Changes in the Understanding of Fungal Diversity Based on Research in the Tropics

Fungal diversity is threatened by climate change, land-use change, and environmental pollution, and requires urgent conservation action. Construction of the fungal species database is an important prerequisite for the study and conservation of fungal diversity. Recently developed DNA barcoding and metabarcoding technologies can provide accurate, rapid, and highly efficient identification on a large scale, and to a large extent compensate for the defects of traditional identification methods. In this paper, we review the application of metabarcoding in fungal species diversity assessment, the study of mechanisms underlying fungal diversity, and the reconstruction of fungal palaeoecology. We emphasize that the application of metabarcoding technology in fungal diversity studies is still in the primary phase, and greater efforts are needed in the construction of reliable reference databases, the optimization of experimental procedures, and updates of bioinformatics tools. Hence, we suggest enhancing cooperation among fungal taxonomists, ecologists, and computer technicians. They should work together to address problems in fungal diversity studies via metabarcoding, which would provide more sound scientific evidence for fungal diversity conservation on a large scale.

Currently, there is a worldwide growing interest in the occurrence and diversity of fungi and their secondary metabolites in aquatic systems, especially concerning their role in water quality and human health. However, this concern is hampered by the scant information that is available in the literature about aquatic fungi and how they affect water quality. There are only few published reports that link certain species of aquatic fungi to human health. The common aquatic fungal species that have been reported so far in African aquatic systems belong to the hyphomycetes kingdom. This paper thus aims to survey the information about the occurrence and factors that control the distribution of different species of fungi in African aquatic systems, as well as their effect on water quality and the possible metabolic pathways that lead to the formation of toxic secondary metabolites that are responsible for the deterioration of water quality. This review will also investigate the analytical and bioanalytical procedures that have been reported for the identification of different species of waterborne fungi and their secondary metabolites.

Fungal abundance and diversity as influenced by properties of Technosols developed from mine wastes containing iron sulphides: A case study from abandoned iron sulphide and uranium mine in Rudki, south-central Poland

Fungi are one of the abundant biodiversity both in Indonesia and in the world, so there are still many species of fungi that have not been successfully identified or known for their benefits. The purpose of this study was to determine the species of macroscopic fungi that can be collected in oil palm plantations in Pantok, West Kalimantan. This study used a qualitative approach, mushroom sampling using the plot method with roaming techniques, all species of macroscopic fungi found in oil palm plantations were recorded morphological characteristics and position of discovery in the observation sheet, then measured environmental factors, and the mushrooms obtained were preserved. Sample identification was carried out by matching morphologies including cup type and edges, cup color, stalk color and surface, stalk mounting type on the cup, and substrate. Using a mushroom identification book that refers to McKnight & McKnight (1987), Roberts & Shelley (2013), Moor and O'Sullivan (2014), and Laessoe (2013). The field data analysis used is descriptive analysis by describing the species of macroscopic fungi found in oil palm plantations. As for the data validity checking technique on the identification results using the website https://www.indexfungorum.org/ to see the validity of the scientific name of each fungus found. In this study there were 17 species of macroscopic fungi found, these fungi belonged to 1 phylum, namely the Basidiomycota phylum and consisted of 11 families, namely the Polyporaceae, Boletaceae, Entolomataceae, Ganodermataceae, Marasmiaceae, Omphalotaceae, Psathyrellaceae, Schizophyllaceae, Tricholomataceae, and Pluteaceae families. The environmental factors of this study were less favorable for fungal growth. From the results of this study it can be concluded that the diversity of fungi in oil palm plantations in Pantok, West Kalimantan is quite varied, this is influenced by environmental factors in the plantation.

The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7–13.2) million compared to 2.2–3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names’ type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded “unculturable fungi” could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the “digital type” could be assigned as the “clade” name + species name. The “clade” name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.

Fungal infections in transplant recipients: pros and cons of immunosuppressive and antimicrobial treatment

Almost all land plant species form a symbiosis with mycorrhizal fungi. These soil fungi provide nutrients and other services to plants in return for plant carbohydrates. The recent application of microbial metagenomics, metatranscriptomics, and metabolomics to plants and their immediate surroundings confirms the key role of mycorrhizal fungi, rhizosphere bacteria and fungi, and suggests a world of hitherto undiscovered interactions (van der Heijden et al., this issue, pp. 1406–1423). This novel knowledge is leading to a paradigm-shifting view: plants cannot be considered as isolated individuals any more, but as metaorganisms, or holobionts (Hacquard & Schadt, this issue, pp. 1424– 1430) encompassing an active microbial community re-programming host physiology (see Pozo et al., this issue, pp. 1431–1436). This bears tremendous implications for plant ecophysiology and evolution, plant breeding, crop management and sustainable ecosystem management.

