Response of Antarctic soil fungal assemblages to experimental warming and reduction of UV radiation

This paper reports the effects of nutrient availability, UV radiation and temperature on the taxa composition and abundance of Antarctic soil mycobiota. Two sites at Edmonson Point were studied: the first was poor in nutrients, near the glacier, and the second was close to bird nesting sites. The highest abundance of soil fungi was recorded at the site adjacent to the bird nesting sites. Phoma herbarum was the most abundant taxon. Lecytophora lignicola and Ascotricha erinacea are new records for continental Antarctica. The fungal assemblage from the nutrient-deficient site was characterized by a dominance-diversity curve approaching the broken-stick model, the assemblage from the soil influenced by birds was characterized by a lognormal distribution. Plastic cloches were used in experiments designed to assess differences in fungal assemblages subjected to altered temperature and/or UV exposure. Dominance-diversity curves and diversity values of soil fungal mycobiota were compared in their natural condition as compared with manipulated conditions. Under the walled cloches, at both sites, artificial warming led to stress on Antarctic soil fungal assemblages. In contrast, UV protection led to a higher equilibrium in the assemblage structure. On the basis of the results obtained, it could be proposed that UV radiation is the most important limiting ecological factor for soil mycobiota in continental Antarctica.     

Spatial-typological differentiation of clavarioid mycobiota in Northern Eurasia

The spatial heterogeneity of mycobiota species composition has been studied. Clavarioid fungi are used as a model group for mycobiota zonation of Northern Eurasia. The differences in the classification of mycobiota of these fungi resulting from the used coefficients of similarity, aggregation algorithms, and opinions of different interpreters are shown. A method of combining different classifications is proposed. A further study on a larger number of fungal groups would be more representative and would contribute to the creation of a unified biogeographic zonation of Northern Eurasia.     

Spatio-temporal,environmental factors,and host identity shape culturable-epibiotic fungi of seaweeds in the Red Sea,Egypt

The study of fungal species diversity from marine algae is in its infancy; as now no studies have been carried out on the distribution and diversity of fungi on the surfaces of marine macroalgae where all fungal–algal interactions tend to begin. The aim of this study was to isolate and describe the culturable part of mycobiota associated with the surface of benthic marine macroalgae (epiphytic or epibiotic fungi). This is an important step in understanding their abundance, diversity and factors influencing their variability and composition. The fungal community was dominated by Ascomycetes (89%) with Eurotiales as the most abundant fungal order followed by Capnodiales, Pleosporales, and Hypocreales, while Zygomycetes was less frequent. The nature of occurrence of fungal genera on different macroalgal hosts suggests that a mix of generalists’ framework applies to fungal epiphytes of seaweeds, but the abundance of fungal taxa varied among ecological functional groups of algae, as well as macroalgal taxonomic groups, which imply host filtering. The fungal assemblages were also characterized by temporal variation with variation in temperature, pH, and salinity as the most important abiotic factors. The structure of fungal assemblages showed high beta diversity and low similarity between hosts.     

Unveiling the fungal mycobiota present throughout the cork stopper manufacturing process

A particular fungal population is present in the main stages of the manufacturing process of cork discs. Its diversity was studied using both dependent (isolation) and independent culture methods (denaturing gel gradient electrophoresis and cloning of the ITS1-5.8S-ITS2 region). The mycobiota in the samples taken in the stages before and after the first boiling seems to be distinct from the population in the subsequent manufacturing stages. Most isolated fungi belong to the genera Penicillium, Eurotium and Cladosporium. The presence of uncultivable fungi, Ascomycota and endophytes in raw cork was confirmed by sequencing. The samples taken after the first boiling contained uncultivable fungi, but in a few samples some isolated fungi were also detected. The main taxa present in the following stages were Chrysonilia sitophila, Penicillium glabrum and Penicillium spp. All applied techniques had complementary outcomes. The main factors driving the shift in cork fungal colonization seem to be the high levels of humidity and temperature to which the slabs are subjected during the boiling process.     

