Ecological processes structuring the ocean microbiome across space and time

Abstract

The marine microbiome, including prokaryotes and minute unicellular eukaryotes, stands for a great part of biodiversity and is essential for ocean food webs and global biogeochemical cycles. Yet, investigating their diversity and ecology was challenging due to sampling and methodological constraints. Modern molecular and bioinformatic tools together with recent large-scale oceanographic sampling cruises (e.g. Tara Oceans and Malaspina) have helped the scientific community to assess the ocean’s microbial diversity with an unprecedented depth of analysis. Recent studies have revealed that microbial communities display latitudinal, seasonal, and depth-related patterns. However, there is still a limited understanding of the mechanisms underlying these biogeographical patterns. In this thesis, I have applied theoretical ecology on DNA sequencing data to disentangle the main ecological processes shaping the ocean’s microbiome across space and time. To do so, I have combined molecular data from two global oceanographic cruises (Tara Oceans and Malaspina), one regional cruise (HotMix Cruise) in the Mediterranean Sea, and from microbial observatories located in different latitudes. First, I demonstrate the high impact of the Theory of Ecological Communities (Vellend 2010, 2016) on the field of microbial ecology using a scientometric approach. Second, I investigated the relative importance of ecological processes (selection, dispersal limitation and ecological drift) shaping picoplankton communities inhabiting different ocean layers. To accomplish this goal, I analyzed 16S- and 18S-rRNA-gene amplicon sequence variants (ASVs) from samples (N=688) covering the epi- (0-200 m), meso- (200-1,000 m) and bathypelagic (1,000-4,000 m) layers of the ocean. I found that the role of selection decreased with depth due to a potential decrease in habitat heterogeneity. Conversely, the relative importance of dispersal limitation increased with depth due to dispersal barriers such as the presence of segregated water masses and bottom topography. Furthermore, I found that the relative importance of selection was stronger in the temperate observatory as compared to the tropical one. Finally, I used 16S-rRNA-gene amplicons as well as metagenome assembled genomes (MAGs) and single-amplified genomes (SAGs) to explore the genomic basis of temperature selection on niche differentiation of an abundant, ubiquitous, but previously overlooked marine bacteria. Overall, this thesis elucidates the ecological processes underlying the biogeographical patterns of microbial communities of the ocean in space, time and depth.