Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research

. 2022 ; 3 () : 860777. [epub] 20220325

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37746218

Understanding and describing the diversity of living organisms is a great challenge. Fungi have for a long time been, and unfortunately still are, underestimated when it comes to taxonomic research. The foundations were laid by the first mycologists through field observations. These important fundamental works have been and remain vital reference works. Nevertheless, a non-negligible part of the studied funga escaped their attention. Thanks to modern developments in molecular techniques, the study of fungal diversity has been revolutionized in terms of tools and knowledge. Despite a number of disadvantages inherent to these techniques, traditional field-based inventory work has been increasingly superseded and neglected. This perspective aims to demonstrate the central importance of field-based research in fungal diversity studies, and encourages researchers not to be blinded by the sole use of molecular methods.

Zobrazit více v PubMed

Abarenkov K., Nilsson R. H., Larsson K. H., Alexander I. J., Eberhardt U., Erland S., et al. . (2010). The UNITE database for molecular identification of fungi–recent updates and future perspectives. New Phytol. 186, 281–285. 10.1111/j.1469-8137.2009.03160.x PubMed DOI

Abdurazakov A. A., Bulgakov T. S., Kholmuradova T. N., Gafforov Y. S. (2021). Powdery mildew fungi (Erysiphaceae) of the Fergana Valley (within Uzbekistan): a first annotated checklist. Nov. Sist. Nizs. Rast. 55, 55–78. 10.31111/nsnr/2021.55.1.55 DOI

Adamčík S., Looney B., Cabon M., Jančovičová S., Adamčíková K., Avis P. G., et al. . (2019). The quest for a globally comprehensible Russula language. Fungal Divers. 99, 369–449. 10.1007/s13225-019-00437-2 DOI

Afkhami M. E., Stinchcombe J. R. (2016). Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi. Mol. Ecol. 25, 4946–4962. 10.1111/mec.13809 PubMed DOI

Aime M. C., Matheny P. B., Henk D. A., Frieders E. M., Nilsson R. H., Piepenbring M., et al. . (2006). An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98, 895–905. 10.1080/15572536.2006.11832619 PubMed DOI

Anderson I. C., Cairney J. W. (2004). Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ. Microbiol. 6, 769–779. 10.1111/j.1462-2920.2004.00675.x PubMed DOI

Antonelli A., Fry C., Smith R. J., Simmonds M. S. J., Kersey P. J., Pritchard H. W., et al. . (2020). State of the World's Plants and Fungi 2020. London: Royal Botanic Gardens, Kew.

Arnolds E. (2001). The future of fungi in Europe: threats, conservation and management. Brit. Mycol. Soc. Symp. Ser. 22, 64–80. 10.1017/CBO9780511565168.005 DOI

Baeza M., Barahona S., Alcaíno J., Cifuentes V. (2017). Amplicon-metagenomic analysis of fungi from antarctic terrestrial habitats. Front. Microbiol. 8, 2235. 10.3389/fmicb.2017.02235 PubMed DOI PMC

Baral H.-O. (1992). Vital versus herbarium taxonomy: morphological differences between living and dead cells of ascomycetes, and their taxonomic implications. Mycotaxon 44, 333–390.

Bardgett R. D., van der Putten W. H. (2014). Belowground biodiversity and ecosystem functioning. Nature 515, 505–511. 10.1038/nature13855 PubMed DOI

Barnosky A. D., Matzke N., Tomiya S., Wogan G. O. U., Swartz B., Quental T. B., et al. . (2011). Has the Earth's sixth mass extinction already arrived? Nature 471, 51–57. 10.1038/nature09678 PubMed DOI

Bauer R., Begerow D., Sampaio J. P., Wei,β M., Oberwinkler F. (2006). The simple-septate basidiomycetes: a synopsis. Mycol. Prog. 5, 41–66. 10.1007/s11557-006-0502-0 DOI

Berbee M. L., Taylor J. W. (2001). “Fungal molecular evolution: gene trees and geologic time,” in Systematics and Evolution, eds. McLaughlin D. J., McLaughlin E. G., Lemke P. A. (New York, NY: Springer–Verlag; ), 229–245. 10.1007/978-3-662-10189-6_10 DOI

Berbee M. L., Taylor J. W. (2010). Dating the molecular clock in fungi – how close are we? Fungal Biol. Rev. 24, 1–16. 10.1016/j.fbr.2010.03.001 DOI

Bernicchia A., Fugazzola M. A., Gemelli V., Mantovani B., Lucchetti A., Cesari M., et al. . (2006). DNA recovered and sequenced from an almost 7000 y-old Neolithic polypore, Daedaleopsis tricolor. Mycol. Res. 110, 14–17. 10.1016/j.mycres.2005.09.012 PubMed DOI

Bjelland T., Ekman S. (2005). Fungal diversity in rock beneath a crustose lichen as revealed by molecular markers. Microb. Ecol. 49, 598–603. 10.1007/s00248-004-0101-z PubMed DOI

Borriello R., Lumini E., Girlanda M., Bonfante P., Bianciotto V. (2012). Effects of different management practices on arbuscular mycorrhizal fungal diversity in maize fields by a molecular approach. Biol. Fertil. Soils 48, 911–922. 10.1007/s00374-012-0683-4 DOI

