https://soilfun.org/, a web-based platform for soil-inhabiting Ascomycota species

Soil is a remarkably complex substrate that provides various niches for microbial communities. In this environment, fungi are the main biotic component and mediate many belowground functions. However, their distribution is variable due to inconsistencies in resource levels (nutrition, soil, water, and air)^[1,2]. Besides, most fungi spend at least one stage of their life in the soil, showing different trophic modes such as pathogenic, saprobic, or mutualistic^[3,4]. Studies have shown that Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Mortierellomycota and Rozellomycota are widely distributed in edaphic habitats^[5−7].

Culturing and high-throughput sequencing (HTS) methods are currently applied for detecting belowground Ascomycota groups^[5,7−9]. Ascomycota is represented by dominant classes in soil, including Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Leotiomycetes, and Sordariomycetes^{[5−7,10,11]}. Of them, some genera, such as Fusarium, Penicillium, and Phoma, are prevalent^[7,12], while others, such as Ambrosiella, Arcopilus, Didymocyrtis, Kionochaeta, and Parathyridaria have rarely been isolated^[13−15]. This is because exclusive adaptations to belowground environments and a lack of isolation techniques make it difficult to recover Ascomycota species. Most soil ascomycetes are identified at higher taxonomic ranks through HTS, which led to many recent publications and databases showing the taxonomy and distribution patterns of belowground fungi only up to the genus level^[16].

High-throughput sequencing has impacted the estimation of the number of fungi and the endemicity of soil taxa in different parts of the world^[8,17,18]. Some databases have attempted to gather information on soil fungal diversity based on HTS. For example, the GlobalFungi (https://globalfungi.com/) provides information on taxonomy, ecology, and reference sequences of taxa from different habitats, including soil^[17]. The Global Soil Mycobiome consortium dataset, a global soil study recovered 722,682 fungal Operational Taxonomic Units (OTUs), representing 62.4% of the total OTUs^[7]. Among them, 330,054 OTUs were assigned to Ascomycota. The total number of fungi is estimated as 6.28 million species^[9] and found the highest diversity from soil and litter samples, revealing that soil fungal sequences have 75% overlap with previously known species. In addition, some studies have recovered unculturable fractions representing several new lineages at the phylum level^{[4−6,10,19]}.

Few studies compare the taxa recovered by HTS and culturing methods from the same sample or location. For example, Stefani et al.^[20]compared the fungal diversity from petrochemical-contaminated soils in Canada. They found that the number of OTUs ranged from 153 to 235 depending on the level of contamination (slightly to highly contaminated), and culturing methods yielded 8 to 43, respectively. Based on these results, we can roughly estimate that only around 5%–65% of the soil fungal community can be cultured in any environment and we need to develop methods to approach the rest of the 35%–95%. A study on Antarctic crypto-endolithic fungal communities identified several black fungal species that were only detectable through cultivation and found a 12% overlap of species from both culture-dependent and -independent approaches, which resulted in 4,618 colonies and 1,439,748 sequences^[21]. The successful isolation of these species highlights the importance of using both complementary techniques^[21]. Compared to overall HTS results, the cultured fraction is smaller as they have vast differences between the two approaches. However, HTS results can excel in culturing the soil taxa, for example, to plan on isolating targeted taxa or selecting suitable fungal isolating methods in a particular area^[8,16]. Culturing is essential to obtain molecular and morphological data of species and recover the undetectable ones from HTS.

However, around 80% of all soil-inhabiting taxa are not assigned to species level, and 20% to known orders^[5,19,22]. Thus, the soil can potentially reveal many undiscovered species in the future^[8,9]. Contemporary studies have described and resolved soil-associated Ascomycota species from Dothideomycetes, Eurotiomycetes, Leotiomycetes, and Sordariomycetes with morpho-molecular support^[23−28]. However, no recently updated study or database shows the total number of species isolated from the soil^[16].

