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Symbioses - the lasting interactions between living organisms - can range from mutually beneficial relationships to harmful pathogenic effects. This interdisciplinary meeting will explore symbiotic interactions in ecological, evolutionary, chemical, spatial, and methodological contexts, ranging from deep mechanistic studies to broader surveys. Our primary objective is to unite researchers and establish new interactions between symbiotic systems and fields. We hope this serves as an incentive to generate new ways of thinking in established fields and spur new directions in symbiosis research.
What are the consequences of symbioses for the partners and other organisms?
Microbes are shaped by their evolutionary history, which provides them the genomic framework to cause disease. Experimental, analytical and technological innovation enables today genomic reconstruction at unprecedented detail. The Key lab aims to uncover the genetic mechanisms and phenotypic variation that underlay emergence, transmission and adaptation of pathogens. We use a systems approach collecting data directly from the host to trace microbial evolution in vivo on dramatically different timescales – ranging from a few weeks to thousands of years. Here I will present work of my lab using ancient metagenomic datasets as well as colony-based sequencing to reconstruct the evolutionary history of human pathogens and identify genetic changes associated with infection. Investigating the genomic footprint of pathogens from the past and the presence holds promise to improve our capacities for disease prevention and intervention.
Metabolic complementarity is hypothesized to underpin beneficial interactions between
symbiotic organisms, allowing the partners to potentially expand their combined metabolic capabilities by offsetting metabolic deficiencies. While genome-based metabolic models offer a promising avenue to predict such complementarity in silico, empirical evidence validating these predictions remains scarce. Here we analyzed 1300 algal-associated bacterial and 40 algal host genomes to investigate the specificity and evolution of metabolic complementarity. We addressed two key questions: 1) Does metabolic complementarity preferentially occur between algae and their direct bacterial associates compared to free-living relatives? and 2) To what extent is complementarity specific to host-bacterial pairs?
The comparative analysis of algal-associated and free-living bacteria did not consistently demonstrate enhanced metabolic complementarity in host-associated strains. However, we identified 38 bacterial taxa exhibiting significantly higher complementarity with their host or closely related algae compared to phylogenetically more distant relatives. Metabolic complementarity varied significantly across bacterial classes, with e.g. Bacteroidia displaying high levels of complementarity but low host specificity, while e.g. Gammaproteobacteria demonstrated greater host specificity. The precise metabolic exchanges underpinning these patterns are currently being explored. Our findings provide novel evidence supporting the co-evolution of metabolic complementarity between algal hosts and specific members of their microbiome.
In animal-microbe interactions, symbiont lifestyles in the host can range from intimate intracellular environments to looser extracellular associations. For each of these lifestyles, symbiont acquisition and maintenance will likely require specific sets of adaptations and interactions between both partners. Deep-sea mussels harbor their symbiotic bacteria in or on specialized gill cells called bacteriocytes with three different morphologies: as endosymbionts engulfed intracellularly in vacuoles, as ectosymbionts in crypts on the outside of host bacteriocytes, or as extracellular endosymbionts. In the latter, the symbionts sit inside bacteriocytes but extracellularly in a complex, interconnected channel system with pores that are open to the environment. The factors driving these different lifestyles and the specific roles of host and symbiont remain unidentified. Our research aims to identify the molecular and cellular determinants involved in the remodeling of the bacteriocytes to better understand each partner's role. By comparing functional capabilities of different symbionts and their free-living relatives, we identified several genes exclusive to the extracellular endosymbionts. Comparing hosts with different symbiont lifestyles, we discovered expanded functions linked to cytoskeleton proteins in mussels with extracellular endosymbionts. Upcoming imaging analyses aim to visualize these candidate factors in situ, comparing symbiotic mussels and cell types to their non-symbiotic counterparts.
The growth of Drosophila melanogaster larvae depend on nutrient-providing and pathogen-suppressing microbial symbionts; these symbionts are transferred through faecal matter deposition by egg-laying females. In different plant substrates, larvae exhibit higher developmental success in the presence of autochthonous versus allochthonous symbionts. This suggests that the capacity of symbiont microbes to maintain a stable development depends on the environmental context. However, the individual contribution of each symbiont to the variation in host developmental success remains unknown. To approach this problem, we have established a collection of microorganisms from microcosms in which Drosophila populations maintain and transfer bacterial and fungal symbionts between insect generations. The microcosms differ in the type of plant substrate, which is expected to be a crucial driver of the symbionts that establish alongside the flies. With this collection in hand, we will be able to create synthetic oligo-symbiont communities to identify key bacterial and fungal symbionts and their specific roles in Drosophila development. By incorporating temporal and spatial variations in substrate availability, we will explore how mutualistic dependence among the insects and specific symbionts, or symbiont consortia is affected. This approach will help us understand how these variations promote or prevent the evolution of host-symbiont specificity in Drosophila.
The Mediterranean Sea, known for its high biodiversity and endemic species, has experienced significant geological events that shaped its current biological landscape. This study focuses on gutless oligochaetes, which rely entirely on symbiotic bacteria for nutrition, and explores their evolutionary path and population structure across the Mediterranean. Gutless oligochaetes and other marine species could have colonized the Mediterranean in two ways. First, from east to west: The ancient Mediterranean was once connected to the Tethys Ocean, allowing colonization from the modern Indian Ocean. The Mediterranean became nearly landlocked and dried out during the Messinian Salinity Crisis (MSC) about 6 million years ago. While most authors argue that all marine life became extinct, some suggest species survived in marine refuges. The second colonization path is from west to east when the Mediterranean reflooded with Atlantic Ocean water about 5.3 million years ago. We are using population genomics to reveal how the gutless oligochaete Olavius algarvensis colonized the Mediterranean, and how and when it acquired its symbiotic consortium of five to six bacterial species. Our initial results show distinct genetic structuring in both host and symbiont populations across the Mediterranean Basin, indicating complex evolutionary dynamics. This research enhances our understanding of how ancient geological events and symbiotic relationships shape marine biodiversity, providing insights into the evolutionary history of Mediterranean fauna.
