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opencc-zeroMay 2023View details →

Supporting isotopic data for: Amino acid isotope analysis reveals variation in gut microbial contribution to host protein metabolism in a wild small mammal community

Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ13C) and nitrogen (δ15N) isotope analysis, we estimated the proportional contributions of essential amino acids (AAESS) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous, and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (Dipodomys spp.) routed a substantial proportion (~40–50%) of their AAESS from gut microbes, while higher trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys arenicola) obtained most of their AAESS (~58%) from plant-based energy channels but still received ~20% of their AAESS from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals.

opencc-by-4.0Dec 2022View details →

[Data from:] Chemical cues involved in the host foraging behavior of Psyttalia concolor wasps to locate the olive fruit fly Bactrocera oleae

Investigate the role of oviposition- (OIPVs) and herbivore-induced plant volatiles (HIPVs) emitted by olive trees upon infestation by Bactrocera oleae as well as cues emitted by the insect host B. oleae.

opencc-zeroMay 2023View details →

Data from: Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund

A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of Streptococcus bovis/Streptococcus equinus complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living on a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.

Data for: Environments and hosts structure the bacterial microbiomes of fungus-gardening ants and their symbiotic fungus gardens

The fungus gardening-ant system is considered a complex, multi-tiered symbiosis between the ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus garden, using 16S rRNA Illumina sequencing, over a large geographical region. Typically microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission, for example. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome were acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which suggests vertical inheritance of the ant associated bacterial microbiome. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some components appear to be structured by the ant host species whereas other by fungal lineage or region. Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.

opencc-by-4.0Jun 2023View details →

[Data S10] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation

Data S10. 10x genomics sequencing data files for Figure 5. Matrix file "sample_filtered_feature_bc_matrix.h5" and V(D)J annotations "filtered_contig_annotations.csv" are included below. Accompanying code can be found at https://github.com/acyeh-lab/2023/tree/main/scseq.

Data from: Widespread amphibian Perkinsea infections associated with Ranidae hosts, cooler months, and Ranavirus co-infection

Amphibians suffer from large-scale population declines globally, and emerging infectious diseases contribute heavily to these declines. Amphibian Perkinsea (Pr) is a worldwide anuran pathogen associated with mass mortality events, yet little is known about its epidemiological patterns, especially in comparison to the body of literature on amphibian chytridiomycosis and ranavirosis. Here, we establish Pr infection patterns in natural anuran populations and identify important covariates including climate, host attributes, and co-infection with Ranavirus (Rv). We used quantitative (q)PCR to determine the presence and intensity of Pr and Rv across 1234 individuals sampled throughout central Florida in 2017-2019. We then implemented random forest ensemble learning models to predict infection with both pathogens based on physiological and environmental characteristics. Perkinsea infected 32% of all sampled anurans, and Pr prevalence was significantly elevated in Ranidae frogs, cooler months, metamorphosed individuals, and frogs co-infected with Rv, while Pr intensity was significantly higher in ranid frogs and individuals collected dead. Ranavirus prevalence was 17% overall and was significantly higher in Ranidae frogs, metamorphosed individuals, locations with higher average temperatures, and individuals co-infected with Pr. Perkinsea prevalence was significantly higher than Rv prevalence across months, regions, life stages, and species. Among locations, Pr prevalence was negatively associated with crayfish prevalence and positively associated with relative abundance of microhylids, but Rv prevalence did not associate with any tested co-variates. Co-infections were significantly more common than single infections for both pathogens, and we propose that Pr infections may propel Rv infections because seasonal Rv infection peaks followed Pr infection peaks and random forest models found Pr intensity was a leading factor explaining Rv infections. Our study elucidates epidemiological patterns of Pr in Florida and suggests that Pr may be under-recognized as a cause of anuran declines, especially in the context of pathogen co-infection.

