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publicOct 2022View details →

Deciphering the interactions between plant species and their main fungal root pathogens in mixed grassland communities

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publicJul 2024View details →

Order of arrival and nutrient supply alter outcomes of coinfection with two fungal pathogens

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publicFeb 2025View details →

Genetic architecture underlying response to the fungal pathogen Dothistroma septosporum in lodgepole pine, jack pine, and their hybrids

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publicMar 2024View details →

Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens

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opencc-zeroJan 2021View details →

Data from: Negative density dependence in the mortality and growth of tropical tree seedlings is strong, and primarily caused by fungal pathogens

<ol> <li class="Body">Natural enemies have been implicated as agents of negative density dependence (NDD) in tropical forests, but their relative contributions to NDD, and thus to the maintenance of diversity, are largely unknown.</li> <li class="Body">We monitored the rates of survival and relative growth rates on seedlings for ten years in tropical moist forest in Manu National Park, Peru. We then experimentally manipulated the plots to exclude fungal pathogens, insects, small mammals, and large mammals for an additional 31 months to assess the influence of these natural enemies on density-dependent interactions among tropical seedlings.</li> <li class="Body">Fungal pathogens made the most important contribution to negative density dependence. The application of fungicide led to lower mortality rates, faster growth rates, and decreased species diversity. Other taxa of natural enemies had at most minor effects on seedling performance.</li> <li class="Body"> Synthesis. We conclude that fungal pathogens are the strongest contributors to the widely observed NDD that occurs among seedlings. Moreover, the presence of fungal pathogens augments the species diversity of seedlings, indicating their critical contribution to the maintenance of species coexistence and the structure of tropical tree communities.</li> </ol>

opencc-zeroApr 2024View details →

Different strategies between queens and workers against fungal pathogens in the termite Reticulitermes chinensis

Social insects are prone to pathogen infection because of high exposure rates from social interactions. However, it remains unclear whether queens have enhanced pathogen resistance, since reproduction is largely confined to queens. Here, we used a natural host-pathogen system, the subterranean termite Reticulitermes chinensis and the entomopathogenic fungus Metarhizium anisopliae, to investigate the differences in allo-grooming, locomotion, and immune gene expression between queens and workers against pathogen infection. We found that fungal infection significantly reduced survival in both queens and workers. Infected queens received significantly more grooming time from sanitary nestmates than infected workers, but they returned much less grooming time to sanitary nestmates than infected workers. Infection resulted in a reduction in the average locomotion speed and distance of queens but had no effect on worker locomotion. Infection resulted in upregulated expression of two immune genes (termicin and transferrin), two antioxidant genes (CAT and SOD), and phosphate genes CYP450 in queens but not in workers. Our results indicated that eusocial termites evolved strategies that prioritize the reproductive castes welfare in defending against the pathogen infection to ensure continued reproduction and colony persistence.

opencc-by-4.0Aug 2024View details →

Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems

This repository contains the data sets from the research paper "Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems"

opencc-by-4.0Dec 2021View details →

The population genetics of adaptation through copy-number variation in a fungal plant pathogen

Supplementary Tables S1-S8 for the manuscript "The population genetics of adaptation through copy-number variation in a fungal plant pathogen"

opencc-zeroMay 2022View details →

Plant-root pathogenic fungal and plant-mycorrhizal fungal association networks in a subtropical forest

Although rhizosphere fungi are essential for plant survival and ecosystem functioning, little is known about the processes that structure plant–fungal association networks. In this study, we constructed association networks between 43 plant species and two groups of root-associated fungi (mycorrhizal and pathogenic fungi; MF and PF, respectively) in a diverse subtropical forest. We then evaluated the modularity of plant–MF and plant–PF networks and linked them to the functional traits and phylogenies of both plants and fungi. We observed strong modularity in both plant–MF and plant–PF networks. Phylogenetically related fungi tended to emerge in the same modules. MF from distinct modules associated with plants with different specific root length and specific root area in plant–MF networks. PF from distinct modules associated with plants with different dark respiration rate and light compensation point in plant–PF networks. Plant affiliation to modules was explained by both plant traits and phylogeny (22% for plant–MF and 37% for plant–PF networks). In contrast, fungal affiliation to modules was explained by fungal phylogeny (16% for plant–MF and 29% for plant–PF networks). Our results elucidate the link between modularity in plant–root fungal networks and the functional traits and phylogeny of the plants and fungi. Our study highlights the importance of traits and phylogeny in governing root fungal community assembly from network perspective.

opencc-zeroMay 2022View details →

Positive allometric growth explains the positive effect of foliar fungal pathogens on plant coexistence