Insects developing on ephemeral patches are always pressed by resource depletion. Host- associated microbial communities (microbiota) may alleviate this stress by interacting with the substrate and temporarily stabilizing the developmental environment. Drosophila melanogaster is breeding on patches of different rotting fruits. Due to the variability of patches, microbial symbionts need to be flexibly adjusted to fluctuating properties. Adult flies replenish their microbiota pool through feeding (horizontal transmission); however, larvae depend on parental feces for microbiota and thus resource availability. This interaction likely results in distinct microbiota forming in different resource patches and possibly over different timescales. As this may influence developmental success of flies, we were interested in the variability of microbial communities that female flies transfer during egg laying. We associated a lab strain of flies with a variety of fruits, previously visited by flying insects in the field (microbiota pool). Egg and microbe disposition was forced on one substrate type (substrate filter), followed by transfer to a new microcosms (isolation). Hence only microbes that allowed fly development on a given substrate type were present in the next generation of adult fly’s fecal material. Using metabarcoding, we identified distinct bacterial and fungal symbiont communities associated with different substrate types, and we were able to link these communities to specific substrate properties.
Chemosynthesis is the basis for symbioses between bacteria and animals forming rich ecosystems in the dark of the deep sea. However, chemosynthesis also fuels symbioses in shallow-water sediments. One group of such coastal chemosymbionts is a diverse genus of sulfur-oxidizing gammaproteobacteria called "Candidatus Thiosymbion". The symbiotic lifestyles of ‘Ca. Thiosymbion’ differ across their three very distantly related host groups: The bacteria are ectosymbionts on stilbonematine nematodes, extracellular endosymbionts in gutless oligochaetes, and intracellular endosymbionts in Astomonema nematodes. In this study, we investigated how these three distinct lifestyles in such closely related symbionts have shaped their genomic content, with a focus on defense mechanisms, as we hypothesized these would be important for ectosymbionts, but less so for endosymbionts. We found that most endosymbionts lacked essential genes for type VI secretion systems, which are often used for interbacterial killing. Additionally, the numbers of CRISPR arrays and spacers, involved in antiviral defense, as well as biosynthetic gene clusters, which produce secondary metabolites often involved in defense, were greatly reduced in endosymbiotic ’Ca. Thiosymbion’. These findings suggest that for endosymbiotic "Ca. Thiosymbion", the protected environment inside their hosts allows the loss of defensive features, while these traits are important for maintaining an ectosymbiotic lifestyle.
Mosquito-borne viruses have emerged as global health threats due to their rapid spread and high disease burden. These viruses share a common feature: the virus is inoculated in the host skin tissue, a tissue colonized by a complex microbial community. The early events at the skin interface are critical for virus replication, yet the role of host skin bacteria remains unclear. In this work, we tested the hypothesis that host skin bacteria impact virus infection (and vice versa) for Ross River virus, an emerging mosquito-borne virus of growing concern. Using a humanized mice model we found that the bacterial load on the skin is higher after virus infection. Flow cytometry further revealed that this effect was independent of the host immune system, suggesting the virus can directly manipulate the host skin microbiota. Additionally, we demonstrated that co-incubation of human skin bacteria together with virus reduced viral infectivity in ex vivo skin biopts. This inhibitory effect was observed for S. epidermidis and B. epidermidis but not for P. aeruginosa and C. minutissimum, indicating the effect is bacterium specific. Together, these results underscore the intricate interplay between skin bacteria and viruses and can provide new insights into other host-microbiota interactions.
Symbiotic relationships are an inevitable part of the existence of all living organisms. Where one may be more beneficial, the other may be very harmful, and in the life of an organism these types of interactions never occur in only one form. As sessile organisms, plants are constantly exposed to mutualistic, commensal, and parasitic interactions, often at the same time. Sweet potato (Ipomoea batatas [L.] Lam) is one of the most widely cultivated crops in the world, largely due to its nutritional value. However, despite its growing importance in agriculture, I. batatas remains a relatively understudied species. There is a notable lack of research examining the interactions between sweet potatoes and mycorrhizal fungi or pathogens, or the consequences when both occur simultaneously. We aim to use modern analytical and computational techniques to investigate plant metabolomics, including primary and secondary metabolites, volatiles and exudates, in the context of beneficial and pathogenic interactions. Although potentially challenging, studying the combination of these relationships will allow us to see the lifestyle of plants in a more natural context and potentially lead us to more sustainable agricultural practices.
Flavobacteriales endosymbionts are well described as obligate endosymbionts of cockroaches (Blattabacterium sp.) and sveral Auchhenorhyncha (Karelsulcia muelleri). In the last years we discovered them also in several beetle families, mostly specialized to provision precursors of tryrosine. Tyrosine is a central building block of the insect cuticle and elimination or inhibition of these endosymbionts results in drastic impairment of the cuticle and tolerance to harsh environmental conditions as well as natural enemies.
After the description of the symbiont identity and metabolic capabilities, we aim on elucidating how they interact with their hosts and each other. I will present current approaches on host symbiont control, as well as interaction between complementary symbionts.
What are the consequences of symbioses for the partners and other organisms?
All mouthless catenulid flatworms of the genus Paracatenula are in a symbiotic relationship with the chemosynthetic bacteria Candidatus Riegeria. This ancient symbiosis has been established more than 400 MYA, the endosymbionts are strictly transmitted vertically and, based on a single symbiont genome, the symbionts still harbour all genes essential for the complete nutrition of their animal host. To reconstruct the evolutionary dynamics of this ancient and stable relationship with very divergent ecophysiological parameters compared to long-term endosymbioses in insects, we sequenced the metagenomes of more than 23 species sampled in different parts of the world. We then used assembly-graph based analyses of the metagenomes to reconstruct complete symbiont genomes as well as host phylogenetic markers. Based on phylogenetic analyses at the gene and genomic level, and chromosome scale comparative methods we detect specific coevolutionary patterns for several host clades, and convergent patterns of streamlining and recombinatory stasis of the symbiont genome. The genome streamlining down to an average genome size of 1.36 Mb from roughly 5 Mb appears to precede the radiation of all extant Paracatenula species. Despite the age of the association, no essential functions show signs of decay, suggesting an immortalizing selection for genomic stability of the symbionts.