Boundy-Mills K., Hess M., Bennett A. R., Ryan M., Kang S., Nobles D., et al. . (2015). The United States Culture Collection Network (USCCN): enhancing microbial genomics research through living microbe culture collections. Appl. Environ. Microbiol. 81, 5671–5674. 10.1128/AEM.01176-15 PubMed DOI PMC

Brock P. M., Döring H., Bidartondo M. I. (2009). How to know unknown fungi: the role of a herbarium. New Phytol. 181, 719–724. 10.1111/j.1469-8137.2008.02703.x PubMed DOI

Bruns T. D., White T. J., Taylor J. W. (1991). Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22, 525–564. 10.1146/annurev.es.22.110191.002521 DOI

Butler G., Heitman J., Idnurm A., James T. Y. (2021). On a special collection in MMBR on sex in fungi: molecular mechanisms and evolutionary implications. Microbiol. Mol. Biol. Rev. 85, e00094–e00021. 10.1128/MMBR.00094-21 PubMed DOI PMC

Cardoza Y. J., Paskewitz S., Raffa K. F. (2006). Travelling through time and space on wings of beetles: a tripartite insect-fungi-nematode association. Symbiosis 41, 71–79.

Ceballos G., Ehrlich P. R., Barnosky A. D., García A., Pringle R. M., Palmer T. M. (2015). Accelerated modern human-induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253. 10.1126/sciadv.1400253 PubMed DOI PMC

Cheek M., Nic Lughadha E., Kirk P., Lindon H., Carretero J., Looney B., et al. . (2020). New discoveries: plants and fungi. Plants People Planet 2, 371–388. 10.1002/ppp3.10148 DOI

Christensen M. (1993). The fungal community: its organization and role in the ecosystem. BioScience 43, 787–789. 10.2307/1312325 DOI

Claridge A. W., Barry S. C., Cork S. J., Trappe J. M. (2000a). Diversity and habitat relationships of hypogeous fungi. II. factors influencing the occurrence and number of taxa. Biodivers. Conserv. 9, 175–199. 10.1023/A:1008962711138 DOI

Claridge A. W., Cork S. J., Trappe J. M. (2000b). Diversity and habitat relationships of hypogeous fungi. I. study design, sampling techniques and general survey results. Biodivers. Conserv. 9, 151–173. 10.1023/A:1008941906441 DOI

Cordier T., Robin C., Capdevielle X., Fabreguettes O., Desprez-Loustau M.-L., Vacher C. (2012). The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient. New Phytol. 196, 510–519. 10.1111/j.1469-8137.2012.04284.x PubMed DOI

Cunha A. O., Bezerra J. D. P., Oliveira T. G. L., Barbier E., Bernard E., Machado A. R., et al. . (2020). Living in the dark: bat caves as hotspots of fungal diversity. PLoS ONE 15, e0243494. 10.1371/journal.pone.0243494 PubMed DOI PMC

Currie C. R. (2000). The ecology and evolution of a quadripartite symbiosis, examining the interactions among Attine ants, fungi, and actinomycetes. Ph.D. thesis. Toronto, ON: University of Toronto.

Dastogeer K. M., Wylie S. J. (2017). “Plant–fungi association: role of fungal endophytes in improving plant tolerance to water stress,” in Plant–Microbe Interactions in Agro-Ecological Perspectives, D. P. eds. Singh, Singh H. B, Prabha R. (Singapore: Springer Nature; ), 143–159. 10.1007/978-981-10-5813-4_8 DOI

Davis T. S., Landolt P. J. (2013). A survey of insect assemblages responding to volatiles from a ubiquitous fungus in an agricultural landscape. J. Chem. Ecol. 39, 860–868. 10.1007/s10886-013-0278-z PubMed DOI

Dayrat B. (2005). Towards integrative taxonomy. Biol. J. Linn. Soc. 85, 407–415. 10.1111/j.1095-8312.2005.00503.x DOI

Dentinger B. T. M., Gaya E., O'Brien H., Suz L. M., Lachlan R., Díaz-Valderrama J. R., et al. . (2016). Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biol. J. Linn. Soc. 117, 11–32. 10.1111/bij.12553 DOI

Deveau A., Bonito G., Uehling J., Paoletti M., Becker M., Bindschedler S., et al. . (2018). Bacterial–fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol. Rev. 42, 335–352. 10.1093/femsre/fuy008 PubMed DOI

Diederich P., Ertz D. (2020). First checklist of lichens and lichenicolous fungi from Mauritius, with phylogenetic analyses and descriptions of new taxa. Plant Fungal Syst. 65, 13–75. 10.35535/pfsyst-2020-0003 DOI

Dighton J. (2003). Fungi in Ecosystem Processes. New York, NY: Marcel Dekker, Inc. 10.1201/9780203911440 DOI

Dirks A., Russell S. D. (2020). DNA barcoding of macrofungi from the 2018 Smith Foray: new fungal records for Wisconsin and the United States of America. Great Bot. 59, 191–201.

