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508 results for “Symbiotes”
Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na+/H+ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.
Data from: Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity
Obligate symbioses occur when organisms require symbiotic relationships to survive. Some parasitic wasps of caterpillars possess obligate mutualistic viruses called "polydnaviruses." Along with eggs, wasps inject polydnavirus inside their caterpillar hosts where the hatching larvae develop inside the caterpillar. Polydnaviruses suppress the immune systems of their caterpillar hosts, which enables egg hatch and wasp larval development. It is unknown whether polydnaviruses also manipulate the salivary proteins of the caterpillar, which may affect the elicitation of plant defenses during feeding by the caterpillar. Here, we show that a polydnavirus of the parasitoid Microplitis croceipes, and not the parasitoid larva itself, drives the regulation of salivary enzymes of the caterpillar Helicoverpa zea that are known to elicit tomato plant-defense responses to herbivores. The polydnavirus suppresses glucose oxidase, which is a primary plant-defense elicitor in the saliva of the H. zea caterpillar. By suppressing plant defenses, the polydnavirus allows the caterpillar to grow at a faster rate, thus improving the host suitability for the parasitoid. Remarkably, polydnaviruses manipulate the phenotypes of the wasp, caterpillar, and host plant, demonstrating that polydnaviruses play far more prominent roles in shaping plant–herbivore interactions than ever considered.
Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus
Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.
Host identity and symbiotic association affects the genetic and taxonomic diversity of the clownfish-hosting sea anemone microbiome
All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly-linked physical interactions that characterize many macroscopic symbioses creates opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the genetic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity shapes the majority of the genetic diversity of the clownfish-hosting sea anemone microbiome, but predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify up-regulated microbial functions in host anemones that are likely affected by clownfish presence. Taken together our study reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes
Data from: Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf
Coral reefs are in rapid decline on a global scale due to human activities and a changing climate. Shallow water reefs depend on the obligatory symbiosis between the habitat forming coral host and its algal symbiont from the genus Symbiodinium (zooxanthellae). This association is highly sensitive to thermal perturbations and temperatures as little as 1°C above the average summer maxima can cause the breakdown of this symbiosis, termed coral bleaching. Predicting the capacity of corals to survive the expected increase in seawater temperatures depends strongly on our understanding of the thermal tolerance of the symbiotic algae. Here we use molecular phylogenetic analysis of four genetic markers to describe Symbiodinium thermophilum, sp. nov. from the Persian/Arabian Gulf, a thermally tolerant coral symbiont. Phylogenetic inference using the non-coding region of the chloroplast psbA gene resolves S. thermophilum as a monophyletic lineage with large genetic distances from any other ITS2 C3 type found outside the Gulf. Through the characterisation of Symbiodinium associations of 6 species (5 genera) of Gulf corals, we demonstrate that S. thermophilum is the prevalent symbiont all year round in the world's hottest sea, the southern Persian/Arabian Gulf.
Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis. However, the mechanisms used by S. meliloti to resist antimicrobial activity of plant peptides are poorly understood. To address this, we applied a global genetic approach using transposon mutagenesis followed by high-throughput sequencing (Tn-seq) to identify S. meliloti genes and pathways that increase or decrease bacterial competitiveness during exposure to the well-studied cationic NCR247 peptide and also to the unrelated model antimicrobial peptide polymyxin B. We identified 78 genes and several diverse pathways whose interruption alters S. meliloti resistance to NCR247. These genes encode the following: (i) cell envelope polysaccharide biosynthesis and modification proteins, (ii) inner and outer membrane proteins, (iii) peptidoglycan (PG) effector proteins, and (iv) non-membrane-associated factors such as transcriptional regulators and ribosome-associated factors. We describe a previously uncharacterized yet highly conserved peptidase, which protects S. meliloti from NCR247 and increases competitiveness during symbiosis. Additionally, we highlight a considerable number of uncharacterized genes that provide the basis for future studies to investigate the molecular basis of symbiotic development as well as chronic pathogenic interactions.
