State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.
Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China.
ISME J. 2021 Oct;15(10):2906-2919. doi: 10.1038/s41396-021-00983-1. Epub 2021 Apr 28.
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.
一氧化碳（CO）是通过混合微生物培养生产生化制品和生物燃料的有前途的底物，其中羧化菌起着关键作用。先前对混合微生物培养的研究主要集中在整体群落结构上，但尚未精确阐明特征不明的分类群和复杂的微生物相互作用。在这里，我们采用基于 DNA-SIP 的宏基因组学来描绘 95%和 35%CO 气氛下厌氧 CO 驱动微生物组。同位素标记的扩增子测序的时间序列分析表明，厚壁菌门和变形菌门分别在高 CO 压力和低 CO 压力下起主要作用，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具有更大的潜力来表达羧酸盐代谢和柠檬酸循环途径。基于基因组的宏基因组学重建了 24 个已发现和 24 个特征不明的宏基因组组装基因组（MAG），涵盖了超过 94%的宏基因组读数。MAG 的代谢重建描述了它们在 CO 驱动微生物组中的潜在功能。一些特征不明的分类群可能在多个过程中具有多功能性；例如，特征不明的 Rhodoplanes sp. 和 Desulfitobacterium_A sp. 可以编码 CO 氧化和羧酸盐产生的完整酶，提高功能冗余性。最后，我们提出了 CO 向羧酸盐和甲烷转化过程中可能存在的微生物相互作用。