Drew L. W. (2011). Are we losing the science of taxonomy? As need grows, numbers and training are failing to keep up. BioScience 61, 942–946. 10.1525/bio.2011.61.12.4 DOI

Edwards R. A., Rodríguez-Brito B., Wegley L., Haynes M., Breitbart M., Peterson D. M., et al. . (2006). Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genom. 7, 57. 10.1186/1471-2164-7-57 PubMed DOI PMC

Egidi E., de Hoog G. S., Isola D., Onofri S., Quaedvlieg W., de Vries M., et al. . (2014). Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies. Fungal Divers. 65, 127–165. 10.1007/s13225-013-0277-y DOI

Fell J. W., Boekhout T., Fonseca A., Scorzetti G., Statzell-Tallman A. (2000). Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int. J. Syst. Evol. Microbiol. 50, 1351–1371. 10.1099/00207713-50-3-1351 PubMed DOI

Fraser J. A., Heitman J. (2004). Evolution of fungal sex chromosomes. Mol. Microbiol. 51, 299–306. 10.1046/j.1365-2958.2003.03874.x PubMed DOI

Fryar S. C., Hyde K. D., Catcheside D. E. (2020). A checklist of marine fungi from Australia. Mycotaxon 135, 465. 10.5248/135.465 DOI

Gafforov Y. (2017). A preliminary checklist of ascomycetous microfungi from Southern Uzbekistan. Mycosphere 8, 660–696. 10.5943/mycosphere/8/4/12 DOI

Gafforov Y., Ordynets A., Langer E., Yarasheva M., Gugliotta A. M., Schigel D., et al. . (2020). Species diversity with comprehensive annotations of wood- inhabiting poroid and corticioid fungi in Uzbekistan. Front. Microbiol. 11, 598321. 10.3389/fmicb.2020.598321 PubMed DOI PMC

Gafforov Y., Riebesehl J., Ordynets A., Langer E., Yarasheva M., Ghobad-Nejhad M., et al. . (2017). Hyphodontia (Hymenochaetales, Basidiomycota) and similar taxa from Central Asia. Botany 95, 1041–1056. 10.1139/cjb-2017-0115 DOI

Geml J., Gravendeel B., van der Gaag K. J., Neilen M., Lammers Y., Raes N., et al. . (2014). The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. PLoS ONE 9, e99852. 10.1371/journal.pone.0099852 PubMed DOI PMC

George P. B., Creer S., Griffiths R. I., Emmett B. A., Robinson D. A., Jones D. L. (2019). Primer and database choice affect fungal functional but not biological diversity findings in a national soil survey. Front. Environ. Sci. 7, 173. 10.3389/fenvs.2019.00173 DOI

Glaeser J. A., Lindner D. L. (2011). Use of fungal biosystematics and molecular genetics in detection and identification of wood-decay fungi for improved forest management. For. Pathol. 41, 341–348. 10.1111/j.1439-0329.2010.00681.x DOI

Gómez-Zapata P. A., Haelewaters D., Quijada L., Pfister D. H., Aime M. C. (2021). Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 78, 21–47. 10.3897/mycokeys.78.62046 PubMed DOI PMC

Gonçalves S. C., Haelewaters D., Furci G., Mueller G. M. (2021). Include all fungi in biodiversity goals. Science 373, 403. 10.1126/science.abk1312 PubMed DOI

Gordon M., van Norman K. (2015). Bridgeoporus nobilissimus is much more abundant than indicated by the presence of basidiocarps in forest stands. North Am. Fungi 10, 1–28.

Grossart H.-P., Van den Wyngaert S., Kagami M., Wurzbacher C., Cunliffe M., Rojas-Jimenez K. (2019). Fungi in aquatic ecosystems. Nat. Rev. Microbiol. 17, 339–354. 10.1038/s41579-019-0175-8 PubMed DOI

Haelewaters D., Dirks A. C., Kappler L. A., Mitchell J. K., Quijada L., Vandegrift R., et al. . (2018). A preliminary checklist of fungi at the Boston Harbor islands. Northeast. Nat. 25, 45–76. 10.1656/045.025.s904 DOI

Haelewaters D., Gorczak M., Kaishian P., De Kesel A., Blackwell M. (2021a). “Laboulbeniomycetes, enigmatic fungi with a turbulent taxonomic history,” in Encyclopedia of Mycology, ed. Zaragoza Ó. (Oxford: Elsevier; ), 263–283. 10.1016/B978-0-12-819990-9.00049-4 DOI

Haelewaters D., Gorczak M., Pfliegler W. P., Tartally A., Tischer M., Wrzosek M., et al. . (2015). Bringing Laboulbeniales to the 21st century: enhanced techniques for extraction and PCR amplification of DNA from minute ectoparasitic fungi. IMA Fungus 6, 363–372. 10.5598/imafungus.2015.06.02.08 PubMed DOI PMC

Haelewaters D., Peterson R. A., Nevalainen H., Aime M. C. (2021b). Inopinatum lactosum gen. & comb. nov., the first yeast-like fungus in Leotiomycetes. Int. J. Syst. Evol. Microbiol. 71, 4862. 10.1099/ijsem.0.004862 PubMed DOI

Haelewaters D., Schoutteten N., Medina-van Berkum P., Martin T. E., Verbeken A., Aime M. C. (2021c). Pioneering a fungal inventory at Cusuco National Park, Honduras. J. Mesoam. Biol. 1, 111–131.

