Fungal Diversity: Global Perspective and Ecosystem Dynamics

Bajpai, Apekcha; Rawat, Seema; Johri, B. N.

doi:10.1007/978-981-13-8315-1_4

Cited by 7 publications

(5 citation statements)

References 165 publications

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“…Numerous genera of common and industrially or agriculturally important fungi such as Penicillium and Aspergillus (Houbraken and Samson 2011;Sklenar et al 2017;Steenwyk et al 2019;Houbraken et al 2020) have been recently taxonomically revised, and ample species combinations were proposed within previous species complexes or clades. Recognition of more species is considered to be a useful practice because it leads to the accurate and precise diagnosis of potential pathogens, prediction of beneficial properties, and an improved overall understanding of fungal diversity and ecology (Hyde et al 2019;Bajpai et al 2019). However, because the identifiability of new taxa (Box 1) is not always evaluated, even well-studied groups of fungi can rapidly move from the rear of fungal taxonomy to its frontline.…”

Section: Introduction Into the Predicament Of Trichoderma Identificationmentioning

confidence: 99%

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

2021

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Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standardized principles of species recognition, at least in a given taxonomic group. However, in fungi, species delimitation is frequently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist. Contrary to it, identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology. The industrial and plant-beneficial fungi from the genus Trichoderma (Hypocreales) offer a suitable model to address this collision between species delimitation and species identification. A few decades ago, Trichoderma diversity was limited to a few dozen species. The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy, with up to 50 new species recognized per year. Here, we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases (the inventory is available at the website of the International Subcommission on Taxonomy of Trichodermawww.trichoderma.info). Among the 375 species with valid names as of July 2020, 361 (96%) have been cultivated in vitro and DNA barcoded. Thus, we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes (ITS, tef1, and rpb2), and it is supported by online tools that are available on www.trichokey.info. We then used all the whole-genome sequenced (WGS) Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification, reveal shortcomings, and discuss possible ambiguities. Based on the Trichoderma example, this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolutionary analysis, and knowledge of taxonomic literature. We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy, and conclude that these fungi are particularly suitable for the implementation of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett (1948–2020), whose work inspired the current study. We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups. An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.

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Section: Introduction Into the Predicament Of Trichoderma Identificationmentioning

confidence: 99%

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

2021

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“…In-depth analysis of fungal diversity provides a better understanding of the plant-fungal interaction framework. Early culture-based methods were unable to accurately identify several isolated strains because (i) many species are uncultivable and (ii) taxonomic discrimination between morphologically similar fungal species is difficult, as exemplified by case of Serendipita vermifera (Cruz et al, 2011;Weiß et al, 2016;Bajpai et al, 2019). However, the development in molecular ecology through Sanger sequencing and high-throughput sequencing (HTS) technologies in the last decade has substantially improved our understanding of plant microbiota (Müller et al, 2016;Nilsson et al, 2019;Toussaint et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Progress and Prospects of Mycorrhizal Fungal Diversity in Orchids

Yang

et al. 2021

Front. Plant Sci.

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Orchids form mycorrhizal symbioses with fungi in natural habitats that affect their seed germination, protocorm growth, and adult nutrition. An increasing number of studies indicates how orchids gain mineral nutrients and sometime even organic compounds from interactions with orchid mycorrhizal fungi (OMF). Thus, OMF exhibit a high diversity and play a key role in the life cycle of orchids. In recent years, the high-throughput molecular identification of fungi has broadly extended our understanding of OMF diversity, revealing it to be a dynamic outcome co-regulated by environmental filtering, dispersal restrictions, spatiotemporal scales, biogeographic history, as well as the distribution, selection, and phylogenetic spectrum width of host orchids. Most of the results show congruent emerging patterns. Although it is still difficult to extend them to all orchid species or geographical areas, to a certain extent they follow the “everything is everywhere, but the environment selects” rule. This review provides an extensive understanding of the diversity and ecological dynamics of orchid-fungal association. Moreover, it promotes the conservation of resources and the regeneration of rare or endangered orchids. We provide a comprehensive overview, systematically describing six fields of research on orchid-fungal diversity: the research methods of orchid-fungal interactions, the primer selection in high-throughput sequencing, the fungal diversity and specificity in orchids, the difference and adaptability of OMF in different habitats, the comparison of OMF in orchid roots and soil, and the spatiotemporal variation patterns of OMF. Further, we highlight certain shortcomings of current research methodologies and propose perspectives for future studies. This review emphasizes the need for more information on the four main ecological processes: dispersal, selection, ecological drift, and diversification, as well as their interactions, in the study of orchid-fungal interactions and OMF community structure.

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“…An in-depth examination of fungal diversity is necessary to understand the relationship between plants and fungal associations. Culture-based methods are difficult to identify the relevant fungi because most of the species are uncultivated and visually similar, which could lead to taxonomically discriminatory outcomes (Cruz et al 2011;Weiß et al 2016;Bajpai et al 2019). However, molecular ecology develops through Sanger sequencing and high-throughput sequencing (HTS) technologies can substantially improve our understanding of plant microbiota (Müller et al 2016;Nilsson et al 2019;Toussaint et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of root-associated fungal diversity and community composition of two Satyrium species

Poudel,

Li,

Anbazhakan

et al. 2024

Preprint

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Root-associated endophytic fungi (REFs) residing within the host plant can significantly impact on the distribution and abundance of host species. The diversity and community composition of endophytic fungi connected to the roots of two terrestrial orchid species with contrasting distribution patterns, remain little explored. Therefore, we used amplicon sequencing method to explore and analyze the diversity and community composition of fungi associated with the roots of two Satyrium Sw. species, including the widely distributed Satyrium nepalense D. Don. and the narrowly distributed Satyrium yunnanense Rolfe. Our study has illuminated that REFs communities did not show significant difference according to the distribution pattern of host species statistically, because the S. yunnanense was rich in different endophytic fungi than S. nepalense. Anyway, S. yunnanense was dominated by uncul-tured_hygrocybe and S. nepalense was dominated by uncultured_fungus species separately. The result of beta-diversity indicated that there were significant differences in fungal com-munities between the two sample species with (P=0.003) value. It provides the strong evidence against the null hypothesis. Similarly, Linear discriminant analysis Effect Size (LEfSe) and Linear Discriminant Analysis (LDA) scored the two sample species as crucial by different biomarkers separately and significantly over the sample groups Satyrium nepalense (SN) and Satyrium yunnanense (SY) for their distribution and population stability. Therefore, the diversity and community composition of endophytic fungi are found to be independent on distribution pattern of host alone.

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Fungal Diversity: Global Perspective and Ecosystem Dynamics

Cited by 7 publications

References 165 publications

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

Progress and Prospects of Mycorrhizal Fungal Diversity in Orchids

Comparative analysis of root-associated fungal diversity and community composition of two Satyrium species

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