Fungal Ecology最新文献

Fungi affect soil aggregation and hence soil structure. Soil aggregation by saprotrophic fungi has been linked to various fungal traits but not tested during interactions with other organisms such as grazing soil fauna. Here we investigated how fungal identity and traits such as mycelial extension rate and biomass production affect aggregation across 49 fungal species isolated from sandy soils with different land uses. We tested each fungus and its effect on aggregation in the presence and absence of a grazer (Folsomia candida). We show that fungal species vary widely in their ability to aggregate soil, that the ability to aggregate soil was not phylogenetically conserved and the best trait predictor for aggregation was mycelial extension rate. Moreover, we show that the interactions between fungi and collembola affect the ability of fungi to aggregate soils. We conclude that identity of fungal species and their interaction with grazers affects soil aggregation and thus soil structure.

While most studies evaluating plant species diversity effects on in-stream fungal decomposers have focused on dominant species, our study simulated different rare species extinction scenarios. We assessed whether the loss of these species altered the fungal biomass and aquatic hyphomycete sporulation, diversity and taxonomic composition in two experiments: even experiment, where we used the same biomass for all species (i.e., even litter mixtures); and natural proportion experiment, where we kept proportions of plant species as found in stream leaf litter (i.e., natural litter mixtures). We found that the loss of litter from rare plant species reduced fungal biomass and the reduction was greater for natural litter mixtures, indicating that evenness modulated the effect of diversity on fungal biomass, possibly through resource dissimilarity. Our findings reveal the relevance of litter from rare plant species and of the maintenance of natural species proportions in tropical riparian forests for the functioning of stream ecosystems.

High throughput sequencing of PCR amplicons derived from environmental DNA (aka DNA metabarcoding) has become an integral part of fungal ecology, enabling in-depth characterization of fungal communities. In most cases, the rDNA Internal Transcribed Spacer (ITS) region, which has a long history as a target in fungal systematics, is used as a DNA barcode marker. Despite improvements in sequencing techniques and bioinformatics approaches, there are inherent limitations associated with the use of a single-locus DNA marker that are often ignored. In this text, I discuss both inherent biological and methodological limitations associated with the use of the ITS marker. For example, proper species delimitation is often not possible with a single marker, and a significant DNA barcoding gap (i.e. interspecific divergence) is often missing between sister taxa in ITS. Further, we can rarely be fully confident about the assigned species-level taxonomy based on available reference sequences. In addition to the inherent limitations, an extra layer of complexity and variation is blended into DNA metabarcoding data due to PCR and sequencing errors that may look similar to natural molecular variation. The bioinformatics processing of ITS amplicons must take into account both the basic properties of the ITS region, as well as the generated errors and biases. In this regard, we cannot adopt approaches and settings from other markers, such as 16S and 18S, blindly. For example, due to intraspecific variability in the ITS region, and sometimes intragenomic variability, ITS sequences must be clustered to approach species level resolution in community studies. Therefore, I argue that the concept of amplicon sequence variants (ASVs) is not applicable. Although the ITS region is by far the best option as a general DNA (meta)barcoding marker for fungi, this contribution is meant to remind against a naive or simplistic use of the ITS region, and for stimulating further discussions.

Prairies were once extensive in the Pacific Northwest, but declined due to Euro-American settlement, agriculture, and fire exclusion. Remnant and restored prairies require frequent management to limit establishment of trees and invasive plants. We asked whether management practices affect sporocarps (“mushrooms”) by quantifying sporocarps in prairie restoration treatments, including fire. Management treatments significantly affected sporocarp production; there were more mushrooms in burned plots and fewer in carbon addition plots. Surveys of fire chronosequences (not burned for >150 years, burned in 2012, 2014 or 2015) revealed significant differences in sporocarp numbers depending on time since fire (more in unburned and in 2015 burns), whether the prairie was an upland or wetland (more in uplands), and when the census occurred. In these now rare habitats, we found over 400 species of macrofungi, some of which were uncommon to rare. These results can inform management to support fungal diversity in Pacific Northwest prairies.

Botrytis cinerea is a necrotrophic fungus causing grey rot (GR) with crucial economic losses in fruit crops. It can also cause the desired noble rot (NR) in grape berries used to produce botrytized wines. In both states, B. cinerea is associated with several other fungi, but the functional role of these is still poorly understood. Metatranscriptomic data was generated from healthy (H), noble rot (NR) and grey rot (GR) grape berries and RNA-seq reads were aligned to the most prevalent filamentous fungi and yeasts based on previous culture-based studies. Differential enrichment analyses and pathway enrichment analyses revealed that all filamentous fungi and yeasts are most active in NR, besides GR and H berries. Beside B. cinerea, several functional genes of other fungi were linked to well-known physico-chemical changes in NR berries and to the production of antagonistic interaction genes. Our study demonstrates the complex interaction dynamics of the grape microbiome.

