Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
330
datasets available to search
ShareScore release 0.7.1
Dataset results
330 results for “symbiosis”
Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis
<p>The upside-down jellyfish <i>Cassiopea</i> engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. In contrast to most other symbiotic cnidarians, algal endosymbionts in <i>Cassiopea</i> are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in <i>Cassiopea</i> remains unknown. By combining isotopic labelling experiments with correlated SEM and NanoSIMS imaging, we quantified the anabolic assimilation of inorganic carbon and nitrogen at the subcellular level in juvenile <i>Cassiopea</i> medusae bell tissue. Amoebocytes were clustered near the sub-umbrella epidermis and facilitated efficient assimilation of inorganic nutrients. Photosynthetically-fixed carbon was efficiently translocated between endosymbionts, amoebocytes and host epidermis at rates similar to or exceeding those observed in corals. The <i>Cassiopea</i> holobionts efficiently assimilated ammonium, while no nitrate assimilation was detected, possibly reflecting adaptation to highly dynamic environmental conditions of their natural habitat. The motile amoebocytes allow <i>Cassiopea</i> medusae to distribute their endosymbiont population to optimize access to light and nutrients, and transport nutrition between tissue areas. Amoebocytes thus play a vital role for assimilation and translocation of nutrients in <i>Cassiopea</i>, providing an interesting new model for studies of metabolic interactions in photosymbiotic marine organisms.</p>
Data from: Cryptic diversity hides host and habitat specialization In a gorgonian-algal symbiosis
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations. Here, we used ribosomal, organelle, and nuclear sequences, along with microsatellite variation, to study the relationship between lineages of a common Caribbean gorgonian and its algal symbionts. The gorgonian Eunicea flexuosa is a broadcast spawner, composed of two recently diverged, genetically distinct lineages largely segregated by depth. We sampled colonies of the two lineages across depth gradients at three Caribbean locations. We find that each host lineage is associated with a unique Symbiodinium B1/184 phylotype. This relationship between host and symbiont is maintained when host colonies are reciprocally transplanted, although cases of within phylotype switching were also observed. Even when the phylotypes of both partners are present at intermediate depths, the specificity between host and symbiont lineages remained absolute. Unrecognized cryptic diversity may mask host-symbiont specificity and change the inference of evolutionary processes in mutualistic associations. Symbiotic specificity thus likely contributes to the ecological divergence of the two partners, generating species diversity within coral reefs.
Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
Data from: Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
Data from: Evolutionary stability of antibiotic protection in a defensive symbiosis
The increasing resistance of human pathogens severely limits the efficacy of antibiotics in medicine, yet many animals, including solitary beewolf wasps, successfully engage in defensive alliances with antibiotic-producing bacteria for millions of years. Here, we report on the in situ production of 49 derivatives belonging to three antibiotic compound classes (45 piericidin derivatives, 3 streptochlorin derivatives, and nigericin) by the symbionts of 25 beewolf host species and subspecies, spanning 68 million years of evolution. Despite a high degree of qualitative stability in the antibiotic mixture, we found consistent quantitative differences between species and across geographic localities, presumably reflecting adaptations to combat local pathogen communities. Antimicrobial bioassays with the three main components and in silico predictions based on the structure and specificity in polyketide synthase domains of the piericidin biosynthesis gene cluster yield insights into the mechanistic basis and ecoevolutionary implications of producing a complex mixture of antimicrobial compounds in a natural setting.
Data from: Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis
Ants have long been renowned for their intimate mutualisms with trophobionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of microbes between interacting macroorganisms, affects the composition and function of symbiotic microbial communities. Here we approached this question by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and quantitative PCR to examine community structure of both bacteria and fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feeding scale insects and honeydew-feeding ants make use of microbial symbionts to subsist on phloem-derived diets of suboptimal nutritional quality. Among the insects examined here, Cephalotes ants and pseudococcid scale insects had the most specialized bacterial symbionts, whereas Azteca ants appeared to consume or associate with more fungi than bacteria, and coccid scale insects were associated with unusually diverse bacterial communities. Despite these differences, we also identified apparent sharing of microbes among the macro-partners. How microbial exchanges affect the consumer-resource interactions that shape the evolution of ant–plant–hemipteran symbioses is an exciting question that awaits further research.
