Interaction variability shapes succession of synthetic microbial ecosystems

Abstract

Cellular interactions are a major driver for the assembly and functioning of microbial communities. Their strengths are shown to be highly variable in nature; however, it is unclear how such variations regulate community behaviors. Here we construct synthetic Lactococcus lactis consortia and mathematical models to elucidate the role of interaction variability in ecosystem succession and to further determine if casting variability into modeling empowers bottom-up predictions. For a consortium of bacteriocin-mediated cooperation and competition, we find increasing the variations of cooperation, from either altered labor partition or random sampling, drives the community into distinct structures. When the cooperation and competition are additionally modulated by pH, ecosystem succession becomes jointly controlled by the variations of both interactions and yields more diversified dynamics. Mathematical models incorporating variability successfully capture all of these experimental observations. Our study demonstrates interaction variability as a key regulator of community dynamics, providing insights into bottom-up predictions of microbial ecosystems.

Regularized S-Map Reveals Varying Bacterial Interactions

“…However, the Jacobian coefficients for two bacteria can provide clues about metabolic exchange in an ecological state. Moreover, the interaction between two species is subject to the presence of a third species (13). Two species may compete with each other in a well-mixed population; however, temporal and spatial separation by a third species can neutralize the competition or even change it to a positive interaction (32)(33)(34).…”

“…ecological state (11). The overall interspecific interactions in a bacterial community determine its assembly and performance in engineered systems (12,13). Therefore, a better understanding of the varying interspecific interactions is critical for regulating the functions of a bacterial community (14).…”

Formation, characterization and modeling of emergent synthetic microbial communities

“…A second approach is to construct synthetic bacterial communities from the bottom-up [24] . In the bottom-up approach, individual bacterial isolates are combined to give rise to a more complex microbial system where the original strains serve as sub-systems in an emergent community [25] , [26] , [27] . These easily manipulated bottom-up assemblies contribute to a promising approach for understanding interactions in natural communities [26] , [28] , [29] .…”

Structured environments foster competitor coexistence by manipulating interspecies interfaces

“…Microbial ecosystems present a particularly attractive test-bed for these ecological ideas. From a practical point of view, they are small and fast growing, relatively easy to genetically manipulate, and can be grown in controlled and customizable synthetic environments [35,[53][54][55][56], such as microfluidics [57,58]. Characterizing the forces and principles that establish and maintain microbial diversity is of significant interest in health-relevant settings like the human gut [59][60][61] and in the myriad contexts where soil microbiota impact natural or agricultural ecosystems [1,62].…”