François Thomas

François Thomas
Station Biologique de Roscoff · Laboratoire de Biologie Intégrative des Modèles Marins UMR8227 CNRS-UPMC

Ph.D

About

108
Publications
13,126
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
2,519
Citations
Introduction
Marine microbiologist and biochemist at Station Biologique de Roscoff. ORCID: 0000-0003-1896-0774 Twitter: @FThomas_Roscoff
Additional affiliations
October 2015 - present
French National Centre for Scientific Research
Position
  • Researcher
April 2014 - September 2015
French National Centre for Scientific Research
Position
  • Postdoctoral Investigator
February 2012 - March 2014
Woods Hole Oceanographic Institution
Position
  • PostDoctoral Investigator
Education
September 2008 - September 2011
Sorbonne Université
Field of study
  • Microbiology and Biochemistry
September 2006 - September 2009
September 2000 - September 2005
Institut National des Sciences Appliquées de Lyon
Field of study
  • Biochemistry and Biotechnologies

Publications

Publications (108)
Article
Full-text available
The marine flavobacterium Zobellia galactanivorans DsijT was isolated from a red alga and by now constitutes a model for studying algal polysaccharide bioconversions. We present an in-depth analysis of its complete genome and link it to physiological traits. Z. galactanivorans exhibited the highest gene numbers for glycoside hydrolases, polysacchar...
Article
Full-text available
Comprehension of the degradation of macroalgal polysaccharides suffers from the lack of genetic tools for model marine bacteria, despite their importance for coastal ecosystem functions. We developed such tools for Zobellia galactanivorans, an algae-associated flavobacterium that digests many polysaccharides, including alginate. These tools were us...
Article
Full-text available
Cell walls of brown algae are complex supramolecular assemblies containing various original, sulfated, and carboxylated polysaccharides. Among these, the major marine polysaccharide component, alginate, represents an important biomass that is successfully turned over by the heterotrophic marine bacteria. In the marine flavobacterium Zobellia galact...
Article
Alginate constitutes a significant part of seaweed biomass and thus a crucial nutrient for numerous marine heterotrophic bacteria. However, the mechanisms for alginate assimilation remain largely unknown in marine microorganisms. We show here that the genome of the marine flavobacterium Zobellia galactanivorans contains seven putative alginate lyas...
Article
Full-text available
Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes a...
Article
Full-text available
Formaldehyde is a toxic metabolite that is formed in large quantities during bacterial utilization of the methoxy sugar 6‐ O ‐methyl‐ d ‐galactose, an abundant monosaccharide in the red algal polysaccharide porphyran. Marine bacteria capable of metabolizing porphyran must therefore possess suitable detoxification systems for formaldehyde. We demons...
Article
Full-text available
Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galac...
Preprint
Full-text available
Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of pioneer bacteria within the flavobacterial genus Zobellia to initiate the degradation of fresh brown macroalgae, which has received little attention compared to the degradation of isolated polysaccharides. Zob...
Chapter
Full-text available
Bacteria are ubiquitous and abundant in the marine environment, playing a multiplicity of roles in marine ecosystems, and are also a source of multiple biotechnological innovations. The well-characterized strains of Escherichia coli, Staphylococcus, Pseudomonas or Bacillus are relevant for medical applications or the study of soil microbiota but ar...
Article
The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) m...
Article
Full-text available
L-2-halocid dehalogenases (L-2-HADs) have been mainly characterized from terrestrial polluted environments. By contrast, knowledge is still scarce about their role in detoxification of predominant halocarbons in marine environments. Here, phylogenetic analyses showed a wide diversity of homologous L-2-HADs, especially among those belonging to marin...
Article
Four marine bacterial strains were isolated from a thallus of the brown alga Ascophyllum nodosum collected in Roscoff, France. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, gliding, rod-shaped and grew optimally at 25–30 °C, at pH 7–8 and with 2–4 % NaCl. Phylogenetic analyses of their 16S rRNA gene sequences showed that the ba...
Article
Full-text available
Alginate is a major compound of brown macroalgae and as such an important carbon and energy source for heterotrophic marine bacteria. Despite the rather simple composition of alginate only comprising mannuronate and guluronate units, these bacteria feature complex alginolytic systems that can contain up to seven alginate lyases. This reflects the n...
Article