Data from: Specificity and stability of the Acromyrmex-Pseudonocardia symbiosis
The stability of mutualistic interactions is likely to be affected by the genetic diversity of symbionts that compete for the same functional niche. Fungus-growing (attine) ants have multiple complex symbioses and thus provide ample opportunities to address questions of symbiont specificity and diversity. Among the partners are Actinobacteria of the genus Pseudonocardia that are maintained on the ant cuticle to produce antibiotics, primarily against a fungal parasite of the mutualistic gardens. The symbiosis has been assumed to be a hallmark of evolutionary stability, but this notion has been challenged by culturing and sequencing data indicating an unpredictably high diversity. We used 454 pyrosequencing of 16S rRNA to estimate the diversity of the cuticular bacterial community of the leaf-cutting ant Acromyrmex echinatior and other fungus-growing ants from Gamboa, Panama. Both field and laboratory samples of the same colonies were collected, the latter after colonies had been kept under laboratory conditions for up to 10 years. We show that bacterial communities are highly colony-specific and stable over time. The majority of colonies (25/26) had a single dominant Pseudonocardia strain, and only two strains were found in the Gamboa population across 17 years, confirming an earlier study. The microbial community on newly hatched ants consisted almost exclusively of a single strain of Pseudonocardia while other Actinobacteria were identified on older, foraging ants in varying but usually much lower abundances. These findings are consistent with recent theory predicting that mixtures of antibiotic-producing bacteria can remain mutualistic when dominated by a single vertically transmitted and resource-demanding strain.
Data from: New insights into carbon acquisition and exchanges within the coral-dinoflagellate symbiosis under NH4+ and NO3- supply
Anthropogenic nutrient enrichment affects the biogeochemical cycles and nutrient stoichiometry of coastal ecosystems and is often associated with coral reef decline. However, the mechanisms by which dissolved inorganic nutrients, and especially nitrogen forms (ammonium versus nitrate) can disturb the association between corals and their symbiotic algae are subject to controversial debate. Here, we investigated the coral response to varying N : P ratios, with nitrate or ammonium as a nitrogen source. We showed significant differences in the carbon acquisition by the symbionts and its allocation within the symbiosis according to nutrient abundance, type and stoichiometry. In particular, under low phosphate concentration (0.05 µM), a 3 µM nitrate enrichment induced a significant decrease in carbon fixation rate and low values of carbon translocation, compared with control conditions (N : P = 0.5 : 0.05), while these processes were significantly enhanced when nitrate was replaced by ammonium. A combined enrichment in ammonium and phosphorus (N : P = 3 : 1) induced a shift in nutrient allocation to the symbionts, at the detriment of the host. Altogether, these results shed light into the effect of nutrient enrichment on reef corals. More broadly, they improve our understanding of the consequences of nutrient loading on reef ecosystems, which is urgently required to refine risk management strategies.
Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
Data from: Transcriptional responses in a Drosophila defensive symbiosis
Inherited symbionts are ubiquitous in insects and can have important consequences for the fitness of their hosts. Many inherited symbionts defend their hosts against parasites or other natural enemies; however, the means by which most symbionts confer protection is virtually unknown. We examine the mechanisms of defence in a recently discovered case of symbiont-mediated protection, where the bacterial symbiont Spiroplasma defends the fly Drosophila neotestacea from a virulent nematode parasite, Howardula aoronymphium. Using quantitative PCR of Spiroplasma infection intensities and whole transcriptome sequencing, we attempt to distinguish between the following modes of defence: symbiont–parasite competition, host immune priming and the production of toxic factors by Spiroplasma. Our findings do not support a model of exploitative competition between Howardula and Spiroplasma to mediate defence, nor do we find strong support for host immune priming during Spiroplasma infection. Interestingly, we recovered sequence for putative toxins encoded by Spiroplasma, including a novel putative ribosome-inactivating protein, transcripts of which are up-regulated in response to nematode exposure. Protection via the production of toxins may be a widely used and important mechanism in heritable defensive symbioses in insects.