Spiroplasma is a gram-positive, cell wall-less, motile bacteria found in plants and animals. In Drosophila, these maternally inheritable bacteria were first found in neotropical willistoni-group samples in the 1960s with low prevalence as a sex-ratio disorder agent. Unfortunately, these strains were lost before being studied by molecular methods. Later, Spiroplasma has been found in different Drosophila species showing various phenotypes ranging from male-killing (MK) to protection against pathogens. Still, far too little attention has been paid to Spiroplasma in neotropical Drosophila to understand long-term interactions with Spiroplasma in their hosts and associations with other symbionts. Here, we investigate both the prevalence of Spiroplasma in neotropical Drosophila populations and further their phenotypic consequences for the hosts. Firstly, we managed to detect asymptomatic Spriroplasma infections that seem almost fixed in natural populations together and without Wolbachia indicating the early introduction of symbionts in the common ancestor. This systemic Spiroplasma infection belongs to the poulsonii clade and the detection by standard PCR is limited by temperature, i.e., infection only appears when flies are exposed to elevated temperatures and thereby express partial MK phenotype. Secondly, we found previously uncovered sex-ratio disorder strains at low prevalence in D. paulistorum hosts in combination with Wolbachia. Our unexpected findings of Spiroplasma in neotropical Drosophila hosts will open a new understanding of their long-term coexistence and dynamics over evolutionary dimensions.
Biotrophic fungal plant pathogens co-evolve with their hosts often leading to narrow host ranges. New host specificities resulting in the emergence of novel plant diseases can arise after so-called host jumps. Resulting from a recent host jump, the biotrophic smut fungus Sporisorium reilianum exists in two distinct formae speciales, S. reilianum f.sp. reilianum (SRS) and S. reilianum f.sp. zeae (SRZ), causing head smut disease in sorghum or maize, respectively. On sorghum, SRZ causes the induction of a strong phytoalexin defense response precluding systemic fungal spread and preventing disease. In spite of genome sequence availability, the evolutionary events leading to host jump, host adaptation and host specificity in S. reilianum are still unknown. Using a combination of classical genetics, next-generation sequencing and gene deletion analysis we identified a nine-gene effector cluster tightly linked with host-specificity of SRS on sorghum. Each effector individually contributes to virulence and has an independent role in host adaptation. One effector supresses the phytoalexin defense response in Sorghum. The orthologous effector from SRZ cannot functionally complement its SRS ortholog. Instead, the SRZ effector leads to phytoalexins via effector-triggered immunity. This highlights the important evolutionary role of effectors in shaping host plant adaptation following a host jump.
Insect-microbe relationships are widespread, traversing a broad spectrum of reciprocal dependency, intimacy, duration, and cooperation. Many insects are only able to establish in their ecological niche because of bacterial partners. The false click beetles (Coleoptera, Throscidae) are a small, but globally distributed family that live in leaf litter and decaying wood and were previously reported to harbor intracellular symbionts in specialized bacteriomes. In this study, we investigated three of the four extant genera of Throscidae beetles for their symbiotic microbes, providing insights into host-symbiont interactions based on symbiont genomes and localization. The ancient Shikimatogenerans symbiont with a highly eroded genome was present in all examined taxa, probably supplying tyrosine precursors for cuticle biosynthesis as its only contribution to the host. Beyond this, several secondary symbionts from the Enterobacterales and Flavobacteriales with variable tissue tropism, genome sizes, and encoded capabilities were present, suggesting multiple symbiont acquisition events. Their inferred roles range from parasitic by manipulating host reproduction, to mutualistic, supplying amino acids and cofactors. Thus, beyond deepening our understanding of tyrosine-supplementing symbionts across a broad range of beetle families, the Throscidae provide insights into a dynamic evolutionary history with multiple co-occurring symbionts, expanding our view on multipartite symbiotic interactions in insects.
Which partners engage (repeatedly) in symbiotic interactions and how did they change during short or long-lasting associations?
Social bees, including honey bees and bumble bees, harbour a highly specialized and conserved gut microbial community. This microbiota has been implicated in beneficial roles in nutrient digestion and pathogen resistance. We are studying mechanisms by which these bacteria interact with each other, and with the host, to form a stable symbiotic community. We are using genomic, transcriptomic, and proteomics to investigate secretion systems and the production of membrane vesicles in the bee gut bacteria, which are two ways in which they may interact within the community. I will also describe work in which we are beginning to characterize the “symbiotic compartment” in which these bacteria reside, namely the bee hindgut. Using single-cell transcriptomics, we are examining how gene expression in the hindgut changes over the natural course of development of the bee and during microbial colonization. We identify previously uncharacterized cell types in the hindgut, and spatially localize these cell types using in-situ hybridization. In doing so, we lay the foundation towards a more mechanistic understanding of the symbiosis between bacteria and bees, which also has ecological and economic implications due to their key role as plant pollinators.
Over ten thousand years ago, Drosophila melanogaster expanded from its sub-Saharan ancestral range to temperate regions, relying on thermotolerance mechanisms to adapt to new abiotic conditions. These mechanisms enable the fruit fly to survive fluctuating temperatures and recover from cold-induced injuries, with their effectiveness closely linked to the insect’s diet and nutritional status. Gut microbes, acquired through food intake, play a crucial role in providing essential nutrients, influencing the fly’s nutritional health. This suggests that gut microbial communities may directly or indirectly contribute to Drosophila melanogaster’s cold tolerance mechanisms. In this study, we demonstrate that the microbial community of wild-caught fruit flies fluctuates with the seasons, with season-specific microbial partners. To investigate the potential role of microbes in Drosophila melanogaster’s cold tolerance, we infected axenic flies with fungal and/or bacterial strains isolated from wild-caught flies and tested their fitness. Our results show that gut microbes can mitigate cold-induced delays in larval development, decreases in reproductive success, and lower mortality rates after cold shock. Further research is essential to unravel the mechanistic basis of these interactions, which is necessary for predicting the survival of natural populations of microbe-associated insects beyond our laboratory strains, particularly in the context of global climate change.
