Nudi-Symb

Title: New culture-independent methods for discovering bacterial symbionts of soft-bodied marine animals and their contribution to chemical defense of their host

Research groups: Microbial Single-Cell Genomics and Theory, Bioinformatics and Computation

Soft-bodied marine animals, such as sponges, corals, tunicates and mollusks, are known to use a variety of bioactive compounds as a protective strategy to fend off their potential predators, however, it is estimated that thousands of novel compounds are yet to be discovered. The presence of these bioactive compounds in tissues of marine soft-bodied animals does not automatically mean that they are produced by these animals. In this sense, our research team was the first to discover that nudibranchs contain novel taxonomic lineages of bacterial symbionts that produce previously unknown bioactive molecules providing chemical defense for their hosts. Its biosynthetic gene cluster (BGC) was discovered by culture-independent genomic techniques with the objetive to produce the bioactive molecule by a heterologous gene expression system. However, it is very common that despite the BGC is expressed by the heterologous culture, the complete synthesis of the final molecule cannot be not achieved. These results inspired us to formulate the principal hypothesis of the Nudi-Symb project: nudibranch hosts might be providing some precursors to their symbiotic bacteria which at the end result in synthesis of the bioactive molecule. So far, only 5% of the 6,000 known nudibranch species have been studied for their bioactive molecules and 0.5% for their microbiome composition, thus new chemical compounds and new uncultured bacterial lineages (new families, orders, classes or even phyla) are surely yet to be discovered. In order to find more nudibranch species harboring novel symbiotic bacteria, we will investigate a large collection of nudibranch species by a variety of innovative and sophisticated approaches. We will develop new methodologies for 1) single-cell genomics of bacteria coming from ethanol preserved tissues of nudibranchs in order to detect novel bacterial lineages and novel BGCs, 2) recovering different sequence variants of the target BGC in other members of the same novel taxonomic lineage by droplet-PCR and subsequent sequencing of selected bacterial cells coming from preserved nudibranchs, fresh nudibranchs and other soft-bodied animals or algae collected on the same site, 3) obtaining draft genomes of the selected nudibranch and analyzing its gene expression profiles from different body sites and stress vs. normal conditions, 4) studying transmission of the target bacterial lineages between nudibranchs and other animals and algae on the same collection site. The methodologies developed in the Nudi-Symb project taken together will provide a complete picture of how symbiotic microbes interact with their hosts when synthesizing the bioactive molecules. This combined approach has not been used in any previous study on nudibranchs, neither in any previous studies on other soft-bodied marine animals. We will produce high impact results on the mechanism behind the interactions between nudibranchs and their symbiotic bacteria, which will be useful for expanding our general knowledge in the fields of microbiology, zoology, ecology and bioinformatics, and also will be of interest for the biotechnological industry. The laboratory and bioinformatic methods, and the molecular structures discovered in the Nudi-Symb project can be used in the future for development of new medical drugs, which is the most important long-term benefit of this project for the whole society.

symbiosis, microbiome, systems biology, microbial single-cell genomics, metagenomics, transcriptomics, biosynthetic gene clusters, uncultured microbes, nudibranchs, marine soft-bodied animals

Ministerio de Ciencia e Innovación

Universitat de València