Data from: Plant-fungal symbiosis affects litter decomposition during primary succession
Microbial symbionts of plants can affect decomposition by altering the quality or quantity of host plant tissue (substrate) or the micro-environment where decomposition occurs (conditioning). In C3 grasses, foliar fungal endophytes (Clavicipitaceae) can increase plant resistance to drought and/or produce alkaloids that reduce herbivory – effects that may also influence host litter composition and subsequent litter decomposition. We studied the effect of the endophyte Epichloë sp. on litter decomposition in the Great Lakes dunes (USA) using a reciprocal design altering endophyte presence/absence in both American beachgrass Ammophila breviligulata substrate (litter bags) and its conditioning of the decomposition microenvironment. Symbiont treatments were crossed with rain-out shelters that altered growing season precipitation. The first year of decomposition, senesced leaf substrate from A. breviligulata with Epichloë decomposed 21% faster than endophyte-free substrate. By the third year, conditioning by live symbiotic plants reduced cumulative decomposition by 33% compared to plots planted with endophyte-free plants. Of the traits we examined – litter quantity, C:N ratio, mineral composition, fungal colonization, and carbon chemistry – increased litter quantity via greater tiller production was the primary trait shift associated with endophyte symbiosis. Epichloë in A. breviligulata litter also altered litter nitrogen decomposition dynamics, as evidenced by lower nitrogen and protein content in decomposed tissue from plants that hosted the endophyte. Differences in initial litter quality and subsequent colonization by saprotrophic fungi were ruled out as key drivers. Altered precipitation had negligible effects on decomposing processes in the dunes. Grass–Epichloë symbiosis altered nutrient cycling through increasing the rate of litter decomposition when present in the litter and through reducing litter decomposition by conditioning the decomposition microenvironment. Epichloë are widespread symbionts of grasses. Thus, their effects on decomposition could be an important, but often overlooked, driver of nutrient cycling in grass-dominated ecosystems.
Data from: Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features
Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA-based methods to identify mycorrhizal fungi from eleven E. firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine-scale environmental factors and macro-evolutionary patterns of change in mycorrhizal specificity. Thus, E. firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.
Data from: Quantifying the climatic niche of symbiont partners in a lichen symbiosis indicates mutualist-mediated niche expansions
The large distributional areas and ecological niches of many lichenized fungi may in part be due to the plasticity in interactions between the fungus (mycobiont) and its algal or cyanobacterial partners (photobionts). On the one hand, broad-scale phylogenetic analyses show that partner compatibility in lichens is rather constrained and shaped by reciprocal selection pressures and codiversification independent of ecological drivers. On the other hand, sub-species-level associations among lichen symbionts appear to be environmentally structured rather than phylogenetically constrained. In particular, switching between photobiont ecotypes with distinct environmental preferences has been hypothesized as an adaptive strategy for lichen-forming fungi to broaden their ecological niche. The extent and direction of photobiont-mediated range expansions in lichens, however, have not been examined comprehensively at a broad geographic scale. Here we investigate the population genetic structure of Lasallia pustulata symbionts at sub-species-level resolution across the mycobiont's Europe-wide range, using fungal MCM7 and algal ITS rDNA sequence markers. We show that variance in occurrence probabilities in the geographic distribution of genetic diversity in mycobiont-photobiont interactions is closely related to changes in climatic niches. Quantification of niche extent and overlap based on species distribution modeling and construction of Hutchinsonian climatic hypervolumes revealed that combinations of fungal-algal interactions change at the sub-species level along latitudinal temperature gradients and in Mediterranean climate zones. Our study provides evidence for symbiont-mediated niche expansion in lichens. We discuss our results in the light of symbiont polymorphism and partner switching as potential mechanisms of environmental adaptation and niche evolution in mutualisms.