Over the last few decades, several books have been published based on morphology, such as Compendium of soil fungi^[29−31], Manual of soil fungi^[32], The Genera of Hyphomycetes from soil^[33], and Soil fungi: diversity and detection^[34], which provided the diversities of worldwide soil species with comprehensive morphological illustrations. The Atlas of soil ascomycetes^[35] illustrated anamorphic and teleomorphic (fruit body and hyphomycetes form on cultures) structures, culture characteristics, and keys to the species. Currently, many taxonomists have adopted DNA sequences to determine species boundaries. However, species delineation criteria can differ among groups, such as cryptic species, pathogenic genera, and species complexes that need solid phylogenetic resolution^[36−39]. In this regard, soil-associated species are a highly complex group, and taxonomists have been using the polyphasic approach, combining morphological, physiological, ecological, and molecular methods to determine species^{[36,38,40,41]}.

Precise identification of fungal species/genera is critical for further use in taxonomy and biotechnology research^{[8,16,42−44]}. For example, pathogens are important in disease management, while soil-borne extremophilic genera (e.g., Verruconis) are sources of bioactive compounds^[42,45,46]. Thus a database integrating taxonomy, ecological, and economic information of soil fungi helps to identify these organisms by end-users. The Soil Fungi website aims to collect and provide accurately identified soil fungi and continuously update checklists and notes on genera. This will increase the availability of information in the field and provide a valuable resource for researchers and students studying soil fungi. The website will be a central database of soil-associated fungal species, including their taxonomic descriptions and other relevant information. Users will be able to easily access and retrieve information from the website, such as the distribution of certain fungal species and their ecological roles. The website will also provide a platform for collaboration between researchers and interested parties, allowing information and idea sharing. Furthermore, the Soil Fungi website will help estimate the number of soil genera discovered over time. This information will be useful for understanding the diversity and distribution of soil fungi and for developing conservation strategies for these important organisms.

The current information on soil fungal taxonomy is available as HTS and culture-dependent data^{[4,6,8,47−50]}. These two forms of data can cause contradictions in species identifications and seem unstable and affect studies. Moreover, the number of fungal species in the soil has been estimated from HTS methods, but there is no updated account for recently identified or recorded species from the soil. In addition, morpho-molecular identifications also face shortfalls as some genera are well-studied, while some have phylogenetic ambiguities^[51−53]. For example, specious genera, such as Aspergillus, Cladosporium, Fusarium, Mucor, Penicillium, and Trichoderma are common in soil. Due to the similar morphologies resulting from hybridization, cryptic speciation, and convergent evolution, their species delineation is difficult^[54]. Therefore, compiling updated phylogenetic and morphological data of the genera/species present in the soil are essential. It is also important to gather data on the type of soil ecosystem, locality, identification method, and economic impact of the species or genera. Since most of the information is scattered among various publications and databases, compiling them into a single database is beneficial for mycologists, ecologists, clinical studies, and the general public.

Even though information about soil fungi is available in online databases e.g., Fungal Genera^[55], GlobalFungi^[17], UNITE^[56], and Global Soil Mycobiome consortium (GSMc)^[7], they lack specific information on fungal species and relevant morpho-molecular data. Further, in other databases like 'Faces of Fungi' (www.facesoffungi.org)^[57] , 'Dothideomycetes' (www.dothideomycetes.org/)^[58], 'Sordariomycetes' (https://sordariomycetes.org/)^[59], GMS microfungi (www.gmsmicrofungi.org/)^[60], and 'Coelomycetes' (https://coelomycetes.org/)^[61] information about Ascomycota studies are commonly found. However, a website compiling morpho-molecular data of soil fungi has not been developed. Therefore, we developed and implemented a web-based platform as the information hub for soil fungi research. The website provides a checklist of all the soil-associated Ascomycota genera. These generic notes include taxonomic descriptions, phylogenetic data, and other hosts/-substrates for each species, accompanied by photographic plates or drawings and detection methods. It also provides a list of novel or existing species of soil fungi for each genus, which will be updated over time. The data from previous studies will be periodically included to disseminate information in a holistic approach, enhancing the in-depth understanding of the soil-inhabiting fungi and resource for retrieving multiple data.

