Understanding Of Fungal Diversity Research Articles

Diversity of Pleosporalean Fungi Isolated from Rice (Oryza sativa L.) in Northern Thailand and Descriptions of Five New Species

Pleosporales represents the largest order within the class Dothideomycetes (Fungi), comprising phytopathogenic, saprobic, and endophytic taxa with a widespread presence in terrestrial and aquatic environments. Rice (Oryza sativa) is a primary economic crop in numerous tropical countries, particularly in Thailand. Studying fungal species associated with rice holds the potential to enhance our understanding of fungal diversity, lifestyles, and biology of rice, offering valuable insights for future research aimed at disease management and yield improvement. Thirty-nine pleosporalean isolates were obtained from various parts of rice plants collected across diverse regions in Chiang Rai Province, Thailand. Species identification involved a combination of morphology and molecular phylogeny, utilizing multi-locus sequence analyses of the ITS, LSU, SSU, gapdh, rpb2, tef1, and tub2 genes. The isolates were identified in 18 taxa distributed across five families and ten genera, including five new species (Bipolaris chiangraiensis, Ophiosphaerella oryzae, Paraphaeosphaeria oryzae, Pyrenochaetopsis oryzicola, and Setophoma oryzicola). Additionally, six new host records and two new geographical records are documented. Photoplates, detailed morphological descriptions, and phylogenetic trees are provided to elucidate the placement of both known and novel taxa.

Entoloma sicoense, a new species in the subgenus Cyanula (Entolomataceae)

Entoloma sicoense, a bluish gray mushroom species belonging to section Poliopodes, is described as a new addition to the subgenus Cyanula. This study presents the phylogeny, taxonomy, and ecological significance of Entoloma sicoense, which inhabits mossy broad-leaved forests in the eastern North Atlantic region. The discovery of this new species expands our understanding of fungal diversity and highlights the ecological significance of the subgenus Cyanula in Serra de Sicó. Entoloma sicoense exhibits specific morphological characteristics, such as slate gray basidiomata, a smooth concolorous stipe, and a sterile gill edge rich in brilliant granules. This research underscores the importance of documenting and describing new species in Serra de Sico´ for comprehensive cataloging, conservation efforts, and further exploration of its ecological role within the local ecosystem. The new species is presented with morphological, illustrated description as well as molecular work and comparison with similar species.

An Integrative Study of Mycobiome in Different Habitats from a High Arctic Region: Diversity, Distribution, and Functional Role.

In the Arctic ecosystems, fungi are crucial for interactions between soil and plants, the cycling of nutrients, and the transport of carbon. To date, no studies have been conducted to thoroughly examine the mycobiome and its functional role in various habitats of the High Arctic region. The aim was to unravel the mycobiome in the nine habitats (i.e., soil, lichen, vascular plant, moss, freshwater, seawater, marine sediment, dung, and marine alga) in the Ny-Ålesund Region (Svalbard, High Arctic) using a high-throughput sequencing approach. A total of 10,419 ASVs were detected. Among them, 7535 ASVs were assigned to unidentified phyla, while the remaining 2884 ASVs were assigned to 11 phyla, 33 classes, 81 orders, 151 families, 278 genera, and 261 species that were known. The distribution of the mycobiome was driven by habitat specificity, indicating that habitat filtering is a crucial factor influencing the fungal assemblages at a local scale in this High Arctic region. Six growth forms and 19 fungal guilds were found. The ecological guild (e.g., lichenized, ectomycorrhizal) and growth form (e.g., yeast, thallus photosynthetic) varied significantly among various habitats. In addition, the occurrence of 31 fungal species that are considered to be potential pathogens was determined. These results will increase our understanding of fungal diversity and its functional significance in this distinctive High Arctic area and thereby establish the groundwork for prediction about how the mycobiome will alter in various environments as a result of anticipated climate change.

A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

BackgroundIn the ice-free area of maritime Antarctica, fungi are the essential functioning group in terrestrial and marine ecosystems. Until now, no study has been conducted to comprehensively assess fungal communities in various habitats in Antarctica. We aimed to characterize fungal communities in the eleven habitats (i.e., soil, seawater, vascular plant, dung, moss, marine alga, lichen, green alga, freshwater, feather) in the Fildes Region (maritime Antarctica) using next-generation sequencing.ResultsA total of 12 known phyla, 37 known classes, 85 known orders, 164 known families, 313 known genera, and 320 known species were detected. Habitat specificity rather than habitat overlap determined the composition of fungal communities, suggesting that, although fungal communities were connected by dispersal at the local scale, the environmental filter is a key factor driving fungal assemblages in the ice-free Antarctica. Furthermore, 20 fungal guilds and 6 growth forms were detected. Many significant differences in the functional guild (e.g., lichenized, algal parasite, litter saprotroph) and growth form (e.g., yeast, filamentous mycelium, thallus photosynthetic) existed among different habitat types.ConclusionThe present study reveals the high diversity of fungal communities in the eleven ice-free Antarctic habitats and elucidates the ecological traits of fungal communities in this unique ice-free area of maritime Antarctica. The findings will help advance our understanding of fungal diversity and their ecological roles with respect to habitats on a neighbourhood scale in the ice-free area of maritime Antarctica.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments.

