Potomac Samples: not what we expected, but still some interesting connections

Last summer I went on a sampling expedition to the Chesapeake Bay for some SAV (submerged aquatic vegetation) collection. I came back with leaf and root samples from the Potomac River from a few different SAV species. Ideally, we thought the microbial community would correlate with the salinity gradient across the sites or the host species.

Neither of those patterns are discernible in this data set as far as the beta diversity plots are concerned, but I found some other interesting things while sifting through these plots. For instance, the samples cluster based on the site location (P1-P4). The communities at P1 and P3 look really similar and P4 is within the tail end of their cluster, while P2 is totally different. location

For reference, here’s a map of our sites:

Screen Shot 2015-06-05 at 11.21.11 AM
Whitehead, Andrew et al. “Genomic Mechanisms of Evolved Physiological Plasticity in Killifish Distributed along an Environmental Salinity Gradient.” Proceedings of the National Academy of Sciences of the United States of America 108.15 (2011): 6193–6198. PMC. Web. 5 June 2015.

Although all the sites were visited, I only found SAV species at P1-4. There are some useful patterns in the water and soil chemistry data (courtesy of Greg Mayer from Texas Tech University) that show the same correlation pattern as the site locations (as expected since each location has its own distinct chemistry data). Some of the chemistry data shows different patterns from site location, so I’ll have to sift through those next and see what looks relevant. I also ran a core microbiome script for each site, but haven’t looked at the output yet.

In addition, the leaf and root samples are pretty distinct:

sampletype

The alpha diversity graphs are a whole ‘nother beast that I’m going to explore some other time. That’s all for now, but I feel that there are some interesting lines of investigation to pursue and more scripts to run.

About aalexiev

I graduated from University of California, Davis with a Microbiology degree, and am now working towards my PhD at the University of Colorado, Boulder. My interest lies in how microbial communities interact with their environments and hosts.

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