metatranscriptomic approaches to unravel taxonomic and functional diversities of a coastal aquatic ecosystem and their reaction to hypoxia. predhypo

Two previous integrative research programs: PREDHYPO (AMIDEX Foundation 2015-2016) and PREDHYP-O2 (EC2CO 2016-2017, CNRS-INSU) have enabled the coupling between physics and biogeochemical processes of the Berre lagoon sediment during laboratory experiments under controlled oxygenation conditions. These programs have also initiated regular in situ measurements during a three-year period, leading to the first-step development of a 1D predictive benthic-pelagic biogeochemical model of the lagoon. We set up a laboratory experiment to follow the biological and chemical dynamics at the sediment-water interface on the short-term period (i.e. one month incubation of sediment core samples), while we conducted an in situ approach to characterize seasonal and yearly dynamics (i.e. from may 2015 to august 2016) of biogeochemical processes at the sediment-water interface for three sites showing contrasted oxygenation conditions. Because microorganisms are key actors of biogeochemical processes and organic matter turnover, we dedicated an important part of these research programs to the characterization of taxonomic and functional responses of the sediment microbiome to hypoxia events. Based on Next Generation Sequencing (NGS) technologies (i.e. ILLUMINA), we developed a metabarcoding approach that aims at exploring taxonomic diversity of Bacteria and Archaea living in the sediment, and we developed a metatranscriptomic approach that aims at identifying metabolic activities and pathways involved in the ecosystem functions. The laboratory experiment considered triplicate samples of sediment at various depth layers and according to oxygenation conditions of the water column ranging from 0% to 100%.