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!
5 thoughts on “Bacterial isolates from seagrass samples: a new approach”
What is the role of these microorganisms in relation with the conservation of seagrass?
We are not sure — but this is definitely an area of interest. We think, for example, that microbes likely influence the effectiveness of restoration projects for seagrass. They also likely affect the resistance of seagrass to stresses such as higher temperature.
How do you estimate abundance of OTU from sediments? Do you know if that can be achieved from historic sediments (cores)? I’m working in a degraded estuary suffering from recent (century-scale) land-use change that used to contain more widespread Zostera marina beds.
All of our OTU studies were based off 16S rRNA gene sequencing. I have no idea how well this translates to older cores, we’ve always used fresh samples. There’s a whole group of micro folks out there that study “ancient DNA” that might have a better sense.