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52 results for “tree pathogen”
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"> <i>Synthesis. </i>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>
Genome sequence resources from three isolates of the apple canker pathogen Neonectria ditissima infecting forest trees
<p><em>Neonectria ditissima</em> is a generalist ascomycete plant pathogen causing canker diseases on a variety of hardwood tree species and can cross-infect many of them. The fungus enters the plants through wounds throughout the year. <em>N. ditissima</em> is considered a major threat to apple production responsible for the fruit tree canker disease which damages trees and causes rotting of fruits in storage. Nearby forests and shelter belts can serve as source of inoculum for well-managed apple orchards. Thus, knowledge about the <em>N. ditissima</em> isolates infecting different host species is essential for designing integrated pest management strategies. Here, we describe the genomes of three <em>N. ditissima</em> isolates, Nd_iso34, Nd_iso35, and Nd_iso36, infecting European beech, American tulip tree, and American beech, respectively. We obtained genome assemblies of ca. 45 megabases for all isolates, covering 94% of the <em>N. ditissima</em> reference annotation, and 97% of the universal single-copy orthologs (BUSCOs). We conclude that these genome assemblies are a highly relevant resource considering the scarcity of genomic data available for <em>N. ditissima</em>.</p>
Comparative transcriptomics reveals divergence in pathogen response gene families amongst twenty forest tree species
<p>Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. <span>In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, </span>we used the RNA-seq data of twenty co-occurring forest tree species from genera including <em>Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, </em>and<em> Ulmus </em>sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.</p>
Effects of tree species diversity and conspecific seedling density on insect herbivory and pathogen infection on big-leaf mahogany seedlings
<p>The Janzen-Connell Hypothesis (JCH) predicts that attack by specialist enemies on seedlings increases with conspecific seedling density, but studies have rarely experimentally tested for the contingency of such effects on tree community context (e.g., diversity, composition) and measured responses by different enemies (e.g. herbivores, pathogens). We conducted a field study in a large-scale system evaluating tree species diversity and conspecific density effects on leaf damage on mahogany (<em>Swietenia macrophylla</em>) seedlings. We established quadrats of eight levels of seedling density across mahogany tree monocultures and species polycultures including mahogany, and recorded percent leaf damage by insects and percent leaf necrosis by a pathogenic fungus on mahogany seedlings. We found contrasting effects of tree species diversity on insects and pathogens. Whereas diversity did not affect leaf damage by insects, it had a significant negative effect on leaf necrosis by pathogens. On average, percent leaf necrosis on mahogany seedlings in polyculture was half of that observed in monoculture. We discuss the potential influences of changes in mahogany tree density vs. frequency (relative to other tree species) driving this diversity effect. Unexpectedly, we found no effect of seedling conspecific density on either leaf insect or pathogen damage (i.e., density-independent attack). Likewise, we found no significant tree diversity by seedling density interaction, indicating that attackers were consistently unresponsive to variation in seedling density across two levels of tree diversity. Overall, this study provides a unique test of the JCH by experimentally evaluating seedling density and tree diversity effects on contrasting plant enemies, shedding light on enemy controls over plant recruitment.</p>
Data from: Negative density dependence in the mortality and growth of tropical tree seedlings is strong, and primarily caused by fungal pathogens
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Pathogen incidence on tree and liana seedlings along a chronosequence of tropical forest recovery in Panama
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Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species
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Effects of tree species diversity and conspecific seedling density on insect herbivory and pathogen infection on big-leaf mahogany seedlings
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Data from: Shade tree traits and microclimate modifications: Implications for pathogen management in biodiverse coffee agroforests
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Fig. 2 Maximum likelihood tree inferred from the combined cmdA, tef1 in New endemic Fusarium species hitch-hiking with pathogenic Fusarium strains causing Panama disease in small-holder banana plots in Indonesia
Fig. 2 Maximum likelihood tree inferred from the combined cmdA, tef1, tub, rpb1, and rpb2 sequence datasets of the Fusarium fujikuroi species complex (FFSC) including eight Indonesian isolates (indicated in blue). Bootstrap support values and Bayesian posterior probabilities are given at each node. The tree is rooted to Fusarium nirenbergiae (CBS 744.97) and F. oxysporum (CBS 716.74).