Indoor fungal diversity and asthma: A meta-analysis and systematic review of risk factors

We conservatively estimate that there is a minimum of 712,000 extant fungal species worldwide, but we recognize that the actual species richness is likely much higher. This estimate was calculated from the ratio of fungal species to plant species for various ecologically defined groups of fungi in well-studied regions, along with data on each groups’ level of endemism. These calculations were based on information presented in the detailed treatments of the various fungal groups published in this special issue. Our intention was to establish a lower boundary for the number of fungal species worldwide that can be revised upward as more information becomes available. Establishing a lower boundary for fungal diversity is important as current estimates vary widely, hindering the ability to include fungi in discussions of ecology, biodiversity and conservation. Problems inherent in making these estimates, and the impact that additional data on fungal and plant species diversity will have on these estimates are discussed.

The impact of aridity on above- and belowground biodiversity can be profound. However, it remains unclear how drought stress influences belowground biodiversity through the complex interplay of soil quality, plant communities, and the direct effects of soil moisture deficit. In this study, we randomly selected 80 sampling plots along a 1000-km natural aridity gradient from east to west of the Inner Mongolia grasslands to identify the factors that influence soil bacterial and fungal diversity in arid and semiarid regions. Our results revealed that both soil bacterial and fungal diversity decreased with increasing aridity. Structural equation models demonstrated that aridity indirectly affected regional-scale soil bacterial and fungal diversity by regulating plant diversity and biomass. Plant biomass and community composition elicited a much stronger impact on soil fungal diversity than on soil bacterial diversity. A detailed analysis revealed that soil fungal and bacterial diversity were significantly correlated with specific plant taxa biomass. However, plant traits did not explain the positive or negative correlations between soil bacterial and fungal diversity and plant species dynamics. Instead, our data suggest that plant biomass is the primary driver controlling soil microbial (mainly fungal) diversity. Our study shows that aridity reduces soil bacterial and fungal diversity on a regional scale and indicates that aridity indirectly influences soil community composition through plant communities. Our findings indicate that plant community dynamics should be considered in assessing soil bacterial and fungal diversity on a regional scale.

The availability and dynamics of airborne fungal spores in the atmosphere are strongly influenced by the meteorological parameters and by other factors such as air pollutants. The aim of this study was to update the knowledge about the seasonal and diurnal variations in airborne fungal spores of Doha area and to correlate these variations with meteorological factors, and to investigate the influence of atmospheric CO2 concentrations and different culture media on the availability of fungal spores. From 106 settle plate exposures (on alternative days) throughout the period April 2015-March 2016, a total of 1197 mould- and 283 yeast colony-forming units (CFU), twenty one genera and 62 species were retrieved. The highest fungal spore's concentration was recorded in February 2016, whereas the lowest concentration occurred in August 2015. The main constituents of the fungal airspora were attributed to Cladosporium (60.2%), Aspergillus (10.4%), Fusarium (9.4%), Alternaria (8.5%), and Ganoderma spp. (2.3%). Cladosporium showed two peaks in April and February, while Fusarium and Alteranria peaked in July. Aspirgillus had one peak in August. The prevalence of Ganoderma spp. were exclusively detected in February and March. Temperature was significantly and negatively correlated with the total colony count and fungal species, however no significant correlation was found between relative humidity and both the total colony count and fungal species. Wind speed was significantly and positively correlated with the total colony count and fungal species. The correlation between rainfalls and either total colony count or fungal species was non-significant. Intra-diurnal fluctuations of fungal spores was investigated during the period of 1st of Feb – 31st of March 2016. The highest dispersal of fungal spores favored 18:00 h, whereas at 00:00 h (midnight) the lowest fungal spores release was recorded. No significant difference was observed in total number of fungal colonies or species collected with the two media Potato Dextrose Agar (PDA) and Rose Bengal media. Nevertheless, certain fungal taxa were highly selective and thus their growth rate was on one media much higher than with another. There were no significant differences in the composition and diversity of the airborne fungal population between two different study sites under the influence of atmospheric CO2 concentration, though daily concentration of CO2 was higher at the Industrial area site than at Qatar University Campus. Remarkably, the concentrations of Alternaria spp. and Fusarium spp. were significantly higher at Industrial area site in corresponding to CO2 than at Qatar University site.

