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Figure 13 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 13. Sponge types which can be used for nematode storage and formulation.

Figure 2 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 2. Endotokia matricida stage of an entomopathogenic nematode.

Figure 12 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 12. Setup of infectivity bioassay in 24-well plates with tape to prevent escape of insects.

Figure 1 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 1. Life cycle of entomopathogenic nematode/bacteria complex in a lepidopteran insect.

Figure 10 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 10. Isolation of Xenorhabdus and Photorhabdus from Galleria mellonella hemolymph.

Figure 4 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts

Figure 4. Steps in isolating entomopathogenic nematodes from soil.

opencc-by-4.0Jul 2024View details →

Transmission of yeast and bacterial symbionts between sexual partners in Drosophila suzukii and Drosophila melanogaster

Data from "Transmission of yeast and bacterial symbionts between sexual partners in Drosophila suzukii and Drosophila melanogaster"

opencc-by-4.0Jul 2021View details →

Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer

Files Uploaded 1.  16S Phylum level LDA analysis of colonoscopy biopsies         16S_LDA_analysis_upload_20210710.tar.gz     2. 16S DNA fastq files FASTQ_Generation_2019-03-16_17_29_28Z-167483978.zip 3. Whole genome sequence analysis of b fragilis isolates from colonoscopy isolates WGS_b_fragilis_analysis_20210709_upload.tar.gz 4. Sample sheet describing the b fragilis sample fastq files. 16S sequencing sample sheet.docx 5. b fragilis whole genome sequence fastq files Sample-*.fastq.gz

opencc-by-4.0Aug 2021View details →

Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

This repository contains annotations for the strains of R. irregularis chromosome assemblies.

opencc-zeroNov 2022View details →

Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.

opencc-zeroDec 2022View details →

An aphid symbiont confers protection against a specialized RNA virus, another increases vulnerability to the same pathogen

Insects often harbor heritable symbionts that provide defense against specialized natural enemies, yet little is known about symbiont protection when hosts face simultaneous threats. In pea aphids (Acyrthosiphon pisum), the facultative endosymbiont Hamiltonella defensa confers protection against the parasitoid, Aphidius ervi, and Regiella insecticola protects against aphid-specific fungal pathogens, including Pandora neoaphidis. Here we investigated whether these two common aphid symbionts protect against a specialized virus A. pisum virus (APV), and whether their anti-fungal and anti-parasitoid services are impacted by APV infection. We found that APV imposed large fitness costs on symbiont-free aphids and these costs were elevated in aphids also housing H. defensa. In contrast, APV titers were significantly reduced and costs to APV infection were largely eliminated in aphids with R. insecticola. To our knowledge, R. insecticola is the first aphid symbiont shown to protect against a viral pathogen, and only the second arthropod symbiont reported to do so. In contrast, APV infection did not impact the protective services of either R. insecticola or H. defensa. To better understand APV biology, we produced five genomes and examined transmission routes. We found that moderate rates of vertical transmission, combined with horizontal transfer through food plants, were the major route of APV spread, although lateral transfer by parasitoids also occurred. Transmission was unaffected by facultative symbionts. In summary, the presence and species identity of facultative symbionts resulted in highly divergent outcomes for aphids infected with APV, while not impacting defensive services that target other enemies. These findings add to the diverse phenotypes conferred by aphid symbionts, and to the growing body of work highlighting extensive variation in symbiont-mediated interactions.

opencc-zeroDec 2022View details →

Data from: Symbiont-specific responses to environmental cues in a threesome lichen symbiosis

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We investigated differential gene expression in photosymbiodemes of the lichen Peltigera britannica at different temperatures representing mild and putatively stressful conditions and compared gene expression of thallus sectors containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts. Firstly, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Secondly, we quantified photobiont-mediated differences in fungal gene expression. High temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data. As expected, the expression of genes involved in photosynthesis was increased in both photobiont types at 15 and 25°C. The green algae exhibited thermal stress responses mainly at 25°C, and the fungus and the cyanobacteria already by 15°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima. Furthermore, photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression.

opencc-zeroDec 2022View details →

Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms

In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e., the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labeled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.