The invasive pathogenic fungus of ash trees alters arthropod predator – prey food webs in forest plantations
<p>The data set contains data on:</p> <p>1] Prey type and size (sheet1: prey type and size). In the cells, prey length in mm is provided for each prey item. NA is stated for a prey item that could not be measured. In this sheet, the plot ids and the spider ids are also stated, which enables connection with other sheets. Note: more prey items caught by an individual are stated in one row if they are of different type. Prey items of a same type caught by an individual are itemized in more rows.</p> <p>2] Information about spider individuals (sheet2: spiders). For each spider individual, it is provided its id, so it can be connected with sheet 1, plot id where it was collected, when it was collected (month), web type, and prosoma length (mm). </p> <p>3] Characteristics of sampling plots (sheet3: environmental data). It is provided plot id, age, infestation degree by H<em>ymenoscyphus fraxineus</em>, canopy openness, shrub coverage, and herb coverage.</p> <p>4] Potential prey of spiders (sheet 4: potential prey). Standardized no. of prey per trap (20 x 15 cm, both sides were sticky) in each plot.</p>
Invasive earthworms reduce chemical defense and increase herbivory and pathogen infection in native trees
<ol> <li>Recent research shows that earthworms can alter defense traits of plants against herbivores and pathogens by affecting soil biochemistry. Yet, the effects of invasive earthworms on defense traits of native plants from previously earthworm-free ecosystems as well as the consequences for multitrophic interactions are virtually unknown.</li> <li>Here we use a combination of an observational study and a complementary experimental study to investigate the effects of invasive earthworms on leaf defense traits, herbivore damage, and pathogen infection in two poplar tree species (<i>Populus balsamifera </i>and <i>Populus tremuloides</i>) native to North American boreal forests.</li> <li>Our observational study showed that earthworm invasion was associated with enhanced leaf herbivory in saplings of both tree species. However, we only detected significant shifts in the concentration of chemical defense compounds in response to earthworm invasion for <i>P. balsamifera</i>. Specifically, leaf phenolic concentrations, including salicinoids and catechin, were lower in <i>P. balsamifera </i>from earthworm-invaded sites.</li> <li>Our experimental study confirmed an earthworm-induced reduction in leaf defense levels in <i>P. balsamifera</i> for one of the defense compounds, tremulacin. The experimental study additionally showed that invasive earthworms reduced leaf dry matter content, potentially increasing leaf palatability, and enhanced susceptibility of trees to infection by a fungal pathogen, but not to aphids, in the same tree species.</li> <li> <i>Synthesis. </i>Our results show that invasive earthworms can decrease the concentrations of some chemical defense compounds in <i>P. balsamifera</i>, which could make them susceptible to leaf-chewing insects. Such potential impacts of invasive earthworms are likely to have implications for tree survival and competition, native tree biodiversity, and ecosystem functioning.</li> </ol>
Neighboring trees regulate the root-associated pathogenic fungi on the host plant in a subtropical forest
<p>Root-associated fungi and host-specific pathogens are major determinants of species coexistence in forests. Phylogenetically related neighboring trees can strongly affect the fungal community structure of the host plant, which, in turn, will affect the ecological processes. Unfortunately, our understanding of the factors influencing fungal community composition in forests is still limited. In particular, investigation of the relationship between the phytopathogenic fungal community and neighboring trees is incomplete. In the current study, we tested the host specificity of members of the root-associated fungal community collected from seven tree species and determined the influence of neighboring trees and habitat variation on the composition of the phytopathogenic fungal community of the focal plant in a subtropical evergreen forest. Using high-throughput sequencing data with respect to the internal transcribed spacer (ITS) region, we characterized the community composition of the root-associated fungi and found significant differences with respect to fungal groups among the seven tree species. The density of conspecific neighboring trees had a significantly positive influence on the relative abundance of phytopathogens, especially host-specific pathogens, while the heterospecific neighbor density had a significant negative impact on the species richness of host-specific pathogens, as well as phytopathogens. Our work provides evidence that the root-associated phytopathogenic fungi of a host plant depends greatly on the tree neighbors of the host plant.</p>
