Abstract
Symbiotic interactions between organisms are important for human health and biotechnological applications. Microbial mutualism is a widespread phenomenon and is important in maintaining natural microbial communities. Although cooperative interactions are prevalent in nature, little is known about the processes that allow their initial establishment, govern population dynamics and affect evolutionary processes. To investigate cooperative interactions between bacteria, we constructed, characterized, and adaptively evolved a synthetic community comprised of leucine and lysine Escherichia coli auxotrophs. The co-culture can grow in glucose minimal medium only if the two auxotrophs exchange essential metabolites — lysine and leucine (or its precursors). Our experiments showed that a viable co-culture using these two auxotrophs could be established and adaptively evolved to increase growth rates (by ∼3 fold) and optical densities. While independently evolved co-cultures achieved similar improvements in growth, they took different evolutionary trajectories leading to different community compositions. Experiments with individual isolates from these evolved co-cultures showed that changes in both the leucine and lysine auxotrophs improved growth of the co-culture. Interestingly, while evolved isolates increased growth of co-cultures, they exhibited decreased growth in mono-culture (in the presence of leucine or lysine). A genome-scale metabolic model of the co-culture was also constructed and used to investigate the effects of amino acid (leucine or lysine) release and uptake rates on growth and composition of the co-culture. When the metabolic model was constrained by the estimated leucine and lysine release rates, the model predictions agreed well with experimental growth rates and composition measurements. While this study and others have focused on cooperative interactions amongst community members, the adaptive evolution of communities with other types of interactions (e.g., commensalism, ammensalism or parasitism) would also be of interest.
Highlights
Microbes are affected by their physical and chemical environment, and they naturally encounter other species that can influence their behaviors
We focused on examining how adaptive evolution affected community growth rates and compositions, and how mono-culture and co-culture phenotypes of individual evolved isolates were affected by adaptive evolution in a co-culture environment
A computational model was used to evaluate how changes in uptake and secretion rates of cross-fed amino acids would influence community growth rates and composition, and predictions were compared to experimental results
Summary
Microbes are affected by their physical and chemical environment, and they naturally encounter other species that can influence their behaviors. Symbiotic interactions between microbes and higher organisms can lead to stable interactions and microbial communities. Mutualism is one type of symbiotic interaction, where both species benefit from the interaction. While symbiotic interactions are important, most of our knowledge of bacterial metabolism has been gathered from studies of individual strains in pure cultures. More than 99 percent of microbes cannot be cultured in mono-culture, since their growth depends on the presence of other species [6]. The phenotypes of cultivatable strains may drastically change when grown in a mixed community as compared to mono-culture [7,8]. Studies are needed on how bacteria interact in mixed cultures
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