Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA.
Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA.
mBio. 2023 Apr 25;14(2):e0318922. doi: 10.1128/mbio.03189-22. Epub 2023 Feb 27.
Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt to changing environments. Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture cooperated via cross-feeding to produce methane using cellulose as the only carbon source and electron donor. The community metabolism of the quad-culture was compared with those of the R. cellulolyticum-containing tri-cultures, bi-cultures, and mono-culture. Methane production was higher in the quad-culture than the sum of the increases in the tri-cultures, which was attributed to a positive synergy of four species. In contrast, cellulose degradation by the quad-culture was lower than the additive effects of the tri-cultures which represented a negative synergy. The community metabolism of the quad-culture was compared between a control condition and a treatment condition with sulfate addition using metaproteomics and metabolic profiling. Sulfate addition enhanced sulfate reduction and decreased methane and CO productions. The cross-feeding fluxes in the quad-culture in the two conditions were modeled using a community stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. cellulolyticum to M. concilii and D. vulgaris and intensified substrate competition between M. hungatei and D. vulgaris. Overall, this study uncovered emergent properties of higher-order microbial interactions using a four-species synthetic community. A synthetic community was designed using four microbial species that together performed distinct key metabolic processes in the anaerobic degradation of cellulose to methane and CO. The microorganisms exhibited expected interactions, such as cross-feeding of acetate from a cellulolytic bacterium to an acetoclastic methanogen and competition of H between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This validated our rational design of the interactions between microorganisms based on their metabolic roles. More interestingly, we also found positive and negative synergies as emergent properties of high-order microbial interactions among three or more microorganisms in cocultures. These microbial interactions can be quantitatively measured by adding and removing specific members. A community stoichiometric model was constructed to represent the fluxes in the community metabolic network. This study paved the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems.
在群落中,微生物之间存在着复杂的相互作用,以进行生态过程并适应不断变化的环境。在这里,我们构建了一个由纤维素分解菌(Ruminiclostridium cellulolyticum)、产氢甲烷菌(Methanospirillum hungatei)、乙酰化甲烷菌(Methanosaeta concilii)和硫酸盐还原菌(Desulfovibrio vulgaris)组成的四元培养物。在四元培养物中,四种微生物通过交叉喂养合作,利用纤维素作为唯一的碳源和电子供体产生甲烷。将四元培养物的群落代谢与含 R. cellulolyticum 的三元培养物、二元培养物和一元培养物进行了比较。四元培养物中的甲烷产量高于三元培养物的总和,这归因于四种物质的正协同作用。相比之下,四元培养物的纤维素降解低于三元培养物的加和效应,这代表了负协同作用。通过元蛋白质组学和代谢组学比较了有硫酸盐添加和无硫酸盐添加两种条件下四元培养物的群落代谢。硫酸盐的添加增强了硫酸盐的还原作用,减少了甲烷和 CO 的产生。使用群落化学计量模型对两种条件下四元培养物的交叉喂养通量进行了建模。硫酸盐的添加加强了 R. cellulolyticum 向 M. concilii 和 D. vulgaris 的代谢传递,并加剧了 M. hungatei 和 D. vulgaris 之间的底物竞争。总的来说,本研究使用一个由四种微生物组成的合成群落,揭示了更高阶微生物相互作用的涌现特性。该合成群落设计使用了四种微生物,它们共同完成了纤维素厌氧降解为甲烷和 CO 过程中的不同关键代谢过程。微生物表现出了预期的相互作用,例如,纤维素分解菌向乙酰化甲烷菌的乙酸交叉喂养,以及硫酸盐还原菌和产氢甲烷菌之间的 H 竞争。这验证了我们基于微生物代谢作用设计微生物相互作用的合理性。更有趣的是,我们还发现了正协同和负协同作用,这是三元或更多微生物共培养物中高阶微生物相互作用的涌现特性。这些微生物相互作用可以通过添加和去除特定成员来定量测量。构建了一个群落化学计量模型来代表群落代谢网络中的通量。本研究为更具预测性地理解环境扰动对维持自然系统中具有地球化学意义的过程的微生物相互作用的影响铺平了道路。