Abstract
Trichoderma bombaxalis isolated from rhizosphere soils of five-year-old Lycium barbarum is described as a novel species. A combined approach is used to characterize T. bombaxalis including cultural and microscopic features, and phylogenetic analyses of the cascaded dataset of internal transcribed spacer (ITS) regions, RNA polymerase II subunit (RPB2), and the translation elongation factor 1-α gene (TEF1-α). The phylogeny reveals that T. bombaxalis belongs to section Hypocreanum, and is closely related to T. austriacum, T. eucorticoides, T. sulphureum, T. subsulphureum and T. victoriense, but represents a novel taxon. These fungi are characterized by often producing verticillium-like conidiophores and ellipsoidal conidia. Distinctions between the new species and its close relatives are compared and discussed. The ability of T. bombaxalis to degrade cellulose and hemicellulose is also estimated.
References
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du Plessis, I.L., Druzhinina, I.S., Atanasova, L., Yarden, O. & Jacobs, K. (2018) The diversity of Trichoderma species from soil in South Africa, with five new additions. Mycologia 110: 559–583. https://doi.org/10.1080/00275514.2018.1463059
Edwards, J.C., Johnson, C., Santos-Medellin, E.L., Podishetty, N.K., Bhatnagar, S., Eisen, J.A. & Sundaresan, V. (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America 112: E911-20. https://doi.org/10.1073/pnas.1414592112
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Guzman-Guzman, P., Porras-Troncoso, M.D., Olmedo-Monfil, V. & Herrera-Estrella, A. (2019) Trichoderma species: versatile plant symbionts. Phytopathology 109: 6–16. https://doi.org/10.1094/PHYTO-07-18-0218-RVW
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Jaklitsch, W.M., Komon, M., Kubicek, C.P. & Druzhinina, I.S. (2017) Hypocrea voglmayrii sp. nov. from the Austrian Alps represents a new phylogenetic clade in Hypocrea/Trichoderma. Mycologia 97: 1365–1378. http://doi.org/10.1080/15572536.2006.11832743
Jang, S., Jang, Y., Kim, C.W., Lee, H., Hong, J.H., Heo, Y.M., Lee, Y.M., Lee, D.W., Lee, H.B. & Kim, J.J. (2017) Five new records of soil-derived Trichoderma in Korea: T. albolutescens, T. asperelloides, T. orientale, T. spirale, and T. tomentosum. Mycobiology 45: 1–8. https://doi.org/10.5941/MYCO.2017.45.1.1
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. https://doi.org/10.1093/molbev/mst010
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Liu, J.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
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Nandini, B., Puttaswamy, H., Saini, R.K., Prakash, H.S. & Geetha, N. (2021) Trichovariability in rhizosphere soil samples and their biocontrol potential against downy mildew pathogen in pearl millet. Scientifc Reports 11: 9517. https://doi.org/10.1038/s41598-021-89061-2
Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author. Available from: https://github.com/nylander/MrModeltest2
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Peciulyte, A., Anasontzis, G.E., Karlström, K., Larsson, P.T. & Olsson, L. (2014) Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates. Fungal Genetics and Biology 72: 64–72. https://doi.org/10.1016/j.fgb.2014.07.011
Rambaut, A. (2012) FigTree version 1.4.0. Program distributed by the author. Available from: http://tree.bio.ed.ac.uk/software/figtree/ (accessed 18 May 2022)
Riley, D. & Barber, S.A. (1970) Salt accumulation at the soybean (Glycine max ( L. ) Merr.) root-soil interface. Soil Science Society of America Journal 34 (1): 154–155. https://doi.org/10.2136/sssaj1970.03615995003400010042x
Ronquist, F., Teslenko, M., Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542. https://doi.org/10.1093/sysbio/sys029
Ryu, S.M., Lee, H.M., Song, E.G., Seo, Y.H., Lee, J., Guo, Y., Kim, B.S., Kim, J.J., Hong, J.S., Ryu, K.H. & Lee, D. (2017) Antiviral activities of trichothecenes isolated from Trichoderma albolutescens against pepper mottle virus. Journal of Agricultural and Food Chemistry 65: 4273–4279. https://doi.org/10.1021/acs.jafc.7b01028
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
