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opencc-by-4.0Feb 2023View details →

Datasets and R script to replicate the statistical analyses from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission

Datasets and R script to replicate the statistical analyses from the article entitled " Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission " by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023

opencc-zeroMay 2023View details →

Grazer host density mediates the ability of parasites to protect foundational plants from overgrazing

Like many top consumers, parasites can regulate feeding of their prey via trait-mediated means. If parasites modify the feeding behavior of ecologically important grazers, they may have cascading effects on the structure and functioning of whole plant communities. The extent to which parasites can influence plant communities in this way is largely dependent on the strength of their behavioral alteration, their prevalence in host grazers, and the density of those hosts. Recent experiments and comparative surveys in southeastern USA salt marshes revealed that common larval trematode parasites suppress the per capita grazing impacts of the marsh periwinkle (Littoraria irrorata), generating a trophic cascade that protects foundational marsh plants from drought-associated overgrazing. Here, we conducted a field manipulation wherein we modified grazer host density while holding infection prevalence constant at an ecologically relevant level (20%) to determine whether the indirect, facilitative effects of parasites on marsh plants varied with the density of grazers. We found that parasites had significant positive impacts on marsh net primary productivity at moderate densities of snails (≥50 snails/ 0.5 m2), but that the positive effects of parasites were negligible at lower densities. Our results confirm the findings of previous studies that parasites can protect marsh plants from overgrazing at sufficiently high prevalence but show that their ability to do so depends on host density.

opencc-zeroMay 2023View details →

Short-term fitness consequences of parasitism depend on host genotype and within-host parasite community

Multi-parasite communities inhabiting individual hosts are common and often consist of parasites from multiple taxa. The effects of parasite community composition and complexity on host fitness are critical for understanding how host-parasite coevolution is affected by parasite diversity. To test how naturally-occurring parasites affect host fitness of multiple host genotypes, we performed a common-garden experiment where we inoculated four genotypes of host plant Plantago lanceolata with six microbial parasite treatments: three single parasite treatments, a fungal mixture, a viral mixture, and a cross-kingdom treatment. Seed production was affected by both host genotype and parasite treatment, and their interaction jointly determined growth of the hosts. Fungal parasites had more consistent negative effects than viruses in both single mixed parasite treatments. These results demonstrate that parasite communities have the potential to affect the evolution and ecology of host populations through their effects on host growth and reproduction. Moreover, the results highlight the importance of accounting for the diversity of parasites as well as host genotypes when aiming to predict the consequences of parasites for epidemics as the effects of multi-parasitism are not necessarily additive of single parasite effects, nor uniform across all host genotypes.

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.

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity

We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH

We used Escherichia coli transformed with pJKR-H-tetR plasmids encoding an inducible GFP gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the GFP gene, used non-transformed E. coli as a negative control, and tested six different FISH protocols.

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping

We used rRNA FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of an active prophage with a sixth fluorophore.  We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump.

[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.

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-by-4.0Jul 2023View details →

Dataset for the paper titled "The Fast X-ray Transient XRT 210423 and its Host Galaxy"

This package is the dataset for the paper titled "The Fast X-ray Transient XRT 210423 and its Host Galaxy". Instructions for analysis and to reproduce the figures: Note: These are minimalistic instructions. Please get in touch with me (deepakeappachen5@gmail.com) for more details.  1a) We used ESO reflex, la cosmic and IRAF for cleaning, cosmic ray removal, astrometric correction and stacking - the wcs corrected, cosmic ray removed FORS images for XRT 210423 are given as xrt210423_astrometrycorrec.fits. 1b) We used the HiPERCAM pipeline to reduce the images. We used the la cosmic and IRAF for astrometric corrections, cosmic removal and stacking. The ugriz fits files are attached. 2) We found the zero point by comparing it with the PanSTARRS  Catalogue (zp.py is the script used, for FORS R band, we converted the PanSTARRS mags to R band using the  transformation_eqn_to_R_band.py) 3) For the artificial star experiment and PSF photometry, we used IRAF/Pyraf (python version 2.7). We modelled the PSF from the FORS and HiPERCAM images. (phot_pyraf_new.py was used for the artificial star experiment)         - the PSF images:                            R: Rfors.fits.psf.1.fits                           u: u.fits.psf.1.fits                           g: g.fits.psf.1.fits                           r: r.fits.psf.1.fits                           i: i.fits.psf.1.fits                           z: z.fits.psf.1.fits          5) For the photometry, we used the  SExtractor.  6) For spectroscopy, we use XSHOOTER pipeline to obtain the cleaned 2D spectrum.         TOO_hard-hostXRT210423_SCI_SLIT_FLUX_MERGE2D_NIR.fits         TOO_hard-hostXRT210423_SCI_SLIT_FLUX_MERGE2D_VIS.fits 7) For SED fitting we used BAGPIPES.          The code used for SED fiiting: photz_bagpipes_n.py         Note: We used the stantard filter profiles from http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=GTC&gname2=HIPERCAM&asttype=astro The codes and the necessary files required for reproducing the Figures are given. Figure 1:     plot_abell.py     plot_n.py Figure 2:     XRT_210423.ipynb     XRT_210423_pow.txt     XRT_210423_HR.txt     XRT_210423_model.txt      Figure 3:     2dspec_plot_O3.py Figure 4:     Obtained by running the BAGPIPES code. Figure 5:     offset.py     usING: comparison_offset_data.txt     fong+22_deepak.txt     and      sfr_mass.py     usING: SNII.dat     SNIc.dat     SNIb.dat     SGRBs_host_properties_fong.txt     Schulze_host_properties.txt Figure 6:     OL_lightcurves.py      using: kilonova.csv     SGRB_AG.dat     SN_2008D.dat

opencc-by-4.0Mar 2021View details →

Fig. 2 in First record of Tettigonia viridissima Linnaeus, 1758 (Orthoptera: Tettigoniidae) as host of the ormiine Therobia leonidei Mesnil, 1964 (Diptera: Tachinidae)

Fig. 2 – Therobia leonidei Mesnil, 1964, adult male.