Hagge J., Bässler C., Gruppe A., Hoppe B., Kellner H., Krah F.-S., et al. . (2019). Bark coverage shifts assembly processes of microbial decomposer communities in dead wood. Proc. R. Soc. B Biol. Sci. 286, 20191744. 10.1098/rspb.2019.1744 PubMed DOI PMC

Halme P., Heilmann-Clausen J., Räm,ä T., Kosonen T., Kunttu P. (2012). Monitoring fungal biodiversity – towards an integrated approach. Fungal Ecol. 5, 750–758. 10.1016/j.funeco.2012.05.005 PubMed DOI

Hawksworth D. L. (1988). The variety of fungal-algal symbioses, their evolutionary significance, and the nature of lichens. Bot. J. Linn. Soc. 96, 3–20. 10.1111/j.1095-8339.1988.tb00623.x DOI

Hawksworth D. L. (2001). The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol. Res. 105, 1422–1432. 10.1017/S0953756201004725 PubMed DOI

Hawksworth D. L. (2011). Naming Aspergillus species: progress towards one name for each species. Med. Mycol. 49, S70–S76. 10.3109/13693786.2010.504753 PubMed DOI

Hawksworth D. L., Lücking R. (2017). Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. 5, 1–17. 10.1128/microbiolspec.FUNK-0052-2016 PubMed DOI PMC

Heilmann-Clausen J., Barron E. S., Boddy L., Dahlberg A., Griffith G. W., Nordén J., et al. . (2014). A fungal perspective on conservation biology. Conserv. Biol. 29, 61–68. 10.1111/cobi.12388 PubMed DOI

Hibbett D., Abarenkov K., Kõljalg U., Öpik M., Chai B., Cole J., et al. . (2016). Sequence-based classification and identification of Fungi. Mycologia 108, 1049–1068. 10.3852/16-130 PubMed DOI

Hibbett D. S., Ohman A., Glotzer D., Nuhn M., Kirk P., Nilsson R. H. (2011). Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol. Rev. 25, 38–47. 10.1016/j.fbr.2011.01.001 DOI

Hock B. (2012). Fungal Associations. Berlin: Springer–Verlag. 10.1007/978-3-642-30826-0 DOI

Hofstetter V., Buyck B., Eyssartier G., Schnee S., Gindro K. (2019). The unbearable lightness of sequenced-based identification. Fungal Divers. 96, 243–284. 10.1007/s13225-019-00428-3 DOI

IPBES (2019). Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Bonn: Secretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.

Irga P. J., Barker K., Torpy F. R. (2018). Conservation mycology in Australia and the potential role of citizen science. Conserv. Biol. 32, 1031–1037. 10.1111/cobi.13121 PubMed DOI

IUCN (2022). The IUCN Red List of Threatened Species. Version 2021-3. Available online at: https://www.iucnredlist.org (accessed January 20, 2022).

Jones M. D., Forn I., Gadelha C., Egan M. J., Bass D., Massana R., et al. . (2011). Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474, 200–203. 10.1038/nature09984 PubMed DOI

Jumbam B., Haelewaters D., Koch R. A., Dentinger B. T., Henkel T. W., Aime M. C. (2019). A new and unusual species of Hericium (Basidiomycota: Russulales, Hericiaceae) from the Dja Biosphere Reserve, Cameroon. Mycol. Prog. 18, 1253–1262. 10.1007/s11557-019-01530-1 DOI

Kaishian P. J. (2021). Insects and their Laboulbeniales (Ascomycota, Fungi) of Lake Eustis and Emeralda Marsh Conservation Area: a case study on urbanization and diversity. Ecol. Evol. 11, 16618–16633. 10.1002/ece3.8246 PubMed DOI PMC

Kendrick B. (2011). “Fungi: ecological importance and impact on humans,” in eLS (Hoboken, NJ: Wiley; ). 10.1002/9780470015902.a0000369.pub2 DOI

Kerekes J., Desjardin D. E. (2009). A monograph of the genera Crinipellis and Moniliophthora from Southeast Asia including a molecular phylogeny of the nrITS region. Fungal Divers. 37, 101–152.

Khan F., Kluting K., Tångrot J., Urbina H., Ammunet T., Eshghi Sahraei S., et al. . (2020). Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi. IMA Fungus 11, 23. 10.1186/s43008-020-00045-9 PubMed DOI PMC

Kim S., Axelsson E. P., Girona M. M., Senior J. K. (2021). Continuous-cover forestry maintains soil fungal communities in Norway spruce dominated boreal forests. For. Ecol. Manag. 480, 118659. 10.1016/j.foreco.2020.118659 DOI

Kõljalg U., Nilsson R. H., Abarenkov K., Tedersoo L., Taylor A. F., Bahram M., et al. . (2013). Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22, 5271–5277. 10.1111/mec.12481 PubMed DOI

Korf R. P. (2005). Reinventing taxonomy: a curmudgeon's view of 250 years of fungal taxonomy, the crisis in biodiversity, and the pitfalls of the phylogenetic age. Mycotaxon 93, 407–415.

