Fungal Ecology最新文献

Accurately identifying entomopathogenic fungi is crucially important, but the current approach of analysing four genes might not provide sufficient resolution. In this study, we investigated the different resolution provided by multilocus phylogenies and approaches based on whole genome sequence data. Fungi were isolated from soil samples that were collected from five different vegetation types (dry sclerophyll forest, agricultural grassland, rainforest, suburban parkland, and sugar cane fields) and across four different suburban soil habitat types in southeast Queensland. Three different agricultural pests were used as live baits, cotton stainer bug, diamondback moth, and rust-red flour beetle. Whole-genome sequencing was conducted for all 83 isolates recovered, and the ITS2 region was extracted from the genome assemblies to make initial species identifications with the UNITE database. We also extracted tef1a 3′, tef1a 5’, rpb1 and rpb2 genes from the Metarhizium genomes and the bloc, tef1a and rpb1 genes from Beauveria genomes to construct multilocus phylogenies and obtain species identification. To investigate the genetic relationships across 14 isolates of Beauveria bassiana and (independently) across 43 isolates of Metarhizium based on whole-genome data, we genotyped single nucleotide polymorphism (SNP) markers and conducted principal components analysis on the whole-genome SNP data. The multilocus methods identified isolates to species more precisely than ITS2, except in the one unresolved clade in the Metarhizium phylogeny. The whole-genome approach identified more genetic clusters than the multilocus phylogenies identified species among the isolates, and the morphological results correlated with some of the genetic clusters, so they likely represent distinct species not detected by the other methods. The genetic clusters were not associated with vegetation type or bait insect species. This is the first comparison of the resolution of multilocus phylogenetics with that of whole-genome SNP data for these genera. We suggest how the genetic clusters identified here may be investigated further to determine whether they represent unrecognised species within these groups.

The amphibian skin pathogen Batrachochytrium dendrobatidis (Bd) has caused an ongoing biodiversity crisis, including in the locally endangered Colorado boreal toad (Anaxyrus boreas). Although researchers have investigated the bacteria living on amphibian skin and how they interact with Bd, there is less information about fungal community members. This study describes (1) the diversity of culturable fungi from boreal toad skin, (2) which subset of these isolates is Bd-inhibitory, and (3) how Bd affects these isolates' growth and morphology. Most isolates were from the orders Capnodiales, Helotiales, and Pleosporales. Of 16 isolates tested for Bd-inhibition, two from the genus Neobulgaria and three from Pseudeurotium inhibited Bd. Fungal growth in co-culture with Bd varied with weak statistical support for Neobulgaria sp. (isolate BTF_36) and cf Psychrophila (isolate BTF_60) (p-values = 0.076 and 0.092, respectively). Fungal morphology remained unchanged in co-culture with Bd, however, these results could be attributed to low replication per isolate. Nonetheless, two fungal isolates’ growth may have been affected by Bd, implying that fungal growth changes in Bd co-culture could be a variable worth measuring in the future (with higher replication). These findings add to the sparse but growing literature on amphibian-associated fungi and suggest further study may uncover the relevance of fungi to amphibian health and Bd infection.

A frequently ignored but critical aspect of microbial dispersal is survival in the atmosphere. We exposed spores of two closely related, morphologically dissimilar, and economically important fungal pathogens to typical atmospheric environments and modeled their movement in the troposphere. Alternaria solani conidia are nearly 10 times larger than A. alternata conidia, but in our experiments, most died within 24 h, while over half of A. alternata conidia remained viable on day 12. Next, we modeled the movement of spores across North America. We predict 99% of the larger A. solani conidia settle within 24 h, with a maximum dispersal distance of 100 km. By contrast, most A. alternata conidia remain airborne for more than 12 days, and dispersal over long distances(2000 km) is likely. Counterintuitively, the larger A. solani conidia survive poorly, as compared to smaller A. alternata conidia, but also land sooner and move over shorter distances.

Physarum polycephalum is a foraging, network-forming organism known for its ability to make complex decisions and maintain memory of past stimuli without use of a complex nervous system. Self-organized peristaltic flows within the network transport nutrients throughout the organism and initiate locomotion and morphological changes. A key step in understanding P. polycephalum's ability to change behavior is therefore forming descriptors of this peristaltic flow. Here, we develop a dynamic network-based method for describing organism-wide patterns of tube contractions from videos of P. polycephalum. Our tool provides robust readouts of the diversity of global modes of tube contraction that could occur within a given network, based on its geometry and topology, and sensitively identifies when global peristaltic patterns emerge and dissipate.

Harpellales, an order of Kickxellomycotina, are commensalistic fungi that live in the digestive tracts of arthropods. They create specialized spores, called trichospores, which are asexual, deciduous, monosporous sporangia that infect individuals in the host population. The trichospores do not produce germ tube(s) and expel the sporangiospore inside very quickly. This germination style is referred to as sporangiospore extrusion. In this study, we were able to record live imaging of the sporangiospore extrusion from trichospores and subsequent morphological changes. Using live image analysis, the rates of spore extrusion, elongation and contraction were determined. When the pH shifted from 10 to 5 in a liquid medium containing potassium, the sporangiospore burst through the sporangial wall in less than 30 s, and rapidly tripled in length (56 μm) from the initial trichospore length (18 μm). During the next 60 s, the spore gradually contracted to be similar to the original length (22 μm) of the trichospore. The mechanisms underlying spore membrane elongation and contraction were revealed by fluorescent staining of the cell wall and plasma membrane. Momentary sporangiospore extrusion from trichospores and its contraction are thought to be an adaptation for quick attachment to the gut cuticle of host insects.

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.