Abstract
Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of these basic mechanisms, which were to some extent anticipated by theoretical predictions. Moreover, synthetic cooperation is a promising lead towards the engineering of novel functions and enhanced productivity of microbial communities. Here, we review recent progress on engineered cooperation in microbial ecosystems. We focus on bottom-up approaches that help to better understand cooperation at the population level, progressively addressing the challenges of tackling higher degrees of complexity: spatial structure, multispecies communities, and host-associated microbiomes. We envisage cooperation as a key ingredient in engineering complex microbial ecosystems.
Highlights
Cooperation emerges at multiple scales of complexity in microbial ecosystems
In response to the amino acid concentrations that were supplemented to the medium, the strains gradually transitioned from a cross-feeding mutualism to parasitism and to competition (Figure 2d)
We reviewed recent work on microbial cooperation from a synthetic biology perspective, taking advantage of both simple ecological principles and a bottom-up approach to tackle the complexity of microbial communities
Summary
Cooperation emerges at multiple scales of complexity in microbial ecosystems. Clonal populations are among the simplest microbial ecosystems that can be studied, and yet, they provide a convenient laboratory arena to analyze several cooperative behaviors in microbes [1,2]. The cooperative strain had instead an intact SUC2 gene, but an engineered auxotrophy for histidine, which allowed tuning its relative fitness in different experiments in which the two strains were cocultured These experiments showed that, as cooperators release the invertase, sucrose digestion occurs at a slightly higher rate in the surroundings of their cell membrane, which gives cooperators a small advantage at capturing the simple sugars. In response to the amino acid concentrations that were supplemented to the medium, the strains gradually transitioned from a cross-feeding mutualism to parasitism and to competition (Figure 2d) These results highlight the plasticity of microbial interactions, as well as the potential to engineer microbial interactions through environmental tuning. An evolutionary race towards minimum metabolic costs could instead promote hierarchical ecosystems in which just one producer strain cross-feeds metabolites with different kinds of cheaters The latter mechanism is known as the Black Queen hypothesis [46,47]. Developing a better understanding of dynamic fitness landscapes will certainly help to unveil how microbial interactions emerge and develop under eco-evolutionary feedbacks
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