About this Research Topic
The field of synthetic ecology relies on a combination of both theoretical and experimental techniques to improve our understanding of the dynamics and functional properties of simple microbial communities. The ultimate goal of this field is to foster stable and robust circuits of interacting organisms based on the rational understanding of the global (consortium-level) behavior resulting from these interactions.
Two broad research goals underpin this ambitious objective:
(i) Building a fundamental understanding of the principles that drive the dynamics and control the community-level properties of microbial consortia; this entails answering questions like "how do higher-order behaviors result from the metabolic and ecological interactions of individual genotypes?" and “how do these interactions and environmental conditions impact the evolutionary stability of cooperation within synthetic communities?“
(ii) Design and engineer synthetic microbial communities to carry out a given biotransformation (e.g. nitrogen removal, mineralisation of a xenobiotic compound) or function (e.g. minimal communities for gut fecal transplant); this is typically carried out in a bottom-up "design and build" manner (akin to synthetic biology), e.g. the engineering of spatially linked microbial consortia. Using a more “top-down“ approach, synthetic communities can also be generated combining different (well-defined) consortia enriched from natural communities, in order to coalesce their properties into a new, synthetic community.
Synthetic microbial ecology (like synthetic biology) is not a completely new discipline, but recent advances in both mathematical modeling, and genetic and metabolic engineering appear to bring us closer to the goal of controling the dynamic behavior of simple synthetic microbial assemblages. Nevertheless, our basic understanding of the principles that control the dynamic and behavior of microbial communities still largely remain elusive, and nowadays we have a better appreciation of how even simple interactions can yield to complex dynamic and unexpected behaviors. This knowledge gap clearly hinders the potential to design and engineer cooperative consortia for our needs (e.g. efficient wastewater treatment plants, bioremediation processes, improved human and animal health).
Addressing this knowledge gap will require to provide answers to broad questions like: how predictable is the outcome of microbial competition, and can the latter be engineered? What is the importance of initiation? How does the number of relevant interactions scale with the number of strains in a consortium? Are multiple stable states common in microbial communities, and do they form the basis of resilience when facing perturbations? How are niches exactly defined, and can niches be engineered? Which level of functional redundancy and complementarity is required for resilient synthetic communities?
This Research Topic could aggregate and make apparent the links between recent and possibly apparently disparate results in mathematical modeling, development of genetic tools and experimental environmental microbiology, that together bring us closer to the synthetic ecology goal. Human microbiome research in particular has a high demand for model systems that are both compositionally defined and of an order of complexity in par with the natural state; achieving this will require addressing the research agenda of synthetic ecology.
The following themes are relevant for this Research Topic, while submissions breeding the first two items are particulalrly encouraged:
• Theoretical modeling of community-level dynamics and control, and prediction of microbial assemblages.
• Experimental design and engineering of synthetic microbial communities in order to perform a given biotransformation, using either bottom-up or top-down approaches.
• Spatial (e.g. niche) or temporal structuring and organisation (e.g. modularity) via interactions (e.g. signaling, trophic,...) in real or reduced systems.
• Model (typically “in vitro“) systems, either continuous or batch.
Modeling papers should either include or explicitely refer to an empirical validation or behavior with actual microbial systems to be considered for review.
Two broad research goals underpin this ambitious objective:
(i) Building a fundamental understanding of the principles that drive the dynamics and control the community-level properties of microbial consortia; this entails answering questions like "how do higher-order behaviors result from the metabolic and ecological interactions of individual genotypes?" and “how do these interactions and environmental conditions impact the evolutionary stability of cooperation within synthetic communities?“
(ii) Design and engineer synthetic microbial communities to carry out a given biotransformation (e.g. nitrogen removal, mineralisation of a xenobiotic compound) or function (e.g. minimal communities for gut fecal transplant); this is typically carried out in a bottom-up "design and build" manner (akin to synthetic biology), e.g. the engineering of spatially linked microbial consortia. Using a more “top-down“ approach, synthetic communities can also be generated combining different (well-defined) consortia enriched from natural communities, in order to coalesce their properties into a new, synthetic community.
Synthetic microbial ecology (like synthetic biology) is not a completely new discipline, but recent advances in both mathematical modeling, and genetic and metabolic engineering appear to bring us closer to the goal of controling the dynamic behavior of simple synthetic microbial assemblages. Nevertheless, our basic understanding of the principles that control the dynamic and behavior of microbial communities still largely remain elusive, and nowadays we have a better appreciation of how even simple interactions can yield to complex dynamic and unexpected behaviors. This knowledge gap clearly hinders the potential to design and engineer cooperative consortia for our needs (e.g. efficient wastewater treatment plants, bioremediation processes, improved human and animal health).
Addressing this knowledge gap will require to provide answers to broad questions like: how predictable is the outcome of microbial competition, and can the latter be engineered? What is the importance of initiation? How does the number of relevant interactions scale with the number of strains in a consortium? Are multiple stable states common in microbial communities, and do they form the basis of resilience when facing perturbations? How are niches exactly defined, and can niches be engineered? Which level of functional redundancy and complementarity is required for resilient synthetic communities?
This Research Topic could aggregate and make apparent the links between recent and possibly apparently disparate results in mathematical modeling, development of genetic tools and experimental environmental microbiology, that together bring us closer to the synthetic ecology goal. Human microbiome research in particular has a high demand for model systems that are both compositionally defined and of an order of complexity in par with the natural state; achieving this will require addressing the research agenda of synthetic ecology.
The following themes are relevant for this Research Topic, while submissions breeding the first two items are particulalrly encouraged:
• Theoretical modeling of community-level dynamics and control, and prediction of microbial assemblages.
• Experimental design and engineering of synthetic microbial communities in order to perform a given biotransformation, using either bottom-up or top-down approaches.
• Spatial (e.g. niche) or temporal structuring and organisation (e.g. modularity) via interactions (e.g. signaling, trophic,...) in real or reduced systems.
• Model (typically “in vitro“) systems, either continuous or batch.
Modeling papers should either include or explicitely refer to an empirical validation or behavior with actual microbial systems to be considered for review.
Keywords: synthetic ecology, mathematical modeling, microbial communities
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
