Prof. Sarahi Garcia (ldenburg University, Germany)
Natural microbial communities have a mixture of both complementary and (seemingly) redundant metabolic capacities. Moreover, much of the complementarity involves metabolically costly compounds that promote not just their own survival and reproduction but can also support neighboring cells. Complementary metabolic interactions develop over an evolutionary time scale as microorganisms utilize metabolites released by other organisms in the same environment. We studied natural microbial communities using both a reductionist approach (dilution-mixed-cultures, a.k.a. model communities) and a holistic (metagenomics) approach. Model communities simplify the community while keeping some genotypic and nutritional diversity and consist of 2 or more microbial strains that would naturally co-occur. We inoculated thousands of model communities from environmental samples, resulting in different success rates depending on the media and the number of cells co-inoculated. Many of these cultures allowed for growing and studying previously uncultivated bacteria. Combined with sequencing techniques, we found complementary metabolic capacities in the genomes of the model community members as well as growth of consortium capable of specific functions, such as methane degradation. Our holistic approach to studying environmental microbial communities with genome-resolved metagenomics and network analyses found correlations between species clusters, their metabolic functions and abiotic factors. By integrating holistic and reductionist approaches, we confirmed that some of the cultivated model communities include abundant members in the environment. Moreover, the different levels of organization of microbial communities start to emerge, showing the intricate network of anabolic and catabolic interactions that play out in the natural environment.