Abstract
In the context of a bioprospection programme for tyrosinase/L-DOPA- and melanin-producing fungal strains for biotechnological purposes, a hyperproducer isolate was obtained from Las Yungas rainforest, a relevant biodiverse ecoregion in North-Western Argentina. The selected strain was preliminarily identified as Paraboeremia sp. This is, to the best of our knowledge, the first native reported species of this genus in South America. Single-gene and multi-locus analyses of the internal transcribed spacer nuclear ribosomal RNA gene region (ITS), partial large subunit 28S nrDNA region (LSU), RNA polymerase II region (RPB2) and partial β-tubulin gene (TUB2) alignments were carried out to define the phylogenetic identity of this strain. As part of a polyphasic identification approach, these results were combined with morphological studies of active cultures growing on malt extract, oatmeal and potato dextrose agar plates. Incubation was performed under diverse conditions to stimulate sporulation for the subsequent micromorphological analysis. Microphotographs of pycnidia and conidia were taken with a scanning electron microscope. Maximum likelihood and Bayesian Inference analyses supported the location of the strain within the genus Paraboeremia, whilst morphological features allowed distinguishing it from previously described species within this genus. Based on the results herein reported, the new South-American species Paraboeremia yungensis is described and proposed.
References
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Cabral, M.E., Delgado, O.D., Sampietro, D.A., Catalan, C.A., Figueroa, L.I.C. & Fariña, J.I. (2010) Antifungal Activity and the Potential Correlation with Statin-Producing Ability: An Optimized Screening Applied to Filamentous Fungi from Las Yungas Subtropical Rainforest. Research Journal of Microbiology 5: 833–848. https://doi.org/10.3923/jm.2010.833.848
Cassago, A., Panepucci, R.A., Tortella Baião, A.M. & Henrique-silva, F. (2002) Cellophane based mini-prep method for DNA extraction from the filamentous fungus Trichoderma reesei. BMC Microbiology 2: 14. https://doi.org/10.1186/1471-2180-2-14
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Chen, Q., Hou, L.W., Duan, W.J., Crous, P.W. & Cai, L. (2017) Didymellaceae revisited. Studies in Mycology 87: 105–159. https://doi.org/10.1016/j.simyco.2017.06.002
Chen, Q., Jiang, J.R., Zhang, G.Z., Cai, L. & Crous, P.W. (2015) Resolving the Phoma enigma. Studies in Mycology 82: 137–217. https://doi.org/10.1016/j.simyco.2015.10.003
Edgar, R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. https://doi.org/10.1186/1471-2105-5-113
Fuller, K.K., Loros, J.J. & Dunlap, J.C. (2015) Fungal photobiology: visible light as a signal for stress, space and time. Current Genetics 61: 275–288. https://doi.org/10.1007/s00294-014-0451-0
De Gruyter, J., Aveskamp, M.M., Woudenberg, J.H.C., Verkley, G.J.M., Groenewald, J.Z. & Crous, P.W. (2009) Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex. Mycological Research 113: 508–519. https://doi.org/10.1016/j.mycres.2009.01.002
Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
Hoog, G.S. & Ende, A.H.G.G. (1998) Molecular diagnostics of clinical strains of filamentous Basidiomycetes. Mycoses 41: 183–189. https://doi.org/10.1111/j.1439-0507.1998.tb00321.x
Hou, L., Hernández-Restrepo, M., Groenewald, J.Z., Cai, L. & Crous, P.W. (2020) Citizen science project reveals high diversity in Didymellaceae (Pleosporales, Dothideomycetes). MycoKeys 65: 49–99. https://doi.org/10.3897/mycokeys.65.47704
Huson, D.H. & Scornavacca, C. (2012) Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61: 1061–1067. https://doi.org/10.1093/sysbio/sys062
Hyde, K.D., Abd-Elsalam, K. & Cai, L. (2010) Morphology: Still essential in a molecular world. Mycotaxon 114: 439–451. https://doi.org/10.5248/114.439
Ishiuchi, K., Hirose, D., Suzuki, T., Nakayama, W., Jiang, W.P., Monthakantirat, O., Wu, J. Bin, Kitanaka, S. & Makino, T. (2018) Identification of Lycopodium Alkaloids Produced by an Ultraviolet-Irradiated Strain of Paraboeremia, an Endophytic Fungus from Lycopodium serratum var. longipetiolatum. Journal of Natural Products 81: 1143–1147. https://doi.org/10.1021/acs.jnatprod.7b00627
Jiang, J.R., Chen, Q. & Cai, L. (2017) Polyphasic characterisation of three novel species of Paraboeremia. Mycological Progress 16: 285–295. https://doi.org/10.1007/s11557-016-1253-1
Kiiskinen, L.L., Rättö, M. & Kruus, K. (2004) Screening for novel laccase-producing microbes. Journal of Applied Microbiology 97: 640–646. https://doi.org/10.1111/j.1365-2672.2004.02348.x
Krishnaveni, R., Rathod, V., Thakur, M.S. & Neelgund, Y.F. (2009) Transformation of L-tyrosine to L-dopa by a novel fungus, Acremonium rutilum, under submerged fermentation. Current Microbiology 58: 122–128. https://doi.org/10.1007/s00284-008-9287-5
Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution 33: 1870–1874. https://doi.org/10.1093/molbev/msw054
Leach, C.M. (1962) Sporulation of Diverse Species of Fungi Under Near-Ultraviolet Radiation. Canadian Journal of Botany 40: 151–161. https://doi.org/10.1139/b62-016
Liu, Y.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerse II subunit. Molecular Biology and Evolution 16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees. In: 2010 Gateway Computing Environments Workshop (GCE). pp. 1–8. https://doi.org/10.1109/GCE.2010.5676129
Rambaut, A. (2017) FigTree-version 1.4. 3, a graphical viewer of phylogenetic trees.