opencc-by-4.0Mar 2023View details →

Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara

Abstract Bacteria colonize specific niches in the animal gut. However, the genetic basis of these associations is often unclear. The proteobacterium Frischella perrara is a widely distributed gut symbiont of honey bees. It colonizes a specific niche in the hindgut and causes a characteristic melanization response. Genetic determinants required for the establishment of this association, or its relevance for the host, are unknown. Here, we independently isolated three point mutations in genes encoding the DNA-binding protein integration host factor (IHF) in F. perrara. These mutants abolished the production of an aryl polyene metabolite causing the yellow colony morphotype of F. perrara. Inoculation of microbiota-free bees with one of the mutants drastically decreased gut colonization of F. perrara. Using RNAseq we found that IHF affects the expression of potential colonization factors, including genes for adhesion (Type 4 pili), interbacterial competition (Type 6 secretion systems), and secondary metabolite production (colibactin and aryl polyene biosynthesis). Gene deletions of these components revealed different colonization defects depending on the presence of other bee gut bacteria. Interestingly, one of the T6SS mutants did not induce the scab phenotype anymore, despite colonizing at high levels, suggesting an unexpected role in bacteria-host interaction. IHF is conserved across many bacteria and may also regulate host colonization in other animal symbionts.

opencc-zeroApr 2023View details →

Data for: Dispersal-limited symbionts exhibit unexpectedly wide variation in host specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.

opencc-by-4.0Jun 2022View details →

Host symbiont gene reconciliation supplementary material

Cinara aphids dataset was obtained from the data of article by Manzano-Marin et al. ISME, 2019, and we chose a representative subset of the species present in the gene trees. We used an exterior source for the phylogeny for the enterobacteria present in the gene trees using Annotree (Mendler et al., Nucleic Acids Research, 2019) (for the one that are not associated to Cinara aphids, and are thus "free living" in this setting).  Helicobacter pylori dataset was constructed by Alexia Nguyen Trung, gathering available whole genome sequences on NCBI with assigned geo populations on NCBI or pubMLST.  A phylogenetic tree was built based on the concatenation of universal-unicopy genes (322 genes), and a sample of 113 strains representing the diversity of H. pylori in the old world (excluding strains from the Americas) was obtained using Treemmer (Menardo et al, BMC Bioinformatics, 2018). Then, 6 non pylori strains were added (H. hepaticus, H. acinonychis, H. canadensis, H felis, H. bizzozeronii, H. cetorum), as an external group.  In this study we considered the 1034 gene families, including 322 universal unicopy family, which displayed strains from the external group and from at least 3 continents. The taleoutput repository contains the recphyloxml outputs of the methods used in the paper, am stands for the approach with amalgamation of the universal unicopy genes to construct a strain tree, while nc refers to the results with the tree constructed from the concatenate, and then the repositories refer to the putative population trees 1, 2, 3 and 4. 0u_0 is the strains genes reconciliation in recphyloxml format. 0upper is the host strains reconciliation in recphyloxml format. Finally, the last repository contains the simulated dataset. It was generated using Sagephy https://compbio.engr.uconn.edu/software/sagephy/ https://doi.org/10.1093/bioinformatics/btz081 For each instance, a host tree, a symbiont tree, and 5 gene trees were generated. We used the parameters proposed in https://doi.org/10.1145/3307339.3342168 \cite{kordi_inferring_2019}, as representative of small (D 0.133, T 0.266, L 0.266), medium (D 0.3, T 0.6, L 0.6) and high (D 0.6, T 1.2, L 1.2) transfer rates, without replacing transfers. The software enables to specify an inter transfer rate, corresponding to the probability for a gene transfer between different hosts. When a horizontal transfer is chosen during generation of the gene tree (inside a symbiont tree and knowing a host/symbiont reconciliation), the transfer is chosen to be an inter host one with the inter transfer rate. So an inter transfer rate of 0 corresponds to only intra transfer, and of 1 corresponds to a case where transfers are only between symbionts in separate hosts. We constructed two simulated datasets, one with a combination of the different rates for the DTL parameters (varrates), and one with only medium rates but with different rates of "inter" and "intra" transfers (coevol). For the first dataset, we used all 9 combinations of small, medium and high rates for the symbiont generation and the gene generation, with only intra host gene transfer (i.e. an inter transfer rate of zero). For the second dataset, we used only medium rates for both symbiont and genes generation, but we used 6 inter transfer rates going from 0 to 1.  For both datasets, and for each set of rates, we generated 50 instances consisting of 1 host tree with 100 leaves, 1 symbiont tree and 5 gene trees, each generated in the pruned version of the other trees (branch that do not reach present are pruned before the generation of the next tree). We then kept each host leaves with a probability of 0.08 to simulate unexhaustive sampling, resulting in host trees with an average size of 8 leaves. This ended up to 399 instances for the first dataset and 226 instances for the second one, and at least 29 instances of 5 genes for each set of parameters. Each repositiory is a simulation instance, varrates_k_l_i correspond to simulation number i with lower rate k and upper rate l. genes, symbiont, species are repositories containing the trees in newick of the genes, symbiont and host in newick. Gene trees are unrooted. Lower matching is a matching between gene and symbiont leaves, upper matching between symbiont and host leaves, gene_host_matching is a matching between gene and host leaves. Transfer list contains one file for each gene and with all transfers simulated, donor and receiver symbiont internal nodes. Each instance also contains the output of tale used in the paper, with the three heuristic, the 2-level symbiont gene (_2l), the 3-level sequential heuristic (_dec) and the 3-level monte carlo approach (_mc) with 50 iterations. All the launch were with 5 rounds of parameters estimation (the default usage). The 0u_0 contain a sampled symbiont gene reconciliation in recphyloxml, and for the 3-level heuristics, 0upper a corresponding host symbiont reconciliation in recphyloxml (multiple ones for the montecarlo i_upper and iu_0 for i from 0 to 49). A known error in the recphyloxml transcription script, now corrected, has induced some errors in some of the recphyloxml files : for some transfers the indicated receiver species is the donor and not the receiver, however redundancy in the format makes it possible to retrieve the information by looking at the matching species in the next event of the gene, that will be the receiver species, we chose to leave it this way instead of relaunching all the computations, as it has no impact on the figures and results presented in our article (mostly constructed using the freq files). The files freq contains information on the frequencies of the different events summed up over gene symbionts reconciliation, lower_log_likelihood contains the log likelihood of the host and symbiont trees knowing the genes (the probability of the genes knowing the host and symbiont).

