Reintjes, G. | Search bioRxiv

bioRxiv2020

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Gut microbiomes have vast catabolic potential and are essential to host health and nutrition. An in-depth understanding of the metabolic pathways in these ecosystems will enable us to design treatments (i.e. prebiotics) that influence microbiome structure and enhance host physiology. Currently, the investigation of metabolic pathways relies on inferences derived from metagenomics or in vitro cultivations, however, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to accurately assess metabolic abilities. Here, we present a multi-faceted study using complimentary next-generation physiology and omics approaches to characterize the microbial adaptation to a prebiotic in the rumen ecosystem. Using fluorescently labeled polysaccharides, we identified bacteria that actively metabolize a glycan prebiotic in the rumen microbiome ex vivo. Subsequently, we characterized strain-level variability in carbohydrate utilization systems and predict metabolic strategies of isolated bovine-adapted strains of Bacteroides thetaiotaomicron using comparative whole genome sequencing, RNA-Seq, and carbohydrate-active enzyme fingerprinting.

microbiology↗

bioRxiv2020

Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom

Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a selfish mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides, and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community. Originality statementThe means by which heterotrophic bacteria cooperate and compete to obtain substrates is a key factor determining the rate and location at which organic matter is cycled in the ocean. Much of this organic matter is high molecular weight (HMW), and must be enzymatically hydrolyzed to smaller pieces to be processed by bacterial communities. Some of these enzyme-producing bacteria are selfish, processing HMW organic matter without releasing low molecular weight (LMW) products to the environment. Other bacteria hydrolyze HMW substrates in a manner that releases LMW products to the wider bacterial community. How these mechanisms of substrate hydrolysis work against a changing background of organic matter supply is unclear. Here, we measured changing rates and mechanisms of substrate processing during the course of a natural phytoplankton bloom in the North Sea. Selfish bacteria generally dominate in the initial bloom stages, but a greater supply of increasingly complex substrates in later bloom stages leads to external hydrolysis of a wider range of substrates, increasing the supply of LMW hydrolysis products to the wider bacterial community.

microbiology↗