How does metal soil pollution change the plant mycobiome?

Microorganisms play a key role in plant adaptation to the environment. The aim of this study was to evaluate the effect of toxic metals present in the soil on the biodiversity of plant-related, endophytic mycobiota. The mycobiome of plants and soil from a Zn–Pb heap and a metal-free ruderal area were compared via Illumina sequencing of the ITS1 rDNA. The biodiversity of plants and fungi inhabiting mine dump substrate was lower than that of the metal free site. In the endosphere of Arabidopsis arenosa from the mine dump the number of endophytic fungal taxa was comparable to that in the reference population, but the community structure significantly differed. Agaricomycetes was the most notably limited class of fungi. The results of plant mycobiota evaluation from the field study were verified in terms of the role of toxic metals in plant endophytic fungi community assembly in a reconstruction experiment. The results presented in this study indicate that metal toxicity affects the structure of the plant mycobiota not by changing the pool of microorganisms available in the soil from which the fungal symbionts are recruited but most likely by altering plant and fungi behaviour and the organisms' preferences towards associating in symbiotic relationships.     

Evaluation of PCR-DGGE methodology to monitor fungal communities on grapes

Aims:  Some fungi present on the surface of grapes may have a negative effect on the quality of wine. The aim of this study was to evaluate PCR-denaturing gradient gel electrophoresis (PCR-DGGE), for the establishment of fungal community profiles from grapes, in order to monitor fungi potentially involved in wine defects.
Methods and Results:  A fragment of the β-tubulin gene was amplified from filamentous fungi and yeasts described from grapes and analysed using two different denaturing gradient gels to constitute a reference database. The use of β-tubulin sequences instead of ITS rDNA in PCR-DGGE showed a progress in the discrimination of these fungal species but comigration problems were still observed. The technique was then applied on grape samples. The profiles counted up to 10 bands of which half corresponded to species which were not recorded in the reference database.
Conclusion:  PCR-DGGE represents a useful tool to compare environmental samples for the study of the dynamics of fungal communities, but comigrations represent a limit in its use to describe the species present.
Significance and Impact of the Study:  A better knowledge of the fungal diversity on grapes, particularly species responsible for wine defect, is necessary to develop accurate molecular detection tools.     

Survey of mycobiota,black <Emphasis Type="Italic">Aspergillus</Emphasis> and ochratoxin A occurrence on Brazilian wine grapes

The southern state of Brazil is responsible for 90 % of the wine produced in the country; however, the mycobiota and the occurrence of ochratoxin A (OTA) on wine grapes produced in this region has never been fully characterized. To evaluate the fungal and OTA contamination in wine grapes of two varieties cultivated in southern Brazil, a survey was conducted in three regions with slightly different climates. From each region, samples were obtained at early ripeness and at harvest stage. Eight genera were isolated; Alternaria and Trichoderma were the most prevalent. Within the Aspergillus genus, the section Nigri was predominant. One uniseriate black Aspergillus was able to produce OTA under the conditions tested but no detectable levels of OTA were found in the grape samples. The low overall incidence of black Aspergillus and the absence of OTA on the grapes may be explained by the meteorological conditions at the analyzed regions, and characterizes a high quality of this product regarding mycotoxigenic contamination. This is the first study to fully describe the mycological biota of two wine grape varieties produced at three different regions of Rio Grande do Sul state.     

Mycobiota of Eucommia ulmoides bark: Diversity,rare biosphere and core taxa

Bark represents a unique microbial habitat. Revealing the interactions among bark-associated microbes is important for understanding their diversity, stability, and function, and how core microbiome influences the health and production of the host plant. We used amplicon sequencing of bark from the medicinal plant Eucommia ulmoides collected across nine distinct biogeographical regions in China, and comprehensively analyzed the diversity, rare biosphere and core taxa of bark fungi. The co-occurrence network results showed significant differences in the compositions of core mycobiota in E. ulmoides bark between the nine regions. Ecological factors (e.g., temperature and rainfall) were crucial determinants of differences in the unique core mycobiota of E. ulmoides from different regions. The metacommunity-scale network indicated that Cladosporium, Alternaria, and Teratosphaeria were core fungal taxa of E. ulmoides bark. Moreover, some core fungal taxa included rare taxa in particular local communities which, despite their relatively low abundance, may play a significant role in the community structure of E. ulmoides bark.     