Data from: Larger plants promote a greater diversity of symbiotic nitrogen-fixing soil bacteria associated with an Australian endemic legume
A major goal in microbial ecology is to understand the factors that structure bacterial communities across space and time. For microbes that are plant symbionts, community assembly processes can lead to either a positive or negative relationship between plant size or age and soil microbe diversity. Here, we evaluated the extent to which such relationships exist within a single legume species (Acacia acuminata) and their naturally occurring symbiotic nitrogen-fixing bacteria (rhizobia). 2. We quantified the diversity of rhizobia that associate with A. acuminata trees of variable size spanning a large environmental gradient in southwest Australia (72 trees in 24 sites spread across ~300,000 km2), using metabarcoding. We modelled rhizobia diversity using 16S exact genetic variants, in a binomial multivariate statistical framework that controlled for climate and local soil characteristics. 3. We identified two major phylogenetic clades of rhizobia that associate with A. acuminata. Soil sampled at the base of larger Acacia trees contained a higher richness of rhizobia genetic variants. Each major clade responds differently to environmental factors (climate and soil characteristics), but the positive association between tree size and rhizobia genetic diversity was mainly driven by responses from one of the two clades. Overall tree size explained more variation than any other factor, resulting in a ~3-fold increase in total richness and clade diversity from the smallest to the largest trees. 4. Synthesis. Previous studies have shown that plant host species is important in structuring microbial soil communities in the rhizosphere. Our results show that host size or age within a single plant species can also structure diversity of at least one group of soil microbes. A positive relationship between plant host size and rhizobia diversity suggests that hosts may modify the niche space of their surrounding soil (niche construction hypothesis) enabling a higher richness of microbial taxa. That different rhizobial groups responded differently to host size and other ecological factors suggests that rhizobia is not an ecologically uniform group, and that entirely neutral explanations for our results are unlikely. Host plants may be analogous to 'islands', where larger plant hosts may accumulate diversity over time, through migration opportunities.
Data from: Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins
The Aiptasia-Symbiodinium symbiosis is a promising model for experimental studies of cnidarian-dinoflagellate associations, yet relatively little is known regarding the genetic diversity of either symbiotic partner. To address this we collected Aiptasia from 17 localities throughout the world and examined the genetic diversity of both anemones and their endosymbionts. Based on newly-developed SCAR markers, Aiptasia consisted of two genetically-distinct populations, one Aiptasia lineage from Florida and a second network of Aiptasia genotypes found at other localities. These populations did not conform to the distributions of described Aiptasia species, suggesting that taxonomic re-evaluation is needed in light of molecular genetics. Associations with Symbiodinium further demonstrated the distinctions among Aiptasia populations. According to 18S-RFLP, ITS2-DGGE, and microsatellite flanker region sequencing, Florida anemones engaged in diverse symbioses predominantly with members of Symbiodinium Clades A and B, but also C, whereas anemones from elsewhere harboured only S. minutum within Clade B. Symbiodinium minutum apparently does not form a stable symbiosis with other hosts, which implies a highly-specific symbiosis. Fine-scale differences among S. minutum populations were quantified using six microsatellite loci. Populations of S. minutum had low genotypic diversity and high clonality (R=0.14). Furthermore, minimal population structure was observed among regions and ocean basins, due to allele and genotype sharing. The lack of genetic structure and low genotypic diversity suggest recent vectoring of Aiptasia and S. minutum across localities. This first ever molecular-genetic study of a globally-distributed cnidarian and its Symbiodinium assemblages reveals host-symbiont specificity and widely-distributed populations in an important model system.
FIGURE 1 in Ankerius aenigmaticus, a new genus and new species of aphanodactylid crab symbiotic with polychaetes from the Red Sea coast of Saudi Arabia (Crustacea: Decapoda: Brachyura: Aphanodactylidae)
FIGURE 1. Ankerius aenigmaticus gen. et sp. nov., female holotype (7.2 × 7.0 mm) (UF), Red Sea coast of Saudi Arabia. Colours in life. Photograph: A. Anker.
FIGURE 4 in Ankerius aenigmaticus, a new genus and new species of aphanodactylid crab symbiotic with polychaetes from the Red Sea coast of Saudi Arabia (Crustacea: Decapoda: Brachyura: Aphanodactylidae)
FIGURE 4. Ankerius aenigmaticus gen. et sp. nov., female holotype (7.2 × 7.0 mm) (UF), Red Sea coast of Saudi Arabia. A, B, left P2; C, D, left P3; E, F, left P4; G, H, left P5; I, J, propodus and dactylus of left P4. A, C, E, J, lateral view; B, D, F, I, mesial view. Scales: A–H = 1.0 mm; I, J = 0.5 mm.
FIGURE 3 in Ankerius aenigmaticus, a new genus and new species of aphanodactylid crab symbiotic with polychaetes from the Red Sea coast of Saudi Arabia (Crustacea: Decapoda: Brachyura: Aphanodactylidae)
FIGURE 3. Ankerius aenigmaticus gen. et sp. nov., female holotype (7.2 × 7.0 mm) (UF), Red Sea coast of Saudi Arabia. A, frontal view of cephalothorax showing orbit, antennule, antenna, epistome and endostome; B, front, orbit and antenna; C, epistome and endostome; D, left third maxiliped; E, female abdomen; F, left chela; G, merus of right cheliped. Scales = 1.0 mm.
