Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation
Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation
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DOI：
10.1021/acssynbio.9b00271
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发表时间：
2019-09-01
影响因子：
4.7
通讯作者：
O'Malley, Michelle A.
中科院分区：
文献类型：
--
作者：
Gilmore, Sean P.;Lankiewicz, Thomas S.;O'Malley, Michelle A.
基于联合体的方法是实现高效生物加工的一种有前途的途径。然而，许多复杂的微生物相互作用决定了必须在合成系统中复制的群落动态和稳定性。大型哺乳动物食草动物的瘤胃和/或后肠含有复杂的生物质降解真菌和细菌群落，以及共同降解木质纤维素的古菌和原生动物，但负责稳定性，弹性和活性的微生物相互作用的社区仍然在很大程度上没有特征。在这项工作中，我们展示了一个“自上而下”的富集为基础的方法，选择一个最小的，但有效的木质纤维素降解社区，产生富含甲烷的发酵气体（沼气）。与来自富集的真菌的单一培养物相比，所得富集聚生体以1.4-2.1倍的速率产生0.75-1.9倍的发酵气体。自上而下富集的财团的宏基因组测序揭示了编码社区功能区室化的基因组，分布在厌氧真菌（Piromyces），细菌（Sphaerochaeta）和两个产甲烷古菌（Methanosphaera和Methanocorpusculum）。由自上而下的富集的组合物的指导下，几个合成的共培养物形成从“自下而上”使用先前分离的真菌，新美鞭菌california和粗壮厌氧酵母配对的产甲烷菌甲烷杆菌bryantii。虽然交叉喂养发生在合成的共培养物，去除真菌代谢产物的产甲烷菌没有增加气体的生产率或基板解构率的合成社区相对于真菌单一栽培。代谢组学表征验证了合成共培养物内建立了互养，其与富集的聚生体相比以相似的浓度产生甲烷，但缺乏在天然系统中看到的时间稳定性（弹性）。总之，破译富集的肠道联合体的成员和代谢潜力使得能够设计产甲烷合成共培养物。然而，在生长速度和稳定性的差异富集与合成财团强调在模拟合成系统中自然发生的互养的困难。
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.