Strakowska, J., B?aszczyk, L. & Che?kowski, J. (2014) The significance of cellulolytic enzymes produced by Trichoderma in opportunistic lifestyle of this fungus. Journal of Basic Microbiology 54: S2–S13. https://doi.org/10.1002/jobm.201300821
Swain, H., Adak, T., Mukherjee, A.K., Mukherjee, P.K., Bhattacharyya, P., Behera, S., Bagchi, T.B., Patro, R., Khandual, A., Bag, M.K., Dangar, T.K. & Jena, M. (2018) Novel Trichoderma strains isolated from tree barks as potential biocontrol agents and biofertilizers for direct seeded rice. Microbiological Research 214: 83–90. https://doi.org/10.1016/j.micres.2018.05.015
White, T.J., Bruns, T., Lee, S. & Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (Eds.) PCR Protocols: a Giude to Methods and Application. Academic Press, San Diego, USA, pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Zhang, J.H., Li, M., Jia, K.L., Zheng, G.Q. & Long, X.E. (2018) Seasonal variation rather than stand age determines bacterial diversity in the rhizosphere of wolfberry (Lycium barbarum L.) associated with soil degradation. Journal of Soils and Sediments 18: 1518–1529. https://doi.org/10.1007/s11368-017-1854-6
Zhang, R. & Wang, D. (2012) Trichoderma spp. from rhizosphere soil and their antagonism against Fusarium sambucinum. African Journal of Biotechnology 11 (18): 4180–4186. https://dx.doi.org/10.5897/ajb11.3426
Zhang, Y.J., Zhang, S., Liu, X.Z., Wen, H.A. & Wang, M. (2010) A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains. Letters in Applied Microbiology 51: 114–118. https://doi.org/10.1111/j.1472-765X.2010.02867.x
Carbone, I & Kohn, L.M. (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553–556. https://doi.org/10.1080/00275514.1999.12061051
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17 (4): 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Chaverri, P., Castlebury, L.A., Samuels, G.J. & David, M.G. (2003) Multilocus phylogenetic structure within the Trichoderma harzianum/Hypocrea lixii complex. Molecular Phylogenetics and Evolution 27 (2): 302–313. https://doi.org/10.1016/S1055-7903(02)00400-1
Chaverri, P., Branco-Rocha, F., Jaklitsch, W., Gazis, R., Degenkolb, T. & Samuels, G.J. (2015) Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains. Mycologia 107 (3): 558–590. https://doi.org/10.3852/14-147
du Plessis, I.L., Druzhinina, I.S., Atanasova, L., Yarden, O. & Jacobs, K. (2018) The diversity of Trichoderma species from soil in South Africa, with five new additions. Mycologia 110: 559–583. https://doi.org/10.1080/00275514.2018.1463059
Edwards, J.C., Johnson, C., Santos-Medellin, E.L., Podishetty, N.K., Bhatnagar, S., Eisen, J.A. & Sundaresan, V. (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America 112: E911-20. https://doi.org/10.1073/pnas.1414592112
Ferreira, F.V., Herrmann-Andrade, A.M., Calabrese, C.D., Bello, F., Vazquez, D. & Musumeci, M.A. (2020) Effectiveness of Trichoderma strains isolated from the rhizosphere of citrus tree to control Alternaria alternata, Colletotrichum gloeosporioides and Penicillium digitatum A21 resistant to pyrimethanil in post-harvest oranges (Citrus sinensis L. (Osbeck)). Journal of Applied Microbiology 129: 712–727. https://doi.org/10.1111/jam.14657
Gu, X., Wang, R., Sun, Q., Wu, B. & Sun, J.Z. (2020) Four new species of Trichoderma in the Harzianum clade from northern China. MycoKeys 73: 109–132. https://doi.org/10.3897/mycokeys.73.51424
Guzman-Guzman, P., Porras-Troncoso, M.D., Olmedo-Monfil, V. & Herrera-Estrella, A. (2019) Trichoderma species: versatile plant symbionts. Phytopathology 109: 6–16. https://doi.org/10.1094/PHYTO-07-18-0218-RVW
Jaklitsch, W.M. (2009) European species of Hypocrea Part I. The green-spored species. Studies in Mycology 63: 1–91. https://doi.org/10.3114/sim.2009.63.01
Jaklitsch, W.M. (2011) European species of Hypocrea part II: species with hyaline ascospores. Fungal Diversity 48: 1–250. https://doi.org/10.1007/s13225-011-0088-y
Jaklitsch, W.M., Komon, M., Kubicek, C.P. & Druzhinina, I.S. (2017) Hypocrea voglmayrii sp. nov. from the Austrian Alps represents a new phylogenetic clade in Hypocrea/Trichoderma. Mycologia 97: 1365–1378. http://doi.org/10.1080/15572536.2006.11832743