Members of the Roseobacter group (class Alphaproteobacteria) can account for up to 25% of the bacterial community in marine ecosystems. They are physiologically versatile, which can be regarded as prerequisite for an adaptation to different ecological niches. Members of the group are morphologically heterogeneous and either form rod- shaped single cells of variable length or multicellular rosettes. Here, we identified triggers for cell elongation in the heterotrophic model strain Phaeobacter inhibens that appear to function in independence of previously studied quorum sensing mechanisms. Using time-lapse microscopy and quantitative image analysis we show that P. inhibens undergoes morphological changes in response to the presence of eukaryotic cells or culture extracts, for example of algae and lysed diatoms. Similar effects were observed with medium containing yeast extract. The longitudinal cell elongation presumably increases the buoyancy of the bacterial cells. Reversal of the morphological phenotype was achieved by removing the trigger with a medium exchange. Continuing cultivation in medium without eukaryotic material results in immediate reinitiation of cell division: elongated cells turn back to rod- shaped single cells and rosettes. We thus hypothesize that P. inhibens uses cell shape modifications to control buoyancy and to enlargen the surface for attachment in nutrient-rich zones.
Which partners engage (repeatedly) in symbiotic interactions and how did they change during short or long-lasting associations?
The arbuscular mycorrhizal symbiosis (AMS) is a crucial partnership that enabled plants to colonize land. However, some plant lineages have evolved to abandon this symbiosis. We explored how these non-mycorrhizal plants obtain phosphorus,a nutrient typically provided by AMS. Our research discovered that these plants have formed new relationships with diverse fungi, especially those belonging to the Helotiales order. These fungi can significantly enhance plant growth and phosphorus uptake, demonstrating that non-mycorrhizal plants have adapted to phosphorus-deficient environments by developing novel partnerships with specific fungal communities.
Beneficial associations between insects and microbes are widespread, however our understanding of complex microbial communities with intricate interactions between the members and their influence on composition and functionality of symbiosis remains limited. We address symbiont-symbiont interactions in the context of a multipartite defensive symbiosis. Lagria villosa (Coleoptera: Tenebrionidae) engage in a symbiosis with multiple strains of Burkholderia gladioli that protect the beetle’s offspring from fungi. B. gladioli Lv-StB produces the antifungal compound lagriamide, B. gladioli Lv-StA is culturable in vitro and has the ability to produce multiple secondary metabolites that confer protection against fungi. To investigate the strain dynamics during colonization, Lv-StA was applied to Lv-StB infected eggs and larvae. Both strains could colonize the beetle’s organs individually, in combination, and in succession, indicating that the strains do not outcompete each other and the symbiosis remains open to environmental microbes. To study the impact of individual secondary metabolites produced by Lv-StA, we generated single knockout mutants and started conducting in vivo bioassays against a fungal antagonist of Lagria villosa. We anticipate to reveal if one compound or a combination of multiple compounds is needed for the defense. We hope to contribute to the understanding of symbiont-symbiont interactions in complex systems.
Microbial communities associated with plants play a crucial role in their host’s health and can influence essential physiological pathways. So far, the dynamic of microbiomes in plant populations from natural ecosystems is poorly described beyond studies in the model plant Arabidopsis thaliana. Through the study of the grass species Agrostis capillaris, we aim to explore the dynamic of microbial communities and to characterize how vegetation management impact the microbiome diversity and composition. Through the analysis of the microbiome diversity, composition and community structure in leaves roots and soil, we looked at the impact of mowing and grazing on the A. capillaris microbiome for 3 consecutive years. Our results highlight a strong impact of the plant tissue on the diversity and microbial composition. Moreover, bacterial communities tend to be stable across 3-year periods, while the diversity and composition of fungal communities change. Finally, the community structure analysis allowed us to identify several fungal and bacterial pathogenic species among the most connected individuals in the leaf microbiome communities, including species of Zymoseptoria. This study represents a first step for investigating the mechanisms shaping the plant microbiome in natural ecosystems, as well as for identifying potential future pathogenic species that could threaten crops.
Fungi of the subphylum Mortierellamycotina occur ubiquitously in soils where they play pivotal roles in carbon cycling, xenobiont degradation, and promoting plant growth. These important fungi are, however, threatened by micropredators such as fungivorous nematodes, and yet little is known about their protective tactics. We have found that Podila verticillata shields itself from fungivorous nematodes with the help of toxin-producing bacterial endosymbionts. We provide evidence that the highly cytotoxic macrolactones (CJ-12,950 and CJ-13,357, syn. necroxime C and D), which were believed to be fungal metabolites, are in fact produced by a previously overlooked bacterial endosymbiont, Candidatus Mycoavidus necroximicus. Using the model organism Caenorhabditis elegans and the fungivorous nematode Aphelenchus avenae, we probed the anthelmintic activity of the necroximes and demonstrated the effective host protection in cocultures of nematodes with symbiotic and chemically complemented aposymbiotic fungal strains. Additionally, we discovered a novel cyclic lipodepsipeptide (symbiosin) produced by the endosymbionts, which synergizes with necroximes and boosts anthelmintic activity. This study reveals an important function for endofungal bacteria as producers of protecting agents and opens the possibility for the development of new biocontrol agents.
What chemical and molecular communication mechanisms are employed by symbiotic partners?
The recent advancements in metabolomics and genomic sequencing technologies have sparked a resurgence in natural product exploration, especially in ecological contexts. Analysing the intricate chemistry of symbiotic systems has become increasingly important given the significance of diverse microbial metabolites in regulating such interactions. Our recent findings highlight that symbiotic microbes present prolific sources of novel biochemistry and secondary metabolites and that we can use the chemical and genomic information to increase the structural diversity of natural products. Here, I will elaborate on two recent examples that highlight the enormous biosynthetic repertoire of protective bacterial symbionts and their unique natural product chemistry. The first example will highlight a novel family of non-ribosomally synthesized peptides, which exhibits unusual combinations of chemical modifications. In a second example I will elaborate on a non-canonical polyketide synthase-derived metabolite family with antimicrobial properties, which exhibits structural features derived from different oxidative rearrangement steps.
Symbiotic relationships between unicellular eukaryotes (protists) and endosymbiotic bacteria are widespread, unexpectedly diverse, dynamic and have been established independently many times. We explore the interactions between intracellular rickettsiae, chlamydiae, and holosporacea and diplonemids, which are extremely diverse, abundant yet understudied free- living marine flagellates. While some diplonemids have no endosymbionts, others host one or even two bacterial species. Interestingly, these endosymbionts can be quite easily removed from and reintroduced into their host, without a growth effect in culture. However, when aposymbiotic diplonemids originally hosting chlamydiae and holosporacea are first infected with chlamydiae, it is impossible to subsequently introduce holosporacea, and the same applies vice versa, a strong indication of protective endosymbiosis. We are also exploring metabolic alterations between the symbiotic and aposymbiotic diplonemids. We propose that diplonemids may serve as vectors for chlamydial pathogens of marine fish. In another endosymbiotic system, we study cytoplasmic β-proteobacteria in the parasitic trypanosomatid flagellates of the genera Angomonas, Strigomonas, Kentomonas and Novymonas. While some endosymbionts can be eliminated when the culture medium is supplemented with heme, most relationships are permanent, as the bacteria provide essential nutrients such as amino acids, purines, vitamins, and heme to their hosts. In some cases, the host keeps a single bacterium per cell, while other flagellates exercise no tight control, resulting in a variable number of bacteria per the protist host. We are in the process of functional characterization of several host genome-encoded proteins that have been neo- functionalized in order to control the number and intracellular position of the endosymbionts.
The Common Symbiosis Signalling Pathway (CSSP) plays a pivotal role in orchestrating symbiotic relationships between plants and arbuscular mycorrhiza fungi, as well as between leguminuos plants and nitrogen-fixing bacteria. These symbioses are vital for optimal plant nutrient acquisition, particularly nitrogen and phosphorous. While the functions of CSSP genes in arbuscular mycorrhizal symbiosis in cereals are well- documented, their impact on other root microbiota, such as free-living nitrogen-fixing bacteria, remains unknown. Understanding interactions between cereals and other potentially beneficial soil microbes is crucial for addressing contemporary environmental challenges related to crop nutrient limitations and organic fertiliser development. In our approach, we employed barley CSSP mutants and combined microbiome profiling and metabolomics to unravel the effect of symbiosis signalling on bacterial assembly, and to identify CSSP-dependent root metabolites that navigate plant-microbe interactions. Our findings reveal that CSSP genes exert distinct effects on various rhizosphere bacteria, including Rhizobiales, which host a broad variety of nitrogen-fixing species. We identified that CSSP genes are involved in the biosynthesis of several signalling molecules, such as flavonoids, known in legumes for attracting nitrogen-fixing bacterial symbionts. These results provide a foundation for future research and engineering efforts to enhance cereal interactions with beneficial soil bacteria, addressing current agricultural challenges.
What chemical and molecular communication mechanisms are employed by symbiotic partners?
Host-microbe associations are essential for the health of seagrass meadows. While the seagrasses themselves host specific and benefical ‘microbiomes’, also symbionts of co-occurring animals can benefit the seagrass ecosystem, such as the sulfur-oxidizing Thiodiazotropha endosymbionts of lucinid clams that ‘detoxify’ seagrass sediments. Molecular surveys are revealing members of the genus Thiodiazotropha in root and rhizome microbiomes of seagrasses, however, their relationships to clam symbionts are unknown. We used a combination of sequencing techniques to reveal the diversity of Thiodiazotropha symbionts in co-occurring lucinids and seagrass Cymodocea nodosa. In >100 clams, within-host symbiont diversity was greater than previously observed, with multiple symbiont types co-occurring regularly. These symbionts were also identified on seagrass roots in the surrounding environment along with many other Thiodiazotropha sequence variants. The environment may therefore have a greater influence on symbiont diversity than previously thought by offering a secondary niche. Using a metacommunity model, we show that the presence of a second co-occurring host type (seagrass) can increase symbiont diversity within clams. Intimate symbionts are usually highly specialized to associate with a particular host species. Thiodiaoztropha would be the first symbiont capable of intimate associations with both a plant and an animal host.
Even though exact ecology and trophic mode of Umbelopsis (Mucoromycota) representatives remain elusive, these fungi are considered soil saprotrophes, often associated with plant matter. Umbelopsis fungi interact frequently with bacteria, and Paraburkholderia are among the most common symbionts. This relationship is facultative, unlike previously described Mucoromycota- Burkholderiaceae interactions. So far, in-depth genomic characterizations are available only for strictly endohyphal bacteria and their mucoralean hosts. As non-obligatory interkingdom interactions are generally more common in nature, Umbelopsis-Paraburkholderia is a particularly good model for studying the evolution of endohyphal interactions. Here, we characterized genomes of both partners, adding close relatives as a reference dataset. Genomes were sequenced using MinION Nanopore and Illumina, then assembled and annotated. Even though studied Paraburkholderia genome is similar to genomes of its free-living relatives, it also contains genes needed for establishment and maintenance of endohyphal interaction, such as genes encoding diacylglycerol kinases. We also detected metabolic intertwinement in wood degrading capacities of both partners potential plant growth promotion factors in bacteria which suggests that the consortium is well adapted to develop in decaying wood from which it was isolated. It thus seems that although partners can live independently, together they may be able to occupy niches otherwise not available.
