CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.

CO 是通过混合微生物培养生产生物化学品和生物燃料的有前景的底物，其中一氧化碳营养菌发挥着至关重要的作用。之前对混合微生物培养物的研究主要集中在整体群落结构上，但尚未明确阐明特征不明的类群和复杂的微生物相互作用。在这里，我们采用基于 DNA-SIP 的宏基因组学来分析 95% 和 35% CO 气氛下厌氧 CO 驱动的微生物组。同位素标记扩增子测序的时间序列分析揭示了厚壁菌门和变形菌门分别在高和低二氧化碳压力下的重要作用，而甲烷杆菌是主要的古菌属。基于同位素标记宏基因组的功能富集分析表明，高CO压力下的微生物培养物在表达羧酸代谢和柠檬酸循环途径方面具有更大的潜力。以基因组为中心的宏基因组学重建了 24 个已发现的宏基因组组装基因组 (MAG) 和 24 个未充分表征的宏基因组组装基因组 (MAG)，覆盖了超过 94% 的宏基因组读数。 MAG 的代谢重建描述了它们在 CO 驱动的微生物组中的潜在功能。一些未充分表征的分类群可能在多个过程中具有多种用途；例如，未充分表征的Rhodoplanes sp。和脱硫杆菌_A sp。可以编码一氧化碳氧化和羧酸盐生成中的完整酶，从而提高功能冗余。最后，我们提出了二氧化碳转化为羧酸盐和甲烷过程中假定的微生物相互作用。