Associational resistance to both insect and pathogen damage in mixed forests is modulated by tree neighbour identity and drought
Tree health declines can be caused by interactions between pests and pathogens and many studies have shown a reduction in their damage in mixed species forests compared to monocultures. Yet few authors have considered tree diversity effects on both groups simultaneously. Moreover, it is unclear whether diversity effects on tree pests and pathogens are robust to changes in abiotic conditions, such as drought. We addressed tree diversity effects on foliar insect herbivory, oak powdery mildew and their interaction under contrasting water regimes in a large-scale tree diversity experiment in SW France. Using an irrigation treatment that alleviated drought conditions, we were able to experimentally assess the effects of tree diversity under contrasting abiotic environments. We surveyed plots along a richness gradient from 1 – 4 tree species, in which a focal study species of oak (Q. robur) was mixed with other oak species (Q. pyrenaica and Q. ilex) and a taller, broadleaved species (Betula pendula). Increasing tree species richness lowered leaf miner abundance, leaf chewer damage and oak powdery mildew infection, consistent with a protective effect of resource dilution. However, richness effects on leaf miners were stronger in irrigated compared to non-irrigated blocks, indicating that environmental conditions can modulate diversity effects. Separate from the effect of tree species richness, the presence of birch in a plot increased damage by leaf chewers and powdery mildew, but lowered leaf miner damage, suggesting additional tree neighbour identity effects potentially linked to modulation of microclimate. We found a negative association between leaf miner abundance and oak powdery mildew, consistent with antagonism between oak damage agents. Overall, our study illustrates the importance of considering both tree diversity and composition (neighbour identity) in designing forests more resistant to pest and pathogen damage.
Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.
The magnitude of large-scale tree mortality caused by the invasive pathogen Phytophthora ramorum
<p>Forest pathogens are important drivers of tree mortality across the globe but it is exceptionally challenging to gather and build unbiased quantitative models of their impacts, which has resulted in few estimates matching the scale of disease. Here we harness the rare dataset matching the spatial scale of pathogen invasion, host, and disease heterogeneity to estimate infection and mortality for the four most susceptible host species of <em>Phytophthora ramorum</em>, an invasive pathogen that drives the most important biological cause of tree mortality in a broad geographic region of coastal California and southwest Oregon. As of 2012, the most current field survey year, we estimate 17.5 (± 4.6 95% CI) million tanoak (<em>Notholithocarpus densiflorus)</em> stems were pathogen-killed with an additional 71 (± 21.5) million infected. We estimated 9.0 million (± 2.2) coast live oak (<em>Quercus agrifolia)</em> and 1.7 million (± 0.5) California black oak (<em>Quercus kelloggii</em>) stems are disease impacted (mortality and infection combined). Lastly, our estimates showed 95.23 million (± 8.6) million infected California bay laurel (<em>Umbellularia californica</em>), which does not suffer mortality from infection and represents a critical source of continued spread. Using an extensive dataset on mortality rates of infected individuals we estimate that cumulative mortality likely increased from 20.8 to 42.8 million individual stems between 2012 and 2019 for all species. While these impacts are substantial, the majority of host populations occur in a yet to be invaded region of northern California indicating that the disease will intensify in the coming decades.</p>
Data from: Do pathogens limit the distributions of tropical trees across a rainfall gradient?