Rambaut, A. & Drummond, A.J. (2007) Tracer v1. 5.
Rayner, A. & Boddy, L. (1988) Fungal decomposition of wood: its biology and ecology. In: John Wiley & Sons Ltd. (ed.) Amoebae and Myxomycetes. Chichester, Sussex, pp. 132–134.
Rayner, R.W. (1972) A Mycological Colour Chart. Mycologia 64: 230. https://doi.org/10.2307/3758035
Rehner, S.A. & Samuels, G.J. (1994) Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycological Research 98: 625–634. https://doi.org/10.1016/S0953-7562(09)80409-7
Ronquist, F., Huelsenbeck, J.P. & Teslenko, M. (2011) Draft MrBayes version 3.2 manual: tutorials and model summaries. pp. 1–105.
Roustaee, A., Dechamp-Guillaume, G., Gelie, B., Savy, C., Dargent, R. & Barrault, G. (2000) Ultrastructural studies of the mode of penetration by Phoma macdonaldii in sunflower seedlings. Phytopathology 90: 915–920. https://doi.org/10.1094/PHYTO.2000.90.8.915
Rovati, J.I., Delgado, O.D., Figueroa, L.I.C. & Fariña, J.I. (2010) A novel source of fibrinolytic activity: Bionectria sp., an unconventional enzyme-producing fungus isolated from Las Yungas rainforest (Tucumán, Argentina). World Journal of Microbiology and Biotechnology 26: 55–62. https://doi.org/10.1007/s11274-009-0142-z
Stalper, J.A. (1978) Identification of Wood-inhabiting Aphyllophorales in Pure Cul- ture. Studies in Mycology 16: 224–225. https://doi.org/10.1080/00275514.1942.12020904
Stamatakis, A. (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Su, Y.Y., Qi, Y.L. & Cai, L. (2012) Induction of sporulation in plant pathogenic fungi. Mycology 3: 195–200. https://doi.org/10.1080/21501203.2012.719042
Sung, G.H., Sung, J.M., Hywel-Jones, N.L. & Spatafora, J.W. (2007) A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44: 1204–1223. https://doi.org/10.1016/j.ympev.2007.03.011
Valenzuela-Lopez, N., Cano-Lira, J.F., Guarro, J., Sutton, D.A., Wiederhold, N., Crous, P.W. & Stchigel, A.M. (2018) Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae. Studies in Mycology 90: 1–69. https://doi.org/10.1016/j.simyco.2017.11.003
Vilgalys, R. & Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
Volossiouk, T., Robb, E.J. & Nazar, R.N. (2021) Direct DNA extraction for PCR-mediated assays of soil organisms. Applied and Environmental Microbiology 61: 3972–3976. https://doi.org/10.1128/aem.61.11.3972-3976.1995
White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, Inc., pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Woudenberg, J.H.C., Aveskamp, M.M., De Gruyter, J., Spiers, A.G. & Crous, P.W. (2009) Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype. Persoonia: Molecular Phylogeny and Evolution of Fungi 22: 56–62. https://doi.org/10.3767/003158509X427808
Yang, J., Stadler, M., Chuang, W.Y., Wu, S. & Ariyawansa, H.A. (2020) In vitro inferred interactions of selected entomopathogenic fungi from Taiwan and eggs of Meloidogyne graminicola. Mycological Progress 19: 97–109. https://doi.org/10.1007/s11557-019-01546-7
Zimowska, B. (2011) Conidiogenesis of Phoma strasseri the fungus responsible for black stem and rhizomes rot in peppermint (Mentha piperita). Acta Scientiarum Polonorum, Hortorum Cultus 10: 171–178.
