Breakthroughs in DNA sequencing have upended our understanding of fungal diversity. Only ∼155,000 of the 2-3 million fungal species on the planet have been formally described and named, and 'dark taxa' - species known only from sequences - represent the vast majority of species within the fungal kingdom. The International Code of Nomenclature requires physical type specimens to officially recognize new fungal species, making it difficult to name dark taxa. This is a significant problem for conservation because, without names, species cannot be recognized for environmental and legal protection. Symbiotic ectomycorrhizal (EcM) fungi play a particularly important role in forest carbon drawdown, but at present we have little understanding of how many EcM fungal species exist, or where to prioritize research activities to survey and describe EcM fungal lineages. In this review, we use global soil metabarcoding databases (GlobalFungi and the Global Soil Mycobiome consortium) to evaluate current estimates of the total number of EcM fungal species on Earth, outline the current state of undescribed EcM dark taxa, and identify priority regions for future dark taxa exploration. The metabarcoding databases include up to 219,730 EcM fungal operational taxonomic units (OTUs) detected from almost 39,500 samples. Using Chao richness estimates corrected for extrapolating species numbers from metabarcoding datasets, we predict that the global diversity of EcM fungi could be ∼25,500-55,500 species. Dark taxa - those that do not match species-level identities - account for 79-83% of OTUs. Oceania contains the highest percentage of dark taxa (87%), and Europe the lowest (78%). Priority 'darkspots' for future research occur predominantly in tropical regions, but also in selected temperate forests at both southern and northern latitudes. We propose concrete steps to reduce the prevalence of EcM darkspots, including performing targeted field surveys, barcoding fungaria voucher specimens, and developing new ways to describe and conserve fungal taxa from DNA alone.
Rocky habitats, globally distributed ecosystems, harbour diverse biota, including numerous endemic and endangered species. Vascular plants thriving in these environments face challenging abiotic conditions, requiring diverse morphological and physiological adaptations. Their engagement with the surrounding microbiomes is, however, equally vital for their adaptation, fitness, and long-term survival. Nevertheless, there remains a lack of understanding surrounding this complex interplay within this fascinating biotic ecosystem. Using microscopic observations and metabarcoding analyses, we examined the fungal abundance and diversity in the root system of the rock-dwelling West Carpathian endemic shrub, Daphne arbuscula (Thymelaeaceae). We explored the diversification of root-associated fungal communities in relation to microclimatic variations across the studied sites. We revealed extensive colonization of the Daphne roots by diverse taxonomic fungal groups attributed to different ecological guilds, predominantly plant pathogens, dark septate endophytes (DSE), and arbuscular mycorrhizal fungi (AMF). Notably, differences in taxonomic composition and ecological guilds emerged between colder and warmer microenvironments. Apart from omnipresent AMF, warmer sites exhibited a prevalence of plant pathogens, while colder sites were characterized by a dominance of DSE. This mycobiome diversification, most likely triggered by the environment, suggests that D. arbuscula populations in warmer areas may be more vulnerable to fungal diseases, particularly in the context of global climate change.
- Klíčová slova
- Carpathians, amplicon sequencing, arbuscular mycorrhiza, dark septate endophytes, endemism, fungal pathogens,
- MeSH
- Daphne * mikrobiologie genetika MeSH
- ekosystém * MeSH
- endofyty genetika MeSH
- fyziologická adaptace genetika MeSH
- houby klasifikace genetika MeSH
- kořeny rostlin * mikrobiologie MeSH
- mykobiom genetika MeSH
- mykorhiza * genetika klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
The ectomycorrhizal fungi Tuber melanosporum Vittad. and Tuber aestivum Vittad. produce highly valuable truffles, but little is known about the soil fungal communities associated with these truffle species in places where they co-occur. Here, we compared soil fungal communities present in wild and planted truffle sites, in which T. melanosporum and T. aestivum coexist, in Mediterranean and temperate regions over three sampling seasons spanning from 2018 to 2019. We showed that soil fungal community composition and ectomycorrhizal species composition are driven by habitat type rather than climate regions. Also, we observed the influence of soil pH, organic matter content and C:N ratio structuring total and ectomycorrhizal fungal assemblages. Soil fungal communities in wild sites revealed more compositional variability than those of plantations. Greater soil fungal diversity was found in temperate compared to Mediterranean sites when considering all fungal guilds. Ectomycorrhizal diversity was significantly higher in wild sites compared to plantations. Greater mould abundance at wild sites than those on plantation was observed while tree species and seasonal effects were not significant predictors in fungal community structure. Our results suggested a strong influence of both ecosystem age and management on the fungal taxa composition in truffle habitats.
- Klíčová slova
- Fungal diversity, Soil fungi, T. aestivum, T. melanosporum, Truffle ecology, Truffle plantation,
- MeSH
- ekosystém MeSH
- mykobiom * MeSH
- mykorhiza * MeSH
- půda MeSH
- půdní mikrobiologie MeSH
- stromy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- půda MeSH
Ambrosia gall midges are endophagous insect herbivores whose larvae live enclosed within a single gall for their entire development period. They may exhibit phytomycetophagy, a remarkable feeding mode that involves the consumption of plant biomass and mycelia of their cultivated gall symbionts. Thus, AGMs are ideal model organisms for studying the role of microorganisms in the evolution of host specificity in insects. However, compared to other fungus-farming insects, insect-fungus mutualism in AGMs has been neglected. Our study is the first to use DNA metabarcoding to characterize the complete mycobiome of the entire system of the gall-forming insects as we profiled gall surfaces, nutritive mycelia, and larvae. Interestingly, larval mycobiomes were significantly different from their nutritive mycelia, although Botryosphaeria dothidea dominated the nutritive mycelia, regardless of the evolutionary separation of the tribes studied. Therefore, we confirmed a long-time hypothesized paradigm for the important evolutionary association of this fungus with AGMs.
