Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padova, Italy.
Water Res. 2019 Mar 15;151:271-279. doi: 10.1016/j.watres.2018.12.041. Epub 2018 Dec 27.
In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.
在典型的厌氧消化（AD）系统中，微生物功能的断言受到异质底物降解所需的同步多功能代谢的阻碍。因此，几十年来的经验操作仍然使复杂的甲烷生成过程成为一个谜。在这项研究中，通过底物规范和连续反应器操作获得了简化的 AD 微生物群落。采用基于基因组的宏基因组方法全面研究 AD 的代谢途径和微生物协同网络。总共从 8 个特定产甲烷小生境中获得的宏基因组中组装了 63 个宏基因组组装基因组（MAG）。从注释基因及其在实验条件下的动态重建代谢途径。结果表明，产甲烷小生境滋养了超出当前基于培养方法获得的知识的独特代谢。在一对共生体：Clostridiaceae sp. 和 Methanoculleus thermophilus 中提出并断言了一种没有乙酸盐形成的新型葡萄糖矿化模型。此外，在未表征的协同乙酸氧化菌 Synergistaceae spp 中阐明了分解代谢途径。一个显著的进化见解是发现电子传递和能量守恒机制对协同伙伴施加选择性压力。总的来说，单个微生物的功能作用紧密依赖于分解代谢途径，并且不能总是根据传统的四步 AD 概念在生理上定义。特定底物的系统提供了一个可追踪的微生物群落，用于剖析 AD 过程。基于基因组的宏基因组成功构建了以前未分离的微生物基因组，并说明了 AD 过程当前知识之外的代谢途径。本研究为揭示 AD 微生物生态学提供了新的视角，并建议特别关注 AD 微生物群落特有的未表征代谢。