The data was collected in the northeastern Qinghai-Tibetan Plateau, Qinghai Province, China (101° 18′ 57″ E, 37° 36′ 50″ N; 3 221 m a.s.l.) in 2019 and 2020, including the species-specific growth allometry (scaling exponent and intercept) fitted by the allometric equation under each treatment in a population-level experiment, i.e., control, fungicide application, neighbor removal (removal), fungicide application × neighbor removal, and the community-level mean and dispersion of the growth allometry (CWM and FDis of growth scaling exponent and intercept, respectively) weighted by the species cover for each plot in a community-level fungicide application experiment.

opencc-zeroJun 2022View details →

Exposure to a fungal pathogen increases the critical thermal minimum of two frog species Datasets

This dataset contains data from a laboratory experiment described in the paper: Siddons, S. R., and Searle, C. L. (Accepted). Exposure to a fungal pathogen increases the critical thermal minimum of two frog species. Ecology and Evolution. The experiment examined how exposure to a virulent fungal pathogen, Batrachochytrium dendrobatidis (Bd), affected the critical thermal minimum (CTmin) of two frog species, Hyla versicolor (gray treefrog) and Lithobates palustris (pickerel frog). The CTmin is the minimum thermal performance point of an organism, which we estimated via righting response trials. For both frog species, the frogs were held in a beaker partially submerged in a circulating water at 15°C. At each 1-degree temperature decrease every 2.5 minutes, the frog was gently flipped onto their back and observed for how quickly they were able to right themselves ("Decreasing" trial). Frogs were considered unable to right themselves when they did not do so within 10 seconds. Another trial was conducted for each frog ("Constant" trial ), in which they were flipped onto their backs every 2.5 minutes while keeping the temperature at a constant 15°C. Main results of the experiment are that, for both species, the CTmin was higher for Bd-exposed frogs than unexposed frogs, and the CTmin of H. versicolor was higher than L. palustris. We also found that Bd-exposed frogs of both species righted themselves significantly fewer times in both decreasing and constant temperature trials. Finally, we observed higher mortality in Bd-exposed individuals throughout the experiment after Bd exposure for both species compared to unexposed individuals, with no difference between species.

opencc-zeroJun 2022View details →

Data from: Metabolites from the fungal pathogen Batrachochytrium dendrobatidis (Bd) reduce Bd load in Cuban treefrog tadpoles

Batrachochytrium dendrobatidis (Bd) has been associated with massive amphibian population declines worldwide. Wildlife vaccination campaigns have proven effective for mitigating damage from other pathogens, and there is evidence that adult frogs can acquire resistance to Bd when exposed to killed Bd zoospores and the metabolites they produced. Here, we investigated whether Cuban treefrogs tadpoles (Osteopilus septentrionalis) can gain protection from Bd through exposure to a prophylaxis treatment composed of killed zoospores or soluble Bd metabolites. We used a 2x2 factorial design, crossing the presence or absence of killed zoospores with the presence or absence of Bd metabolites. All hosts were subsequently exposed to live Bd to evaluate susceptibility. Exposure to killed zoospores did not induce a protective response. However, tadpoles exposed to Bd metabolites had significantly lower Bd intensity and prevalence than tadpoles that were not exposed to metabolites. The metabolites Bd produce pose no risk of Bd infection and therefore make an epidemiologically safe prophylaxis treatment, protecting tadpoles against Bd. This work provides a promising potential for protecting amphibians in the wild as a disease management strategy for controlling Bd associated declines.

opencc-zeroAug 2022View details →

Data from: Comparative host-pathogen associations of Snake Fungal Disease in sympatric species of water snakes (Nerodia)

The ascomycete fungus Ophidiomyces ophiodiicola (Oo) is the causative agent of ophidiomycosis (Snake Fungal Disease), which has been detected globally. However, surveillance efforts in the central U.S., specifically Texas, have been minimal. The threatened and rare Brazos water snake (Nerodia harteri harteri) is one of the most range restricted snakes in the U.S. and is sympatric with two wide-ranging congeners, N. erythrogaster transversa and N. rhombifer, in north central Texas; thus, providing an opportunity to test comparative host-pathogen associations in this system. To accomplish this, we surveyed a portion of the Brazos river drainage (~400 river km) over 29 months and tested 150 Nerodia individuals for the presence of Oo via quantitative PCR and recorded any potential signs of Oo infection. We found Oo was distributed across the entire range of N. h. harteri, Oo prevalence was 46% overall, and there was a significant association between Oo occurrence and signs of infection in our sample. Models indicated adults had a higher probability of Oo infection than juveniles and subadults, and adult N. h. harteri had a higher probability of infection than adult N. rhombifer but not higher than adult N. e. transversa. High Oo prevalence estimates (94.4%) in adult N. h. harteri has implications for their conservation and management owing to their patchy distribution, comparatively low genetic diversity, and threats from anthropogenic habitat modification.