Boerema, G.H. & De Gruyter, J. (1997) Contributions towards a monograph of Phoma (Coelomycetes) IV. Persoonia 16: 335–371.
Boerema, G.H., De Gruyter, J., Noordeloos, M.E. & Hamers, M.E.C. (2004) Phoma identification manual. Differentiation of specific and infra-specific taxa in culture. https://doi.org/10.1079/9780851997438.0000
Boom, R., Sol, C.J.A., Salimans, M.M.M., Jansen, C.L., Wertheim-Van Dillen, P.M.E. & Van Der Noordaa, J. (1990) Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28: 495–503. https://doi.org/10.1128/jcm.28.3.495-503.1990
Cabral, M.E., Delgado, O.D., Sampietro, D.A., Catalan, C.A., Figueroa, L.I.C. & Fariña, J.I. (2010) Antifungal Activity and the Potential Correlation with Statin-Producing Ability: An Optimized Screening Applied to Filamentous Fungi from Las Yungas Subtropical Rainforest. Research Journal of Microbiology 5: 833–848. https://doi.org/10.3923/jm.2010.833.848
Cassago, A., Panepucci, R.A., Tortella Baião, A.M. & Henrique-silva, F. (2002) Cellophane based mini-prep method for DNA extraction from the filamentous fungus Trichoderma reesei. BMC Microbiology 2: 14. https://doi.org/10.1186/1471-2180-2-14
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Chen, Q., Hou, L.W., Duan, W.J., Crous, P.W. & Cai, L. (2017) Didymellaceae revisited. Studies in Mycology 87: 105–159. https://doi.org/10.1016/j.simyco.2017.06.002
Chen, Q., Jiang, J.R., Zhang, G.Z., Cai, L. & Crous, P.W. (2015) Resolving the Phoma enigma. Studies in Mycology 82: 137–217. https://doi.org/10.1016/j.simyco.2015.10.003
Edgar, R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. https://doi.org/10.1186/1471-2105-5-113
Fuller, K.K., Loros, J.J. & Dunlap, J.C. (2015) Fungal photobiology: visible light as a signal for stress, space and time. Current Genetics 61: 275–288. https://doi.org/10.1007/s00294-014-0451-0
De Gruyter, J., Aveskamp, M.M., Woudenberg, J.H.C., Verkley, G.J.M., Groenewald, J.Z. & Crous, P.W. (2009) Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex. Mycological Research 113: 508–519. https://doi.org/10.1016/j.mycres.2009.01.002
Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
Hoog, G.S. & Ende, A.H.G.G. (1998) Molecular diagnostics of clinical strains of filamentous Basidiomycetes. Mycoses 41: 183–189. https://doi.org/10.1111/j.1439-0507.1998.tb00321.x
Hou, L., Hernández-Restrepo, M., Groenewald, J.Z., Cai, L. & Crous, P.W. (2020) Citizen science project reveals high diversity in Didymellaceae (Pleosporales, Dothideomycetes). MycoKeys 65: 49–99. https://doi.org/10.3897/mycokeys.65.47704
Huson, D.H. & Scornavacca, C. (2012) Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61: 1061–1067. https://doi.org/10.1093/sysbio/sys062
Hyde, K.D., Abd-Elsalam, K. & Cai, L. (2010) Morphology: Still essential in a molecular world. Mycotaxon 114: 439–451. https://doi.org/10.5248/114.439
Ishiuchi, K., Hirose, D., Suzuki, T., Nakayama, W., Jiang, W.P., Monthakantirat, O., Wu, J. Bin, Kitanaka, S. & Makino, T. (2018) Identification of Lycopodium Alkaloids Produced by an Ultraviolet-Irradiated Strain of Paraboeremia, an Endophytic Fungus from Lycopodium serratum var. longipetiolatum. Journal of Natural Products 81: 1143–1147. https://doi.org/10.1021/acs.jnatprod.7b00627
Jiang, J.R., Chen, Q. & Cai, L. (2017) Polyphasic characterisation of three novel species of Paraboeremia. Mycological Progress 16: 285–295. https://doi.org/10.1007/s11557-016-1253-1
Kiiskinen, L.L., Rättö, M. & Kruus, K. (2004) Screening for novel laccase-producing microbes. Journal of Applied Microbiology 97: 640–646. https://doi.org/10.1111/j.1365-2672.2004.02348.x
Krishnaveni, R., Rathod, V., Thakur, M.S. & Neelgund, Y.F. (2009) Transformation of L-tyrosine to L-dopa by a novel fungus, Acremonium rutilum, under submerged fermentation. Current Microbiology 58: 122–128. https://doi.org/10.1007/s00284-008-9287-5
Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution 33: 1870–1874. https://doi.org/10.1093/molbev/msw054
Leach, C.M. (1962) Sporulation of Diverse Species of Fungi Under Near-Ultraviolet Radiation. Canadian Journal of Botany 40: 151–161. https://doi.org/10.1139/b62-016
Liu, Y.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerse II subunit. Molecular Biology and Evolution 16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees. In: 2010 Gateway Computing Environments Workshop (GCE). pp. 1–8. https://doi.org/10.1109/GCE.2010.5676129
Rambaut, A. (2017) FigTree-version 1.4. 3, a graphical viewer of phylogenetic trees.
