Host-symbiont Interactions Research Articles

Changes in the microbiome and associated host tissue structure in the blue mussel (Mytilus edulis) following exposure to polystyrene microparticles

Marine life is increasingly exposed to microplastics, which can be ingested and disrupt the relationship between host tissues and their microbiomes. We investigated the effects of microplastics (5 µm polystyrene beads) on the microbial community and host tissue structure in organs at high risk of exposure (digestive gland and gills) in blue mussels ( Mytilus edulis Linnaeus, 1758). We exposed mussels to concentrations of microplastic consistent with levels found in local coastal waters. High exposures (1000 particles per m3 per mussel) decreased the alpha and beta diversity in the microbiome of the digestive gland, with an increase in relative abundance of Polaribacter and a decrease in other species in the Flavobacteriaceae. Both low (10 particles per m3 per mussel) and high exposures to polystyrene also changed tissue structure in the hosts, with an increase in immune cells (hemocytes) and reactive lysosomes in the gills, and in the digestive gland, a loss of cell specialization in digestive cells and an increase in cell breakdown products. Thus, exposure to particles of polystyrene in concentrations consistent with levels detected in local coastal zones reduces microbial biodiversity of the digestive gland and disrupts host tissues, which may indicate a loss of the host–symbiont interactions that support tissue homeostasis.

Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont

Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.

Priority effects alter the colonization success of a host-associated parasite and mutualist.

Priority effects shape the assembly of free-living communities and host-associated communities. However, the current literature does not fully incorporate two features of host-symbiont interactions, correlated host responses to multiple symbionts and ontogenetic changes in host responses to symbionts, leading to an incomplete picture of the role of priority effects in host-associated communities. We factorially manipulated the inoculation timing of two plant symbionts (mutualistic rhizobia bacteria and parasitic root-knot nematodes) and tested how host age at arrival, arrival order, and arrival synchrony affected symbiont colonization success in the model legume Medicago truncatula. We found that host age, arrival order, and arrival synchrony significantly affected colonization of one or both symbionts. Host age at arrival only affected nematodes but not rhizobia: younger plants were more heavily infected than older plants. By contrast, arrival order only affected rhizobia but not nematodes: plants formed more rhizobia nodules when rhizobia arrived before nematodes. Finally, synchronous arrival decreased colonization both symbionts, an effect that depended on host age. Our results demonstrate that priority effects compromise the host's ability to control colonization by two major symbionts and suggest that the role of correlated host responses and host ontogeny in the assembly of host-associated communities deserve further attention.

Intrapopulation adaptive variance supports thermal tolerance in a reef-building coral

Coral holobionts are multi-species assemblages, which adds significant complexity to genotype-phenotype connections underlying ecologically important traits like coral bleaching. Small scale heterogeneity in bleaching is ubiquitous in the absence of strong environmental gradients, which provides adaptive variance needed for the long-term persistence of coral reefs. We used RAD-seq, qPCR and LC-MS/MS metabolomics to characterize host genomic variation, symbiont community and biochemical correlates in two bleaching phenotypes of the vertically transmitting coral Montipora capitata. Phenotype was driven by symbiosis state and host genetic variance. We documented 5 gene ontologies that were significantly associated with both the binary bleaching phenotype and symbiont composition, representing functions that confer a phenotype via host-symbiont interactions. We bred these corals and show that symbiont communities were broadly conserved in bulk-crosses, resulting in significantly higher survivorship under temperature stress in juveniles, but not larvae, from tolerant parents. Using a select and re-sequence approach, we document numerous gene ontologies selected by heat stress, some of which (cell signaling, antioxidant activity, pH regulation) have unique selection dynamics in larvae from thermally tolerant parents. These data show that vertically transmitting corals may have an adaptive advantage under climate change if host and symbiont variance interact to influence bleaching phenotype.

Complex effects of environment and Wolbachia infections on the life history of Drosophila melanogaster hosts.