opencc-by-4.0Dec 2023View details →

Datasets for Twort et al. Signals of positive selection in Palearctic bat species coexisting with a fungal pathogen

Datasets used in Twort et al: Signals of positive selection in Palearctic bat species coexisting with a fungal pathogen Included are final gene alignments and tree files from the Phylogenetic Dataset (2515 genes) and the curated dataset (300 genes). Phylogenetic Dataset Files: <ul> <li>BUSCO Dataset: 2515 genes extracted from the Mammalia_odb10 BUSCO database. This dataset was used for phylogeney construction and branch tests</li> <li>Align_BUSCO: Contains the final cleaned alignments used for the 2515 Phylogenetic dataset genes (after gblocks) in fasta format</li> <li>Contree_BUSCO.zip: Contains the consensus tree constructed with IQ-Tree for the 2,515 phylogenetic gene dataset (used as input for ASTRAL,and for branch tests)  </li> <li>Ufboot_BUSCO.zip: Contains the bootstrap trees from IQ-Tree for the 2,515 gene dataset</li> <li>Branch_Myoluc_labelled_BUSCO.zip: Final labelled trees, with Myotis lucifugus labelled as foreground branch  from the 2,515 gene dataset used for PAML branch tests, all bootstrap values and branch lengths have been removed.</li> <li>Branch_Myomyo_labelled_BUSCO.zip: Final labelled trees, with Myotis myotis labelled as foreground branch  from the 2,515 gene dataset used for PAML branch tests, all bootstrap values and branch lengths have been removed.</li> </ul> Curated Dataset Files: <ul> <li>PAML Dataset - 300 gene set, This dataset was used for codon tests (PAML)</li> <li>Align_Paml: Contains the final cleaned alignments for the 300 gene dataset (after gblocks) in fasta format</li> <li>Contree_PAML: Contains the consensus trees constructed with IQ-Tree for the 300 gene dataset </li> </ul> Version 2 corrects a sample labelling mistake present in Version 1.

opencc-by-4.0Jun 2024View details →

Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen - Supplementary Data files

Supplementary Data file 3-4 included in the manuscript Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen.

opencc-zeroJul 2024View details →

Achieving bio-protection in New Zealand ecosystems mesocosm fungal pathogen OTU table

We established 80 experimental ecosystems (mesocosms), manipulated interactions between plants and soil biota in a fully factorial design. Each mesocosm was grown in a 125 L pot (575 mm diameter), and comprised one of 20 unique, eight-species plant communities varying orthogonally in the proportion of exotic and woody shrub/tree species (0-100% and 0-63%, respectively). These plants were taken from a pool of 20 exotic and 19 native/endemic New Zealand plant species. Soil biota were manipulated using a modified plant-soil feedback approach, where each plant species was grown in monoculture in 10 L pots containing field-collected soil for 9-10 months, allowing the conditioning of typical associated soil biota for each of the plant species. We created 'home' soils by taking the conditioned soil from each of the eight representative species in a mesocosm and mixing it together to create a single inoculum. Each 'home' soil mixture was also used as an 'away soil' in a different mesocosm that did not contain any of the representative plants in that inoculum. These soils were intended to increase the relative biomass in inocula of specialized and preferred interaction partners of the resident (or non-resident) plant species. After approximately one year of growth, we harvested all plants from each mesocosm, took root samples from each individual plant (n=491), extracted DNA and sequenced the fungi in the roots. Fungal sequences were paired and clustered into operational taxonomic units (OTUs) at 97% similarity. We assigned functional attributes to fungal OTUs using the FUNGUILD database and retained only the taxa assigned as "probable" or "highly probable" plant pathogens.

opencc-zeroSep 2021View details →

Feedbacks between forest structure and an opportunistic fungal pathogen

Abiotic stresses, physiological dysfunction, forest stand dynamics, and primary tree attackers (native and non-native) are all recognized as important contributors to both anomalous tree mortality and background tree mortality, and thus as important influences on biogeochemical cycling and habitat for associated terrestrial organisms. Opportunistic and latent tree pathogens and insect pests have largely been left out of this discussion, probably because they are difficult to monitor and their effects sometimes more diffuse, yet they play important roles in tree mortality scenarios. We know very little about the influence of biotic gradients, e.g., forest dynamics and forest structure, on the occurrence and effects of these opportunistic biotic enemies. To better understand the influence of an important biotic gradient—forest structure as represented by tree density and competition—on the occurrence and distribution of a typical opportunistic pathogen, we analyzed the relationship between tree neighborhood competition and soil-dwelling rhizomorphs of the fungus Armillaria gallica in regenerating (20-yr-old) and mature (80-100-yr-old) hardwood-dominated forest stands in central Missouri following a severe drought. We detected A. gallica, rhizomorphs in twice as many sampling sites in young (dense) plots as in mature (open) plots, and by contrast, found a twofold occurrence of other saprophytic fungi in the soil of mature plots compared to young plots. Mean tree density and competition index were significantly higher in subplots where A. gallica was found than in those with no A. gallica detections, and the pattern of A. gallica occurrence tracked closely with the occurrence of dense "hotspots" of competition in the plots. Synthesis. Early stages of forest structure and succession—potentially through initial inputs of disturbance-produced woody biomass, increased host connectivity and competition-influenced host tree susceptibility to fungal colonization—provide important feedbacks to A. gallica foraging, which in turn influences forest development. The recognition that tree density and competition influence A. gallica foraging suggests that in order to achieve a more comprehensive understanding of forest growth, development, and biogeochemical cycling, it may be necessary to increase life-history studies and basic occurrence surveys for opportunistic tree pathogens and insect pests.