Aerial photos and Google Earth images of the Laramie Basin in Wyoming were used to measure size, and calculate species-specific growth rates and ages for 304 rings comprising eight species of fairy ring forming fungi. Estimated age was used to explore establishment, dynamics and persistence in relation to historic precipitation and drought data. Size of fairy rings ranged from 4 to 272 meters, and age from 15 to 522 years. 90% of all rings were younger than 80 years. Species-specific growth rates varied from 0.131 to 0.364 meters per year. All fairy ring species became established over a wide range of precipitation, although most rings established during years with 25–30 centimeters of precipitation. Little correlation was observed between establishment and precipitation patterns for some fungi, however others exhibited a significant relationship between year of establishment and both August precipitation and the Palmer Modified Drought Index. Expansion of one large ring was followed for 75 years. These data demonstrate that turnover in fairy rings is quite high and that fairy ring fungi can establish over a wide range of moisture levels.

We investigated the wood fungal community composition in stems of living Norway spruce (Picea abies (L.) Karst.) trees in 20–40 year-old forest stands from Latvia that differed in recent management history (stands with or without thinning) and former land use (former agricultural or former forest lands). Fungal internal transcribed spacer (ITS2) amplicons of DNA extracted from wood were sequenced to assess wood fungal communities. Alternaria, Ascocoryne, Didymella, Heterobasidion, Ophiostoma, Orbilia, Pesotum, Phoma and Pseudocercosporella were the dominant wood pathogen and wood saprotroph genera in the analysed samples. PERMANOVA analysis identified some differences in fungal communities among site types analysed (p < 0.001); tree height and presence/absence of rot in the wood samples (mainly Heterobasidion rot) significantly influenced fungal community composition (p < 0.001). Significant negative co-occurrence (p < 0.05) was observed between Heterobasidion and Ascocoryne genera indicating the differing wood colonizing niches of these taxa. Both stand level factors, such as management history and former land use, and tree level parameters are significant for wood inhabiting fungal communities of living spruces.

Forests can experience negative feedbacks in the growth of tree populations but positive feedbacks within the two dominant mycorrhizal types of trees: ectomycorrhizal (EM) and arbuscular mycorrhizal (AM). Positive feedbacks within mycorrhizal types may provide communities with resistance to climate change. We tested whether each mycorrhizal type led to positive feedbacks on seedling survival, while statistically controlling for the effect of congeneric trees in ambient versus rainfall reduced conditions. We explored two potential drivers: the variation in soil fungal community structure and soil chemistry. Seedlings benefited from growing in stands dominated by their own mycorrhizal type, and simultaneously, tree seedlings performed worse in the presence of adult trees of their own genus, but only in rainfall reduced conditions. We found that the composition of the EM fungal community differed between plots dominated by EM versus AM trees. These results indicated that mycorrhizal types may create positive feedbacks in dry conditions that should be considered when predicting future states.

The generalist entomophthoralean insect pathogen Batkoa major was recorded causing epizootics in populations of a new invasive fulgorid in North America, the spotted lanternfly (Lycorma delicatula). We conducted studies on the basic biology and ecology of B. major using Galleria mellonella larvae exposed to conidial showers. Death of G. mellonella followed a diurnal cycle with most larvae dying within 4 h before or after the end of photophase. Time for initiation of rhizoid emergence also followed a diurnal rhythm and, on average occurred 3.6 h after host death. While B. major sometimes began producing rhizoids to attach cadavers to substrates while G. mellonella were alive (but moribund), often hosts were dead before rhizoids began emerging. On average, conidial discharge began 18.6 h after host death and was greater 4–8 h before the end of photophase, compared with 4–8 h after scotophase began. At 20 °C under high humidity, initiation of conidial discharge was 95% complete within 24 h after host death. To evaluate B. major activity by temperature, we tested percent conidial germination over 24 h from 5 to 35 °C. When showered onto water agar, all primary conidia produced secondary conidia. At 20 and 25 °C, at 3 h ≥89% of primaries had produced and discharged secondaries and from 10 to 30 °C, secondaries were produced by over 75% of primary conidia within 12 h. When cover slips were placed over primary conidia to force production of germ tubes, germination was much slower, with >85% germination from 20 to 30 °C only by 24 h. Batkoa major therefore times host death and initiation of conidial discharge for night-time hours and conidial germination occurs within 24 h over a broad temperature range (10–30 °C).

There is substantial fungal diversity in marine environments where uncharacterized species may play important ecological roles. Malassezia, a genus of yeast generally associated with mammalian skins, is an example of a seemingly abundant marine fungus in ocean environments. Accumulating evidence indicates that Malassezia is widespread in the ocean. However, we know little about its diversity, role, and distribution. To address these gaps in our knowledge, we analyzed 127 marine samples collected from marine rocks, sediment, water, and various organisms, from the coasts of Hawaiʻi, Washington, and Massachusetts. We then used Malassezia-specific 28S primers in a nested PCR approach to amplify all present Malassezia, and performed Illumina sequencing from which we generated a possible phylogeny. Based on our phylogenetic results, we circumscribed 20 potentially novel clades that might represent new species. Our findings are consistent with Malassezia having substantial novel diversity and a high prevalence in the marine environment.