Kress W. J., Erickson D. L. (2012). DNA barcodes: methods and protocols. Methods Mol. Biol. 858, 3–8. 10.1007/978-1-61779-591-6_1 PubMed DOI

Kuhar F., Furci G., Drechsler-Santos E. R., Pfister D. H. (2018). Delimitation of Funga as a valid term for the diversity of fungal communities: the Fauna, Flora & Funga proposal (FF&F). IMA Fungus 9, A71–A74. 10.1007/BF03449441 DOI

Léveillé-Bourret É., Eggertson Q., Hambleton S., Starr J. R. (2021). Cryptic diversity and significant cophylogenetic signal detected by DNA barcoding the rust fungi (Pucciniaceae) of Cyperaceae–Juncaceae. J. Syst. Evol. 59, 833–851. 10.1111/jse.12740 DOI

Lienhard P., Terrat S., Prévost-Bour,é N. C., Nowak V., Régnier T., Sayphoummie S., et al. . (2014). Pyrosequencing evidences the impact of cropping on soil bacterial and fungal diversity in Laos tropical grassland. Agron. Sustain. Dev. 34, 525–533. 10.1007/s13593-013-0162-9 DOI

Lin H., Peddada S. D. (2020). Analysis of compositions of microbiomes with bias correction. Nat. Commun. 11, 3514. 10.1038/s41467-020-17041-7 PubMed DOI PMC

Liu B., Fu R., Wu B., Liu X. Z., Xiang M. (2021). Rock-inhabiting fungi: terminology, diversity, evolution and adaptation mechanisms. Mycology 13, 1–31. 10.1080/21501203.2021.2002452 PubMed DOI PMC

Liu J., Haelewaters D., Pfliegler W. P., Page R. A., Dick C. W., Aime M. C. (2020). A new species of Gloeandromyces from Ecuador and Panama revealed by morphology and phylogenetic reconstruction, with a discussion of secondary barcodes in Laboulbeniomycetes taxonomy. Mycologia 112, 1192–1202. 10.1080/00275514.2020.1781496 PubMed DOI

López-Quintero C. A., Straatsma G., Franco-Molano A. E., Boekhout T. (2012). Macrofungal diversity in Colombian Amazon forests varies with regions and regimes of disturbance. Biodivers. Conserv. 21, 2221–2243. 10.1007/s10531-012-0280-8 DOI

Lücking R., Aime M. C., Robbertse B., Miller A. N., Ariyawansa H. A., Aoki T., et al. . (2020). Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11, 14. 10.1186/s43008-020-00033-z PubMed DOI PMC

Lücking R., Dal-Forno M., Sikaroodi M., Gillevet P. M., Bungartz F., Moncada B., et al. . (2014). A single macrolichen constitutes hundreds of unrecognized species. Proc. Natl. Acad. Sci. U.S.A. 111, 11091–11096. 10.1073/pnas.1403517111 PubMed DOI PMC

Marinho F., da Silva I. R., Oehl F., Maia L. C. (2018). Checklist of arbuscular mycorrhizal fungi in tropical forests. Sydowia 70, 107–127. 10.12905/0380.sydowia70-2018-0107 DOI

McMurdie P. J., Holmes S. (2014). Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comp. Biol. 10, e1003531. 10.1371/journal.pcbi.1003531 PubMed DOI PMC

Meswaet Y., Mangelsdorff R., Yorou N. S., Piepenbring M. (2021). Unravelling unexplored diversity of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) in tropical Africa. MycoKeys 81, 69–138. 10.3897/mycokeys.81.67850 PubMed DOI PMC

Moore D., Nauta M. M., Evans S. E., Rotheroe M. (2001). Fungal Conservation: Issues and Solutions. Cambridge: Cambridge University Press. 10.1017/CBO9780511565168 DOI

Morange M., Lagerkvist C., Helix D. (1998). A history of molecular biology. Endeavour 22, 165–166. 10.1016/S0160-9327(99)80026-X DOI

Mueller G. M. (2017). Progress in conserving fungi: engagement and red listing. BGjournal 14, 30–33.

Mueller G. M., Bills G. F., Foster M. S. (2004). Biodiversity of Fungi: Inventory and Monitoring Methods. Burlington, MA: Elsevier Academic Press.

Nilsson R. H., Anslan S., Bahram M., Wurzbacher C., Baldrian P., Tedersoo L. (2019). Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat. Rev. Microbiol. 17, 95–109. 10.1038/s41579-018-0116-y PubMed DOI

Nilsson R. H., Hyde K. D., Pawłowska J., Ryberg M., Tedersoo L., Aas A. B., et al. . (2014). Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Divers. 67, 11–19. 10.1007/s13225-014-0291-8 DOI

Nilsson R. H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.-H., Kõljalg U. (2006). Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1, e59. 10.1371/journal.pone.0000059 PubMed DOI PMC

Noordeloos M. E., Antonín V. (2008). Contribution to a monograph of marasmioid and collybioid fungi in Europe. Czech Mycol. 60, 21–27. 10.33585/cmy.60103 DOI

Nuñez N. F., Maggia L., Stenger P. L., Lelièvre M., Letellier K., Gigante S., et al. . (2021). Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: the case study of the New Caledonian biodiversity hotspot. Ecol. Eng. 173, 106416. 10.1016/j.ecoleng.2021.106416 DOI

Oberwinkler F. (2018). “How to understand cryptogams? The development of research methods and their impact on the knowledge of cryptogams,” in Biodiversity and Ecology of Fungi, Lichens, and Mosses. Kerner von Marilaun Workshop 2015 in memory of Josef Poelt, Vol. 34, ed. Blanz P. (Budapest: Austrian Academy of Sciences; ), 106–186.

