All posts by aalexiev

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.

Genome of Z. marina Sequenced

A paper on the genome of Z. marina was released early this year. This is the first marine angiosperm genome to be sequenced, and since it’s our main host organism, we are fairly excited. This opens up a couple research possibilities, like studying host-microbe coevolution between Z. marina and its microbiome. We can also use the plant reference genome with RNA-seq data to filter out reads from the microbes, which will make it easier to look at the gene functions represented in the seagrass microbiome. Having a reference genome for our host will definitely come in handy, and has opened some exciting new doors for us.

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:


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.

Potomac River Samples – Finally, DNA

At last, all the Potomac River Seagrass samples have had their DNA extracted via MoBio Powersoil kits (reagents, tubes, and pipettes, oh my!). All the samples showed promising amounts of DNA going into PCR. Unfortunately, after doing the first 12 samples and finding only 4 that amplified, I’m a little discouraged. I still have the rest of the ~60 samples to go through, so hopefully there will be enough bacterial DNA to amplify in the rest of the samples to do some meaningful analyses. I suspect most of the DNA extracted was non-bacterial though, so it might be hard getting sequences from these plants.

Seagrasses and Other SAVs at Chesapeake Bay

I recently went to Chesapeake Bay to collect submerged aquatic vegetation (SAV) for the Seagrass Microbiome Project. I found a lot of aquatic plants that were related to seagrass, which will be useful for comparing the SAV microbiome between species, not just within seagrass (Zostera marina). The plan was to embark on a five-day trip down the Potomac and James Rivers, hitting 12 sites and a 13’th out in the Bay. The rivers provide a near-replicate salinity gradient, allowing us to observe microbiome changes across varying salinities as well as species. Unfortunately, the amount of sampling we planned to get done was a bit too ambitious. We got through 11 sites, only 3 of which had SAVs, all on the Potomac. So goes field sampling, I guess.

Here is a selection of pictures of what was found at some of the sites with tentative identifications:


Ceratophyllum demersum, found at the most freshwater site on the Potomac


Really dead Vallisneria americana, tons of which was found at the most freshwater site on the Potomac


Myriophyllum spicatum, found in a very muddy and sedimented wetlands area, surrounded by Spartina.


Vallisneria again? Wasn’t sure at first since it had those oddly curly leaves, but it seems Vallisneria has a lot of leaf morphologies and this is one of them. Found at the second most freshwater sight, happily growing on a rocky coast.

Sadly, a lot of the sites were boating areas or were otherwise heavily impacted by human activities. Almost all the sites had water with boating oil floating atop it. Most of the coasts were filled with terrestrial and semi-aquatic plants, but no aquatic vegetation whatsoever. Just bare, sandy coasts and water filled with oil. It really solidified how important seagrasses and SAVs are to ecosystems. They thrived in areas of the Potomac with higher biodiversity and less anthropogenic influence. And having waded through tangles of SAVs, I can assure everyone that they really do a great job filtering trash that flows outward from land.