Reproductive synchronization between hosts and guests is a defining feature of obligatory endosymbioses. However, the evolutionary stability of synchronization remains unclear when hosts and guests battle to control resource allocation to maximize their own fitness. Here, we examine how control exerted by the host over the guest (or vice versa) affects the evolution of synchronization. We employ genome-scale metabolic network models from the AGORA and CarveMe databases to systematically analyze host-guest interactions. Leveraging thousands of host-guest pairs, we found that synchronization rarely emerges naturally when hosts and guests strive to maximize their own finesses. Our results indicate that the cost of synchronization is context-dependent on control and whether the controller is a host or guest. We then develop a mathematical model and find a simple rule determining what conditions favor synchronization against transient endosymbioses. Ultimately, our results suggest that the path to synchronization is unlikely to emerge without costs and requires a particular tradeoff to be evolutionarily stable.
Leaf bacteria are critical for plant health, but little is known about how plant traits control their recruitment. Aliphatic glucosinolates (GLSs) are metabolites usually associated with defense that are present in leaves of Brassicaceae plants in genotypically-defined mixtures. Upon plant cell damage, they break down into products that deter herbivory and inhibit pathogens. We studied natural colonization of commensal leaf bacteria in the model A. thaliana genotype Col-0 which produces mainly 4-methylsulfinylbutyl-GLS and NG2, a genotype isolated from a local wild population, with mainly allyl-GLS. Comparing colonization in WT and GLSs-free mutants in both backgrounds showed that GLSs differentially affect leaf communities. In Col-0, GLSs had no measurable effect, but in NG2 they surprisingly enriched certain bacteria. Allyl-GLS likely functions as a resource, since similar leaf bacteria were enriched on it as a sole carbon source in-vitro, but not on 4MSOB-GLS. All enriched bacteria were fully dependent on a specialized Yersiniaceae strain that metabolized allyl-GLS and detoxified the resulting breakdown products. Further evidence supported GLS substrate specificity arising at the GLS hydrolysis step, catalyzed by myrosinase. Together, these results suggest that well-studied defense metabolites can have broader roles in the plant microverse, providing important insight into recruitment of bacterial symbionts.
This session is dedicated to student talks from any field of study.
Bacteria of the family Cand. Midichloriaceae (Rickettsiales, Alphaproteobacteria) like Aquarickettsia spp. or Grellia spp. are common intracellular symbionts in a wide range of aquatic protists and animals, such as euglenozoans, placozoans or cnidarians. They have been detected in almost 10% of all aquatic microbiomes, but their pathogenic or beneficial roles in the associations remain unclear. To better understand the ecophysiology and the molecular mechanisms behind these symbioses, we combine RNASeq data from experiments with high-resolution imaging techniques such as immunofluorescence and fluorescence in-situ hybridization in a 3D context and at sub-cellular resolution. A special focus of our work are effector proteins of the symbionts that are secreted into the host cells and that appear to modulate host cell biology to create and stabilize the intracellular niche of the symbionts. We use structural modelling, phylogenetic analyses and recombinant expression-based experiments for the characterization of these effectors and the validation of their function. Based on our preliminary results, the Midichloriaceae symbionts in our protist and animal models are in mutualistic rather than parasitic interactions and likely support their hosts with the digestion of energy rich and commonly available fungal and algal carbohydrates.
Nutritional symbioses between chemosynthetic bacteria and animals form the base of the food web at hydrothermal vent ecosystems. Deep-sea mussels are among the most successful host groups in these ecosystems, and many species harbor sulfur-oxidizing (SOX) bacteria. We discovered that SOX symbionts in deep-sea mussels differ in their morphology: some mussels have endosymbionts, while others have ectosymbionts. Endosymbionts live inside specialized gill cells, whereas ectosymbionts colonize the surfaces of gill cells. Our study examined how these lifestyles influence the metabolic potential and strain diversity of SOX symbionts in five mussel species. We found no significant differences between endo- and ectosymbionts in genome size, GC content, or central metabolic pathways. The only notable difference was the higher strain diversity of ectosymbionts, with four times higher single nucleotide variants in ectosymbionts compared to endosymbionts. This higher strain diversity could be shaped by relaxed host selectivity in ectosymbiotic associations, or the ectosymbionts' exposure to more heterogeneous environments compared to the relatively stable environment inside host cells. Ongoing analyses of symbiont population sizes and the influence of selection on genes (pN/pS) aim to elucidate the processes shaping the genetic diversity of ectosymbionts.
The flourishing of nutrient-providing and pathogen-suppressing microbiota is a prerequisite within the ontogenetic environment of Drosophila melanogaster fruit flies. In different plant substrates, larvae achieve higher developmental success with autochthonous vs. allochthonous microbial symbionts, vertically inherited through fecal matter deposition by egg-laying females. This indicates that certain groups of microbes contribute to maintaining developmental stability in a changing environment, but which and how many microbial symbionts are key to successful developmental niche construction? And which mechanisms regulate microbial dynamics that feedback on insect phenotypic trait expression? In our study, we aim to create a standardized gnotobiotic fly model that can be manipulated to mirror the environmental changes faced by D. melanogaster in the wild. We are establishing a substrate-specific library of symbiont bacteria and fungi from fly populations maintained in various environments. We will present simplified microbiota used to quantify dynamics in symbiont succession and explore their individual and combined capacity to nourish larvae and/or defend them against pathogens. In particular, we are interested in how symbiont dynamics feedback on the quality of insects’ ontogenetic environment and shape their phenotypes when flies are subject to environmental variation in plant substrate properties and abiotic stressors.
Beetles have a hard cuticle that protects them against biotic and abiotic threats. Tyrosine is essential for cuticle synthesis but insects cannot synthesize it and must obtain it with their diet. Our study investigates the symbiotic relationship between Dinoderus porcellus and its two bacterial symbionts focusing on their contribution to the host’s cuticle development. The symbiont Shikimatogenerans retained the shikimate pathway that produces the precursor of tyrosine. The second symbiont, Bostrichidicola, retained genes involved in urea recycling and the biosynthesis of lysine. We assessed the symbionts’ contribution to the host by supplementing the beetle’s diet with antibiotics or inhibitors of metabolic pathways, then evaluating the effects on symbiont titers, cuticle thickness, and pigmentation. Antibiotics and glyphosate significantly reduced Shikimatogenerans titers and compromised cuticle pigmentation, supporting our hypothesis that the host benefits from symbiont-derived tyrosine precursors. Inhibitor of lysine metabolic pathway resulted in increased Bostrichidicola titers but no cuticle changes, suggesting its alternative roles for host metabolism. Furthermore, injection of 15N-urea into resulted in broad incorporation of the 15N-label into adults’ amino acids attesting to the importance of Bostrichidicola ability to recycle nitrogen and potential tripartite metabolite exchange although not necessarily in the context of cuticle synthesis.
