In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time.

Fungal Guttation, a Source of Bioactive Compounds and Its Ecological Role—A Review

Guttation is a common phenomenon in the fungal kingdom. Its occurrence and intensity depend largely on culture conditions, such as growth medium composition or incubation temperature. As filamentous fungi are a rich source of compounds, possessing various biological activities, guttation exudates could also contain bioactive substances. Among such molecules, researchers have already found numerous mycotoxins, antimicrobials, insecticides, bioherbicides, antiviral, and anticancer agents in exudate droplets. They belong to either secondary metabolites (SMs) or proteins and are secreted with different intensities. The background of guttation, in terms of its biological role, in vivo, and promoting factors, has been explored only partially. In this review, we describe the metabolites present in fungal exudates, their diversity, and bioactivities. Pointing to the significance of fungal ecology and natural products discovery, selected aspects of guttation in the fungi are discussed.

Substrate-Specific Differential Gene Expression in the Brown Rot Fungus Fomitopsis pinicola (Retracted and Republished from: “Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola ”)

All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes.

Fungal ethnoecology: observed habitat preferences and the perception of changes in fungal abundance by mushroom collectors in Poland

Background Scientists frequently raise the topic of data deficiency related to the abundance and distribution of macrofungi in the context of climate change. Our study is the first detailed documentation on locals’ perception of fungal ecology which covers a large mycophilous region of Europe (Mazovia, Poland). Methods A total of 695 semi-structured interviews were carried out among local informants in 38 localities proportionally distributed throughout the study area (one locality approximately every 30 km). Interview questions concerned fungi species collected, their perceived habitats, and whether any changes had been noted in their abundance. As many as 556 respondents provided information concerning fungal ecology. In these descriptions, 35 taxa were mentioned by at least 5 respondents. Results The data collected during interviews allowed us to create collective folk descriptions of habitat preferences and a list of 98 different macro-, meso-, and microhabitats of macrofungi described by the respondents. This list of recurring habitats assigned to particular macrofungal taxa coincides with, and sometimes exceeds, data available in scientific publications. Some habitat preferences observed by the informants have not yet been researched or tested by science. Out of 695 respondents, 366 (53%) noticed a steady decrease in local macrofungi abundance, and only one person claimed to have observed a steady increase. Imleria badia was the only species with increased abundance, as noted by fifteen independent respondents. The main listed reason for abundance decrease was drought (f = 186). Conclusions Collected information on the ecology of fungi shows that local knowledge does not generally diverge from scientific knowledge. The acquired information related to macrofungal abundance and ecology may also be used as a tool for the formulation of new scientific questions and theories. The analysis of local fungi observations might contribute to broadening knowledge about local changes in fungi and enable new estimations related to large-scale analysis of macrofungal abundance.

Palaeomycology: A modern mycological view of fungal palynomorphs

Fungal spores are increasingly used as reliable proxies in paleoenvironmental reconstructions; however, little attention is paid to the ecological tolerances of the fungi themselves and the signal the fungi provide. This chapter provides a much-needed background in fungal biology and ecology of monophyletic Dikarya (Ascomycota and Basidiomycota), as well as taphonomic considerations which could be included in any use as palaeoecological indicators. It is intended to help those who are interested in using fungal spores as palaeoecological indicators to make more informed interpretations. A recapitulation of spore dispersal strategies and distances is presented for a better understanding of the transport mechanisms of fungal spores. Likewise, pigmentation is discussed, as it results in significant taphonomic bias in fossil fungal assemblages and, as some dark-colored pigmentation is authigenic while some develops during taphonomy. A key element of this chapter is discussion of the environmental role of fungi, including modern versus palaeo-approaches to fungal ecology, fungal assemblages, and diversity patterns as diagnostic tools to infer paleoenvironments.Supplementary material at https://doi.org/10.6084/m9.figshare.c.5342039

Pulmonary Coccidioidomycosis

Coccidioidomycosis is an infection caused by the geographically restricted dimorphic fungus, Coccidioides. Coccidioidomycosis occurs endemically in the southwestern and western United States, mainly in focused regions of Arizona and California where the incidence is highest, and in Central and South America. Patients with impaired immunity, especially those with impaired cellular immunity, are at higher risk of severe and disseminated disease. In this review, we describe the fungal ecology and mycology, epidemiology, pathophysiology, and normal immune defenses to Coccidioides as well as address current concepts in diagnosis, treatment, and continued care of patients with pulmonary coccidioidomycosis. We also present and answer our most frequently asked questions regarding patients with primary pulmonary coccidioidomycosis.