Wolbachia bacteria are common endosymbionts of many arthropods found in gonads and various somatic tissues. They manipulate host reproduction to enhance their transmission and confer complex effects on fitness‐related traits. Some of these effects can serve to increase the survival and transmission efficiency of Wolbachia in the host population. The Wolbachia–Drosophila melanogaster system represents a powerful model to study the evolutionary dynamics of host–microbe interactions and infections. Over the past decades, there has been a replacement of the ancestral wMelCS Wolbachia variant by the more recent wMel variant in worldwide D. melanogaster populations, but the reasons remain unknown. To investigate how environmental change and genetic variation of the symbiont affect host developmental and adult life‐history traits, we compared effects of both Wolbachia variants and uninfected controls in wild‐caught D. melanogaster strains at three developmental temperatures. While Wolbachia did not influence any developmental life‐history traits, we found that both lifespan and fecundity of host females were increased without apparent fitness trade‐offs. Interestingly, wMelCS‐infected flies were more fecund than uninfected and wMel‐infected flies. By contrast, males infected with wMel died sooner, indicating sex‐specific effects of infection that are specific to the Wolbachia variant. Our study uncovered complex temperature‐specific effects of Wolbachia infections, which suggests that symbiont–host interactions in nature are strongly dependent on the genotypes of both partners and the thermal environment.

Wolbachia pipientis modulates metabolism and immunity during Aedes fluviatilis oogenesis

Wolbachia pipientis is a maternally transmitted bacterium that mostly colonizes arthropods, including the mosquito Aedes fluviatilis, potentially affecting different aspects of host physiology. This intracellular bacterium prefers gonadal tissue cells, interfering with the reproductive cycle of insects, arachnids, crustaceans, and nematodes. Wolbachia's ability to modulate the host's reproduction is related to its success in prevalence and frequency. Infecting oocytes is essential for vertical propagation, ensuring its presence in the germline. The mosquito Ae. fluviatilis is a natural host for this bacterium and therefore represents an excellent experimental model in the effort to understand host-symbiont interactions and the mutual metabolic regulation. The aim of this study was to comparatively describe metabolic changes in naturally Wolbachia-infected and uninfected ovaries of Ae. fluviatilis during the vitellogenic period of oogenesis, thus increasing the knowledge about Wolbachia parasitic/symbiotic mechanisms.

Zooming in on host-symbiont interactions: advances in cryo-EM sample processing methods and future application to symbiotic tissues

Animals, plants, and fungi live in a microbe-dominated world. Investigating the interactions and processes at the host-microbe interface offers insight to how bacteria influence the development, health, and disease of the host. Optimization of existing imaging technologies and development of novel instrumentation will provide the tools needed to fully understand the dynamic relationship that occurs at the host-microbe interface throughout the lifetime of the host. In this review, we describe the current methods used in cryo-electron microscopy (cryo-EM) including cryo-fixation, sample processing, FIB-SEM, and cryotomography. Further, we highlight the new advances associated with these methods that open the cryo-EM discipline to large, complex multicellular samples, like symbiotic tissues. We describe the advantages and challenges associated with correlative imaging techniques and sample thinning methods like lift-out. By highlighting recent pioneering studies in the large-volume or symbiotic sample workflows, we provide insight into how symbiotic model systems will benefit from cryo-EM methods to provide artefact-free, near-native, macromolecular-scale resolution imaging at the host-microbe interface throughout the development and maintenance of symbiosis. Cryo-EM methods have brought a deep fundamental understanding of prokaryotic biology since its conception. We propose the application of existing and novel cryo-EM techniques to symbiotic systems is the logical next step that will bring an even greater understanding how microbes interact with their host tissues.

The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host

Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses.

Mechanisms for establishing primary and secondary endosymbiosis in Paramecium.

Primary (eukaryote and procaryote) and secondary (eukaryote and eukaryote) endosymbioses are driving forces in eukaryotic cell evolution. These phenomena are still contributing to acquire new cell structures and functions. To understand mechanisms for establishment of each endosymbiosis, experiments that can induce endosymbiosis synchronously by mixing symbionts isolated from symbiont-bearing host cells and symbiont-free host cells are indispensable. Recent progress on endosymbiosis using Paramecium and their endonuclear symbiotic bacteria Holospora or symbiotic green alga Chlorella has been remarkable, providing excellent opportunities for elucidating host-symbiont interactions. These organisms are now becoming model organisms to know the mechanisms for establishing primary and secondary endosymbioses. Based on experiments of many researchers, we introduce how these endosymbionts escape from the host lysosomal fusion, how they migrate in the host cytoplasm to localize specific locations within the host, how their species specificity and strain specificity of the host cells are controlled, how their life cycles are controlled, how they escape from the host cell to infect more young host cell, how they affect the host viability and gene expression, what kind of substances are needed in these phenomena, and what changes had been induced in the symbiont and the host genomes.