Insects frequently form symbioses with beneficial bacteria that are passed onto subsequent generations. While these heritable bacterial symbionts often play important roles in host biology, experimental approaches often are limited by an inability to independently cultivate such symbionts. Here, we demonstrate the independent cultivation of Fukatsuia symbiotica, a vertically transmitted endosymbiont of the pea aphid, Acyrthosiphon pisum. Whole-genome sequencing revealed that this strain shares similar genomic features with vertically transmitted Fukatsuia strains of pea aphids and other distantly related host species, suggesting these methods might be broadly applicable. Microinjection of the symbiont cultures into uninfected hosts revealed that this strain is capable of re-establishing stable, transgenerational infections. Once established, these artificially generated infections exhibit similar phenotypic effects on hosts, including protection against a fungal pathogen and disruption of embryonic development. Overall, our results indicate that Fukatsuia symbiotica is a valuable tool for understanding the genetic basis for vertical transmission and antifungal defenses.
The brown alga Ascophyllum nodosum and its microbiota form a dynamic functional entity named holobiont. The microbial partners play a role in seaweed health by producing bioactive compounds crucial for normal morphology and development. Ascophyllum is also an important raw material to produce plant biostimulants. However, we need more knowledge about the microbiome of Ascophyllum to understand the role of symbionts in bioactive molecule production. Within the SEABIOZ project, we are studying the roles of microorganisms associated with Ascophyllum through multi-omics approaches. By combining long-read and short-read metabarcoding approaches, we examined the composition of the microbiome (bacteria, archaea, fungi, and other eukaryotes) over a year, including algal tissue, and site as covariables. We identified three major player symbionts as there are almost always associated with the host and found in high relative abundance: the two fungi Mycophycias ascophylli and Moheitospora sp., and the bacterium Granulosicoccus sp.. Moheitospora sp. and Granulosicoccus sp. were successfully cultured and sequenced. However, Mycophycias ascophylli is still uncultivable and to obtain its genome sequence, we used Illumina metagenome assembly, real-time read enrichment during long-read metagenome re-sequencing, and hybrid assemblies. The analysis of microbial genomes provided access to their potential metabolic and biological functions in the holobiont ecosystem.
In biofilms, host tissues, or intracellular environments - what consequence does spatial localization have on individual organisms?
Understanding symbiotic interactions between soil organisms is important to understand how edaphic ecosystems contribute to ecosystem functioning, as well as plant health and nutrition. Traditional techniques are limited in their ability to capture the spatial and temporal dynamics of these interactions. Microfluidic, or "on-a-chip", technology aims to fill this methodological gap through the manufacturing of custom-designed simplified micro-environments. Current microfluidic research has focused on single organism studies, but the next frontier is combining multiple interacting organisms into a "symbiosis-on-a-chip".
Many insects have evolved in beneficial associations with microorganisms, among which is the supplementation of nutrients. Some grain pest beetles have successfully adapted to dry conditions due to their thick cuticles, which is attributed to their ancient endosymbiont. Among the grain pest beetles with tyrosine supplementing symbionts, Prostephanus truncatus harbors the ancient symbiont, Shikimatogenerans bostrichidophilus, which diverged into three lineages with complementary gene repertoires. Symbiont genomic analyses revealed complementary gene distributions among the three strains, suggesting obligate metabolic exchange among the symbionts. Different Fluorescence in situ hybridization (FISH) techniques were used to localize bacterial lineage-specific DNA and RNA molecules. Macromolecular distribution and ultra-structure imaging demonstrated host-life-stage-dependent symbiont dynamics and presumable interactions among symbiont cells via connections and transport. Finally, experimental manipulation of symbionts resulted in thinner and brighter beetle cuticles, verifying the functional integrity of metabolically fragmented symbiont genomes. The results suggest that Prostephanus necessarily need to maintain and transmit three lineages of symbionts, which is widely considered to be non-adaptive. Applying different imaging techniques, we present potential mechanisms of interactions among the interdependent bacteria and illustrate the context- dependent FISH results in endosymbiont research.
Leaf-associated microbial communities are shaped by diverse factors including host species, environmental conditions, and heterogeneous microenvironments across leaf surfaces. This environmental heterogeneity results in each bacterial cell experiencing unique local conditions, driving individual behaviours that influence not only survival but also the broader community dynamics. By focusing on single-cell resolution, we can reveal key microbial adaptations, such as reproductive success and resource utilisation, and gain insights into how individual cells contribute to population-level functionality and the assembly of microbial communities. To explore these complex dynamics, bioreporter technology and single-cell analysis have emerged as key approaches, enabling detailed studies of gene expression and interactions at the individual cell level. Our research has focused on developing a suite of genetic tools for studying leaf-associated bacteria, including fluorescent markers for the in situ visualisation of bacterial arrangements on leaf surfaces, reporters to track reproductive success in varied contexts, and substrate- dependent reporters to investigate how bacteria respond to their environment. This approach has deepened our understanding of how individual bacteria contribute to populations, community functions, and bacterium-host interactions. This knowledge is key for designing synthetic bacterial communities from the ground up, allowing us to understand emergent properties and processes underlying community assembly.
Chemical interactions enable bacteria to associate closely with organisms across all domains of life. Beyond mutualistic and pathogenic interactions, small molecules known as metabolites not only provide essential building blocks for cellular membranes but also facilitate interactions between microbes and their hosts. A major challenge in studying metabolites involved in host-microbe interactions is determining whether a given metabolite corresponds to the site of colonization. Mass spectrometry imaging (MSI) offers a powerful approach for unraveling the metabolic fingerprints and interactions of microbes within animal tissues.
