So for the last couple of years I’ve supervised a series of undergraduates who have spent some time isolating bacteria from seagrass samples… sometimes from the plants themselves and sometimes from associated sediment. We usually used non-specific aerobic media such as Marine Broth and Seawater Nutrient Agar. The result has been a series of the usual suspects; Vibrio, Shewanella, Pseudoalteromonas, etc. We’ve sequenced a number of these genomes, examples of Genome Announcements papers like this can be found here, here, here, here, here, here and here. The goals of this culturing were three-fold; cool undergraduate projects (check), add seagrass-associated genome data to the database to aid in metagenomics and such (check), and to characterize isolates that might be important in seagrass biology (unknown).
In regards to the last goal, we’ve attempted to use abundance of taxa as one rough proxy of “importance” and significant changes within an experiment as another. We have several large 16S projects to work with, but in most cases the isolates that we have generated are not found at particular abundance or significance in these datasets. And perhaps that’s not surprising, non-specific media is good at isolating widely distributed generalists.
So now we plan to approach the problem from the opposite direction, we’re picking the OTUs from our 16S data that are the most interesting and attempting to selectively culture them. #1 on our hit list is Sulfurimonas which crops up over and over again.
Stay tuned for results on this approach!