Diversity, Ecology and Evolution of Microbes

ERC AdG - ProtistWorld: Protist evolution in suboxic environments

(PI Puri Lopez-Garcia, 2013-2019)

How and when eukaryotes evolved remain major open questions. Also the phylogenetic relationships and the emergence order of major eukaryotic lineages remain unresolved, despite progress in phylogenomic analyses based on genome and transcriptome data across the eukaryotic tree. However, this information is biased towards multicellular taxa. Yet, environmental molecular analyses have uncovered a vast diversity of protists (broadly, microbial eukaryotes), many of which have uncertain phylogenetic position. Phylogenomics also suggests that endosymbiosis (e.g. mitochondrial acquisition) played a key role in eukaryotic evolution, shaping their genomes and leading to innovations. Different competing models try to explain such transition, but most of them propose that the first eukaryotes evolved in anoxic or transition-to-oxic (broadly, suboxic) environments, from where they colonized new niches thanks to the oxygen-respiring capacity of mitochondria. Therefore, suboxic ecosystems may hold clues as to the type of environmental constraints and selective forces that led to the evolution of eukaryotes and their early diversification.

Despite so, little is known about the diversity and mode of evolution of eukaryotes in suboxic worlds, including microbial mats and stromatolites, where many inter-species interactions are likely to exist. In this project, we take an integrative interdisciplinary approach to gain significant knowledge about early eukaryotic evolution on the following premises:

i) High-diversity suboxic environments, such as microbial mats, hide novel divergent protist lineages.

ii) Microbial eukaryotes fossilize in calcifying microbial mats (e.g. stromatolites), leaving biosignatures in the past fossil record that may be useful to date the origin of eukaryotes and/or particular eukaryotic taxa.

iii) Phylogenomic analysis of divergent protist lineages from suboxic environments will help resolving the eukaryotic tree of life.

iv) Protist symbiosis with prokaryotes is widespread in suboxic worlds and is stabilized by (endo)symbiotic-gene transfer.

Major achievements

WP1. Protist diversity in microbial communities of suboxic environments potentially harboring novel lineages. We characterized microbial diversity via 18S rRNA metabarcoding and direct metagenomics in poorly studied ecosystems, including temporal series in suboxic lakes (France), spatial vertical and horizontal transects in Lake Baikal (Russia), methane-rich caves in Romania and polyextreme ponds in Ethiopia. We identified eukaryotes from all known supergroups, including lineages previously thought exclusively marine and novel divergent clades in freshwater systems (Simon 2015a,b, 2016; Reboul 2019; David, in prep). We also explored microbial mats along redox gradients (Atacama Desert; Saghaï, 2017) and microbialites from alkaline crater lakes (Mexico), as analogues of past microbial ecosystems, detecting many divergent microbial lineages including Asgard archaea (phylogenetically closer to eukaryotes). Our work suggests that functional shifts in metagenomes across redox gradients recapitulates early metabolic transitions in the early Earth (Gutiérrez-Preciado 2018). Also, anoxygenic photosynthesizers and photosynthetic protists likely contribute to microbialite carbonate precipitation in addition to cyanobacteria (Saghaï 2015), with implications for fossilization. We enriched the known diversity of novel divergent protist lineages, including apusomonads (Torruella 2017), nucleariids (Lopez-Escardo 2018), sanchytrids (Karpov 2018) and aphelids and other fungal relatives (Karpov, 2016-2019).

WP2. Protist fossilization in microbialites. We explored early fossilization in modern microbialites through interdisciplinary collaboration, identifying exquisitely preserved microbial cells down to the nm-scale. This preservation is achieved by permineralization with a newly identified poorly-crystalline hydrated silicate phase (Zeyen 2015). We have also identified the abiotic formation of silica biomorphs in extreme environments. These precipitates likely induce cell fossilization but, in the absence of cellular life, might be misinterpreted as tiny cells (Belilla 2019)

WP3. Phylogenomics of deeply divergent protists. To enrich protist taxon sampling and improve the resolution of the eukaryotic tree of life, we generated genomes/transcriptomes from cultures or single cells of divergent protists. Phylogenomic analysis of Incisomonas and Opalina improved the resolution of the Stramenopiles (Derelle 2016, Yubuki, 2020), that of Metchnikovella incurvata helped unraveling early Microsporidia evolution towards extreme parasitism (Galindo 2018). We generated the first transcriptome for aphelids, showing that they are the closest relatives to fungi, which likely evolved from phagotrophic free-living predators (Torruella 2018) and not parasites, as previously suggested. We have also discovered a divergent lineage of pseudoflagellated fungi, the sanchytrids, for which the phylogenomic analyses of single cell genomes and transcriptomes reveal reductive steps in fungal evolution (Galindo, in prep).

WP4. Symbiosis and eukaryotic evolution. We postulated that inter-domain horizontal gene transfer, important for the adaptation to novel ecological niches (Lopez-Garcia 2015), may stabilize endosymbioses. We helped showing that symbiosis of deltaproteobacteria and euglenozoans were at the origin of protist magnetoreception (Monteil, 2019). We discovered the closest lineage of cyanobacteria at the origin of eukaryotic plastids (Ponce-Toledo 2017) and explored endosymbiotic gene transfer during the evolution of photosynthetic eukaryotes (Ponce-Toledo, 2018, 2019). We have significantly contributed to the debate on the role of symbiosis in eukaryogenesis (Lopez-Garcia & Moreira, 2015, 2019, 2020; Lopez-Garcia 2017) and revised the Syntrophy hypothesis for the origin of eukaryotes (Lopez-Garcia & Moreira, 2020).