Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India
Abstract Plant disease management based on pesticide use has numerous detrimental effects on health and the environment. As a result, the adoption of environment-friendly disease management options is the best alternative to pesticide use. Therefore, the identification of locally available bio-agent...
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2025-07-01
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| author | Sana Surma Sumaira H. Misbah M. M. S. Dar Bilal A. Padder Imran Khan Khalid Mushtaq Maheen M. Sehla K. Asha Nabi Mushtaq A. Lone Snober S. Mir Ozer Callis Mehraj D. Shah |
| author_facet | Sana Surma Sumaira H. Misbah M. M. S. Dar Bilal A. Padder Imran Khan Khalid Mushtaq Maheen M. Sehla K. Asha Nabi Mushtaq A. Lone Snober S. Mir Ozer Callis Mehraj D. Shah |
| author_sort | Sana Surma |
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| description | Abstract Plant disease management based on pesticide use has numerous detrimental effects on health and the environment. As a result, the adoption of environment-friendly disease management options is the best alternative to pesticide use. Therefore, the identification of locally available bio-agents like Trichoderma species using morpho-cultural and molecular approaches specifically targeting the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (TEF 1-α) and RNA polymerase B subunit II (RPB2) is necessary. In this study, we characterized 24 Trichoderma strains isolated from the apple rhizosphere. Significant variations were observed in the morpho-cultural characteristics of Trichoderma isolates and categorized them into four groups (I-IV) that were identified as T. harzianum complex, T. koningiopsis, T. viride, and T. hamatum, comprising 4, 4, 6 and 10 isolates, respectively. The concatenated sequence data set derived from the ITS region, TEF 1-α and RPB2 grouped 24 Trichoderma isolates into 03 independent clades. Specifically, the sequencing based on ITS region grouped them into four sub-clades, which were identified as T. harzianum complex, T. viride, T. asperelloides, and T. koningiopsis, comprising 4, 6, 5 and 7 isolates, respectively, and two independent lineages, each represented by a single isolate. In contrast, sequencing of the TEF 1-α and RPB2 genes grouped 24 Trichoderma isolates into two distinct clades and six sub-clades that were identified as T. asperelloides, T. asperellum, T. hamatum, T. viride, T. koningiopsis and T. harzianum complex, comprising 5, 5, 3, 4, 3 and 4 isolates, respectively. Thus, the final identification of 24 Trichoderma strains was achieved through a combined morpho-cultural and molecular approach, resulting in the identification of six species viz., T. koningiopsis, T. viride, T. asperellum, T. asperelloides, T. hamatum and T. harzianum complex comprising 5, 5, 3, 4, 3 and 4 isolates, respectively in accordance with the reference sequences retrieved from NCBI. Notably, to our knowledge, this is the first report of T. koningiopsis, T. viride, T. asperellum, T. asperelloides, and T. hamatum from the apple rhizosphere. |
| format | Article |
| id | doaj-art-41697c552d5f4c1d9882ab0dfb2d8d11 |
| institution | DOAJ |
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| publishDate | 2025-07-01 |
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| spelling | doaj-art-41697c552d5f4c1d9882ab0dfb2d8d112025-08-20T03:05:25ZengNature PortfolioScientific Reports2045-23222025-07-0115111710.1038/s41598-025-12086-4Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of IndiaSana Surma0Sumaira H.1Misbah M.2M. S. Dar3Bilal A. Padder4Imran Khan5Khalid Mushtaq6Maheen M.7Sehla K.8Asha Nabi9Mushtaq A. Lone10Snober S. Mir11Ozer Callis12Mehraj D. Shah13Plant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarDepartment of Biosciences and Bioengineering, Integral UniversityPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarDivision of Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, ShalimarDivision of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, ShalimarPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarDivision of Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, ShalimarDepartment of Biosciences and Bioengineering, Integral UniversityDepartment of Plant Protection, Akdeniz UniversityPlant Virology and Molecular Pathology Lab, Division of Plant Pathology, Sher-e-Kashmir, University of Agricultural Sciences and Technology of Kashmir, ShalimarAbstract Plant disease management based on pesticide use has numerous detrimental effects on health and the environment. As a result, the adoption of environment-friendly disease management options is the best alternative to pesticide use. Therefore, the identification of locally available bio-agents like Trichoderma species using morpho-cultural and molecular approaches specifically targeting the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (TEF 1-α) and RNA polymerase B subunit II (RPB2) is necessary. In this study, we characterized 24 Trichoderma strains isolated from the apple rhizosphere. Significant variations were observed in the morpho-cultural characteristics of Trichoderma isolates and categorized them into four groups (I-IV) that were identified as T. harzianum complex, T. koningiopsis, T. viride, and T. hamatum, comprising 4, 4, 6 and 10 isolates, respectively. The concatenated sequence data set derived from the ITS region, TEF 1-α and RPB2 grouped 24 Trichoderma isolates into 03 independent clades. Specifically, the sequencing based on ITS region grouped them into four sub-clades, which were identified as T. harzianum complex, T. viride, T. asperelloides, and T. koningiopsis, comprising 4, 6, 5 and 7 isolates, respectively, and two independent lineages, each represented by a single isolate. In contrast, sequencing of the TEF 1-α and RPB2 genes grouped 24 Trichoderma isolates into two distinct clades and six sub-clades that were identified as T. asperelloides, T. asperellum, T. hamatum, T. viride, T. koningiopsis and T. harzianum complex, comprising 5, 5, 3, 4, 3 and 4 isolates, respectively. Thus, the final identification of 24 Trichoderma strains was achieved through a combined morpho-cultural and molecular approach, resulting in the identification of six species viz., T. koningiopsis, T. viride, T. asperellum, T. asperelloides, T. hamatum and T. harzianum complex comprising 5, 5, 3, 4, 3 and 4 isolates, respectively in accordance with the reference sequences retrieved from NCBI. Notably, to our knowledge, this is the first report of T. koningiopsis, T. viride, T. asperellum, T. asperelloides, and T. hamatum from the apple rhizosphere.https://doi.org/10.1038/s41598-025-12086-4Trichodema speciesMorphological characterizationCultural characterizationInternal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α)RNA polymerase B subunit II (RPB2) |
| spellingShingle | Sana Surma Sumaira H. Misbah M. M. S. Dar Bilal A. Padder Imran Khan Khalid Mushtaq Maheen M. Sehla K. Asha Nabi Mushtaq A. Lone Snober S. Mir Ozer Callis Mehraj D. Shah Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India Scientific Reports Trichodema species Morphological characterization Cultural characterization Internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α) RNA polymerase B subunit II (RPB2) |
| title | Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India |
| title_full | Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India |
| title_fullStr | Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India |
| title_full_unstemmed | Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India |
| title_short | Morpho-cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of India |
| title_sort | morpho cultural and molecular characterization of trichoderma species from the northwestern himalayan apple rhizosphere of india |
| topic | Trichodema species Morphological characterization Cultural characterization Internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α) RNA polymerase B subunit II (RPB2) |
| url | https://doi.org/10.1038/s41598-025-12086-4 |
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