The website provides a comprehensive checklist of all the soil-associated genera in Ascomycota essential for identifying and classifying soil fungi. The generic notes contain morphological descriptions, information on phylogenetic analyses such as gene regions, a summary of the latest phylogenetic revisions, ecological and economic impacts and the distribution. For each genus, a list of novel or existing soil-inhabiting species is provided, which will be uploaded and updated over time. Each species is accompanied by taxonomic descriptions, photographic plates or drawings, and detection methods. Each species/genera description is linked to the original publication(s), thus, users have-real time access to further details (Fig. 4). The website ensures that researchers can access the latest information about soil fungal taxonomy and keep up with the latest research developments. The data from previous studies are rearranged, and future studies will be periodically included to disseminate information in a holistic approach. Therefore, the website remains an up-to-date resource for researchers, providing them access to the latest research on soil fungi. These data will enhance an in-depth understanding of the soil-inhabiting fungi and will be important for future research. We encourage all the taxonomists and interested parties who work on soil fungi to contribute their published data to this website which will enhance the information availability and ensures that the website becomes an invaluable resource for retrieving multiple data, providing researchers a platform to share their research and collaborate with others in the field.

On the website, taxa are arranged according to the latest classification^[53]. The history of soil taxonomy is briefly described, and links to related literature are provided. All taxonomic entries are checked by the curators prior to uploading and published in a consistent format. The list of curators and their contact details are displayed in Table 1.

The website is available at https://soilfun.org/ and provides a user-friendly interface to retrieve updated information on the classification of soil-inhabiting Ascomycota. It is easy to access and navigate. The homepage comprises a navigation bar and a search tool to retrieve information.

Home page

The Home page displays the summary of the project (Fig. 1). A navigation bar is displayed at the top of the page. Below the navigation bar, the main objectives of the webpage are displayed in the left column, while the right column displays the search tool and the recently updated entries. The bottom of the page shows the publisher details, copyright information, and contact details. The navigation bar consists of eight menu items (Home, Outline, Archives, Reference, Curators, History, Reference, Notes, and Contact). These menu items facilitate easy navigation throughout the website, allowing users to access the information they need, quickly and efficiently

Figure 1. 

Home page of the Soil Fungi website.

Outline

Under this navigation menu item, the website presents the latest taxonomic representation of genera that are recorded from soil obtained from peer-reviewed publications (Fig. 2). The user can scroll down to find any taxa or the search bar is optional, where the user can type preferred taxa, and be directed to the exact location. Each taxon is linked to its corresponding taxonomic description, which can be accessed by clicking on the relevant name.

Figure 2. 

'Outline' contains soil inhabiting Ascomycota taxa according to the latest classification.

Archives

The orders to which different fungi isolated from soil belong are listed alphabetically under this menu item (Fig. 3). When the user clicks on a preferred order, a dropdown list containing its families and a 'Read more about…' link to the description of each hierarchical taxonomic level is displayed. Similarly, when the user clicks on a family, it shows the related genera and a 'Read more about…' link to the family description. When the user selects a preferred genus, a 'Read more about…' link to the description of the genus and a list of soil-associated species linked to their taxonomic descriptions and illustrations are shown (Fig. 4). Each taxonomic description includes a web source link, enabling the reader to access the original publication directly. This information is continuously updated according to the latest publications, ensuring user access to the most up-to-date and accurate information on soil-inhabiting Ascomycota.

Figure 3. 

'Archives' configured with a dropdown list of taxonomic hierarchy with links to order, family, genera, and species descriptions.

Figure 4. 

Information provided for the soil-inhabiting species with taxonomic description.

Curators

Curators and contact details are provided under this menu item (Fig. 5). These curators are expert fungal taxonomists who continuously monitor the webpage and suggest improvements.

Figure 5. 

'Curators' provides the list of curators with their contact details.

History

Under this menu item, the evolution of soil fungal taxonomy is briefly discussed, together with the available culture-dependent and independent approaches (Fig. 6).

Figure 6. 

'History' provides the history and development of studies on soil fungal taxonomy.

References

References used in the entries are provided under this menu.

Notes

Important events, information, and the latest trends in soil fungal taxonomy are provided here.

Contact

Under this menu item, a dialogue box is provided for the users to exchange information directly or share their suggestions and/or comments. Furthermore, the email and the address of the publisher are also given.