opencc-zeroSep 2021View details →

Data from: Alternative food sources interfere with removal of a fungal amphibian pathogen by zooplankton

1. While the amphibian disease chytridiomycosis is causing ongoing population declines and biodiversity losses around the globe, efficient mitigation strategies are lacking. The free-living zoospores of the causative agents of this disease, the chytrid pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal), are a potential food source for filter-feeding micropredators as part of the aquatic food web. While consumption of zoospores can lower environmental pathogen loads, alternative food sources may interfere with pathogen removal rates. 2. We compared the ability of three filter-feeding zooplankton species, i.e. the cladoceran Daphnia magna, the rotifer Brachionus calyciflorus and the ostracod Heterocypris incongruens, to remove Bd zoospores in water and investigated the effect of alternative food sources, i.e. the green algae Pseudokirchneriella subcapitata and Chlorella vulgaris, on zoospore ingestion by D. magna. 3. D. magna was the only micropredator candidate that effectively removed Bd zoospores from its environment, with an average removal rate of 1,012 ± 542 GE ind.-1 h-1 within our test system. High concentrations (1x105 cells/mL) of large and easily ingestible P. subcapitata reduced pathogen removal rates, whereas the small and less edible C. vulgaris did not interfere with pathogen removal. 4. Synthesis and applications: We showed that Daphnia spp., which are keystone species in all sorts of aquatic habitats worldwide, are promising target agents for biologically mitigating chytridiomycosis infections and how natural food sources may interfere with this strategy. We also suggest potential management actions for biological disease mitigation, aiming to optimize environmental conditions for these target filter-feeders, thereby reducing pathogen densities and eventually infection pressure in amphibian hosts. Examples of such management actions include, but are not limited to, removal of planktivorous fish, habitat restoration, nutrient control or agrochemical regulation in the vicinity of amphibian breeding ponds. Further studies, including field trials, are needed to confirm the effects of pathogen consumption on infection dynamics in natural situations and investigate the impact of intervention actions.

opencc-zeroJan 2023View details →

Data from: Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation

Nitrogen enrichment can alter soil communities and their functioning directly, via changes in nutrient availability and stoichiometry, or indirectly, by changing plant communities or the abundance of consumers. However, most studies have only focused on one of these potential drivers and we know little about the relative importance of the different mechanisms (changes in nutrient availability, in plant diversity or functional composition, or in consumer abundance) by which nitrogen enrichment affects soil functioning. In addition, soil functions could vary dramatically between seasons, however, they are typically measured only once during the peak growing season. We therefore know little about the drivers of intra-annual stability in soil functioning. In this study, we measured activities of β-glucosidase and acid phosphatase, two extracellular enzymes that indicate soil functioning. We did so in a large grassland experiment which tested the effects, and relative importance, of nitrogen enrichment, plant functional composition and diversity, and foliar pathogen presence (controlled by fungicide) on soil functioning. We measured the activity of the two enzymes across seasons and years to assess the stability and temporal dynamics of soil functioning. Overall β-glucosidase activity was slightly increased by nitrogen enrichment over time but did not respond to the other experimental treatments. Conversely, plant functional diversity, and interactions between plant attributes and fungicide application, were important drivers of mean acid phosphatase activity. The temporal stability of both soil enzymes was differently affected by two facets of plant diversity: species richness increased temporal stability and functional diversity decreased it; however, these effects were dampened when nitrogen and fungicide were added. Synthesis: The fungicide effects on soil enzyme activities suggest that foliar pathogens can also affect belowground processes and the interacting effect of fungicide and plant diversity suggests that these plant enemies can modulate the relationship between plant diversity and ecosystem functioning. The contrasting effects of our treatments on the mean versus stability of soil enzyme activities clearly show the need to consider temporal dynamics in belowground processes, to better understand the responses of soil microbes to environmental changes such as nutrient enrichment.