The main scientific objectives of the project “Functional Redundancy of the Global Ocean Microbiome (FROM)” were to develop approaches to study microbial functional redundancy and diversity and explain their patterns in the global ocean. The ideas leading to the development of FROM were first summarized in an opinion/review piece we called: “Microbial functional diversity and redundancy: moving forward”. In this piece, we review the state of the field of microbial functional ecology, we identify limiting factors and outline a framework to circumvent them. Finally, we detail ensuing perspectives for the field. We then applied this new found framework using public data, namely: a) a collection of prokaryotic genomes (Paoli et al., 2022), b) methods to predict biogeochemically relevant traits from genomes (Zhou et al., 2022), c) metagenomes and meta-transcriptomes (Sunagawa et al., 2020), and d) an unpublished collection of prokaryotic genomes, metagenomes and meta-transcriptomes from the ICM-CSIC (host institution) (
http://bbmo.icm.csic.es/(opens in new window)) to compute microbial functional diversity and redundancy in the global ocean. We first evidence that potential and expressed microbial redundancy generally correlate in the ocean, suggesting that, when present, microbes express their traits. We then evidence that deeper layers harbor more versatile microbes which leads to a lowering of redundancy in deep microbiomes. In the surface ocean, functional diversity was homogeneous but redundancy was markedly lower between the temperate and the polar area. Polar areas harbor lower microbial richness, higher dominance from opportunistic taxa, and larger community turnover. Finally, using machine learning and earth model projections, we predict further losses of redundancy at the horizon of 2100, notably in surface temperate and the equatorial Pacific Ocean. Being able to quantify microbes' functional diversity and redundancy, we are now poised to test the significance of these metrics for the functioning of present and future ecosystems facing climate change.
To apply this method to microbial eukaryotes, we started an international working group on Protists Trait Annotation. The aims of this working group are: 1) to identify a key set of traits representing the ecological functions of protists and their roles in ecosystems. 2) To annotate all known protistan taxa with these traits, and find experts to perform and supervise this task. 3) To analyze and explain patterns of protists functional ecology across biomes. In a preliminary approach, a MSc student (Louise Pietri from Aix-Marseille Université, France) joined FROM to annotate the protist taxa in the collection of oceanic metabarcoding datasets (Vaulot et al., 2022). After a successful work of annotation, Louise then explored patterns of protist traits in the ocean. In the samples analyzed, we highlight that the majority of oceanic protists harbor simple morphology (round naked cells), are able to swim in order to predate or avoid predation, they also generally lack of defense appendages and are unable to perform dormancy. A promising result was the apparent correlation between protists feeding strategy and cell size with estimations of oceanic carbon bottom export, suggesting that this key ecosystem process could be predicted from functionally characterized marine protistan communities. The next step with this approach is to predict and explain patterns microbial eukaryotes functional redundancy in the ocean. Another underlying project is using the traits of marine protists to functionally characterize network-predicted interactions in marine microbiome and potentially unveil general rules of microbial interactions in time and space. This project will be offered as new MSc study in autumn 2024.
