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

Informations

Funding country

Norway

Acronym

-

URL

-

Start date

1/1/2015

End date

12/31/2019

Budget

851,529 EUR

Fundings

Abstract

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.