Using ecological theory to increase microbial coexistence under controlled conditions

Our ability to predict and manage ecosystem dynamics is limited by complex, emergent properties that arise as individuals interact with one another and their environment. Information is particularly deficient for microbes, despite the fact that they make up the majority of Earth's biodiversity and harbor the majority of life's metabolic capabilities. We need controlled model ecosystems to learn how to predict microbial dynamics and derive fundamental principles; however, most laboratory-based, synthetic microbial communities are composed of only a few species and do not reflect natural diversity. The aquatic communities living in carnivorous pitcher plants are an emerging model system for community ecology, and have many characteristics that make them tractable for research. Furthermore, a recent experiment has shown that pitcher bacterial community function can significantly improve plant growth. In this empirical study, we used bacteria isolated from pitcher plant microcosms to explore if and how different equalizing and stabilizing mechanisms promote coexistence and lead to species-rich microbial communities under controlled conditions. We ran two experiments, starting with either 17 or 26 distinct bacterial taxa, and added spatial and temporal structure as well as varying resource complexity. We used a full factorial design and measured composition across multiple transfers. Our results show that, as hypothesized, more complex media, no shaking, and temperature fluctuations all increased bacterial coexistence. However, we saw unexpected tradeoffs and interactions among treatments, with more complex media plus no shaking or less complex media plus temperature fluctuations having the largest increases in biodiversity. Our results highlight how small environmental changes can alter community dynamics, and also how we do not yet understand the interactive effects of different mechanisms driving microbial coexistence.