Biology subjects

THOMAS, F.

Publications and source records attributed to THOMAS, F..

5 recordsLinked to original sources

bioRxiv2026

A novel membrane-spanning one-component system controls β-glucan utilization in marine Bacteroidota

One of the most prevalent and bioavailable glycans in marine systems is the {beta}-glucan laminarin. Members of the phylum Bacteroidota are particularly well adapted to degrade this and other polysaccharides. Here, we describe a membrane-spanning one-component system that regulates laminarin utilization in marine Bacteroidota. We analyzed this {beta}-glucan utilization regulator (BguR) type in the marine model bacterium Formosa agariphila KMM3901T. Deletion of the regulator gene abolishes growth on laminarin, whereas the wild type exhibits more than 80-fold induction of the associated genomic gene cluster, indicating the regulators role as a transcriptional activator for laminarin utilization. Structural predictions show that its periplasmic sensor domain resembles those of hybrid two-component systems (HTCSs), although the absence of phosphorylation domains and distinct architecture indicate a completely different, ATP-independent mode-of-action. Comparative genomics show that this regulator is widespread among Bacteroidota, exhibiting lineage-specific distribution patterns similar to hallmark features such as tandem SusCD-like pairs. BguR is frequently found in close proximity to {beta}-glucan-targeting PULs in the genome, implying a defined substrate preference that extends beyond laminarin. These findings suggest a previously unrecognized regulatory mechanism for glycan sensing in marine bacteria, shedding light on an important facet of the marine carbon cycle. IMPORTANCEAlthough recent research has provided detailed insights into the enzymatic breakdown of algal glycans by marine bacteria, the regulatory mechanisms that govern specific carbohydrate utilization strategies remain largely unexplored. This study reveals a novel regulatory mechanism for {beta}-glucan use by marine Bacteroidota. We identified a membrane-embedded one-component regulator that directly links sensing and utilization of laminarin, a major algal polysaccharide in the oceans. Unlike traditional two-component systems, the new regulator operates without phosphorelays. The regulator and its associated laminarin PULs are widely conserved across diverse marine bacteria and even linked to other {beta}-glucan types, indicating a shared regulatory strategy for carbon acquisition from structurally related substrates. These findings advance our understanding of how key ocean microbes coordinate polysaccharide breakdown.

microbiology↗

bioRxiv2024

Year-round quantification, structure and dynamics of epibacterial communities from diverse macroalgae reveal a persistent core microbiota and strong host specificities

Macroalgae-bacteria interactions play pivotal ecological roles in coastal ecosystems. Previous characterization of surface microbiota from various macroalgae evidenced fluctuations based on host tissues, physicochemical and environmental parameters. However, the dynamics and degree of similarity of epibacterial communities colonizing phylogenetically distant algae from the same habitat are still elusive. We conducted a year-long monthly epimicrobiota sampling on five algal species inhabiting an English Channel rocky shore: Laminaria digitata, Ascophyllum nodosum, Fucus serratus (brown algae), Palmaria palmata (red alga) and Ulva sp. (green alga). To go beyond relative compositional data and estimate absolute variations in taxa abundance, we combined qPCR measurements of 16S rRNA gene copies with amplicon metabarcoding. A core microbiome composed of 10 genera was consistently found year-round on all algae. Notably, the abundant genus Granulosicoccus stood out for being the only one present in all samples and displayed an important microdiversity. Algal host emerged as the primary driver of epibacterial community composition, before seasonality, and bacterial taxa specifically associated with one or several algae were identified. Moreover, the impact of seasons on the epimicrobiota varied depending on algal tissues. Overall, this study provides an extensive characterization of the microbiota of intertidal macroalgae and enhances our understanding of algal-bacteria holobionts.

microbiology↗

bioRxiv2023

Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally-mixed coastal temperate habitat

Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonization by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally-mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low-abundance component of healthy macroalgal microbiota and can also colonize particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling. Originality-significance statementGlycan-degrading bacteria play a crucial role in marine habitats to remineralize organic carbon sequestered in algal biomass. Yet, resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we investigate the seasonal dynamics of abundance and activity of an environmentally relevant glycan-degrading bacterial genus in two constrasted compartments of the same coastal habitat, i.e. the surface of diverse macroalgae and the water column. These results provide insights into the recurring temporal patterns and environmental constraints driving natural populations of alga-degrading bacteria that influence ocean carbon cycling.

microbiology↗

bioRxiv2023

Zobellia alginoliquefaciens sp. nov. , a new flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C.Agardh) Molinari & Guiry 2020

Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected in Mediterranean Sea near Bastia in Corsica, France, was characterized using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30-33 {degrees}C, at pH 8-8.5 and with 4-5 % NaCl. Strain LLG6346-3.1T used the seaweed polysaccharide alginic acid as sole carbon source which was vigorously liquefied. Phylogenetic analyses showed that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae, class Flavobacteriia). Strain LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.5 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis respectively, and of 97.4-98.2 % to other species of the genus Zobellia. The DNA G+C content of strain LLG6346-3.1T was determined to be 38.28 mol%. Digital DNA-DNA hybridization predictions by the ANI and GGDC methods between strain LLG6346-3.1T and other members of the genus Zobellia showed values of 76-88 %, and below 37 %, respectively. The phenotypic, phylogenetic and genomic analyses show that strain LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia, for which the name Zobellia alginoliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (RCC 7657T = LLG 32918T).

microbiology↗

bioRxiv2020

Hypoxia Drives Dihydropyrimidine Dehydrogenase Expression in Macrophages and Confers Chemoresistance in Colorectal Cancer

Colon adenocarcinoma is characterized by an infiltration of tumor-associated macrophages (TAMs). TAMs are associated with a chemoresistance to 5-Fluorouracil (5-FU), but the mechanisms involved are still poorly understood. In the present study, we found that macrophages specifically overexpress dihydropyrimidine dehydrogenase (DPD) in hypoxia, leading to a macrophage-induced chemoresistance to 5-FU by inactivation of the drug. Macrophage DPD expression in hypoxia is translationally controlled by the cap-dependent protein synthesis complex eIF4FHypoxic, which includes HIF-2. We discovered that TAMs constitute the main contributors to DPD activity in human colorectal primary or secondary tumors where cancer cells do not express significant levels of DPD. Together, these findings shed light on the role of TAMs in forming chemoresistance in colorectal cancers and offer the identification of new therapeutic targets. Additionally, we report that, contrary to what is found in humans, macrophages in mice do not express DPD.

cell biology↗