Microbes encounter a slew of abiotic and biotic factors that determine their success in the ocean. These factors, or niche dimensions, are often studied individually by growing organisms under defined conditions, or by linking microbes to environmental parameters measured in the field. Trying to gain a more comprehensive picture of the importance and roles of these factors determining microbial viability is a challenge, however, as there is great complexity in a drop of seawater involving many interacting species and up to hundreds of thousands of unique organic molecules.
In our recent study, we used the marine bacterium Ruegeria pomeroyi DSS-3 as an invader of intact seawater sampled from a declining dinoflagellate bloom in Monterey Bay, California. This bacterium has been a model organism for lab studies to better understand important currencies in carbon and sulfur cycling and interactions with phytoplankton, and it is able to rapidly respond to dynamic conditions. We sought to determine how its transcriptomic response in bloom seawater could reveal niche dimensions important to bacterial survival in the coastal ocean.
These invasion studies were carried out as part of a broader sampling of the native microbial bloom community in collaboration with the Monterey Bay Aquarium Research Institute, providing an inventory of other organisms and environmental parameters encountered by the invading bacterium. At intervals during the bloom, we added the bacterium into seawater, gave it 90 minutes to assess the environment, and analyzed its differential gene expression patterns across the serial invasions.
En route to sampling site in Monterey Bay, CA
We identified about 100 niche dimensions of R. pomeroyi including organic nitrogen and sulfur metabolites, vitamins and cofactors, and transported metals. A number of interesting genes encoding biotic interactions were differentially expressed, including genes for a diffusible killing mechanism targeting diverse bacterial taxa, as well as a gene transfer agent system that packages random fragments of the genome into virus-like particles released for intraspecific gene transfer.
Invasion studies coupled with transcriptomics can be used in a variety of natural systems to better understand microbial ecological niches.