Ecological and metabolic strategies of specialist bacteria mediating macroalgae breakdown – ALGAVOR

We combine culture-dependent and «omics« approach to reach our objectives.

Analysis of public metagenomes has shown a primarily coastal distribution of the genus Zobellia, with a greater abundance on macroalgal surfaces. To complement this data, we developed and validated deux new protocols to detect and quantify Zobellia by qPCR and FISH. We now apply these protocols to environmental samples. A sampling campaign targeting specifically flavobacteria allowed to isolate 109 novel strains, of which 12 were selected for a complete genome sequencing. Among them, we isolated a new member of the genus Zobellia, potentially representing a new species. Furthermore, we conducted the catabolic profiling of 40 macroalga-associated flavobacteria (including 5 Zobellia) by testing their utilization of 35 different substrates. The genomes of these strains have been submitted to the MAGE platform and are being annotated. In parallel, we performed a taxonomic and phenotypic characterization for 4 new Zobellia strains that represent 2 new species.
In addition, we demonstrated the strong potential of Zobellia galactanivorans to degrade intact tissues from several brown algae. RNA-seq transcriptomic data were obtained for Z. galactanivorans cultures grown with fresh algal tissues (3 brown algal species, in triplicate), separating free and alga-attached cells, and compared to cultures on 2 purified brown algal polysaccharide (alginate and fucane) or maltose used as a control. Transcriptomic analyses are in progress. They have already shown that 7-20% of the genes are differentially expressed by cells when degrading fresh algal biomass compared to purified alginate.

We will continue the analysis of public marine metagenomes and the annotation of new flavobacterial genomes, together with the monitoring of Zobellia in environmental samples. Transcriptome analysis will allow the identification of genes determining the behavior of Zobellia as a pioneer of macroalgal biomass degradation. The functions of some of these genes could further be characterized using genetic and/or biochemical approaches.

Book chapters :
Thomas F, Le Duff N, Leroux C, Dartevelle L & Riera P (2020). Isotopic labeling of cultured macroalgae and isolation of 13C-labeled cell wall polysaccharides for trophic investigations. Advances in Botanical Research 95, 1-17

Communications during conférences :
Brunet M, Fuchs B, Amann R, Barbeyron T & Thomas F (2019) Stratégies métaboliques de bactéries spécialistes de la dégradation des macroalgues. IX° colloque de l'Association Francophone d'Ecologie Microbienne, 5-8 novembre, Bussang (France) oral
Thomas F (2019) Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsiJt. POMPU meeting, 20-21 novembre, Berlin (Allemagne) oral
Thomas F, Le Duff N, Riera P, Cébron A, Leroux C, Tanguy G, Legeay E, Uroz S, Wu TD, Guerquin-Kern JL (2019) IX° colloque de l'Association Francophone d'Ecologie Microbienne, 5-8 novembre, Bussang (France), poster
Brunet M, Fuchs B, Amann R, Barbeyron T & Thomas F (2019) Degradation of fresh macroalgae by Zobellia galactanivorans. First Symposium on Symbiosis, 9-10 Décembre, Roscoff (France), oral
Brunet M, Fuchs B, Amann R, Barbeyron T & Thomas F (2019) Ecological and metabolic strategies of specialist bacteria mediating macralgae breakdown. 12° journées du Réseau Français des Parois, 14-16 mai, Roscoff (France)

In coastal regions, seaweed biomass turnover influences ecosystem functions both at local and global scales. It largely relies on specialized bacteria able to breakdown intact algal tissues and release degradation products in the water column. The ALGAVOR project will explore the ecological and metabolic strategies of such poorly known specialized marine bacteria of the genus Zobellia. We will combine cultivation-dependent and 'omics approaches to (i) evaluate the biodiversity, distribution, abundance, activity and catabolic functions of Zobellia spp in marine environments, (ii) decipher which metabolic pathways they use to degrade fresh seaweed biomass and (iii) study their cooperative interactions with scavenger bacteria that can profit from degradation products. Altogether, ALGAVOR will unveil the strategies of crucial bacteria considered as a bottleneck controlling the fate of organic matter in coastal habitats.