Tuning Microbial Diversity Using Temporal Structure in High-Throughput Continuous Culture

Many microbiomes exhibit remarkable diversity, even within the same ecosystem. The mechanisms that enable such broad coexistence are critical to understanding the composition and function of microbiomes. Network structure (e.g. cross-feeding) or spatial structure (e.g. compartmentalization) are well-studied mechanisms that promote coexistence in microbial communities. Temporal structure, in which nutrients or stresses change over time in an ecosystem, is a third mechanism that can promote coexistence between competing microbes. An improved understanding of temporal structure could unlock new approaches to tune the diversity or composition of microbiomes in-situ. In prior work, we developed eVOLVER, a DIY automated culture platform that enables real-time monitoring and feedback control over culture parameters (e.g. culture density, temperature, media composition) across an array of independent cultures for long-term experiments (>100 hours). Recently, eVOLVER enabled us to vary the temporal structure in microbial co-cultures by independently tuning mean dilution rate (i.e. cumulative media consumption) and dilution frequency (i.e. from “batch-Like” to “chemostat-like”). Starting >100 continuous cultures from the same highly diverse soil microbiome sample, we observed large differences in the composition and diversity of communities grown in different dilution schemes. Notably, our results diverged in multiple ways from the classic diversity-disturbance relationship models that are used to relate environmental fluctuations to ecosystem diversity. In collaborative work, we found our observations are well-captured by a modified consumer-resource model. We believe these results reinforce the role of temporal structure in stabilizing microbial communities, and highlight the need to consider these effects in both experimental and modeling efforts to study and engineer microbiomes.