Two new endophytic species enrich the Coniochaeta endophytica / C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov.
More details
Hide details
School of Plant Sciences, The University of Arizona, Tucson, AZ 85721 USA
Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721 USA
Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
Indigo Agriculture, Boston, MA 02129 USA
Online publication date: 2021-07-30
Publication date: 2021-07-30
Plant and Fungal Systematics 2021; 66(1): 66–78
Coniochaeta (Coniochaetaceae, Ascomycota) is a diverse genus that includes a striking richness of undescribed species with endophytic lifestyles, especially in temperate and boreal plants and lichens. These endophytes frequently represent undescribed species that can clarify evolutionary relationships and trait evolution within clades of previously classified fungi. Here we extend the geographic, taxonomic, and host sampling presented in a previous analysis of the clade containing Coniochaeta endophytica, a recently described species occurring as an endophyte from North America; and C. prunicola, associated with necroses of stonefruit trees in South Africa. Our multi-locus analysis and examination of metadata for endophyte strains housed in the Robert L. Gilbertson Mycological Herbarium at the University of Arizona (ARIZ) (1) expands the geographic range of C. endophytica across a wider range of the USA than recognized previously; (2) shows that the ex-type of C. prunicola (CBS 120875) forms a well-supported clade with endophytes of native hosts in North Carolina and Michigan, USA; (3) reveals that the ex-paratype for C. prunicola (CBS 121445) forms a distinct clade with endophytes from North Carolina and Russia, is distinct morphologically from the other taxa considered here, and is described herein as Coniochaeta lutea; and (4) describes a new species, Coniochaeta palaoa, here identified as an endophyte of multiple plant lineages in the highlands and piedmont of North Carolina. Separation of CBS 120875 and CBS 121445 into C. prunicola sensu stricto and C. lutea is consistent with previously described genomic differences between these isolates, and morphological and functional differences among the four species (C. endophytica, C. prunicola, C. palaoa, and C. lutea) underscore the phylogenetic relationships described here. The resolving power of particular loci and the emerging perspective on the host- and geographic range of Coniochaeta and the C. endophytica / C. prunicola clade are discussed.
Agrawal, T. & Kotasthane, A. S. 2012. Chitinolytic assay of indigenous Trichoderma isolates collected from different geographical locations of Chhattisgarh in central India. SpringerPlus 1: 73. https://doi.org/10.1186/2193-1....
Asgari, B., Zare, R. & Gams, W. 2007. Coniochaeta ershadii, a new species from Iran, and a key to well-documented Coniochaeta species. Nova Hedwigia 84: 175–187. https://doi.org/10.1127/0029-5....
Bills, G. F., González-Menéndez, V., Martín, J., Platas, G., Fournier, J., PerŠoh, D. & Stadler, M. 2012. Hypoxylon pulicicidum sp. nov. (Asco­mycota, Xylariales), a pantropical insecticide-producing endophyte. PLoS One 7: e46687. https://doi.org/10.1371/journa....
Bussaban, B., Lumyong, S., Lumyong, P., Hyde, K. D. & McKenzie, E. H. C. 2003. Three new species of Pyricularia are isolated as zingiberaceous endophytes from Thailand. Mycologia 95: 519–524. https://doi.org/10.2307/376189....
Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U’Ren, J. M., May, G. & Lutzoni, F. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 33: 1160–1168. https://doi.org/10.1093/bioinf....
Chen, K.-H., Miadlikowska, J., Molnár, K., Arnold, A. E., U’Ren, J. M., Gaya, E., Gueidan, C. & Lutzoni, F. 2015. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales and a new order – Phaeomoniellales. Molecular Phylogenetics and Evolution 85: 117–130. https://doi.org/10.1016/j.ympe....
Chen, K.-H. 2017. Evolution of fungal endophytes and their functional transitions between endophytism and saprotrophism. PhD Dissertation, Duke University, Durham, NC, USA.