Temporal and spatial microbiome dynamics across natural populations of the social spider Stegodyphus dumicola.

Host-symbiont interactions may form obligatory or facultative associations that are context dependent. Long-term studies on microbiome composition from wild populations should assess the temporal and spatial dynamics of host-microbe associations. We characterized the temporal and spatial variation in the bacterial microbiome composition in six populations of the social spider Stegodyphus dumicola for 2.5 years, using 16S rRNA gene amplicon sequencing of whole spiders. Individuals within a nest exhibit highly similar microbiomes, which remain stable over several generations and are not predictably affected by seasonal variation in temperature or humidity. This stability in nest microbiome is likely due to social transmission, whereas drift-like processes during new nest foundations explain variation in host microbiomes between nests. This is supported by the lack of obligate symbionts (i.e. no symbionts are present in all spider individuals). Quantitative PCR analyses showed that the bacterial load of individual spiders is stable in healthy nests but can increase dramatically in perishing nests. These increases are not driven by specific bacterial taxa but likely caused by loss of host immune control under deteriorating conditions. Spider nests show an annual survival rate of approximately 45%, but nest death is not correlated to microbiome composition, and the bacteria found in S. dumicola are not considered to be high virulence pathogens.

Distribution and phenotypic effect of Wolbachia in natural population of Indian Drosophila

Background & objectives: Wolbachia (alpha-proteobacteria, Rickettsiaceae) undergoes maternal transmission and manipulates host reproductive fitness. Wolbachia strains in the Drosophila host (wMel, wRi) have significant implications in controlling arboviral diseases and are being transfected into the mosquito population. The efficient use of Wolbachia as a biocontrol agent calls for a need to understand its biology and host-symbiont interactions. The present work is a baseline study to explore the distribution of Wolbachia strains and their effect on the reproductive fitness of Drosophila (Drosophilidae, Diptera) hosts from India. Methods: The distribution and strain identification of Wolbachia was done by PCR and sanger sequencing method in Indian Drosophila host species. For further setting up of host-phenotype experiments, control (nature-caught Wolbachia- infected) and treated (antibiotics-treated Wolbachia-uninfected) host Drosophila laboratory-established lines were used. Results: The presence of Wolbachia was found to be limited to only three Drosophila host species i.e. D. melanogaster, D. simulans and D. ananassae and their distribution frequency was not influenced by host ecological background. Wolbachia infection was seen to provide a fitness advantage in terms of reproductive success in D. melanogaster; however, tetracycline treatment could not remove Wolbachia from D. ananassae, preventing us from conducting experiments in this species. Interpretation & conclusion: These results reaffirm the host specific nature of Wolbachia infection and highlight for the first time Wolbachia distribution and phenotypic effect in Indian Drosophila host. In the wake of world mosquito programme, it is crucial to identify Wolbachia strains in natural population and evaluate their effects on host species for making it an effective bio-control agent.

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont.

Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.

Positive selection on mitochondria may eliminate heritable microbes from arthropod populations.

Diverse eukaryotic taxa carry facultative heritable symbionts, microbes that are passed from mother to offspring. These symbionts are coinherited with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria, but with currently unknown consequences for symbiont evolution. We therefore employed a population genetic mean field framework to model the impact of selection on mitochondrial DNA (mtDNA) upon symbiont frequency for three generic scenarios of host–symbiont interaction. Our models predict that direct selection on mtDNA can drive symbionts out of the population where a positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, by contrast, the positively selected mtDNA mutation occurs in a symbiont-infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. We conclude that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA.