Carbon fixation and transfer in the Olavius spp. symbiosis studied with microautoradiography
<p>Microautoradiographic images of thin sections from <em>Olavius</em> spp. worms that were incubated with <sup>14</sup>C-labelled bicarbonate in a pulse chase experiment. After 10 days chase, radioactive label is not only present in the outer region of the worm that harbors the chemosynthetic symbionts but is also detected over symbiont-free regions, i.e. the coelomic fluid (A) or the chloragogen tissue (B), indicating carbon transfer to the host.</p>
FIGURE 2 in The rare deep-living hyperiid amphipod Megalanceoloides remipes (Barnard, 1932): complementary description and symbiosis
FIGURE 2. Megalanceoloides remipes (Barnard, 1932), ovigerous female from the Gulf of California photographed in vivo, ventral view. Scale bar: 5 mm.
FIGURE 3 in The rare deep-living hyperiid amphipod Megalanceoloides remipes (Barnard, 1932): complementary description and symbiosis
FIGURE 3. Megalanceoloides remipes (Barnard, 1932) from the Gulf of California. A. antenna I; B, C. details of apical segments; D. antenna II, lateral view; E. details of proximal segments of antenna II, ventral view; F. same, lateral view; G, H. details of apical segments of antenna II; I. mandibular palp; J. mouthparts, ventral view including antenna II (ant2), mandible (md), first maxilla (mx1), second maxilla (mx2), and maxilliped (mxp); K. second maxilla; L, M. PI and details of distal segments. Scale bars: A, D–F, I, J, L = 1 mm; B, G, K, M = 0.25 mm; C, H= 0.1 mm.
FIGURE 4 in The rare deep-living hyperiid amphipod Megalanceoloides remipes (Barnard, 1932): complementary description and symbiosis
FIGURE 4. Megalanceoloides remipes (Barnard, 1932) from the Gulf of California. A–C. PII with details of distal segment and ornamentation of S6; D–F. PIII with details of S6; G. P IV S6 and S7; H. PV; I. PV detail of S6 and S7; J. PVI; K. same, detail of S6 and S7; L. PVII; M. same, detail of S6 and S7; N. UR1, dorsal view; O. UR2, dorsal view; P. same, ornamentation pattern. Scale bars: A, D, H, J, L = 1 mm (B, I, K, M = 0.25 mm; E, F = 0.5 mm).
FIGURE 1 in The rare deep-living hyperiid amphipod Megalanceoloides remipes (Barnard, 1932): complementary description and symbiosis
FIGURE 1. Megalanceoloides remipes (Barnard, 1932) ovigerous female from the Gulf of California photographed in vivo (2.5 mm), lateral view. Scale bar: 5 mm.
FIGURE 4 in Phyllodesmium rudmani (Mollusca: Nudibranchia: Aeolidoidea), a new solar powered species from the IndoWest Pacific with data on its symbiosis with zooxanthellae
FIGURE 4. Phyllodesmium rudmani, histology: A: Ramification of the digestive glandular branches beneath epidermis in large ceras. B: Multiple saclike structures of the digestive glandular branches beneath epidermis of ceras. Note the zooxanthellae inside the digestive glandular cells and the lumen of the branches. C: Zooxanthellae inside the tissue of the terminal digestive glandular branches. Note the highly vacuolated cells of the epidermis. D: Zooxanthellae surrounded by digestive glandular cells from the lumen of a midgut branch. Note the dividing zooxanthellae cell (left middle).
FIGURE 3 in Phyllodesmium rudmani (Mollusca: Nudibranchia: Aeolidoidea), a new solar powered species from the IndoWest Pacific with data on its symbiosis with zooxanthellae
FIGURE 3. Phyllodesmium rudmani, hard structures in digestive system: A: Radula of holotype, CASIZ 103747. B: Closeup of radula of holotype, CASIZ 103747.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
International Brain Laboratory public data
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.