Data for: Intraspecific variation for host immune activation by the spider mite Tetranychus evansi

Many parasites can interfere with their host's defences to maximize their fitness. Here, we investigated if there is heritable variation in the spider mite Tetranychus evansi for traits associated with how they interact with their host plant. We also determined if this variation correlates with mite fecundity. Tetranychus evansi can interfere with jasmonate (JA) defences which are the main determinant of anti-herbivore immunity in plants. We investigated (i) variation in fecundity in the presence and absence of JA defences, making use of a wild-type tomato cultivar and a JA-deficient mutant (defenseless-1), and (ii) variation in the induction of JA defences, in four T. evansi field populations and 59 inbred lines created from an outbred population originating from controlled crosses of the four field populations. We observed a strong positive genetic correlation between fecundity in the presence (on wild-type) and the absence of JA defences (on defenseless-1). However, fecundity did not correlate with the magnitude of induced JA defences in wild-type plants. Our results suggest that the performance of the specialist T. evansi is not related to their ability to manipulate plant defences, either because all lines can adequately reduce levels of defences, or because they are resistant to them.

Spot test and spore count assay data for combinations of dictyostelid hosts infected by Paraburkholderia spp.

The social amoeba Dictyostelium discoideum engages in a complex relationship with bacterial endosymbionts in the genus Paraburkholderia, which can benefit their host by imbuing it with the ability to carry prey bacteria throughout its life cycle. The relationship between D. discoideum and Paraburkholderia has been shown to take place across many strains and a large geographical area, but little is known about Paraburkholderia's potential interaction with other dictyostelid species. We explore the ability of three Paraburkholderia species to stably infect and induce bacterial carriage in other dictyostelid hosts. We found that all three Paraburkholderia species successfully infected and induced carriage in seven species of Dictyostelium hosts. While the overall behavior was qualitatively similar to that previously observed in infections of D. discoideum, differences in the outcomes of different host/symbiont combinations suggest a degree of specialization between partners. Paraburkholderia was unable to maintain a stable association with the more distantly related host Polysphondylium violaceum. Our results suggest that the mechanisms and evolutionary history of Paraburkholderia's symbiotic relationships may be general within Dictyostelium hosts, but not so general that it can associate with hosts of other genera. Our work further develops a emerging model system for the study of symbiosis in microbes.

Data from: Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals

Differences in the bacteria inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiosis pattern associated with the different body sizes and diets of the mammalian lineages present. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker than comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or dietary composition, while subtler microbiome differences reflected variation in ecologically important traits between closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.

Data for: Host infection dynamics and disease induced mortality modify species contributions to the environmental reservoir

Environmental pathogen reservoirs exist for many globally important diseases and can fuel epidemics, influence pathogen evolution, and increase the threat of host extinction. Species composition can be an important factor that shapes reservoir dynamics and ultimately determines the outcome of a disease outbreak. However, disease-induced mortality can change species communities, indicating that species responsible for environmental reservoir maintenance may change over time. Here we examine reservoir dynamics of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We quantified changes in pathogen shedding, infection prevalence and intensity, host abundance, and the subsequent propagule pressure imposed by each species over time. We find that highly shedding species are important during pathogen invasion, but contribute less over time to environmental contamination as they also suffer the greatest declines. Less infected species remain more abundant, resulting in equivalent or higher propagule pressure. More broadly, we demonstrate that high infection intensity and subsequent mortality during disease progression can reduce the contributions of high-shedding species to long-term pathogen maintenance.

opencc-by-4.0Jun 2023View details →

Supplementary Data for "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates"

Supplementary data includes original sample names and locations, raw geochemical and granulometric data, and calculated geochemical data represented as figures for the manuscript titled "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates". All datasets are in the same excel file on separate tabs. All data were processed according to established procedures cited in the manuscript text. All software used is open access: ImageJ, adobe illustrator, and Microsoft excel.

opencc-zeroJul 2023View details →

Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.

opencc-zeroJul 2023View details →

Data from: When perfection isn't enough: host egg signatures are an effective defence against high-fidelity African cuckoo mimicry

