Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium
Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium
复制标题
微生物生态系统的组装和多样性的热力学约束在接近和远离平衡时是不同的
DOI：
10.1101/2021.04.19.440392
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Cook J
中科院分区：
文献类型：
--
作者：
Cook J
长期以来，非平衡热力学一直是生态学家非常感兴趣的领域，因为大多数基本的生物过程，如蛋白质合成和呼吸，本质上都是耗能的。然而，这些兴趣大多集中在开发粗略的生态系统水平最大化原则上，对导致这种新出现的限制的潜在机制提供的洞察力很少。微生物群落是破译这一机制基础的自然系统，因为它们以底物消耗、代谢物生产和交叉喂养的形式存在的相互作用可以用热力学的术语明确描述。以前的工作考虑了热力学约束如何影响物种对之间的竞争，但没有分析这如何在复杂的动力系统中表现出来。为了解决这一差距，我们开发了一个具有完全可逆反应动力学的热力学微生物群落模型，该模型允许直接考虑自由能耗散。这也允许物种通过产品而不仅仅是底物进行相互作用，增加了动态复杂性，并允许出现更细微的相互作用类型分类。使用这个模型，我们发现群落多样性随着底物的不稳定而增加，因为更大的自由能可获得性允许更快地产生生态位。因此，在群落建立的时间框架内会产生更多的生态位，从而导致更高的最终物种多样性。我们还发现，允许物种利用接近平衡的反应增加了低自由能区域的多样性。在这种情况下，我们在这里确定的两种新的热力学相互作用类型达到了与传统(竞争和促进)类型相当的优势，强调了热力学在群落动力学中所起的关键作用。我们的结果表明，考虑到现实的热力学约束对于理解现实世界微生物群落的动态至关重要。
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.
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影响因子：
8.6
作者：
Posfai A;Taillefumier T;Wingreen NS
通讯作者：
Wingreen NS
影响因子：
4.3
作者：
Noor E;Flamholz A;Bar-Even A;Davidi D;Milo R;Liebermeister W
通讯作者：
Liebermeister W
动力学校对和热力学不确定性的极限
DOI：
10.1101/845164
发表时间：
2019
期刊：
bioRxiv
影响因子：
--
作者：
W. Piñeros;Tsvi Tlusty
通讯作者：
Tsvi Tlusty
影响因子：
2
作者：
Michaelian, K
通讯作者：
Michaelian, K
影响因子：
16.6
作者：
Smith, Thomas P.;Thomas, Thomas J. H.;Pawar, Samrat
通讯作者：
Pawar, Samrat