Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples

Methodology comparison of environmental sediment fungal community analysis

Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.

A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms

Diatoms (Bacillariophyta) are a major source of primary production on Earth, generating between 1/4 to 1/2 of all oxygen. They are found in almost all bodies of water, the ice of mountains, the arctic and the antarctic, and soils. Diatoms are also a major source of food in aquatic systems, a key component of the silica cycle, and are carbon capturers in oceans. Recently, diatoms have been examined as sources of biofuels, food, and other economic boons. Chytrids are members of the Kingdom fungi comprising, at a minimum, Chytridiomycota, Blastocladiomycota, and Neocallimastigales. Most chytrids are saprobes, plant pathogens, or parasites, and play an important role in aquatic ecosystems. Chytrid parasitism of diatoms has been reported to cause epidemics of over 90% fatality, though most of the information regarding these epidemics is limited to interactions between just a few hosts and parasites. Given the ubiquity of diatoms, their importance in natural and economic systems, and the massive impact epidemics can have on populations, the relative lack of knowledge regarding parasitism by chytrids is alarming. Here we present a list of the firsthand accounts of diatoms reported parasitized by chytrids. The list includes 162 named parasitic chytrid-diatom interactions, with 63 unique chytrid taxa from 11 genera, and 74 unique diatom taxa from 28 genera. Prior to this review, no list of all documented diatom-chytrid interactions existed. We also synthesize the currently known methods of infection, defense, and experiments examining diatoms and chytrids, and we document the great need for work examining both a greater breadth of taxonomic diversity of parasites and hosts, and a greater depth of experiments probing their interactions. This resource is intended to serve as a building block for future researchers studying diatom-parasite interactions and global planktonic communities in both fresh and marine systems.

Exploring the mycobiota of bromeliads phytotelmata in Brazilian Campos Rupestres

The phytotelmata is a water-filled tank on a terrestrial plant, and it plays an important role in bromeliad growth and ecosystem functioning. Even though previous studies have contributed to elucidate the composition of the prokaryotic component of this aquatic ecosystem, its mycobiota (fungal community) is still poorly known. In the present work, ITS2 amplicon deep sequencing was used to examine the fungal communities inhabiting the phytotelmata of two bromeliads species that coexist in a sun-exposed rupestrian field of Southeastern Brazil, namely Aechmea nudicaulis (AN) and Vriesea minarum (VM). Ascomycota was the most abundant phylum in both bromeliads (57.1 and 89.1% in AN and VM respectively, on average), while the others were present in low abundance (< 2%). Mortierellomycota and Glomeromycota were exclusively observed in AN. Beta-diversity analysis showed that samples from each bromeliad significantly clustered together. In conclusion, despite the considerable within-group variation, the results suggested that each bromeliad harbor a distinct fungi community, what could be associated with the physicochemical characteristics of the phytotelmata (mainly total nitrogen, total organic carbon, and total carbon) and plant morphological features.

Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.

Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon

Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.

OMICS and Other Advanced Technologies in Mycological Applications

Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.

Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data

Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes.

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

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.