils of different natures, water from different sources, and with samples from different plant tissues. The mBCA detection limits and population dynamics in the different matrices are similar to those in qPCR assays designed by other means. In summary, a new accessible, cost-effective, and robust workflow to obtain a large number of strain-specific qPCR markers is presented.
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Affiliation(s)
| | - Clara Sant
- Futureco Bioscience S.A., Barcelona, Spain
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Kredics L, Chen L, Kedves O, Büchner R, Hatvani L, Allaga H, Nagy VD, Khaled JM, Alharbi NS, Vágvölgyi C. Molecular Tools for Monitoring Trichoderma in Agricultural Environments. Front Microbiol 2018; 9:1599. [PMID: 30090089 PMCID: PMC6068273 DOI: 10.3389/fmicb.2018.01599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Various Trichoderma species possess significance in agricultural systems as biofertilizers or biocontrol agents (BCAs). Besides these beneficial features, certain Trichoderma species can also act as agricultural pests, causing the green mold disease of cultivated mushrooms. This double-faced nature of the genus in agricultural environments points at the importance of proper monitoring tools, which can be used to follow the presence and performance of candidate as well as patented and/or registered biocontrol strains, to assess the possible risks arising from their application, but also to track harmful, unwanted Trichoderma species like the green molds in mushroom growing facilities. The objective of this review is to discuss the molecular tools available for the species- and strain-specific monitoring of Trichoderma, ranging from immunological approaches and fingerprinting tools to exogenous markers, specific primers used in polymerase chain reaction (PCR) as well as "omics" approaches.
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Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Orsolya Kedves
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Rita Büchner
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lóránt Hatvani
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Henrietta Allaga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Viktor D Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Morales MC, Verdejo V, Orlando J, Carú M. Fungal communities as an experimental approach to Darwin's naturalization hypothesis. Res Microbiol 2015; 167:126-32. [PMID: 26506029 DOI: 10.1016/j.resmic.2015.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Darwin's naturalization hypothesis suggests that the success of an invasive species will be lower when colonizing communities are formed by phylogenetically related rather than unrelated species due to increased competition. Although microbial invasions are involved in both natural and anthropogenic processes, factors affecting the success of microbial invaders are unknown. A biological invasion assay was designed using Trichoderma cf. harzianum as the invader and two types of recipient communities assembled in microcosm assays: communities phylogenetically related to the invader, and communities phylogenetically unrelated to it. Both types of communities were invaded by T. cf. harzianum, and the success of colonization was monitored by qPCR; its effect on the genetic structure of recipient fungal communities was then assessed by DGGE profiles. T. cf. harzianum established itself in both communities, reaching 1000-10,000 times higher copy numbers in the non-related communities. However, invader establishment does not affect the structure of the invaded communities. These results suggest that the composition of recipient communities and their phylogenetic relationship to the invader affect the success of colonization by T. cf. harzianum. While this approach represents a very simplified assay, these microcosms enable an experimental test of Darwin's hypothesis in order to understand the biological invasion process in microbial communities.
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Affiliation(s)
- María Camila Morales
- Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Valentina Verdejo
- Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Julieta Orlando
- Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Margarita Carú
- Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Casilla 653, Santiago, Chile.
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