FIGURE 2. Uruma ourana n. gen., n in A new genus and new species of symbiotic crab (Crustacea: Brachyura: Pinnotheroidea) from Okinawa, Japan
FIGURE 2. Uruma ourana n. gen., n. sp. Holotype, male, 4.2 × 9.2 mm, RUMF-ZC-907. a, cephalothorax, anterior view; b, anterior thoracic sterna, ventral view; c, posterior thoracic sterna, posterior ventral view. Abbreviations: p = penis, pb = press button of abdominal locking mechanism, st 4–8 = thoracic sternites 4–8.
FIGURE 3. Uruma ourana n. gen., n in A new genus and new species of symbiotic crab (Crustacea: Brachyura: Pinnotheroidea) from Okinawa, Japan
FIGURE 3. Uruma ourana n. gen., n. sp. Holotype, male, 4.2 × 9.2 mm, RUMF-ZC-907. a, cephalothorax, anterior view; b, right third maxilliped; c, carpus and distal lobe of merus of left cheliped, anterior-upper view; d, right chela, outer view; e, left third ambulatory leg, dorsal view; f, propodus and dactylus of left third ambulatory leg, ventral-inner view; g, right fourth ambulatory leg, dorsal view. Scales = 1 mm.
FIGURE 5 in A new genus and new species of symbiotic crab (Crustacea: Brachyura: Pinnotheroidea) from Okinawa, Japan
FIGURE 5. Holotype of Gandoa zanzibarensis (Lenz, 1905) (after Lenz, 1905: pl. 47 figs. 9–9c). a, habitus; b, cephalothorax, frontal view; c, left third maxilliped; d, abdomen and telson.
FIGURE 4. Uruma ourana n. gen., n in A new genus and new species of symbiotic crab (Crustacea: Brachyura: Pinnotheroidea) from Okinawa, Japan
FIGURE 4. Uruma ourana n. gen., n. sp. Holotype, male, 4.2 × 9.2 mm, RUMF-ZC-907. a, telson, abdomen, and posterior margin of carapace; b, right G1, ventral view; c, right G2, dorsal view. Scales = 1 mm.
FIGURE 1 in A new genus and new species of symbiotic crab (Crustacea: Brachyura: Pinnotheroidea) from Okinawa, Japan
FIGURE 1. Live colouration of Uruma ourana n. gen., n. sp. Holotype, male, 4.2 × 9.2 mm, RUMF-ZC-907.
FIGURE 1. A in Isozoanthus antumbrosus, a new species of zoanthid (Cnidaria: Anthozoa: Zoanthidea) symbiotic with Hydrozoa from the Caribbean, with a key to hydroid and sponge-symbiotic zoanthid species
FIGURE 1. A. Line drawing showing Isozoanthus antumbrosus colonized Dentitheca dendritica. Scale bar is solid for colony and checkered for polyp detail inset. Drawing by J. Putnam H. of Florida State University. B. In situ macrophotograph of Isozoanthus antumbrosus with Dentitheca dendritica zooids visible in background.
FIGURE 3 in Aphanodactylidae, a new family of thoracotreme crabs (Crustacea: Brachyura) symbiotic with polychaete worms
FIGURE 3. Gandoa zanzibarensis (Lenz, 1905), female holotype. A, habitus. B, cephalothorax, frontal view. C, left maxilliped 3. D, abdomen. (After Lenz 1905: pl. 47 figs. 9–9c).
FIGURE 7. A, Gustavus mecognathus n. gen., n in Aphanodactylidae, a new family of thoracotreme crabs (Crustacea: Brachyura) symbiotic with polychaete worms
FIGURE 7. A, Gustavus mecognathus n. gen., n. sp., male holotype, cl. 6.1 mm, cw. 8.8 mm (ZRC) (lower) and female paratype, cl. 8.0 mm, cw. 13.9 mm (ZRC) (upper) (photo: G. Paulay). B, Uruma ourana Naruse, Fujita & Ng, 2009, male holotype, cl. 4.2 mm, cw. 9.2 mm (RUMF-ZC-907) (after Naruse et al. 2009: fig. 1).
FIGURE 2 in Aphanodactylidae, a new family of thoracotreme crabs (Crustacea: Brachyura) symbiotic with polychaete worms
FIGURE 2. Aphanodactylus loimiae, ovigerous female, cl. 8.6 mm, cw. 13.9 mm (CBM 5341). A, habitus. B, cephalothorax, anterior view. C, thoracic sternum. D, right chela. E, right P4. Scales A, C, D = 3.0 mm; B, E = 1.5 mm.
ScienceDex guides
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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.