Rambaut, A. & Drummond, A.J. (2007) Tracer v1. 5.
Rayner, A. & Boddy, L. (1988) Fungal decomposition of wood: its biology and ecology. In: John Wiley & Sons Ltd. (ed.) Amoebae and Myxomycetes. Chichester, Sussex, pp. 132–134.
Rayner, R.W. (1972) A Mycological Colour Chart. Mycologia 64: 230. https://doi.org/10.2307/3758035
Rehner, S.A. & Samuels, G.J. (1994) Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycological Research 98: 625–634. https://doi.org/10.1016/S0953-7562(09)80409-7
Ronquist, F., Huelsenbeck, J.P. & Teslenko, M. (2011) Draft MrBayes version 3.2 manual: tutorials and model summaries. pp. 1–105.
Roustaee, A., Dechamp-Guillaume, G., Gelie, B., Savy, C., Dargent, R. & Barrault, G. (2000) Ultrastructural studies of the mode of penetration by Phoma macdonaldii in sunflower seedlings. Phytopathology 90: 915–920. https://doi.org/10.1094/PHYTO.2000.90.8.915
Rovati, J.I., Delgado, O.D., Figueroa, L.I.C. & Fariña, J.I. (2010) A novel source of fibrinolytic activity: Bionectria sp., an unconventional enzyme-producing fungus isolated from Las Yungas rainforest (Tucumán, Argentina). World Journal of Microbiology and Biotechnology 26: 55–62. https://doi.org/10.1007/s11274-009-0142-z
Stalper, J.A. (1978) Identification of Wood-inhabiting Aphyllophorales in Pure Cul- ture. Studies in Mycology 16: 224–225. https://doi.org/10.1080/00275514.1942.12020904
Stamatakis, A. (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Su, Y.Y., Qi, Y.L. & Cai, L. (2012) Induction of sporulation in plant pathogenic fungi. Mycology 3: 195–200. https://doi.org/10.1080/21501203.2012.719042
Sung, G.H., Sung, J.M., Hywel-Jones, N.L. & Spatafora, J.W. (2007) A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44: 1204–1223. https://doi.org/10.1016/j.ympev.2007.03.011
Valenzuela-Lopez, N., Cano-Lira, J.F., Guarro, J., Sutton, D.A., Wiederhold, N., Crous, P.W. & Stchigel, A.M. (2018) Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae. Studies in Mycology 90: 1–69. https://doi.org/10.1016/j.simyco.2017.11.003
Vilgalys, R. & Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
Volossiouk, T., Robb, E.J. & Nazar, R.N. (2021) Direct DNA extraction for PCR-mediated assays of soil organisms. Applied and Environmental Microbiology 61: 3972–3976. https://doi.org/10.1128/aem.61.11.3972-3976.1995
White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, Inc., pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Woudenberg, J.H.C., Aveskamp, M.M., De Gruyter, J., Spiers, A.G. & Crous, P.W. (2009) Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype. Persoonia: Molecular Phylogeny and Evolution of Fungi 22: 56–62. https://doi.org/10.3767/003158509X427808
Yang, J., Stadler, M., Chuang, W.Y., Wu, S. & Ariyawansa, H.A. (2020) In vitro inferred interactions of selected entomopathogenic fungi from Taiwan and eggs of Meloidogyne graminicola. Mycological Progress 19: 97–109. https://doi.org/10.1007/s11557-019-01546-7
Zimowska, B. (2011) Conidiogenesis of Phoma strasseri the fungus responsible for black stem and rhizomes rot in peppermint (Mentha piperita). Acta Scientiarum Polonorum, Hortorum Cultus 10: 171–178.