Abstract
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, with many insights about an organism’s ecological niche arising from metabolic reconstruction of its genome content. In this work, we demonstrate how the “seed set framework” enables high-throughput, computational analysis of metabolic reconstructions, while providing new insights into a microbe’s metabolic capabilities, such as nutrient sources and essential metabolites. We apply this framework to members of the ubiquitous freshwater Actinobacterial lineage acI, confirming and extending previous experimental and genomic observations that suggest acI bacteria exhibit a heterotrophic lifestyle reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage. These results reveal strong expression of transport proteins and the light-harvesting protein actinorhodopsin, suggesting the acI are capable of photoheterotrophy.