Weinrich Sören, Koch Sabine, Bonk Fabian, Popp Denny, Benndorf Dirk, Klamt Steffen, Centler Florian
Biochemical Conversion Department, Deutsches Biomasseforschungszentrum gGmbH, Leipzig, Germany.
Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
Front Microbiol. 2019 May 17;10:1095. doi: 10.3389/fmicb.2019.01095. eCollection 2019.
The process of anaerobic digestion in which waste biomass is transformed to methane by complex microbial communities has been modeled for more than 16 years by parametric gray box approaches that simplify process biology and do not resolve intracellular microbial activity. Information on such activity, however, has become available in unprecedented detail by recent experimental advances in metatranscriptomics and metaproteomics. The inclusion of such data could lead to more powerful process models of anaerobic digestion that more faithfully represent the activity of microbial communities. We augmented the Anaerobic Digestion Model No. 1 (ADM1) as the standard kinetic model of anaerobic digestion by coupling it to Flux-Balance-Analysis (FBA) models of methanogenic species. Steady-state results of coupled models are comparable to standard ADM1 simulations if the energy demand for non-growth associated maintenance (NGAM) is chosen adequately. When changing a constant feed of maize silage from continuous to pulsed feeding, the final average methane production remains very similar for both standard and coupled models, while both the initial response of the methanogenic population at the onset of pulsed feeding as well as its dynamics between pulses deviates considerably. In contrast to ADM1, the coupled models deliver predictions of up to 1,000s of intracellular metabolic fluxes per species, describing intracellular metabolic pathway activity in much higher detail. Furthermore, yield coefficients which need to be specified in ADM1 are no longer required as they are implicitly encoded in the topology of the species' metabolic network. We show the feasibility of augmenting ADM1, an ordinary differential equation-based model for simulating biogas production, by FBA models implementing individual steps of anaerobic digestion. While cellular maintenance is introduced as a new parameter, the total number of parameters is reduced as yield coefficients no longer need to be specified. The coupled models provide detailed predictions on intracellular activity of microbial species which are compatible with experimental data on enzyme synthesis activity or abundance as obtained by metatranscriptomics or metaproteomics. By providing predictions of intracellular fluxes of individual community members, the presented approach advances the simulation of microbial community driven processes and provides a direct link to validation by state-of-the-art experimental techniques.
复杂微生物群落将废弃生物质转化为甲烷的厌氧消化过程，已经通过参数化灰箱方法进行了16年多的建模，这些方法简化了过程生物学，并未解析细胞内微生物活性。然而，通过元转录组学和元蛋白质组学的最新实验进展，关于这种活性的信息已经以前所未有的细节呈现出来。纳入这些数据可能会产生更强大的厌氧消化过程模型，能更忠实地反映微生物群落的活性。我们通过将1号厌氧消化模型（ADM1）与产甲烷菌的通量平衡分析（FBA）模型耦合，对作为厌氧消化标准动力学模型的ADM1进行了扩充。如果对非生长相关维持（NGAM）的能量需求选择得当，耦合模型的稳态结果与标准ADM1模拟结果相当。当将玉米青贮料的恒定进料从连续进料改为脉冲进料时，标准模型和耦合模型的最终平均甲烷产量非常相似，而脉冲进料开始时产甲烷菌群的初始响应及其脉冲间动态变化则有很大差异。与ADM1不同，耦合模型可为每个物种提供多达1000个细胞内代谢通量的预测，更详细地描述细胞内代谢途径活性。此外，ADM1中需要指定的产率系数不再需要，因为它们隐含地编码在物种代谢网络的拓扑结构中。我们展示了通过实施厌氧消化各个步骤的FBA模型来扩充ADM1（一个基于常微分方程的模拟沼气生产模型）的可行性。虽然将细胞维持作为一个新参数引入，但由于不再需要指定产率系数，参数总数减少。耦合模型提供了关于微生物物种细胞内活性的详细预测，这些预测与通过元转录组学或元蛋白质组学获得的酶合成活性或丰度的实验数据兼容。通过提供单个群落成员细胞内通量的预测，本文提出的方法推进了微生物群落驱动过程的模拟，并为通过先进实验技术进行验证提供了直接联系。