To study the endosymbionts of chemosynthetic mussels of the genus Bathymodiolus from deep-sea vents, I integrated high-resolution MSI with fluorescence labeling of the intracellular symbionts. With this correlative approach, I was able to assign hundreds of metabolite distributions to either the host or its symbionts within a single measurement, revealing the heterogeneous metabolic landscape of the animals’ symbiotic organ on a micrometer scale.
To investigate the site-specific metabolism of another intimate microbe that colonizes specific micro-niches in its host, I applied my approach to study the interaction between the pathogen Helicobacter pylori and stomach epithelium. H. pylori colonizes the human stomach and can persist for decades. Since MSI is limited to metabolic snapshots, the next frontier in studying spatial metabolism involves mimicking and experimentally perturbing the tissue microenvironments that arise from host-microbe interactions. I use a novel gastric organoid model to monitor and manipulate the cell-cell interactions between bacteria and host, ultimately resolving micrometer-scale metabolic interactions between clonal microcolonies and the gastric epithelium through MSI.
By pivoting between research on environmental symbioses and pathogenesis, my goal is not only to discover but also to test the factors that drive the metabolic heterogeneity underlying host-microbe interactions.
What are cutting-edge methods in symbiosis research and how are they applied across systems?
The astonishing diversity of eukaryotes results from a continuous evolution process and the emergence of functional traits. Such innovations allowed eukaryotes to adapt to all biomes and conditions on Earth and are regulated by complex genetic mechanisms. One of the key innovations that paved the way of eukaryotes diversity is their ability to establish mutualistic interactions with microorganisms such as plant and fungi. Mutualistic interactions are diverse and can be intra- or extracellular. Understanding the genetic mechanisms regulating such interactions is one of the key questions in biology. For example, deciphering these mechanisms in plant-microbe interactions open the perspectives of symbiotic-improved crops demanding fewer chemical intrants. In insects, understanding their interactions with microorganisms can improve their protection or pave the way for more environmental-friendly management plans. Most of the interactions have been studied in model species. However, such approaches are sensitive to the species-specific genetic background. With the genomic era, genomes from multiple species are now available covering the diversity of species but also of their symbiotic abilities. By comparing large numbers of genomes in an evolutionary context, phylogenomic is a powerful tool to identify genetic mechanisms associated with the ability to establish symbiotic relationships. In addition, integrating additional data such as transcriptomics, we are able to identify shared and specific modules of regulatory networks associated with mutualistic interactions and their evolution in multiple species.
The Eurasian spruce bark beetle (Ips typographus) is currently the most economically relevant pest of Norway spruce (Picea abies). This insect associates with filamentous fungi that may help it overcome the tree’s chemical defenses. However, the involvement of other microbial partners in this pest’s ecological success is unclear. In past works, we have shown that the core fungal and bacterial gut microbiota is stable across life stages, geographic location, seasonality, and rearing conditions. Further, we have shown that I. typographus females transfer part of its microbiota to the eggs via the deposition of an bark plug treated with maternal secretions, and by inducing an increase in abundance of a subset of taxa from the adjacent phloem. While the taxanomic characterization transmission routes of the core taxa are important groundwork to understand the importance of the microbiota for the host, the location of the bacterial partners in the gut has remained elusive. The use of advanced microscopy techniques, such as Fluorescence Lifetime Imaging (FLIM) and Stimulated-Emission Depletion (STED), could be the key to overcome the difficulties of imaging symbionts in the gut of bark-feeding insects. Imaging the distribution of key microbial taxa along the alimentary canal would provide valuable information to understand this complex microorganism-plant-arthropod study system.
Mosquito saliva was shown to play a key role in arbovirus transmission and pathogenesis. In this study, we explored the presence of microbiota (fungi and bacteria) in mosquito saliva and their effect on mosquito-borne virus infection in vitro. Culturable fungal and bacterial colonies were isolated and identified from saliva harvested from Aedes aegypti (lab strain mosquitoes) and Culex pipiens (field-collected mosquitoes). For the first time, the fungal species Penicillium crustosum was discovered in mosquitoes. Culturable bacteria detected in the mosquito saliva included Serratia marcescens, Serratia nematodiphila, Enterobacter spp., and Klebsiella spp., which were previously identified as mosquito or insect endosymbionts in the midgut or other mosquito organs. Oral treatment of adult mosquitoes with antibiotics or an antifungal drug resulted in a significant reduction of bacteria or fungi in saliva. (Pre-) Incubation of Semliki Forest virus with saliva from antibiotic or antifungal treated mosquitoes triggered a decrease in viral infection in human skin fibroblasts compared to non-treated saliva. These results demonstrate an important role for the mosquito saliva microbiota in mosquito-borne virus replication and further in vivo studies are required to better understand its impact on viral transmission.
Endosymbioses can give rise to new combinations of biochemical capabilities that promote evolutionary innovation and diversification. But despite the many examples of known endosymbioses across the tree of life, their de novo emergence is rare and challenging to uncover in retrospect. Using fluidic force microscopy (FluidFM), we directly implant bacteria into the filamentous fungus Rhizopus microsporus to follow the fate of artificially induced endosymbioses. While Escherichia coli implanted into the cytosol induced septum formation, effectively halting endosymbiogenesis, Mycetohabitans rhizoxinica was transmitted vertically to the progeny at low frequency. Continuous positive selection on endosymbiosis through cell sorting mitigated initial fitness constraints by several orders of magnitude upon adaptive evolution. These phenotypic changes were underscored by the accumulation of mutations in the host as the system stabilized. In the new host, the bacterium produced rhizoxin congeners, demonstrating the transfer of a metabolic function through induced endosymbiosis. Single cell implantation thus provides a powerful experimental approach to study critical events at the onset of endosymbiogenesis, highlights associated costs and opportunities, and opens possibilities for synthetic approaches towards designing endosymbioses with desired traits.