Towards a genomic and ecological atlas of the marine microbes of the Southern Ocean – ACE-Ecogenomics

In this project we will obtain the largest environmental DNA dataset to date from all biological compartments the Southern Ocean plankton, covering a wide variety of bathyal, ecological and latidunal gradients. These dataset will be composed of:
- Archaeal and Bacterial and eukaryotic metabarcode libraries using ribosmal rRNA genes as marker genes. These will be used to uncover the biogeography, the taxonomic diversity and the keys microorganisms involved in the oceanic carbon pump.
- Archaeral and bacterial metagenomes to elucidate the functional role of these microorganisms and the genomic blueprint of polar environment adaptations
- eukaryotic metatranscriptomes to enrich the TARA plankton gene catalogue and characterize genes unique to the SO as well as genetic repertoires of phytoplankton involved in massive SO summer blooms.
- metavirome to understand the viral diversity and its contribution to the carbon pump viral shunt, as well as their role as genetic shuttles among microbial populations.
We will deploy a large array of bioinformatics tools, from NGS read analysis to genome-centric approaches to understand diversity in each of these biological compartments, how they are interconnected and their relation to environmental metadata acquired in parallel during the sampling campaign.

To date, the first step of the project is nearly complete as partners have extracted DNA from over 900 seawater filters of different pore sizes, constructed environmental DNA libraries and sequenced 80% of the samples. The completion of this first step is scheduled for the end of 2020.

This project has already reached a major deliverable, as we have produced the largest and most geographically and ecologically diverse molecular dataset from the SO to date, bringing this Ocean at the same level as the other oceans explored by e.g. the TARA ocean initiative.
The analysis of this unknown and overlooked diversity will constitute an important contribution to ocean sciences and microbiology.
For public outreach, the ACE expedition benefited from an excellent media coverage, including a 1 h documentary available online («Thalassa: coup de chaud sur l'Antarctique« www.youtube.com/watch,

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This project aims at exploiting samples and data acquired during the ACE cruise, an international expedition that explored the Southern Ocean (SO) during the austral summer 2016/2017 in a circumpolar path from and to Cape Town, South Africa. This expedition has allowed the coordinated sampling of different Southern Ocean systems (including areas never visited by scientific expeditions before) and gathered 22 research projects providing a rich set of ancillary geochemical parameters to explore the environmental drivers of biodiversity. During ACE, PI Maignien and collaborators have collected over 1000 samples from 5-1000 m water depth, suitable for environmental DNA sequencing and analysis of planktonic viral, archaeal, bacterial and picoeukaryote diversity.
The overarching goal of this proposal is thus to better understand the ecology of SO plankton, identify biotic and abiotic factors controlling its distribution, and its implication in the biogeochemical cycling in this ocean based on a spatial and depth resolved analysis of microbial taxonomic and genomic diversity in austral summer waters.
To achieve these objectives, we will use a combination of metabarcoding, metagenomics metatranscritomics on different size fractions to describe microbial communities at high geographic and genetic resolution. This project will thus produce SO reference datasets comprising over 60 trillion reads. The correlation biological patterns with a set of geochemical parameters acquired during the expedition will provide an opportunity to better understand SO plankton ecology and contribution to carbon cycling.