Unraveling the metabolic mechanisms of pioneer bacteria during the utilization of fresh macroalgae. Unraveling the metabolic mechanisms of pioneer bacteria during the utilization of fresh macroalgae

We cultivated the flavobacterium Zobellia galactanivorans DsijT with fresh brown macroalgae with distinct chemical compositions. Its capacity to use macroalgae as the sole carbon source via the secretion of extracellular enzymes, leading to extensive tissue damages, highlights a sharing pioneer degrader behavior. RNA-seq transcriptome analysis revealed a metabolic shift toward the utilization of brown algal polysaccharides during tissue degradation. A subset of genes was specifically induced in cells grown with intact algae compared to purified polysaccharides. It notably includes genes involved in protection against oxidative burst, type IX secretion system proteins and novel uncharacterized Polysaccharides Utilization Loci (PULs). Comparative growth experiments and genomics between Zobellia members brought out putative genetic determinants of the pioneer behavior of Z. galactanivorans, whose in vitro role could be further characterized. This work constitutes the first investigation of the metabolic mechanisms of bacteria mediating fresh macroalgae breakdown, and will help unravel the role of marine microbes in the fate of macroalgal biomass. Overall design: RNAseq profiles of Zobellia galactanivorans DsijT when grown with different carbon sources. Profiles of free-living cells were assessed with Laminaria digitata, Fucus serratus, Ascophyllum nodosum, Maltose, Alginate or Fucose-containing sulfated polysaccharides (FCSP) as the sole carbon source. Profiles of algae-attached cells were assessed with Laminaria digitata and Fucus serratus as the sole carbon source. Experiments were done in triplicates for each condition (except for free-living cells with F. serratus and algae-attached cells where n=2). 21 samples in total. Maltose condition was used as a control.

我们使用化学成分各异的新鲜大型褐藻，培养黄杆菌属菌株半乳聚糖降解佐贝尔菌（Zobellia galactanivorans）DsijT。该菌株可通过分泌胞外酶将大型褐藻作为唯一碳源进行利用，进而引发褐藻组织的广泛降解，这一特性彰显了其作为共享型先驱降解者的行为特征。
RNA测序（RNA-seq）转录组分析显示，在褐藻组织降解过程中，菌株的代谢模式发生转向，以褐藻多糖为核心底物进行利用。与以纯化多糖为碳源培养的菌体相比，以完整褐藻培养的菌体中存在一组基因被特异性诱导表达，该诱导基因集显著包含抗氧化爆发相关基因、IX型分泌系统蛋白编码基因，以及全新的未表征多糖利用基因座（Polysaccharides Utilization Loci, PULs）。
通过对佐贝尔菌属不同菌株的比较生长实验与基因组学分析，我们明确了半乳聚糖降解佐贝尔菌先驱降解行为的潜在遗传决定因子，其体外功能有待进一步表征。
本研究是首个针对介导新鲜大型褐藻降解的细菌代谢机制的探索，将有助于阐明海洋微生物在大型藻生物质归宿中发挥的作用。
实验整体设计：以不同碳源培养半乳聚糖降解佐贝尔菌DsijT，获取其转录组表达谱。以掌状海带（Laminaria digitata）、锯齿墨角藻（Fucus serratus）、泡叶藻（Ascophyllum nodosum）、麦芽糖、褐藻胶或含岩藻糖硫酸多糖（Fucose-containing sulfated polysaccharides, FCSP）作为唯一碳源，检测游离态菌体的转录谱；以掌状海带和锯齿墨角藻作为唯一碳源，检测附着于藻体的菌体的转录谱。除以锯齿墨角藻培养的游离态菌体组与附着态菌体组（n=2）外，其余所有实验组均设置3次生物学重复，总计21个样本。其中麦芽糖组作为对照。