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

The critical role of tree species and human disturbance in determining the macrofungal diversity in Europe

AbstractAimKnowledge concerning species distribution is important for biodiversity conservation and environmental management. Fungi form a large and diverse group of species and play a key role in nutrient cycling and carbon storage. However, our understanding of fungal diversity and distribution remains limited, particularly at large spatial scales. Here, we predicted the diversity and distribution of ectomycorrhizal and saprotrophic macrofungi at relatively fine spatial resolution at a continental scale and examined the importance of variables that affect the distribution of these two functional groups.LocationEurope.Time period1990–2018.Major taxa studiedMacrofungi.MethodsFrom observations of 1,845 macrofungal species, we predicted the diversity and distribution of two functional groups of macrofungi at a resolution of 5 km across eight European countries based on 25 environmental variables using the MaxEnt model. We determined the importance of variables that affect the distribution of these two functional groups of macrofungi using the built‐in jackknife test in the model.ResultsAnalysis of the modelling results showed that eastern Denmark and southern Sweden are biodiversity hotspots for both functional groups of macrofungal species. Tree species and human disturbance (i.e., the human footprint index) were found to be the two most important predictor variables explaining the distribution of ectomycorrhizal and saprotrophic macrofungi.Main conclusionsOverall, our study demonstrates that tree species and human disturbance have played a more important role than climatic factors in determining the diversity and distribution of macrofungi at the continental scale. Our study suggests that fungal diversity and distribution might change considerably if the strongest predictors (i.e., tree species) were to be affected by climate change and/or human activity. Changes in fungal diversity might, in turn, influence other processes, because fungi are important in driving ecosystem processes, such as nutrient and carbon cycling.

Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds

Our understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept, Hesperomyces virescens (Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest that H. virescens could be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades within Hesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.

DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists?

Although significant progress has been made in our understanding of fungal diversity, identification based on phenotype can be difficult, even for trained experts. Fungi typically have a cryptic nature and can have a similar appearance to distantly related species. Moreover, the appearance of industrially processed mushrooms complicates species identification, as they are often sold sliced and dried. Here we present a small-scale citizen science project, wherein the participants generated and analyzed DNA sequences from fruiting bodies of dried and fresh fungi that were sold for commercial use in New York City supermarkets. We report positive outcomes and the limitations of a youth citizen scientist, aiming to identify dried mushrooms, using established DNA barcoding protocols and exclusively open-access data analysis tools for species identification. Our results indicate that the single-locus nuclear ribosomal internal transcribed spacer (ITS) DNA barcoding approach allowed for identification of only a subset of all of the samples at the species level, although the generated high-quality DNA barcodes were submitted to three different databases. Our results highlight the need for a curated, centralized, and open access ITS reference database that allows rapid third-party annotations for the benefit of both traditional research as well as the emerging citizen science community.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea

Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments.

Insights into deep-sea sediment fungal communities from the East Indian Ocean using targeted environmental sequencing combined with traditional cultivation.

The fungal diversity in deep-sea environments has recently gained an increasing amount attention. Our knowledge and understanding of the true fungal diversity and the role it plays in deep-sea environments, however, is still limited. We investigated the fungal community structure in five sediments from a depth of ∼4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation. This approach resulted in the recovery of a total of 45 fungal operational taxonomic units (OTUs) and 20 culturable fungal phylotypes. This finding indicates that there is a great amount of fungal diversity in the deep-sea sediments collected in the East Indian Ocean. Three fungal OTUs and one culturable phylotype demonstrated high divergence (89%–97%) from the existing sequences in the GenBank. Moreover, 44.4% fungal OTUs and 30% culturable fungal phylotypes are new reports for deep-sea sediments. These results suggest that the deep-sea sediments from the East India Ocean can serve as habitats for new fungal communities compared with other deep-sea environments. In addition, different fungal community could be detected when using targeted environmental sequencing compared with traditional cultivation in this study, which suggests that a combination of targeted environmental sequencing and traditional cultivation will generate a more diverse fungal community in deep-sea environments than using either targeted environmental sequencing or traditional cultivation alone. This study is the first to report new insights into the fungal communities in deep-sea sediments from the East Indian Ocean, which increases our knowledge and understanding of the fungal diversity in deep-sea environments.

Fungal Community Ecology: A Hybrid Beast with a Molecular Master

ABSTRACT Fungi play a major role in the function and dynamics of terrestrial ecosystems, directly influencing the structure of plant, animal, and bacterial communities through interactions that span the mutualism-parasitism continuum. Only with the advent of deoxyribonucleic acid (DNA)-based molecular techniques, however, have researchers been able to look closely at the ecological forces that structure fungal communities. The recent explosion of molecular studies has greatly advanced our understanding of fungal diversity, niche partitioning, competition, spatial variability, and functional traits. Because of fungi's unique biology, fungal ecology is a hybrid beast that straddles the macroscopic and microscopic worlds. While the dual nature of this field presents many challenges, it also makes fungi excellent organisms for testing extant ecological theories, and it provides opportunities for new and unanticipated research. Many questions remain unanswered, but continuing advances in molecular techniques a...

Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity

Fungal endophytes have been found in every plant species examined to date and appear to be important, but largely unquantified, components of fungal biodiversity. Endophytes are especially little known in tropical forest trees, where their abundance and diversity are thought to be greatest. Here, we explore the occurrence of endophytes in a broad diversity of woody, angiospermous taxa in a lowland, moist tropical forest in central Panamá. We use similarity indices to assess host preference and spatial heterogeneity of endophytes associated with two co-occurring, but distantly related, understorey tree species in two sites of that forest, and assess the utility of indices based on frequencies of morphospecies occurrence (Morisita-Horn index) and on presenceabsence data (Sørensen's index). We suggest that our understanding of fungal diversity will be enhanced by exploring ecological patterns underlying endophyte occurrence in host species, and discuss methods for assessing the proportion of fungal biodiversity represented by tropical endophytes.