Penicillium astrolabium and Penicillium neocrassum, two new species isolated from grapes and their phylogenetic placement in the P. olsonii and P. brevicompactum clade

We describe two new terverticillate Penicillium species isolated from grapes on the basis of phenotypic and phylogenetic differences from known species. The strains were isolated in the course of a study to establish the mycobiota of grapes in Portugal. Penicillium astrolabium is phenotypically similar to P. olsonii but differs from it by two cultural characters, growth rates and the colony reverse color. P. neocrassum is similar to P. brevicompactum but is readily distinguished by sclerotia production. Phylogenetically P. astrolabium and P. neocrassum are placed respectively in the P. olsonii and P. brevicompactum clade. Multilocus analysis confirmed the genetic distinctiveness of both species. The parsimony trees obtained for ITS-lsu rDNA region and two protein coding genes, calmodulin and beta-tubulin, show congruence for all the species in the Olsonii series: P. brevicompactum, P. bialowiezense, P. olsonii, P. astrolabium and P. neocrassum, indicating that these taxa are genetically well isolated.     

Diversity of the endophytic fungi associated with the ancient and narrowly endemic neotropical plant Vellozia gigantea from the endangered Brazilian rupestrian grasslands

This study focused on the taxonomy and diversity of the endophytic fungi associated with Vellozia gigantea, an endemic, ancient, and endangered plant species that occurs only in the rupestrian grasslands of Brazil. A total of 285 fungal isolates were recovered from leaves and roots of the V. gigantea, which were identified in 27 genera and 87 different taxa using molecular taxonomy methods. Xylaria berteri, Diaporthe sp. 1, Nigrospora oryzae, Muscodor sp. 1, Colletotrichum aeschynomene, and Trichoderma viride occurred in the highest frequency in both the leaf and root. Diaporthe was the most abundant genus, with 70 endophytic isolates recovered from the leaves and roots. Among all the taxa identified, 62 occurred as singlets, including those of the genera Clonostachys, Coccomyces, Crucellisporiopsis, Daldinia, Myxotrichum, Pallidocercospora, Pezicula, Peyronellaea, and Pseudocercospora. The diversity indices displayed high values, showing that V. gigantea shelters a diverse and rich mycobiota. Our results indicate that V. gigantea shelters in its tissues a highly diverse and cryptic mycobiota, including several rare species previously unreported as endophytes, but that are reported to have different ecological functions, which might be an important biological component contributing to the fitness of the plants living in the rupestrian grassland.     

Yeast communities associated withDrosophila species and related flies in an eastern oak-pine forest: A comparison with western communities

Summary Intestinal yeast mycobiota were studied in 14 species ofDrosophila and in the drosophilid speciesChymomyza amoena, captured at Pinery Provincial Park, Ontario. Over 56 yeast species, some undescribed, were isolated. These yeast communities were compared with those from two similar surveys conducted in western portions of North America. The community structures were influenced significantly by the habitat rather than phylogeny of the flies. Geographic separation was a factor affecting yeast taxa frequencies in the fly species, but it was largely overshadowed by ecological factors when the communities were described physiologically. The notion that habitats are filled by yeasts which add up to a suitable physiological potential, more or less independently of their taxonomic affinities, was thus confirmed.This paper is dedicated to Professor Herman Jan Phaff in honor of his 50 years of active research which still continues.     