Full-text available
Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate uti...
Article
Full-text available
Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its ac...
Article
Full-text available
Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT...
Article
A high proportion of the kelp Laminaria hyperborea production is exported from kelp forests following seasonal storms or natural annual old blades loss. Transport of drifting kelp fragments can lead to temporarily accumulations in benthic subtidal habitats. We investigated the degradation processes of L. hyperborea in a low subtidal sandy bottom ec...
Article
Plant‐ and alga‐associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these datasets frequently contain >90% plastidial sequences, and the bacterial diversity may be under‐sampled. To overcome this limitation we evaluated in silico th...
Article
Full-text available
Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promisi...
Data
Summary of above and belowground plant biomass, carbon dioxide flux, and chemical composition of pore water at 21 cm depth. (PDF)
Data
Description of the samples and alpha-diversity measures. (PDF)
Data
Summary of permutational analysis of variance (PERMANOVA with 999 permutations) testing the difference in bacterial community structure according to sediment source (on all samples together) and elevation and depth (separately for natural and sand-amended sediments). (PDF)
Data
Natural and sand-amended mesocosms with inserts and lysimeters, and elevation levels labelled. (TIF)
Data
Phylum-level taxonomic distribution of all sequences retrieved during this study (singleton-free, n = 68,123). "Others" comprises phyla accounting less than 1%. (PNG)
Article
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contam...
Presentation
Full-text available
Major part of the Laminaria hyperborea kelp forest production is exported due to storm events or to natural annual old blade losses. Drift kelps are transported and can accumulate temporarily over benthic subtidal habitats. We investigated the degradation processes and the macrofaunal colonization of L. hyperborea on low subtidal (-8 m) sandy botto...
Article
Full-text available
Below the seafloor at deep-sea hot springs, mixing of geothermal fluids with seawater supports a potentially vast microbial ecosystem. Although the identity of subseafloor microorganisms is largely known, their effect on deep-ocean biogeochemical cycles cannot be predicted without quantitative measurements of their metabolic rates and growth effici...
Article
Full-text available
Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria using largely uncharacterized mechanisms. Here we describe the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macro...
Article
Full-text available
Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have...
Article
At centimeter scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a planted industrial soil, contaminated with polycyclic aromatic hydrocarbons (PAHs), pollution was previously shown to be distributed randomly with hot and cold spots, using rhizoboxes. We therefore investig...
Article
Full-text available
Kelps are founding species of temperate marine ecosystems, living in intertidal coastal areas where they are often challenged by generalist and specialist herbivores. As most sessile organisms, kelps develop defensive strategies to restrain grazing damage and preserve their own fitness during interactions with herbivores. To decipher some inducible...
Data
Primers used in the qPCR analysis study. (XLSX)
Data
Statistical analysis comparing ion relative abundances of Grazed vs. Control Lessonia spicata samples, collected after 6, 12, 24 and 48h (n = 3, except for Control-48h n = 2). Peak assignation, ion identification and relative abundance calculation were processed by XCMS analysis. Each ion is identified by a unique ID (MxTy) indicating its mass (Mx,...
Data
List of 122 putative differentially expressed unigenes under grazing pressure in Laminaria digitata, identified by 454 sequencing and EST analysis. (XLSX)
Data
Detailed list of identified ions by LC/MS analysis and their relative abundance from Laminaria digitata samples, under control and grazed conditions, collected after 6, 12, 24 and 48h (n = 4, except for Grazed-48h n = 2). Peak assignation, ion identification and relative abundance calculation were processed by XCMS analysis. Each ion is identified...
Data
Detailed list of identified ions by LC/MS analysis and their relative abundance from Lessonia spicata samples, under control and grazed conditions, collected after 6, 12, 24 and 48h (n = 3, except for Control-48h n = 2). Peak assignation, ion identification and relative abundance calculation were processed by XCMS analysis. Each ion is identified b...
Data
List of 132 putative differentially expressed unigenes under grazing pressure in Lessonia spicata, identified by 454 sequencing and EST analysis. (XLSX)