In silico insights into potential gut microbial modulation of NAD+ metabolism and longevity

Recent evidence has prompted the notion of gut-microbial signatures as an indirect marker of aging and aging-associated decline in humans. However, the underlying host-symbiont molecular interactions contributing to these signatures remain poorly understood. In this study, we address this gap using cheminformatic analyses to elucidate potential gut microbial metabolites that may perturb the longevity-associated NAD+ metabolic network. In silico ADMET, KEGG interaction analysis, molecular docking, molecular dynamics simulation, and molecular mechanics calculation predict a large number of safe and bioavailable microbial metabolites to be direct and/or indirect activators of NAD+-dependent sirtuin proteins. Our simulation results suggest dihydropteroate, phenylpyruvic acid, indole-3-propionic acid, phenyllactic acid, all-trans-retinoic acid, and multiple deoxy-, methyl-, and cyclic nucleotides from intestinal microbiota as the best-performing regulators of NAD+ metabolism. Retracing these molecules to their source microorganisms also suggest commensal Escherichia, Bacteroides, Bifidobacteria, and Lactobacilli to be associated with the highest number of pro-longevity metabolites. These findings from our early-stage study, therefore, provide an informatics-based context for previous evidence in the area and grant novel insights for future clinical investigation intersecting anti-aging drug discovery, probiotics, and gut microbial signatures.

Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A.

SummaryThe symbiotic cyanobacterium UCYN‐A is one of the most globally abundant marine dinitrogen (N2)‐fixers, but cultures have not been available and its biology and ecology are poorly understood. We used cultivation‐independent approaches to investigate how UCYN‐A single‐cell N2 fixation rates (NFRs) and nifH gene expression vary as a function of depth and photoperiod. Twelve‐hour day/night incubations showed that UCYN‐A only fixed N2 during the day. Experiments conducted using in situ arrays showed a light‐dependence of NFRs by the UCYN‐A symbiosis, with the highest rates in surface waters (5–45 m) and lower rates at depth (≥ 75 m). Analysis of NFRs versus in situ light intensity yielded a light saturation parameter (I k ) for UCYN‐A of 44 μmol quanta m−2 s−1. This is low compared with other marine diazotrophs, suggesting an ecological advantage for the UCYN‐A symbiosis under low‐light conditions. In contrast to cell‐specific NFRs, nifH gene‐specific expression levels did not vary with depth, indicating that light regulates N2 fixation by UCYN‐A through processes other than transcription, likely including host–symbiont interactions. These results offer new insights into the physiology of the UCYN‐A symbiosis in the subtropical North Pacific Ocean and provide clues to the environmental drivers of its global distributions.

A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence.

Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.

Pervasive effects of Wolbachia on host activity.

Heritable symbionts have diverse effects on the physiology, reproduction and fitness of their hosts. Maternally transmitted Wolbachia are one of the most common endosymbionts in nature, infecting about half of all insect species. We test the hypothesis that Wolbachia alter host behaviour by assessing the effects of 14 different Wolbachia strains on the locomotor activity of nine Drosophila host species. We find that Wolbachia alter the activity of six different host genotypes, including all hosts in our assay infected with wRi-like Wolbachia strains (wRi, wSuz and wAur), which have rapidly spread among Drosophila species in about the last 14 000 years. While Wolbachia effects on host activity were common, the direction of these effects varied unpredictably and sometimes depended on host sex. We hypothesize that the prominent effects of wRi-like Wolbachia may be explained by patterns of Wolbachia titre and localization within host somatic tissues, particularly in the central nervous system. Our findings support the view that Wolbachia have wide-ranging effects on host behaviour. The fitness consequences of these behavioural modifications are important for understanding the evolution of host-symbiont interactions, including how Wolbachia spread within host populations.

Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement.

“Omics” techniques (including genomics, transcriptomics, metabolomics, proteomics, and metagenomics) have been employed with huge success in the improvement of agricultural crops. As marine aquaculture of macroalgae expands globally, biologists are working to domesticate species of macroalgae by applying these techniques tested in agriculture to wild macroalgae species. Metabolomics has revealed metabolites and pathways that influence agriculturally relevant traits in crops, allowing for informed crop crossing schemes and genomic improvement strategies that would be pivotal to inform selection on macroalgae for domestication. Advances in metagenomics have improved understanding of host–symbiont interactions and the potential for microbial organisms to improve crop outcomes. There is much room in the field of macroalgal biology for further research toward improvement of macroalgae cultivars in aquaculture using metabolomic and metagenomic analyses. To this end, this review discusses the application and necessary expansion of the omics tool kit for macroalgae domestication as we move to enhance seaweed farming worldwide.

Assessing the role of host-symbiont interactions in maternal care behaviour

A recommendation of: Sophie Van Meyel, Séverine Devers, Simon Dupont, Franck Dedeine and Joël Meunier Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig https://doi.org/10.1101/2020.10.08.331363

Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis

Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host–symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.