Oliver R. P., Schweizer M. (1999). Molecular Fungal Biology. Cambridge: Cambridge University Press Oliver. 10.1017/CBO9781139163972 DOI

Osiewacz H. D. (2002). Genes, mitochondria and aging in filamentous fungi. Ageing Res. Rev. 1, 425–442. 10.1016/S1568-1637(02)00010-7 PubMed DOI

Osmundson T. W., Robert V. A., Schoch C. L., Baker L. J., Smith A., Robich G., et al. . (2013). Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS ONE 8, e62419. 10.1371/journal.pone.0062419 PubMed DOI PMC

Pante E., Schoelinck C., Puillandre N. (2015). From integrative taxonomy to species description: one step beyond. Syst. Biol. 64, 152–160. 10.1093/sysbio/syu083 PubMed DOI

Paton A., Antonelli A., Carine M., Forzza R. C., Davies N., Demissew S., et al. . (2020). Plant and fungal collections: current status, future perspectives. Plants People Planet 2, 499–514. 10.1002/ppp3.10141 PubMed DOI

Peay K. G. (2014). Back to the future: natural history and the way forward in modern fungal ecology. Fungal Ecol. 12, 4–9. 10.1016/j.funeco.2014.06.001 DOI

Peay K. G., Kennedy P. G., Bruns T. D. (2008). Fungal community ecology: a hybrid beast with a molecular master. BioScience 58, 799–810. 10.1641/B580907 DOI

Peay K. G., Kennedy P. G., Talbot J. M. (2016). Dimensions of biodiversity in the Earth mycobiome. Nat. Rev. Microbiol. 14, 434–447. 10.1038/nrmicro.2016.59 PubMed DOI

Peay K. G., Matheny P. B. (2016). “The biogeography of ectomycorrhizal fungi – a history of life in the subterranean,” in Molecular Mycorrhizal Symbiosis, ed. Martin F. (Hoboken, NJ: John Wiley & Sons, Ltd.), 341–361. 10.1002/9781118951446.ch19 DOI

Penton C. R., StLouis D., Cole J. R., Luo Y., Wu L., Schuur E. G., et al. . (2013). Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions. Appl. Environ. Microbiol. 79, 7063–7072. 10.1128/AEM.01702-13 PubMed DOI PMC

Pérez-Izquierdo L., Zabal-Aguirre M., Verdú M., Buée M., Rincón A. (2020). Ectomycorrhizal fungal diversity decreases in Mediterranean pine forests adapted to recurrent fires. Mol. Ecol. 29, 2463–2476. 10.1111/mec.15493 PubMed DOI

Petisco C., Downey G., Murray I., Zabalgogeazcoa I., García-Criado B., García-Ciudad A. (2008). Direct classification of related species of fungal endophytes (Epichloë spp.) using visible and near-infrared spectroscopy and multivariate analysis. FEMS Microbiol. Lett. 284, 135–141. 10.1111/j.1574-6968.2008.01186.x PubMed DOI

Phengsintham P., Braun U., McKenzie E. H. C., Chukeatirote E., Hyde K. D. (2013). Monograph of cercosporoid fungi from Thailand. Plant Pathol. Quar. 3, 67–138. 10.5943/ppq/3/2/2 DOI

Piepenbring M. (2015). Introduction to Mycology in the Tropics. St. Paul, MN: American Phytopathological Society. 10.1094/9780890546130 DOI

Piepenbring M., Caballero E., Fournier J., Guzmán G., Hou C.-L., Kirschner R., et al. . (2011). Pioneer forays for fungi in the Darién Province in eastern Panama: quintuplicating the knowledge on fungi in this area by five days of fieldwork. Biodivers. Conserv. 20, 2511–2526. 10.1007/s10531-011-0085-1 DOI

Piepenbring M., Hofmann T. A., Miranda E., Cáceres O., Unterseher M. (2015). Leaf shedding and weather in tropical dry-seasonal forest shape the phenology of fungi–lessons from two years of monthly surveys in southwestern Panama. Fungal Ecol. 18, 83–92. 10.1016/j.funeco.2015.08.004 DOI

Piepenbring M., Lotz-Winter H., Hofmann T. A. (2018). Incentives and challenges for mycologists in the tropics. Biosyst. Ecol. Ser. 34, 481–514.

