Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate

The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were "trained" to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs

Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean

Members of the class Flavobacteria in the phylum Bacteroidetes are among the most abundant picoplankton in coastal and polar oceans. Their diversity is high in marine waters. However, quantitative information about distribution patterns of flavobacterial clades is scarce. We analyzed the diversity and clade-specific abundances of individual Flavobacteria in different oceanic provinces in the North Atlantic Ocean. Samples were taken along the 30 degrees W meridian between the East Greenland current and the North Atlantic subtropical gyre. Comparative sequence analysis of 16S ribosomal RNA (rRNA) gene libraries revealed high diversity and significant spatial variability within the class Flavobacteria. Published and newly designed oligonucleotide probes were used to enumerate eleven flavobacterial clades by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). We found that different provinces harbor distinct flavobacterial communities. Clade DE2 accounted for a substantial fraction of total Flavobacteria only in the Polar Biome (BPLR), whereas the VISION clades VIS1 and VIS4 significantly increased in the Arctic (ARCT) province. Members of the genus Polaribacter were the most abundant clade in all the water masses analyzed, with highest absolute numbers in BPLR and ARCT. We improved the CARD-FISH protocol to quantify the rare clades VIS2, VIS3, VIS5 and VIS6, which were present in abundances below 0.5%. They all showed pronounced regional distribution patterns. Microscopic analysis proved a specific enrichment of Flavobacteria in the phycosphere of nanophytoplankton of BPLR and ARCT. Our results suggest that different marine flavobacterial clades have distinct niches and different life strategies