opencc-zeroMay 2023View details →

Defensive symbiosis in the wild: seasonal dynamics of parasitism risk and symbiont-conferred resistance

Parasite-mediated selection can rapidly drive up resistance levels in host populations, but fixation of resistance traits may be prevented by costs of resistance. Black bean aphids (Aphis fabae) benefit from increased resistance to parasitoids when carrying the defensive bacterial endosymbiont Hamiltonella defensa. However, due to fitness costs that come with symbiont infection, symbiont-conferred resistance may result in either a net benefit or a net cost to the aphid host, depending on parasitoid presence as well as on the general ecological context. Balancing selection may therefore explain why in natural aphid populations, H. defensa is often found at intermediate frequencies. Here we present a two-year field study where we set out to look for signatures of balancing selection in natural aphid populations. We collected temporally well-resolved data on the prevalence of H. defensa in A.f. fabae and estimated the risk imposed by parasitoids using sentinel hosts. Despite a marked and consistent early-summer peak in parasitism risk and significant changes in symbiont prevalence over time, we found just a weak correlation between parasitism risk and H. defensa frequency dynamics. H. defensa prevalence in the populations under study was, in fact, better explained by the number of heat days that previous aphid generations were exposed to. Our study grants an unprecedentedly well-resolved insight into the dynamics of endosymbiont and parasitoid communities of A.f. fabae populations, and it adds to a growing body of empirical evidence suggesting that not only parasitism risk but rather multifarious selection is shaping H. defensa prevalence in the wild.

opencc-zeroMay 2023View details →

Corals adapted to extreme and fluctuating seawater pH increase calcification rates and have unique symbiont communities

Ocean acidification (OA) is a severe threat to coral reefs mainly by reducing their calcification rate. Identifying the resilience factors of corals to decreasing seawater pH is of paramount importance to predict the survivability of coral reefs in the future. This study compared corals adapted to variable pHT (i.e., 7.23–8.06) from the semi-enclosed lagoon of Bouraké, New Caledonia, to corals adapted to more stable seawater pHT (i.e., 7.90-8.18). In a 100-day aquarium experiment, we examined the physiological response and genetic diversity of Symbiodiniaceae from three coral species (Acropora tenuis, Montipora digitata and Porites sp.) from both sites under three stable pHNBS conditions (8.11, 7.76, 7.54) and one fluctuating pHNBS regime (between 7.56 and 8.07). Bouraké corals consistently exhibited higher growth rates than corals from the stable pH environment. Interestingly, A. tenuis from Bouraké showed the highest growth rate under the 7.76 pHNBS condition, whereas for M. digitata and Porites sp. from Bouraké, growth was highest under the fluctuating regime and the 8.11 pHNBS conditions, respectively. While OA generally decreased coral calcification by ca. 16%, Bouraké corals showed higher growth rates than corals from the stable pH environment (21% increase for A. tenuis to 93% for M. digitata, with all pH conditions pooled). This superior performance coincided with divergent symbiont communities that were more homogenous for Bouraké corals. Corals adapted to variable pH conditions appear to have a better capacity to calcify under reduced pH compared to corals native to more stable pH conditions. This response was not gained by corals from the more stable environment exposed to variable pH during the 100-day experiment, suggesting that long-term exposure to pH fluctuations and/or differences in symbiont communities benefit calcification under OA.

opencc-zeroMay 2023View details →

Plant productivity response to inter- and intra-symbiont diversity: mechanisms, manifestations, and meta-analyses

Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality, and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns, and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context-dependency in these relationships.