Assembling a Micro Eco-System: Unveiling the network of ecological interactions in a marine microbial community using Next-Generation omics

Biological communities are ecosystem composed of many interacting parts (species) that in combination constitute the basis of the functioning of the biosphere as a self-sustaining entity. The study of animals and plants has advanced substantially our understanding of ecosystems, providing mathematical models where species and their ecological interactions (for example, predation, parasitism, symbiosis, competition) are understood as networks, which have specific architectures that can influence ecosystem functioning. In comparison with animals and plants, our knowledge of microbial interaction networks is rudimentary, and in most community studies, microbes are still pooled by their function (e.g. all grazers are lumped together as one entity), thus missing species-specific interactions. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans. Without a thorough understanding of microbial interactions we cannot increase our understanding of the functioning of the biosphere, which is particularly needed in a context of global climate change. The reason for the current state-of-affairs is that investigating microbial interactions and diversity has proven to be extremely challenging. However, recent technological advance in microfluidics, Single-Cell genomics, Next-Generation DNA sequencing, and High-Performance computing makes now feasible to capture important microbes of a given community and explore their ecological interactions. In this project we have gathered information about these interactions by assembling networks of co-occurring organisms covering each month during a ten year period. We have sequenced a barcode region of eukaryotes and one of prokaryotes and have built complex networks to investigate which species are consistently appearing together and which are co-excluding themselves in the ecosystem. A co-occurrence network of 2987 species (smaller than 20 micro-meters and present in at least 20% of the time period) showed that the microbial community is highly connected. Only 5% of the connections were negative (co-exclusion) suggesting a predominance of cooperative associations or similar habitat preferences. A computer program was made to exclude environmental components and to identify the ecological interactions between microorganisms. To verify the known interactions, but also to identify novel and previously unknown interactions we have constructed a database of microbial interactions based on literature, going back to the mid 1800s. This has allowed us to predict diverse ecological interactions, increasing our knowledge of the marine microbial interactome.

This projects has contributed to increase the bioinformatics skills of the participants, as well as their skills in analysing association networks. Two PhD students will benefit from the large amount of data produced by this project. In addition, the datasets generated by this project will be available to the scientific community for future explorations. Thus, other questions unrelated to this project may be explored in the future, contributing to the increase in our understanding of marine systems. This project has also contributed significantly to improve the project management skills of the PI.

Biological communities are systems (ecosystems) composed of many interacting parts (species) that in combination constitute the basis of the functioning of the biosphere as a self-sustaining entity. Macro ecologists have advanced substantially our understanding of ecosystems involving mainly animals and plants, generating models where species and their ecological interactions are understood as networks, which have specific characteristics and architectures that can influence ecosystem functioning. In comparison, our knowledge of microbial interaction networks is rudimentary, and in most community studies, microbes are still pooled by their function (e.g. grazers), thus missing their species-specific interactions. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans, and without comprehending their interactions we cannot increase our understanding of the functioning of the biosphere, which is particularly needed in a context of global change. The reason for the current state-of-affairs is that understanding microbial interactions (and diversity) has proven to be highly challenging. However, I am convinced that recent technological advance in High-Throughput microfluidics, Single-Cell genomics, Next-Generation sequencing, and High-Performance computing makes now feasible to capture all important microbes of a given community and determine their ecological interactions. Therefore, here I propose to assemble the first exhaustive network of ecological interactions for a natural marine microbial community. I will analyse in depth the architecture of this network and its connections with ecosystem functioning. Then, I will use models to explore questions on e.g. stability and robustness of the network, extrapolating the results to the global ocean. Constructing this network is a challenging and multidisciplinary venture, but the risks are compensated by the benefits of moving forward the research frontier.