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Symbiomics: Molecular Ecology and Evolution of Bacterial Symbionts

Final Report Summary - SYMBIOMICS (Symbiomics: Molecular Ecology and Evolution of Bacterial Symbionts)

Symbiosis research is currently in the midst of a revolution as molecular techniques are leading to major breakthroughs in our understanding of interactions between animals and microbes. There is an emerging recognition that all animals are intimately associated with a complex community of beneficial microbes that are essential for their development, nutrition, and health. Thus, modern symbiosis research has become a newly emerging supra-disciplinary field with novel and innovative methods for examining microbial symbionts, the vast majority of which remain as yet uncultivable. As so often when novel technologies open up new areas of research, training for students lags behind. We closed this gap by offering a comprehensive and innovative training in the microbial ecology and evolution of animal symbionts.

The ITN Symbiomics started with 14 leading research groups and 4 top-tier participants from the private sector to provide 14 early stage researchers (ESR, i.e. PhD students) and 1 experienced research (ER, i.e. postdoctoral fellow) with an interdisciplinary and synergistic training. Symbiomics provided training through a combination of local and network-wide activities that included research, secondments, workshops and courses including soft skills training, networking and meetings, regular thesis committee meetings, and mentoring. The ITN-wide training workshops included training in diverse cutting edge microscopic and molecular techniques combined with confocal Raman and secondary ion mass microspectroscopy, initial steps into the world of genomics, proteomics and metabolomics, courses in phylogenetics and basic bioinformatics, as well as two field workshops on the ecology of marine symbioses. As a response to scientific progress in the course of the project and to provide additional highest quality secondments for the individual early stage researchers, the consortium even broadened its competence spectrum in the second project half by taking up five additional partners from academia and one from the private sector. By pooling the scientific, technological, and entrepreneurial expertise of the Symbiomics partners, this ITN provided a training that extends far beyond what each partner would be able to offer with local training alone.

The ITN was structured in three scientific Workpackages (WPs) and one for the project management. The individual Research Tasks of the ESR and ER in the scientific WPs used cutting edge methods in molecular biology, image analysis and bioinformatics to analyze a broad range of hosts from protozoan and invertebrate animal groups.

The goal of WP 1 (Evolutionary Symbiomics) was to test hypotheses about functional convergence in endosymbionts and their hosts that go along with evolutionary symbiont genome reduction. One focus has been on insect symbionts such as Lactobacillus species in honey bees and Serratia symbiotica in aphids. While the genomes of these symbionts have undergone significant size reductions, they revealed remarkable and unexpected variability in certain metabolic genes or variations in genome sizes that was due to accumulation of junk DNA. Another focus was on symbionts from deep-sea invertebrates such as the chemosynthetic Bathymodiolus mussels. A novel epsilonproteobacterial ectosymbiont of these mussels revealed the presence of a carbon fixation pathway that was most likely received by lateral gene transfer from gammaproteobacterial endosymbionts. To explore the extreme limits of reductive evolution in one of the most ancient symbioses, the functions and metabolic interdependencies between microsporidian parasitic protists and their tiny remnant mitochondria (mitosomes) were examined. A quantitative analysis of the cellular distribution of specific proteins has revealed life cycle stage-specific functions of the mitosome. Global analyses of endosymbiont genomes with bioinformatics methods showed that most symbionts are highly specific for one or a few hosts, and thus that hosts can be distinguished from their content of endosymbionts. A data base was constructed that consists of more than 900 symbiont genomes, including metadata.

WP2 (Metabolic Symbiomics) used advanced proteomics, metabolomics and isotope-detection techniques to reveal the function of amoebal and sponge symbionts from shallow water environments and mussel symbionts from deep-sea hydrothermal vents. Research on Chlamydiae, in particular the deep branching member symbiont of the marine worm Xenoturbella bocki, focused on insight into putative past and current interactions between these organisms and their hosts. Metabolomic studies on the nephridial earthworm symbionts Verminephrobacter monitored the uptake of nutrients and the subsequent intracellular metabolism of the endosymbiotic bacteria. The search for secondary metabolites in the limnetic fungus Pseudohalonectria lignicola revealed both antibacterial and cytotoxic effects, suggesting that this fungus could be a promising candidate for cancer research. Metagenomic and proteomic studies on the dual symbiotic deep-sea mussel Bathymodiolus azoricus suggest that the sulfur-oxidizing symbiont follows an obligate autotrophic lifestyle while the methane-oxidizing symbiont has a potential for heterotrophy. “Omics” studies and experiments with the tropical sponge Iantella basta indicated that its symbiome is strongly dominated by two proteobacterial symbionts and a Thaumarchaeon that live in a synthrophic relationship.

The goal of WP 3 (Ecological Symbiomics) was to study key ecological aspects in a wide range of symbiotic systems to cover the variety of characteristics related to transmission: intracellular endosymbionts in the trophosome of vestimentiferan tubeworms from hydrothermal vents, extracellular endosymbionts in the body wall of gutless oligochaetes, gill intracellular endo- and ectosymbionts in lucinid, mytilid and thyasirid bivalves, and extracellular endosymbionts in the nephridia of earthworms. A multilocus sequencing typing study on the symbionts of the East Pacific Rise vestimentiferan tube worm Riftia pachyptila indicated that free-living symbiont populations were present at vents, on basalt, in sediment and in the water column, and that host-associated and free-living bacteria form a monomorphic population. Metagenomic analyses of colonization experiments with organic substrates that had been deployed in deep-sea environments of the North-East-Atlantic and the Mediterranean indicated that the geographical distribution of free-living symbionts resembled that of their hosts. Investigations on the transmission of multiple extracellular endosymbionts in the gutless oligochaete Olavius algarvensis showed that some bacterial phylotypes are already present in early developmental stages of the eggs suggesting vertical transmission as a possible transfer mode between host generations. Metagenomics and proteomics of shallow water Codakia clams gave insight to a diversity of co-existing pathways for sulfur oxidation in the symbionts. “Omics” analyses of the earthworm symbiont Verminephrobacter eiseniae EF01-2 revealed high abundance of “nanopod” proteins that form recently discovered cell appendices which may play a role in symbiont-host interaction.

The ITN started and continued throughout the project time in a mutually stimulating spirit. The excellent atmosphere led to many bi- or multilateral collaborations among ITN partners that resulted in preparations of several joint scientific manuscripts from which some are already published. To date the ITN ESR and ER have published 2 book sections and 23 publications in peer reviewed journals. Four manuscripts are currently under revision and 29 additional manuscripts are in preparation. Three ESR have finished their theses and defended successfully. All others are in a final phase and are expected to finish within 2015.