1. Organisms are adapted to particular habitats; consequently, community composition changes across environmental gradients, enhancing regional diversity. In Panama, a rainfall gradient correlates with the spatial turnover of tree species. While strong evidence suggests that tree species common in the wetter forests are excluded from the drier forests by seasonal drought, the factor(s) excluding drought-tolerant species, common in the drier forests, from the wetter forests remain ambiguous. 2. Here, we show that seedlings were significantly more likely to suffer pathogen-caused damage and mortality in the wetter forest. While seedlings of dry- and wet-forest species were equally likely to suffer pathogen attack, seedlings of dry-forest species were significantly more likely to die when attacked and tended to suffer more pathogen-caused mortality overall. Furthermore, seedlings of dry-forest species suffered pathogen-caused mortality in the forest in which they do not naturally occur and in which conspecific and/or congeneric adults are absent or rare, indicating that some pathogens are relatively widespread and/or are capable of damaging multiple host species. 3. Synthesis. Elevated risk of pathogen-caused damage and mortality in the wetter forests and a greater impact to host fitness from pathogen attack for seedlings of dry-forest species suggest that pathogens may enhance regional forest diversity by contributing to changes in tree species composition via the exclusion of dry-forest tree species from the wetter forests. This study highlights a potentially widespread and under explored mechanism by which pathogens shape plant communities at the landscape scale. An understanding of how species' distributions are shaped by the interplay between abiotic and biotic factors is essential for conservation biology.
Data from: Adaptive variation for growth and resistance to a novel pathogen along climatic gradients in a foundation tree
Natural ecosystems are under pressure from increasing abiotic and biotic stressors, including climate change and novel pathogens, which are putting species at risk of local extinction, and altering community structure, composition, and function. Here, we aim to assess adaptive variation in growth and fungal disease resistance within a foundation tree, Corymbia calophylla to determine local adaptation, trait heritability, and genetic constraints in adapting to future environments. Two experimental planting sites were established in regions of contrasting rainfall with seed families from 18 populations capturing a wide range of climate origins (~4000 individuals at each site). Every individual was measured in 2015 and 2016 for growth (height, basal diameter) and disease resistance to a recently introduced leaf blight pathogen (Quambalaria pitereka). Narrow-sense heritability was estimated along with trait covariation. Trait variation was regressed against climate-of-origin and multivariate models were used to develop predictive maps of growth and disease resistance. Growth and blight resistance traits differed significantly among populations, and these differences were consistent between experimental sites and sampling years. Growth and blight resistance were heritable, and comparisons between trait differentiation (QST) and genetic differentiation (FST) revealed that population differences in height and blight resistance traits are due to divergent natural selection. Traits were significantly correlated with climate-of-origin, with cool and wet populations showing the highest levels of growth and blight resistance. These results provide evidence that plants have adaptive growth strategies and pathogen defense strategies. Indeed, the presence of standing genetic variation and trait heritability of growth and blight resistance provide capacity to respond to novel, external pressures. The integration of genetic variation into adaptive management strategies, such as assisted gene migration and seed sourcing, may be used to provide greater resilience for natural ecosystems to both biotic and abiotic stressors.
Data from: Genetic signatures of variation in population size in a native fungal pathogen after the recent massive plantation of its host tree
Historical fluctuations in forests' distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Armillaria ostoyae, one of the major pathogens of the maritime pine (Pinus pinaster), in the largest monospecific pine planted forest in Europe (south-western France). Genetic structure analyses and approximate Bayesian computation approaches revealed that a single pathogen population underwent a severe reduction in effective size (12 times lower) 1080-2080 generations ago, followed by an expansion (4 times higher) during the last 4 generations. These results are consistent with the history of the maritime pine forest in the region characterized by a strong recession during the last glaciation (~19 000 years ago) and massive plantations during the second half of the nineteenth century. Results suggest that recent and intensive plantations of a host tree population have offered the opportunity for a rapid spread and adaptation of their pathogens.
FIGURE 1. Phylogenetic tree inferred from a in Ophiocordyceps ovatospora sp. nov. (Ophiocordycipitaceae, Hypocreales), pathogenic on termites from China
FIGURE 1. Phylogenetic tree inferred from a combined ITS, nrSSU, nrLSU, tef-1a, rpb1, rpb2 dataset based on Bayesian inference (BI) and maximum likelihood (ML) analyses. Values at the nodes are BI posterior probabilities (BP) and ML bootstrap proportions (PP), the scale bar 0.02 indicates the number of expected mutations per site. Cordyceps militaris and C. kyusyuensis in the Cordycipitaceae were used as the outgroup. The new species is in bold.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.