Piepenbring M., Maciá-Vicente J. G., Codjia J. E. I., Glatthorn C., Kirk P., Meswaet Y., et al. . (2020). Mapping mycological ignorance – checklists and diversity patterns of fungi known for West Africa. IMA Fungus 11, 13. 10.1186/s43008-020-00034-y PubMed DOI PMC

Piepenbring M., Yorou N. S. (2017). Promoting teaching and research on African fungi by field schools on tropical mycology in Benin. IMA Fungus 8, 74–77. 10.1007/BF03449467 DOI

Pitt J. I., Hocking A. D., Glenn D. R. (1983). An improved medium for the detection of Aspergillus flavus and A. parasiticus. J. Appl. Bacteriol. 54, 109–114. 10.1111/j.1365-2672.1983.tb01307.x PubMed DOI

Powell J. R., Rillig M. C. (2018). Biodiversity of arbuscular mycorrhizal fungi and ecosystem function. New Phytol. 220, 1059–1075. 10.1111/nph.15119 PubMed DOI

Purahong W., Wubet T., Krüger D., Buscot F. (2019). Application of next-generation sequencing technologies to conservation of wood-inhabiting fungi. Conserv. Biol. 33, 716–724. 10.1111/cobi.13240 PubMed DOI

Reynolds N. K., Jusino M. A., Stajich J. E., Smith M. E. (2021). Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples. Mol. Ecol. Resour. 10.1111/1755-0998.13540 PubMed DOI

Ríos-Saldaña C. A., Delibes-Mateos M., Ferreira C. C. (2018). Are fieldwork studies being relegated to second place in conservation science? Glob. Ecol. Conserv. 14, e00389. 10.1016/j.gecco.2018.e00389 DOI

Rivas-Ferreiro M. (2021). Exploring the potential of opportunistic surveys and sequence databases: revealing the fungal diversity of Madagascar and the arrival of ectomycorrhizal fungi in the island. M.Sc. thesis. London: Royal Botanic Gardens, Kew.

Rodrigues P., Santos C., Venâncio A., Lima N. (2011). Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches. J. Appl. Microbiol. 111, 877–892. 10.1111/j.1365-2672.2011.05116.x PubMed DOI

Rosa L. H., Pinto O. H. B., Šantl-Temkiv T., Convey P., Carvalho-Silva M., Rosa C. A., et al. . (2020). DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica. Sci. Rep. 10, 21793. 10.1038/s41598-020-78630-6 PubMed DOI PMC

Runnel K., Drenkhan R., Adamson K., Lõhmus P., Rosenvald K., Rosenvald R., et al. . (2021). The factors and scales shaping fungal assemblages in fallen spruce trunks: a DNA metabarcoding study. For. Ecol. Manag. 495, 119381. 10.1016/j.foreco.2021.119381 DOI

Ryberg M., Nilsson R. H. (2018). New light on names and naming of dark taxa. MycoKeys 30, 31–39. 10.3897/mycokeys.30.24376 PubMed DOI PMC

Sadiković D., Kuštera M. (2013). Fungal conservation: protected species of fungi in South Serbia region. Biol. Nyssana 4, 35–40.

Schmit J. P., Lodge D. J. (2005). “Classical methods and modern analysis for studying fungal diversity,” in The Fungal Community, ed. Dighton J. (Boca Raton, FL: Marcel Dekker, Inc.), 193–214. 10.1201/9781420027891.ch10 DOI

Selbmann L., Isola D., Egidi E., Zucconi L., Gueidan C., de Hoog G. S., et al. . (2014). Mountain tips as reservoirs for new rock-fungal entities: Saxomyces gen. nov. and four new species from the Alps. Fungal Divers. 65, 167–182. 10.1007/s13225-013-0234-9 DOI

Sharma S. K., Saini S., Verma A., Sharma P. K., Lal R., Roy M., et al. . (2019). National agriculturally important microbial culture collection in the global context of microbial culture collection centres. Proc. Natl. Acad. Sci. India Sect. B Biol. Sci. 89, 405–418. 10.1007/s40011-017-0882-8 DOI

Shrestha U. B., Bawa K. S. (2014). Impact of climate change on potential distribution of Chinese caterpillar fungus (Ophiocordyceps sinensis) in Nepal Himalaya. PLoS ONE 9, e106405. 10.1371/journal.pone.0106405 PubMed DOI PMC

Simões M. F., Pereira L., Santos C., Lima N. (2013). “Polyphasic identification and preservation of fungal diversity: Concepts and applications,” in Management of Microbial Resources in the Environment, eds. Malik A., Grohmann E., Alves M. (Dordrecht: Springer; ), 91–117. 10.1007/978-94-007-5931-2_5 DOI

Simpson G. (1960). Principles of Animal Taxonomy. New York, NY: Columbia University Press. 10.7312/simp92414 DOI

Spatafora J. W., Aime M. C., Grigoriev I. V., Martin F., Stajich J. E., Blackwell M. (2018). “The fungal tree of life: from molecular systematics to genome-scale phylogenies,” in The Fungal Kingdom, eds. Heitman J., Howlett B. J., Crous P. W., Stukenbrock E. H., James T. Y., Gow N. A. R. (Washington, DC: ASM Press; ), 1–34. 10.1128/9781555819583.ch1 PubMed DOI PMC

Stewart J. E., Kim M. S., Klopfenstein N. B. (2018). Molecular genetic approaches toward understanding forest-associated fungi and their interactive roles within forest ecosystems. Curr. For. Rep. 4, 72–84. 10.1007/s40725-018-0076-5 DOI

Suh S.-O., Zhang N., Nguyen N., Gross S., Blackwell M. (2008). Lab Manual for Yeast Study. Baton Rouge, LA: Louisiana State University.