Damm, U., Fourie, P. H. & Crous, P. W. 2010. Coniochaeta (Lecythophora), Collophora gen. nov. and Phaemoniella species associated with wood necroses of Prunus trees. Persoonia – Molecular Phylogeny & Evolution of Fungi 24: 60–80. https://doi.org/10.3767/003158....
Del Olmo-Ruiz, M. 2012. Diversity, distributions, and host affiliations of fungal endophytes associated with seedless vascular plants (Ph.D dissertation). University of Arizona.
Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792–1797. https://doi.org/10.1093/nar/gk....
Ewing, B., Hillier, L., Wendl, M. C. & Green, P. 1998. Base-calling of automated sequencer traces with phred. Genome Research 8: 175–185. https://doi.org/10.1101/gr.8.3....
Friebes, G., Jaklitsch, W. M., Garcia, S. & Voglmayr, H. 2016. Lopadostoma taeniosporum revisted and a new species of Coniochaeta. Sydowia 68: 87–97.
Gams, W. & McGinnis, M. R. 1983. Phialemonium, a new anamorph genus intermediate between Phialophora and Acremonium. Mycologia 75: 977–987. https://doi.org/10.1080/002755....
García, D., Stchigel, A. M., Cano, J., Calduch, M., Hawksworth, D. L. & Guarro, J. 2006. Molecular phylogeny of Coniochaetales. Mycological Research 110: 1271–1289. https://doi.org/10.1016/j.mycr....
Gazis, R., Rehner, S. & Chaverri, P. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Molecular Ecology 20: 3001–3013. https://doi.org/10.1111/j.1365....
Gazis, R., Miadlikowska, J., Lutzoni, F., Arnold, A. E. & Chaverri, P. 2012. Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes. Molecular Phylogenetics and Evolution 65: 294–304. https://doi.org/10.1016/j.ympe....
Han, J., Liu, C., L. Li, Zhou, H., Liu, L., Bao, L., Chen, Q., Song, F., Zhang, L., Li, E., Liu, L., et al. 2017. Decalin-containing tetramic acids and 4-Hydroxy-2-pyridones with antimicrobial and cytotoxic activity from the fungus Coniochaeta cephalothecoides collected in Tibetan Plateau (Medog). Journal of Organic Chemistry 82: 11474–11486. https://doi.org/10.1021/acs.jo....
Harrington, A. H., Del Olmo-Ruiz, M., U’Ren, J. M., Garcia, K., Pignatta, D., Wespe, N., Sandberg, D. C., Huang, Y.-L., Hoffman, M. T. & Arnold, A. E. 2019. Coniochata endophytica sp. nov., a foliar endophyte associated with healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae). Plant and Fungal Systematics 64: 65–79. https://doi.org/10.2478/pfs-20....
Hoffman, M. T. & Arnold, A. E. 2008. Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycological Research 112: 331–344. https://doi.org/10.1016/j.mycr....
Huang, Y.-L., Devan, M. M. N., U’Ren, J. M., Furr, S. H. & Arnold, A. E. 2016. Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microbial Ecology 71: 452–468. https://doi.org/10.1007/s00248....
Huhndorf, S. M., Miller, A. N. & Fernández, F. A. 2004. Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia 96: 368–387. https://doi.org/10.1080/155725....
Ivanová, H. & Bernadovičová, S. 2012. New record of the fungus Coniochaeta prunicola on peaches from Slovakia. Biologia (Bratisl) 67: 269–273. https://doi.org/10.2478/s11756....
Kamiya, S., Uchiyama, S. & Udagawa, S. 1995. Two new species of Coniochaeta with a cephalothecoid peridium wall. Mycoscience 36: 377–383. https://doi.org/10.1007/bf0226....
Khan, Z., Gene, J., Ahmad, S., Cano, J., Al-Sweih, N., Joseph, L., Chandy, R. & Guarro, J. 2013. Coniochaeta polymorpha, a new species from endotracheal aspirate of a preterm neonate, and transfer of Lecythophora species to Coniochaeta. Antonie van Leeuwenhoek 104: 243–252. https://doi.org/10.1007/s10482....
