New paper on seagrass microbial ecology

We have a new paper out today on the impacts of coastal seagrasses on the microbial community structure of San Diego Bay.  I’m excited about this paper as the first student-led study to come out of my lab.  The study was conceived by Tia Rabsatt, an undergraduate from UVI, during a SURF REU in 2017.  Tia carried out the sample collection, DNA extractions, and flow cytometry, then handed the project off to Sahra Webb.  Sahra carried out the remainder of the project as her Masters thesis.

Tia filters water just outside the mouth of San Diego Bay.  Coronado Island is in the background.

Why the interest in seagrass?  Unlike kelp, seagrasses are true flowering plants.  They’re found around the world from the tropics to the high latitudes and perform a number of important ecosystem functions.  Considerable attention has been given to their importance as nursery habitat for a number of marine organisms.  More recently we’ve come to appreciate the role they play in mediating sediment transport and pollution.  Recent work in Indonesia (which inspired Tia to carry out this study) even showed that the presence of seagrass meadows between inhabited beaches and coral reefs reduced the load of human and coral pathogens within the reefs.

Seagrass, barely visible on a murky collection day.  Confirming seagrass presence/absence was a considerable challenge during the field effort, and one we hadn’t anticipated.  There’s always something…

There are a number of good papers out on the seagrass microbiome – epibionts and other bacteria that are physically associated with the seagrass (see here and here) – but not so many on water column microbes in the vicinity of seagrass meadows.  In this study we took paired samples inside and outside of seagrass beds within and just outside of San Diego Bay.  I’ll be the first to admit that our experimental design was simple, with a limited sample set, and we look forward to a more comprehensive analysis at some point in the future.  Regardless, it worked well for a factor-type analysis using DESeq2; testing for differentially present microbial taxa while controlling for the different locations.

What we found was that (not surprisingly) the influence of seagrass is pretty minor compared to the influence of sample location (inside vs. outside of the bay).  There were, however, some taxa that were more abundant near seagrass even when we controlled for sample location.  These included some expected copiotrophs including members of the Rhodobacteraceae, Puniceispirillum, and Colwellia, as well as some unexpected genera including Synechococcus and Thioglobus (a sulfur oxidizing gammaproteobacteria).  We spent the requisite amount of time puzzling over some abundant Rickettsiales within San Diego Bay.  We usually take these to mean SAR11 (though our analysis used paprica, which usually picks up Pelagibacter just fine), but didn’t look like SAR11 in this case.  An unusual coastal SAR11 clade?  A parasite or endosymbiont with a whonky GC ratio?  TBD…