Diversity, Ecology and Evolution of Microbes

We have broad interest in different questions on the ecology and evolution of microbial life, from the origin of microbial diversity and its evolution since life emerged on Earth to the role of microbial communities in biogeochemical cycles. We combine complementary approaches including the exploration of extant prokaryotic and eukaryotic diversity by metabarcoding analysis, metagenomics, single cell ‘omics’ and phylogenomics to infer microbial functions and to elucidate the order of emergence of the different microbial groups and unravel their early evolutionary history. We have also broad interdisciplinary questions, in particular at the biology-geology interface.

The DEEM team, initially co-founded by Puri Lopez-Garcia and David Moreira, is one of the six research components in the Ecology, Systematics and Evolution unit (UMR 8079, CNRS – Université Paris-Sud – AgroParisTech).

Latest in press

Rafael, Puri and David (New Phytologist, 2019) discuss the impact of HGT on plastid evolution and introduce the "red carpet hypothesis" for the origin of secondary green plastids.

Reboul et al. (Environ Microbiol Rep, 2019) describe the diversity of protists in the chemosynthetic ecosystem of Movile Cave in Romania.

Puri (Nature Microbiology) has participated to the description of the first magnetotatic protist, a consortium of a Symbiontida euglenozoan and ectosymbiotic magnetotactic deltaproteobacteria.

Puri and David (Mol Ecol, 2019) elaborate on the importance of time series to understand microbial ecology.

Guifré Torruella et al. (Commun Biol, 2018) have produced the first almost complete transcriptome of one aphelid, Paraphelidium tribonemae. Careful phylogenomic analyses show that aphelids are the closest relatives to fungi and provide the basis to understand the transition from phagotrophic ancestors to the osmotrophic lifestyle that characterizes fungi.

Gutiérrez-Preciado et al. (Nature Ecol Evol, 2018) carried out comparative metagenomic analyses of microbial mats across a redox gradient. Taking a space-for-time substitution approach, we hypothesize that the functional shifts in core metabolism observed across the redox gradient recapitulate early metabolic transitions in the early Earth.

Field trips

May 2019, Mexican crater lakes: With our mineralogist and geochemist colleagues, we have sampled microbialites, plankton, and sediment of several crater lakes in different Mexican regions (Puebla, Michoacan, Chiapas) in the framework of our ANR project “Microbialites”. We will specifically focus on gene expression during diurnal cycles.

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Open positions

New postdoc and PhD positions will be soon available within the framework of Laura’s and David’s ERC Starting and Advanced grants. Keep an open eye!

If you are a motivated graduate or PhD student or a young postdoc interested in our research activities and wishing to develop an original research project, please do not hesitate to contact us for an internship, a prospective position or to prepare an application to funding agencies.

Contact us

Address :
DEEM team - Unité d’Ecologie, Systématique et Evolution
Rue Doyen André Guinier, bâtiment 360
91400 Orsay, France

Phone: +33 (0)1 69 15 76 08