Animal host control of beneficial bacteria

What keeps non-pathogenic microorganisms at bay? Despite our genome-based understanding of the metabolic capacities of microbial symbionts is steadily increasing, little is known about how the host controls and confines them. All the same, it is primal to know how the symbiont manipulates host physiology to stably associate with it. In vertebrates, the microbiome plays a fundamental role in the bidirectional axis that integrates the gut and central nervous system activities, but the mechanisms responsible for microbiota-nervous system interactions are largely unknown. Marine nematode-bacterium associations are exquisitly specific i.e. only one bacterial species can associate to the surface of one nematode species. Additionally, the symbiont spatial organization on the host surface is exact and faithfully maintained throughout host and symbiont generations via epidermal glandular sensory organs. In this research proposal we want to understand (1) how the animal immune and nervous systems control the identity, number and spatial distribution of their beneficial bacteria and (2) what is the ecological and evolutionary significance of specific symbiosis outfits (i.e. bacterial coat architectures). We will address these questions by comparing transcriptomes of symbiotic vs non- symbiotic tissues, as well as those of four selected host species. Moreover, we will compare the transcriptomes and proteomes of the four corresponding symbionts. Upon employment of omics techniques, we will analyze the function of selected molecules such as host immune effectors and neuropeptides, or symbiont secretion systems. Moreover, omics data will be employed to predict host-symbiont molecular exchange via metabolic modeling.

This project aimed at understanding the unique symbiosis between and animal, the nematode L. oneistus, and the single bacterial species coating its surface, the gammaproteobacterium Candidatus Thiosymbion oneisti. Namely, by applying omics and stable isotope-based techniques, we wanted to know how (1) the animal selects and control symbiont proliferation, (2) the symbiont is kept by its host and (3) how the nematode-bacterium consortium reacts to environmental changes (in particular to oxygen, as the worm is thought to migrate between the sand redox boundary). Concerning (1), we found that when anoxic, L. oneistus upregulated genes putatively involved in specific symbiont recruitment (e.g., lectins, mucins, lysozymes) and likely supported symbiont proliferation by providing phospholipids. Remarkably, the worm could engage in this and in other energy-demanding processes (e.g., ribosome biogenesis) likely by rewiring its electron transfer chain in such way as to use rhodoquinone as electron carrier and fumarate as electron acceptor. Concerning (2), we found that symbiont sulfur oxidation is upregulated in anoxia, which may help the worm avoiding sulfide poisoning when crawling in predator-free sand. However, when exposed to oxygen, symbiont proliferation was hampered, apparently due to oxidative stress and to the upregulation of host immune pathways (e.g., Toll). Concerning (3), we propose that wherever in the sand the consortium is, one of the two partners is bound to be stressed and to proliferate less: in anoxia, the symbiont multiplies rapidly (by relying on sulfur oxidation coupled to denitrification), while its animal host mainly engages in degradation of damaged proteins and mitochondria. In the presence of oxygen, the situation is inverted: the symbiont is stressed, while the animal host can afford energy costly biosynthetic processes to develop and reproduce. Based on all the above data (Paredes et al., 2021; Paredes et al., in preparation), we also propose that, although the symbiont is a mixotrophic nitrogen-fixing rod, the possibility of exploiting host-derived nutrients (e.g., phospholipids, small organic compounds, ammonia) may have driven longitudinal division - a reproduction mode which guarantees host attachment to both daughter cells. Concerning symbiont cell biology, although originally not planned, we also discovered that, in a longitudinally dividing rod, a bidimensional segregation mode endows maintenance of a fixed chromosome configuration (Weber et al., 2019) and that bacterial symbiont can be cuboid (Weber et al., 2021). In conclusion, our research showed that two dramatically incompatible partners, an animal and an anaerobic bacterium, can hold onto each other thanks to an exquisitely fine environmental regulation of their symbiosis.