Kirk, P., Cannon, P. F., Minter, D. W. & Stalpers, J. A. 2008. Ainsworth & Bisby’s Dictionary of the Fungi. 10th edn. CAB International, Wallingford, UK.
Maddison, W. P. & Maddison, D. R. 2017. Mesquite: a modular system for evolutionary analysis. Version 3.2.
Malloch, D. & Cain, R. F. 1971. New cleistothecial Sordariaceae and a new family, Coniochaetaceae. Canadian Journal of Botany 49: 869–880. https://doi.org/10.1139/b71-12....
Melin, E. & Nannfeldt, J. A. 1934. Researches into the blueing of ground woodpulp. Svenska Skogsvårdsföreningens Tidskrift 32: 397–616.
Nasr, S., Bien, S., Soudi, M. R., Alimadadi, N., Fazeli, S. A. S. & Damm, U. 2018. Novel Collophorina and Coniochaeta species from Euphorbia polycaulis, an edemic plant in Iran. Mycological Progress 17: 755–771. https://doi.org/10.1007/s11557....
Oita, S., Carey, J., Kline, I., Ibáñez, A., Yang, N., Hom, E. F. Y., Carbone, I., U’Ren, J. M. & Arnold, A. E. 2021. Methodological approaches frame insights into endophyte richness and community composition. Microbial Ecology 82: 21–34. https://doi.org/10.1007/s00248....
Réblová, M., Miller, A. N., Rossman, A. Y., Seifert, K. A., Crous, P. W., Hawksworth, D. L., et al. 2016. Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales). IMA Fungus 7: 131–153. https://doi.org/10.5598/imafun....
Rehner, S. & Buckley, E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-a sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97: 84–98. https://doi.org/10.1080/155725....
Rojas, E. I., Herre, E. A., Mejía, L. C., Arnold, A. E., Chaverri, P. & Samuels, G. J. 2008. Endomelanconiopsis, a new anamorph genus in the Botryosphaeriaceae. Mycologia 100: 760–775. https://doi.org/10.3852/07-207.
Rojas, E. I., Rehner, S. A., Samuels, G. J., Van Bael, S. A., Herre, E. A., Cannon, P., Chen, R., et al. 2010. Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia 102: 1318–1338. https://doi.org/10.3852/09-244.
Torres-Cruz, T. J., Billingsley, T. T. L., Almatruk, M., Hesse, C. N., Kuske, C. R., Desiro, A., et al. 2017. Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia 109: 363–378. https://doi.org/10.1080/002755....
U’Ren, J. M., Lutzoni, F., Miadlikowska, J., Laetsch, A. D. & Arnold, A. E. 2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany 99: 898–914. https://doi.org/10.3732/ajb.11....
U’Ren, J. M., Lutzoni, F., Miadlikowska, J., Zimmerman, N. B., Carbone, I., May, G. & Arnold, A. E. 2019. Host availability drives distributions of fungal endophytes in the imperiled boreal realm. Nature Ecology & Evolution 3: 1430–1437. https://doi.org/10.1038/s41559....
Vázquez-Campos, X., Kinsela, A. S., White, T. D., Collins, R. N. & Neilan, B. A. 2014. Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine-inhabiting Ascomycota fungi from northern Australia. Mycologia 106: 1073–1089. https://doi.org/10.3852/14-013.
Weber, E. 2002. The Lecythophora-Coniochaeta complex I. Morphological studies on Lecythophora species isolated from Picea abies. Nova Hedwigia 74: 159–185. https://doi.org/10.1127/0029-5....
Weber, E., Görke, C. & Begerow, D. 2002. The Lecythophora-Coniochaeta complex II . Molecular studies based on sequences of the large subunit of ribosomal DNA. Nova Hedwigia 74: 187–200.
Xie, J., Strobel, G. A., Feng, T., Ren, H., Mends, M. T., Zhou, Z. & Geary, B. 2015. An endophytic Coniochaeta velutina producing broad spectrum antimycotics. Journal of Microbiology 53: 390–397. https://doi.org/10.1007/s12275....
Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the Maximum Likelihood Criterion (PhD thesis). University of Texas at Austin.