Soil fungi play a crucial role in soil quality and fertility in being able to break down organic matter but are frequently also observed to play a role as important plant pathogens. As part of a Citizen Science Project initiated by the Westerdijk Fungal Biodiversity Institute and the Utrecht University Museum, which aimed to describe novel fungal species from Dutch garden soil, the diversity of fusarioid fungi (Fusarium and other fusarioid genera), which are members of Nectriaceae (Hypocreales) was investigated. Preliminary analyses of ITS and LSU sequences from more than 4 750 isolates obtained indicated that 109 strains belong to this generic complex. Based on multi-locus phylogenies of combinations of cmdA, tef1, rpb1, rpb2 and tub2 alignments, and morphological characteristics, 25 species were identified, namely 22 in Fusarium and three in Neocosmospora. Furthermore, two species were described as new namely F. vanleeuwenii from the Fusarium oxysporum species complex (FOSC), and F. wereldwijsianum from the Fusarium incarnatum-equiseti species complex (FIESC). Other species encountered in this study include in the FOSC: F. curvatum, F. nirenbergiae, F. oxysporum and three undescribed Fusarium spp.; in the FIESC: F. clavus, F. croceum, F. equiseti, F. flagelliforme and F. toxicum; Fusarium tricinctum species complex: F. flocciferum and F. torulosum; the Fusarium sambucinum species complex: F. culmorum and F. graminearum; the Fusarium redolens species complex: F. redolens; and the Fusarium fujikuroi species complex: F. verticillioides. Three species of Neocosmospora were encountered, namely N. solani, N. stercicola and N. tonkinensis. Although soil fungal diversity has been well studied in the Netherlands, this study revealed two new species, and eight new records: F. clavus, F. croceum, F. flagelliforme, F. odoratissimum, F. tardicrescens, F. toxicum, F. triseptatum and N. stercicola.

Fungal-fungal and fungal-bacterial interactions in aquatic decomposer communities: bacteria promote fungal diversity.

Uncommon ectomycorrhizal networks: richness and distribution of <i>Alnus</i>‐associating ectomycorrhizal fungal communities

The gold and uranium mines of the Free State gold fields in South Africa are no longer mined underground but provide a rich source of biological data for analysis from the different rehabilitation programmes designed to revegetate the above-ground tailings. Some of the programmes have incorporated the application of mycorrhizal fungal inoculum and the aim of this study was to assess the arbuscular mycorrhiza (AM) fungal diversity in the roots of trees being used for two different phytoremediation trials. The trees sampled were indigenous acacias (Vachellia and Senegalia spp.) and two tailings assessed were (i), planted with trees which had been inoculated with crude AM fungal inocula in the nursery and received no organic inputs and (ii), ameliorated with garden refuse, on which the acacias were natural colonisers. The approach was to target and amplify the small subunit rRNA gene sequences, a marker gene widely used in ecological studies for phylogenetic analysis to determine AM fungal diversity. This study identified 17 different AM fungal species that fell within 8 genera, namely, Diversispora, Rhizophagus, Scutellospora, Claroideoglomus, Cetraspora, Sclerocystis, Glomus and Redecker. From the planted mine tailing 8 genera and 13 species were identified of which 5 species were unique to the tailing, and from the garden refuse-ameliorated mine tailing 6 genera and 12 species were identified of which 4 species were unique to the tailing. A limited soil physico-chemical analysis of the substrata revealed no significant difference between the sites except for the element Al, whose concentration on site (i) was almost double that of site (ii). The elements Pb, Hg, Mo, Ni, Pt and Th were not detected. The results represent the first AM fungal diversity study from South Africa sampling root DNA and report 9 first records of AM fungal species in South Africa. A high number of AM fungal taxa were identified when compared with other diversity studies on metal-contaminated sites, all of which exhibited substantially higher levels of pollutant elements than the Free State sites.