In this manuscript we study a key, but poorly understood determinant of microbial ecosystem structure: the number of different molecules available as substrates in the environment. How does a microbiome respond to a more diverse set of available food sources? How does a marine microbiome respond to diverse pollutants? These are very difficult questions that will require years of biomedical and field research. What is stunning, however, is that we lack an even basic understanding of how the number of environmental molecules (“environmental complexity”) would affect a microbial ecosystem in a well controlled laboratory setting. In our paper, we fill this fundamental gap by implementing hundreds of combinatorial experiments with synthetic consortia to systematically measure vital microbial ecosystem phenotypes (yield and diversity) as a function of increasing environmental complexity.
Our work, at the crossroads of microbial ecology and systems biology, has important implications for our fundamental understanding of complex microbiomes, as well as for future efforts to engineer synthetic microbial consortia for metabolic engineering and therapeutic applications.
Our article explores the effects of multiple nutrients on the growth and diversity of microbial communities. In this photograph, inspired by the work of the 16th century Italian painter Giuseppe Arcimboldo, we portray two microbes as an arrangement of fruits and vegetables to capture the variety of resources that these organisms can use as building blocks for biomass. We also highlight the exchange of nutrients between different organisms, which is prevalent in microbial communities and can further modulate how they behave in complex environments.
Abstract and link to paper:
Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non- additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.
Alan R Pacheco, Melisa Osborne & Daniel Segrè: “Non-additive microbial community responses to environmental complexity”, Nature Communications 12, 2365 (2021). https://www.nature.com/articles/s41467-021-22426-3