Jang, S., Jang, Y., Kim, C.W., Lee, H., Hong, J.H., Heo, Y.M., Lee, Y.M., Lee, D.W., Lee, H.B. & Kim, J.J. (2017) Five new records of soil-derived Trichoderma in Korea: T. albolutescens, T. asperelloides, T. orientale, T. spirale, and T. tomentosum. Mycobiology 45: 1–8. https://doi.org/10.5941/MYCO.2017.45.1.1
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. https://doi.org/10.1093/molbev/mst010
Liu, B., Ji, S., Zhang, H., Wang, Y. & Liu, Z. (2020) Isolation of Trichoderma in the rhizosphere soil of Syringa oblata from Harbin and their biocontrol and growth promotion function. Microbiological Research 235: 126445. https://doi.org/10.1016/j.micres.2020.126445
Liu, J.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Na, X.F, Ma, S., Ma, C., Liu, Z., Xu, P., Zhu, H., Liang, W. & Kardol, P. (2021) Lycium barbarum L. (goji berry) monocropping causes microbial diversity loss and induces Fusarium spp. enrichment at distinct soil layers. Applied Soil Ecology 168: 104–107. https://doi.org/10.1016/j.apsoil.2021.104107
Nandini, B., Puttaswamy, H., Saini, R.K., Prakash, H.S. & Geetha, N. (2021) Trichovariability in rhizosphere soil samples and their biocontrol potential against downy mildew pathogen in pearl millet. Scientifc Reports 11: 9517. https://doi.org/10.1038/s41598-021-89061-2
Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author. Available from: https://github.com/nylander/MrModeltest2
Overton, B.E., Stewart, E.L. & Geiser, D.M. (2006) Taxonomy and phylogenetic relationships of nine species of Hypocrea with an amorphs assignable to Trichoderma section Hypocreanum. Studies in Mycology 56: 39–65. https://doi.org/10.3114/sim.2006.56.02
Peciulyte, A., Anasontzis, G.E., Karlström, K., Larsson, P.T. & Olsson, L. (2014) Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates. Fungal Genetics and Biology 72: 64–72. https://doi.org/10.1016/j.fgb.2014.07.011
Rambaut, A. (2012) FigTree version 1.4.0. Program distributed by the author. Available from: http://tree.bio.ed.ac.uk/software/figtree/ (accessed 18 May 2022)
Riley, D. & Barber, S.A. (1970) Salt accumulation at the soybean (Glycine max ( L. ) Merr.) root-soil interface. Soil Science Society of America Journal 34 (1): 154–155. https://doi.org/10.2136/sssaj1970.03615995003400010042x
Ronquist, F., Teslenko, M., Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542. https://doi.org/10.1093/sysbio/sys029
Ryu, S.M., Lee, H.M., Song, E.G., Seo, Y.H., Lee, J., Guo, Y., Kim, B.S., Kim, J.J., Hong, J.S., Ryu, K.H. & Lee, D. (2017) Antiviral activities of trichothecenes isolated from Trichoderma albolutescens against pepper mottle virus. Journal of Agricultural and Food Chemistry 65: 4273–4279. https://doi.org/10.1021/acs.jafc.7b01028
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
Strakowska, J., B?aszczyk, L. & Che?kowski, J. (2014) The significance of cellulolytic enzymes produced by Trichoderma in opportunistic lifestyle of this fungus. Journal of Basic Microbiology 54: S2–S13. https://doi.org/10.1002/jobm.201300821
Swain, H., Adak, T., Mukherjee, A.K., Mukherjee, P.K., Bhattacharyya, P., Behera, S., Bagchi, T.B., Patro, R., Khandual, A., Bag, M.K., Dangar, T.K. & Jena, M. (2018) Novel Trichoderma strains isolated from tree barks as potential biocontrol agents and biofertilizers for direct seeded rice. Microbiological Research 214: 83–90. https://doi.org/10.1016/j.micres.2018.05.015
White, T.J., Bruns, T., Lee, S. & Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (Eds.) PCR Protocols: a Giude to Methods and Application. Academic Press, San Diego, USA, pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Zhang, J.H., Li, M., Jia, K.L., Zheng, G.Q. & Long, X.E. (2018) Seasonal variation rather than stand age determines bacterial diversity in the rhizosphere of wolfberry (Lycium barbarum L.) associated with soil degradation. Journal of Soils and Sediments 18: 1518–1529. https://doi.org/10.1007/s11368-017-1854-6
Zhang, R. & Wang, D. (2012) Trichoderma spp. from rhizosphere soil and their antagonism against Fusarium sambucinum. African Journal of Biotechnology 11 (18): 4180–4186. https://dx.doi.org/10.5897/ajb11.3426
Zhang, Y.J., Zhang, S., Liu, X.Z., Wen, H.A. & Wang, M. (2010) A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains. Letters in Applied Microbiology 51: 114–118. https://doi.org/10.1111/j.1472-765X.2010.02867.x