Transcriptional Markers of Organic Substrate Utilization in a Marine Bacterium

The marine carbon pool is a complex source of nutrients for microbes, found within a diverse microbial community, making it difficult to identify which carbon substrates are supporting which microbes. One approach is to use bacterial transcriptomes as biosensors of labile substrates. To investigate the reliability of transcriptomics, the transcriptomes of Ruegeria Pomeroyi were analyzed under growth on a carbon mix and glucose treatment, containing substrates many orders-of-magnitude higher than in situ to maximize metabolic responses. We observed strong correlations between transcriptional enrichment of a metabolic pathway with its associated substrate, with signals strongest at initial steps, but found that the presence of multiple substrates blurs the metabolic signatures of individual compounds. However, we observed some enrichments did not relate back to substrates we added within our treatments, indicating false negatives/positives. This work elucidates relationships between substrate availability and metabolic responses, and how a complex mixture obscures these signals.