背景:尽管基因组解析宏基因组学的快速发展和宏基因组组装基因组(MAG)的显着爆炸,未培养的厌氧谱系的功能及其在碳矿化中的相互作用仍然很大程度上不确定,这对生物技术和生物地球化学有着深远的影响。
结果:在这项研究中,我们将长读测序和超转录组学指导的代谢重建相结合,以提供厌氧生物反应器中碳矿化从聚合物到甲烷的全基因组视角。我们的结果表明,合并长读数导致宏基因组装配质量的实质性改善,实现132个高质量基因组的有效回收,这些基因组符合宏基因组组装基因组(MIMAG)最低信息的严格标准.此外,与短只读组装相比,杂交组装获得的原核基因多51%。超转录组学指导的代谢重建揭示了Mesotogasp的几种新型拟杆菌附属细菌和种群的显着代谢灵活性。清除氨基酸和糖。除了回收先前已知但分裂的共生细菌的两个环状基因组,发现Syntrophales中的两种新发现的细菌通过与主要的产甲烷菌Methanoculraceaebin的互养关系高度参与脂肪酸氧化。74和Methanothrixsp。bin.206。随着负载的增加,优选乙酸盐作为底物的bin.206的活性超过了bin.74的活性,加强底物的决定性作用。
结论:总体而言,我们的研究发现了一些关键的活跃厌氧谱系及其在这个复杂的厌氧生态系统中的代谢功能,为理解厌氧消化中的碳转化提供了一个框架。这些发现促进了对代谢活动和营养相互作用的理解厌氧行会,提供对工程和自然生态系统中碳通量的基本见解。视频摘要。
BACKGROUND: Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.
RESULTS: In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.
CONCLUSIONS: Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.