Photosynthetic microalgae have potential as a renewable bioenergy source, but the role of their microbiome in outdoor ponds is poorly understood. While the bacteria can consume up to 50% of the fixed carbon, they are unavoidable and are known to impact the algal productivity. In this work we present a novel co-culture method (“porous microplate”) to study how the associated bacteria spatiotemporally respond to algal exometabolites in vivo. Mechanistic design of the porous microplate allowed us to identify taxonomically distinct responses in or between bacterial isolates. The results were consistent with their individual consumption patterns of the algal exometabolites, identified using untargeted metabolomics, suggesting a competitive interaction in our co-culture system. Our systems biology approach exemplifies how the microbes spatiotemporally interact while competing for limited resources. The presented method can also be useful in understanding more advanced manufacturing systems examining interactions in, and between, other biological domains such as bacteria, fungi and yeast.