Sundberg H., Ekman S., Kruys Å. (2018). A crush on small fungi: an efficient and quick method for obtaining DNA from minute ascomycetes. Methods Ecol. Evol. 9, 148–158. 10.1111/2041-210X.12850 DOI

Taylor D. L., Hollingsworth T. N., McFarland J. W., Lennon N. J., Nusbaum C., Ruess R. W. (2014). A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecol. Monogr. 84, 3–20. 10.1890/12-1693.1 DOI

Taylor J. W., Jacobson D. J., Kroken S., Kasuga T., Geiser D. M., Hibbett D. S., et al. . (2000). Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31, 21–32. 10.1006/fgbi.2000.1228 PubMed DOI

Tedersoo L., Bahram M., Põlme S., Kõljalg U., Yorou N. S., Wijesundera R., et al. . (2014). Global diversity and geography of soil fungi. Science 346, 1256688. 10.1126/science.1256688 PubMed DOI

Teke N. A., Kinge T. R., Bechem E., Nji T. M., Ndam L. M., Mih A. M. (2018). Ethnomycological study in the Kilum-Ijim mountain forest, Northwest Region, Cameroon. J. Ethnobiol. Ethnomed. 14, 25. 10.1186/s13002-018-0225-8 PubMed DOI PMC

Tomao A., Bonet J. A., Castaño C., de-Miguel S. (2020). How does forest management affect fungal diversity and community composition? Current knowledge and future perspectives for the conservation of forest fungi. For. Ecol. Manag. 457, 117678. 10.1016/j.foreco.2019.117678 DOI

Truong C., Mujic A. B., Healy R., Kuhar F., Furci G., Torres D., et al. . (2017). How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. New Phytol. 214, 913–919. 10.1111/nph.14509 PubMed DOI

Turland N. J., Wiersema J. H., Barrie F. R., Greuter W., Hawksworth D. L., Herendeen P. S., et al. . (2018). “International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code),” in The Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159 (Glashütten: Koeltz Botanical Books; ). 10.12705/Code.2018 DOI

van der Linde S., Suz L. M., Orme C. D. L., Cox F., Andreae H., Asi E., et al. . (2018). Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558, 243–248. 10.1038/s41586-018-0189-9 PubMed DOI

Vargas-Gastélum L., Romero-Olivares A. L., Escalante A. E., Rocha-Olivares A., Brizuela C., Riquelme M. (2015). Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing. FEMS Microbiol. Ecol. 91, fiv044. 10.1093/femsec/fiv044 PubMed DOI

Vega F. E., Blackwell M. (2005). Insect-Fungal Associations: Ecology and Evolution. New York, NY: Oxford University Press.

Velázquez M. S., Biganzoli F., Cabello M. N. (2010). Arbuscular mycorrhizal fungi in El Palmar National Park (Entre Rios Province, Argentina) – a protected reserve. Sydowia 62, 149–163.

Wang X. W., Jiang J. H., Liu S. L., Gafforov Y., Zhou L. W. (2021). Species diversification of the coniferous pathogenic fungal genus Coniferiporia (Hymenochaetales, Basidiomycota) in association with its biogeography and host plants. Phytopathology. 112, 404–413. 10.1094/PHYTO-05-21-0181-R PubMed DOI

Weiss M., Selosse M. A., Rexer K. H., Urban A., Oberwinkler F. (2004). Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol. Res. 108, 1003–1010. 10.1017/S0953756204000772 PubMed DOI

Weiss S., Xu Z. Z., Peddada S., Amir A., Bittinger K., Gonzalez A., et al. . (2017). Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 104. 10.1186/s40168-017-0237-y PubMed DOI PMC

Wu B., Hussain M., Zhang W., Stadler M., Liu X., Xiang M. (2019). Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi. Mycology 10, 127–140. 10.1080/21501203.2019.1614106 PubMed DOI PMC

Wutkowska M., Vader A., Mundra S., Cooper E. J., Eidesen P. B. (2019). Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in high arctic soil. Front. Microbiol. 9, 3243. 10.3389/fmicb.2018.03243 PubMed DOI PMC

Yan D., Mills J. G., Gellie N. J., Bissett A., Lowe A. J., Breed M. F. (2018). High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration. Biol. Conserv. 217, 113–120. 10.1016/j.biocon.2017.10.035 DOI

Yan Y., Li Y., Wang W. J., He J. S., Yang R. H., Wu H. J., et al. . (2017). Range shifts in response to climate change of Ophiocordyceps sinensis, a fungus endemic to the Tibetan Plateau. Biol. Conserv. 206, 143–150. 10.1016/j.biocon.2016.12.023 DOI

Zhang Y., Qiao M., Xu J., Cao Y., Zhang K.-Q., Yu Z.-F. (2013). Genetic diversity and recombination in natural populations of the nematode-trapping fungus Arthrobotrys oligospora from China. Ecol. Evol. 3, 312–325. 10.1002/ece3.450 PubMed DOI PMC

Zhang Y., Zhang S., Wang M., Bai F., Liu X. (2010). High diversity of the fungal community structure in naturally-occurring Ophiocordyceps sinensis. PLoS ONE 5, e15570. 10.1371/journal.pone.0015570 PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...