Complexes of soil micromycetes in the area of the influence of the Chernobyl Atomic Electric Power Station]

Complexes of soil micromycetes in the Chernobyl 30-km zone of the Ukrainian Polesye were studied for 1986-1989 with regard for such ecological parameters as the level of radiation contamination, a particular observation site, depth of soil horizon and season. As a result of the study correlation pleiads of soil micromycete complexes have been revealed with their structure and fungal genera characteristic of such complexes determined. The overwhelming majority of correlation pleiads of fungal complexes are attributed to complex-organized ones and this indicated high radioresistance of mycobiota in the studied, soils. Melanine-containing genera of fungi rank among the first in formation of correlation pleiads of soil micromycete complexes.     

Unusual fungal niches

Fungi are found in all aerobic ecosystems, colonizing a diversity of substrates and performing a wide diversity of functions, some of which are not well understood. Many spices of fungi are cosmopolitan and generalists or habitats. Unusual fungal niches are habitats where extreme conditions would be expected to prevent the development of a mycobiota. In this review we describe five unusual fungal habitats in which fungi occupy poorly understood niches: Antarctic dry valleys, high Arctic glaciers, salt flats and salterns, hypersaline microbial mats and plant trichomes. Yeasts, black yeast-like fungi, melanized filamentous species as well as representatives of Aspergillus and Penicillium seem to be dominant among the mycobiota adapted to cold and saline niches. Plant trichomes appear to be a taxa. The advent of new sequencing technologies is helping to elucidate the microbial diversity in many ecosystems, but more studies are needed to document the functional role of fungi in the microbial communities thriving in these unusual environments.     

Intra- and inter-cores fungal diversity suggests interconnection of different habitats in an Antarctic frozen lake (Boulder Clay,Northern Victoria Land)

A perennially frozen lake at Boulder Clay site (Victoria Land, Antarctica), characterized by the presence of frost mounds, have been selected as an in situ model for ecological studies. Different samples of permafrost, glacier ice and brines have been studied as a unique habitat system. An additional sample of brines (collected in another frozen lake close to the previous one) was also considered. Alpha- and beta-diversity of fungal communities showed both intra- and inter-cores significant (p < 0.05) differences, which suggest the presence of interconnection among the habitats. Therefore, the layers of frost mound and the deep glacier could be interconnected while the brines could probably be considered as an open habitat system not interconnected with each other. Moreover, the absence of similarity between the lake ice and the underlying permafrost suggested that the lake is perennially frozen based. The predominance of positive significant (p < 0.05) co-occurrences among some fungal taxa allowed to postulate the existence of an ecological equilibrium in the habitats systems. The positive significant (p < 0.05) correlation between salt concentration, total organic carbon and pH, and some fungal taxa suggests that a few abiotic parameters could drive fungal diversity inside these ecological niches.     

Fungal community composition in the gut of rove beetles (Coleoptera: Staphylinidae) from the Canadian boreal forest reveals possible endosymbiotic interactions for dietary needs

The goal of this study was to investigate the fungal community composition in the gut of Staphylinidae from boreal forest in order to better understand the diversity and the complexity of fungus-insect relationships. DNA gut content analyses of nine abundant rove beetle species (Coleoptera, Staphylinidae) living in the boreal balsam fir forest ecosystem (Montmorency Forest, Quebec, Canada) were performed to identify the fungal taxa present either as endosymbiotic taxa or as a source of nutrition. A total of 42 fungal operational taxonomic units (OTUs) were recorded from the analysis of 441 fungal ITS rDNA sequences recovered from gut extracts. The OTU richness per species ranged between four in Tachinus quebecensis and 16 in Atheta ventricosa. The fungal mycobiota in posterior gut extracts was dominated by Saccharomycetales (12 OTUs), followed by Sordariomycetes (nine OTUs). No significant difference was observed between the OTU richness recorded within each of the three subfamilies of rove beetles investigated. The core mycobiome of the posterior gut extracts was dominated by three OTUs related to yeasts, with ITS sequences having pairwise similarities equal to or greater than 99% with Candida mesenterica, Debaryomyces spp. and Ophiostoma pluriannulatum. These results provide some evidence of the consumer-resource relationships of these beetles. Predominance of yeast and fungal spores in the posterior gut of rove beetles suggests that they may play an important role in their dietary requirements and as endosymbionts.     