- Klíčová slova
- Asphondylia, Cecidomyiidae, Lasioptera, ambrosia gall midge, fungiculture, larval mycobiome, metabarcoding, nutritive mycelium, phytomycetophagy,
- MeSH
- Ambrosia MeSH
- Diptera * MeSH
- hmyz MeSH
- larva MeSH
- mykobiom * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The caterpillar gut is an excellent model system for studying host-microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.
- Klíčová slova
- bacterial and fungal microbiomes, invertebrate–microbe interactions, network stability, plant secondary metabolite, salicylic acid, tannin, tannivin,
- MeSH
- Bacteria genetika MeSH
- mikrobiota * MeSH
- mykobiom * MeSH
- rostliny MeSH
- Publikační typ
- časopisecké články MeSH
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
- Klíčová slova
- bacteria, core microbiome, decomposition, fungi, necromass soil organic matter,
- MeSH
- ekosystém MeSH
- lesy MeSH
- mykobiom * MeSH
- mykorhiza * MeSH
- uhlík MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Názvy látek
- uhlík MeSH
Despite the growing interest in using mixed-culture aerobic denitrifying fungal flora (mixed-CADFF) for water remediation, there is limited research on their nitrogen removal performance in low C/N polluted water bodies. To address this knowledge gap, we isolated three mixed-CADFFs from overlying water in urban lakes to evaluate their removal performance. The total nitrogen (TN) removal efficiencies were 93.60 %, 94.64 %, and 95.18 %, while the dissolved organic carbon removal efficiencies were 96.64 %, 95.12 %, and 96.70 % for mixed-CADFF LN3, LN7, and LN15, respectively in the denitrification medium under aerobic conditions at 48 h cultivation. The three mixed-CADFFs could utilize diverse types of low molecular weight carbon sources to drive the aerobic denitrification processes efficiently. The optimal C/N ratio for the mixed-CADFFs were C/N = 10, and then C/N = 15, 7, 5, and 2. The high-throughput sequencing analysis of three mixed-CADFFs indicated that Eurotiomycetes, Cystobasidiomycetes, and Sordariomycetes were the dominant class in the communities at class level. The network analysis showed that the rare fungal species, such as Scedosporium dehoogii Saitozyma, and Candida intermedia presented positively co-occurred with the TN removal and organic matter reduction capacity. Immobilization mixed-CADFFs treatment raw water experiments indicated that three mixed-CADFFs could reduce nearly 62.73 % of TN in the low C/N micro-polluted raw water treatment. Moreover, the cell density and cell metabolism indexes were also increased during the raw water treatment. This study will provides new insight into resource utilization of the mixed-culture aerobic denitrifying fungal community in field of environment restoration.
- Klíčová slova
- Aerobic denitrification, C/N, Cell metabolism, Micro-polluted water bodies, Mixed-culture aerobic denitrifying fungal flora,
- MeSH
- aerobióza MeSH
- denitrifikace * MeSH
- dusičnany MeSH
- dusík metabolismus MeSH
- mykobiom * MeSH
- uhlík MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- dusičnany MeSH
- dusík MeSH
- uhlík MeSH
Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance indicating that human-mediated transport may serve as a pathway of the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.
- MeSH
- ekosystém * MeSH
- fylogeneze MeSH
- hmyz MeSH
- klimatické změny MeSH
- lesy MeSH
- lidé MeSH
- mykobiom * MeSH
- zeměpis MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
- MeSH
- biologická evoluce MeSH
- feces mikrobiologie MeSH
- fylogeneze MeSH
- mykobiom * genetika MeSH
- savci MeSH
- trávicí systém MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports high microbial diversity, opening questions of how forest management practices impact belowground associated diversity as research related to this issue is scarce. This study aims to investigate the effects of different fire prevention treatments and site history on bacterial and fungi co-response and co-occurrence patterns over a fire-risky scrubland ecosystem. Two different site histories were studied by applying three different fire prevention treatments and samples were analyzed by amplification and sequencing of ITS2 and 16S rDNA for fungi and bacteria, respectively. The data revealed that site history, especially regarding fire occurrence, strongly influenced the microbial community. Young burnt areas tended to have a more homogeneous and lower microbial diversity, suggesting environmental filtering to a heat-resistant community. In comparison, young clearing history also showed a significant impact on the fungal community but not on the bacteria. Some bacteria genera were efficient predictors of fungal diversity and richness. For instance, Ktedonobacter and Desertibacter were a predictor of the presence of the edible mycorrhizal bolete Boletus edulis. These results demonstrate fungal and bacterial community co-response to fire prevention treatments and provide new tools for forecasting forest management impacts on microbial communities.
- Klíčová slova
- Cistus ladanifer, Fire prevention, Forestry, Microbial communities, Predictive bacteria,
- MeSH
- Bacteria MeSH
- ekosystém MeSH
- lesy MeSH
- mikrobiota * MeSH
- mykobiom * MeSH
- požáry * MeSH
- půda MeSH
- půdní mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- půda MeSH