Most mimicry systems involve imperfect mimicry, whereas perfect and high-fidelity mimicry are rare. When the fidelity of mimicry is high, mimics might be expected to have the upper hand against their antagonists. However, in coevolving systems, diversification of model phenotypes may provide an evolutionary escape, because mimics cannot simultaneously match all model individuals in the population. Here we investigate high-fidelity mimicry in a highly specialised, Afrotropical brood parasite-host system: the African cuckoo and fork-tailed drongo. Specifically, we test whether host egg polymorphisms are an effective defence against such mimicry. We show, using a combination of image analysis, field experiments, and simulations, that 1) egg colour and pattern mimicry of fork-tailed drongo eggs by African cuckoos is near-perfect on average; 2) drongos show fine-tuned rejection of foreign eggs, exploiting unpredictable pattern differences between parasitic eggs and their own; and 3) the high degree of interclutch variation (polymorphic egg 'signatures') exhibited by drongos gives them the upper hand in the arms race, with 93.7% of cuckoo eggs predicted to be rejected, despite cuckoos mimicking the full range of drongo egg phenotypes. These results demonstrate the effectiveness of model diversification as a defence against mimics, even when mimicry is highly accurate.

opencc-zeroJul 2023View details →

Data from: Dissecting molecular evolution of class 1 integron gene cassettes and their bacterial hosts in suburban creeks via epicPCR

Horizontal gene transfer (HGT) of class 1 integrons plays a key role in the dissemination of antimicrobial resistance (AMR) with clinical consequences worldwide. Class 1 integrons in clinical pathogens are commonly associated with AMR genes and embedded in mobile genetic elements. Over time, these mobile class 1 integrons have spread to diverse environmental bacterial hosts via HGT. We applied a single-cell fusion PCR-based technique to link class 1 integron gene cassette arrays to the phylogenetic markers in their bacterial hosts. Class 1 integrons and associated gene cassettes were detected in Alpha- and Gammaproteobacteria hosts from freshwater samples from two creeks in suburban Sydney. Molecular and bioinformatic characterisations of altered gene cassettes generated new insights into mechanisms that contribute to the evolution of class 1 integron gene cassettes. Here, we present experimental and bioinformatic evidence for key signatures of molecular evolution of gene cassettes, including the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an insertion sequence (IS) element. Notably, our experimental testing of a new variant of the aminoglycoside adenylyltransferase encoding aadA11 gene cassette demonstrated that the gain of 5'-UTR contributed to a 3-fold increase in the minimum inhibitory concentration of streptomycin relative to the ancestral reference gene cassette. Understanding these signatures of molecular evolution allows us to explain their effects on AMR phenotypes and offers the potential to better predict evolutionary trajectories of class 1 integrons.

opencc-by-4.0Apr 2023View details →

Understanding the impact of host networking elements on traffic bursts: Raw measurement data

This record contains the raw trace files gathered by the Valinor network traffic burst measurement framework in Redis dump (rdb) format. Please refer to the artifact repository for instructions on how to parse and use the datasets: <a href="https://github.com/hopnets/valinor-rawdata">hopnets/valinor-rawdata: Raw Redis datasets containing the measurement results of Valinor NSDI '23 paper (github.com)</a>

opencc-zeroAug 2023View details →

Data from: Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional traits. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e., plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly by increasing the maximum plant height, rather than altering soil properties. Our results highlight that plant height drives the AMF community dynamics under nitrogen enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic nitrogen deposition.

opencc-by-4.0Aug 2023View details →

Data for Torppa et al. 2023 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety'

The dataset consists of the data that supports the findings of the article 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety’ written by Torppa et al. and published in Plant and Soil in 2023. The data consists of arbuscular mycorrhizal colonization, fatty acid and community data, as well as soil and crop nutrient and yield data.

opencc-by-4.0Nov 2023View details →

Spatial metatranscriptomics resolves host-bacteria-fungi interactomes, Source Data

Source Data for a publication: Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.  Includes the data sets to generate the results.  Contains five different experiment types: - Pst  bacterial infiltration experiment - Enrichment experiment with different array types - Comparison between SmT vs. Amp-seq - Outdoor-grown leaf experiments - Sterile leaf experiment For each of the experiments are included (if generated, see the README file): - Gene count matrices - Microbial taxa count matrices - Bright field images - Alignment files (Spot files) - Putative microbial reads and related probe information - Data for enrichment analysis - Fluorescent images and corresponding fluorescent values

publicOct 2020View details →

Data for: Environmentally-driven escalation of host egg-rejection decimates success of an avian brood parasite

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