Fungal contamination of some imported spices

Seventeen imported raw spice samples obtained from retail outlets were examined for spoilage mould profile. A total of 665 fungal isolates, representing 14 species, were recovered and identified from dried and ground spice samples on several media using standard dilution plate method. Moisture content varied greatly among various samples and were generally high. The most heavily contaminated spice samples examined were observed in red chili and black pepper in order of magnitude of 1580 and 1120 cfu/g, respectively. The most predominant fungal genera encountered were Aspergillus, Penicillium, Rhizopus, Cladosporium and Trichoderma. Yeasts were also frequently recovered, but not identified. Relative occurrence values of taxa disclosed ranged between 36.4% for A. flavus and 0.6% for A. parasiticus and Absidia corymbifera. Samples obtained from gunny bags encounter higher colony counts and contamination frequency than other packing methods. The present magnitude of contamination and spectra of mycobiota approximate those reported for similar spice samples. Although several potentially mycotoxigenic fungi were isolated during the present study, neither the foodstuff nor the fungi were assayed for the presence of these toxins.     

Non-systemic fungal endophytes of grasses

Many fungi behave as endophytes in grasses. Unlike the well known Epichloë/Neotyphodium species, most other endophytes are not capable of systemic colonization of plant organs, or seed transmission. The species diversity of the non-systemic endophytic mycobiota of grasses is large, dominated by ascomycetes. The relative abundance of species is very unequal, a few dominant taxa like Acremonium, Alternaria, Cladosporium, Epicoccum and Penicillium spp., occur in many grasses and locations. In contrast, many rare species are isolated only once in endophyte surveys. The possible ecological functions of endophytes are diverse, and often unknown. Latent pathogens represent a small fraction of endophytic mycobiotas, indicating that many non-pathogenic fungal taxa are able to enter plants overriding defence reactions. Some dominant species behave as latent saprotrophs, sporulating when the host tissue dies. Endofungal viruses and bacteria occur among endophytic species, but their effect in their hosts is largely unknown.     

Fungi populate deep-sea coral gardens as well as marine sediments in the Irish Atlantic Ocean

Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small molecules. Despite their ecophysiological and biotechnological relevance, fungal deep-sea biodiversity has not yet been thoroughly characterized. In this study, we describe the culturable mycobiota associated with the deepest margin of the European Western Continental Shelf: sediments sampled at the Porcupine Bank and deep-water corals and sponges sampled in the Whittard Canyon. Eighty-seven strains were isolated, belonging to 43 taxa and mainly Ascomycota. Ten species and four genera were detected for the first time in the marine environment and a possible new species of Arachnomyces was isolated from sediments. The genera Cladosporium and Penicillium were the most frequent and detected on both substrates, followed by Candida and Emericellopsis. Our results showed two different fungal communities: sediment-associated taxa which were predominantly saprotrophic and animal-associated taxa which were predominantly symbiotic. This survey supports selective fungal biodiversity in the deep North Atlantic, encouraging further mycological studies on cold water coral gardens, often overexploited marine habitats.     

Canopy tree species and openness affect foliar endophytic fungal communities of understory seedlings

There is growing evidence demonstrating the diversity of foliar endophytic fungi and their ecological roles in the survival of tree seedlings. However, the factors that shape fungal communities in tree seedlings within natural forest ecosystems remain poorly understood. Here, we evaluated the composition of foliar endophytic fungi growing in current-year seedlings of Cornus controversa and Prunus grayana in a cool temperate deciduous forest through a seed-sowing experiment and fungal isolation. The composition of endophytic fungi was affected by canopy tree species, canopy openness, and time after germination. In total, 27 and 22 fungal taxa were isolated from C. controversa and P. grayana seedlings, respectively. The dominant fungal taxa in both seedling species were Colletotorichum spp., and their isolation frequencies were higher under C. controversa canopies than under P. grayana canopies; the frequencies also increased with time after germination. These results suggest that overstory tree species strongly influences the endophytic fungal communities of understory seedlings.