Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org

Repeating this with KOs, a map of functional potential emerged. Different regions had specialized functions. E.g. new bottom water had in genes that allow cells to become dormant, protect themselves from salt stress, and have flexible membranes that allow division despite cold and high pressure.

I also clustered our genomes based on just where they were most abundant. 6 cohorts emerged. 3 were divided on the basis of depth: a surface, mesopelagic, and deep water cohort. Another 2 followed deep water circulation: an Upper Circumpolar Deep Water cohort and Antarctic Bottom Water cohort.

This is clearer when you consider the number of species shared between any two given samples. Surface water samples share few species and samples of old water share many.

In fact, prokaryotic diversity increases rapidly across the mixed layer and then is stable to the full depth of the ocean. This trend is akin to a pycnocline, which is a rapid change in water density with depth separating surface water from deeper water. Thus, we call it the “phylocline.”

So without further ado, HERE is the preprint: www.biorxiv.org/content/10.1.... The answer is YES—water masses do structure microbial communities for both prokaryotes and eukaryotes. In fact, they seem to be the single most important factor structuring microbial communities in the pelagic ocean.

My incredible graduate advisor, Andy Allen, committed to sequencing > 1000 samples, but by the time I graduated in 2020, we still needed to sequence our shotgun metagenomics samples. Reagents for library prep were hard to come by for anything except covid screens.

Back in San Diego, Hong Zheng expertly extracted DNA from my filters, finessing even the lowest biomass samples. We spent months calibrating the right concentration of controls to add to samples from different depths so that we could estimate absolute abundance of each species per mL of seawater.

When we docked, my now-husband James Giammona flew out for what he thought was a vacation. He ended up bundled up with me in the ship’s walk-in freezer, re-sealing sample tubes that had exploded in liquid nitrogen. Here he is after lugging my peristaltic pump around Punta Arenas.

At sea I shared a lab space with Cathy Garcia, who became a great friend and indispensable to my project. Everyone on the cruise was incredible, from the captain and crew to the chief and co-chief scientists Rolf Sonnerup and Sarah Purkey, who taught me how to date seawater and define water masses.

Miraculously, the organizers of the GO-SHIP program let me join the team. My incredible graduate advisors Eric Allen and Andy Allen encouraged me to go on this cruise. I went and if there was extra water not allocated to other analyses, I was up any time day or night, filtering it!

Then, I got an email asking for volunteers for the GO-SHIP P18 cruise, running from Easter Island to Antarctica. It was perfect—spanning newly formed bottom water and some of the oldest water in the world.

When I first posed this question, the data to answer it didn't exist. The most state-of-the art global ocean survey, TARA Oceans, only sampled to about 1000 m deep. To find out, you'd need to charter a ship equipped to sample to full ocean depth (~$50k/day). I put it out of my mind.

Or, put another way, do “water masses”, which are defined in temperature and salinity space, represent biomes, the way rainforests and grasslands can be defined by temperature and precipitation on land?

Physical oceanographers make beautiful section plots that slice the ocean like a cake and show how temperature, salinity, and many other variables change across an ocean basin. My reaction was, could we make a map like this of microbes? Would individual species be confined by water mass boundaries?

Below the mixed layer, water is divided into “water masses” that stack like iced tea and lemonade in an Arnold Palmer drink. These water masses circulate based on their densities but very, very slowly. Some of the “oldest” water in the ocean hasn’t seen the surface in over 1000 years.

I’m very excited to finally share the results of a passion project that has been on my mind for nearly a decade. You can find the pre-print below, but what follows is the saga of how this project came to be: