Multiple omics data is key to understand ecological processes

The data we intend to generate for this project is rich not only in itself, but also because is will complement previously published data.

Indeed, we have already sequenced and published the DNA of many samples from the deep-sea sediment of the Clarion-Clipperton Zone (CCZ) and other regions of the world, but this data only informs on the diversity of small animals, and Foraminifera (an amazing group of single-celled eukaryotes).

This data showed that the CCZ - which is going to be mined for precious metals - also harbour the most unique and diverse communities of organisms, as indicated by the blue dots (samples), separated from the other regions (other colors) on the plot below, showing how different the communities are from each other. There, the arrows indicate the most important organism that explain this separation:

 

Robust-PCA showing the difference between samples based on their compositions in small animals From Lejzerowicz et al. 2021, Frontiers in Marine Sciences.

But in itself, this data hardy informs us or the governing bodies - that will have the difficult talk of managing mining impacts - on the ecological and biogeochemical mechanisms at play in the different area, whether these are also different, and if they could determine the evolution of species in specific niches, where by definition these species would interact more specifically.

This is why we propose in our Experiment project, to augment this diversity data with new, metagenomics data on the metabolic potential of the microbes that live n the sample few grams of samples from which the diversity data was generated, This approach of combining different types of "omics" data is called multi-omics.

In the global dataset of the Earth Microbiome Project, combining two omics datasets using multi-omics allowed us to strongly suggest the existence of a niche that is specific to the saline water environment.

 

Summary of the co-occurrences between the microbes (arrows: most important ones) and metabolites (all the dots, coloured per strength of association with the saline water environment). From Shaffer et al. 2022 Nature Microbiology.

This is shown by the yellow dots (= strong association with the saline water environment) that form a separate group, a bit like for the figure above. The difference here below is that the dots are not samples but the data analyzed inside all the samples, which is the case of the Earth Microbiome Project, are small metabolic compounds. But... the arrows also represent data analysed inside all the samples? Yes, the data from the other dataset. Indeed, this figure is the result of combining metagenomics (arrows = genomes) with metabolomics (dots = compounds) and the whole plot is influenced by the strengths of the co-occurrences between these genomes and compounds in the samples.

The hypothesis now is that in saline water ecological niches, there are interactions that are very important, and this could motivate new research on specific compounds and genomes! We will do something similar with diverse deep-sea sediment niches, but this time, using association of (electroactive / metal-utilizing) microbial genomes vs animal and Foraminifera taxa, which could indicate the existence of specific niches and ecological mechanisms that would motivate more research before mining happens.

Exciting no?