Bethany Kolody, PhD

Overturning circulation structures the microbial functional seascape of the South Pacific Global overturning circulation partitions the deep ocean into regions, each with different physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems rem...

manuscript here! www.science.org/doi/10.1126/...

Thanks also to
@jjminich.bsky.social
ial for advising me on how to process low-yield deep sea samples, Drishti Kaul and
@rhlampe.bsky.social
for bioinformatic consultation, James Giammona for help with MOANA and tireless moral support, and Karen Selph for processing flow cytometry samples.

Special thanks to the GO-SHIP program, especially Lynne Talley and P18 Chief Scientists Brendan Carter and Rolf Sonnerup and the crew of the Ronald H. Brown for making this project possible.

Huge thanks to my co-authors: Rohan Sachdeva, Hong Zheng, Zoltán Füssy, Eunice Tsang, Rolf Sonnerup, Sarah Purkey, Eric Allen, Jill Banfield
@banfieldlab.bsky.social and Andy Allen!!

You can find a great summary of our research by JCVI's Matt LaPointe here: bsky.app/profile/jcvi...

To celebrate, here are some home videos from our GO-SHIP P18 cruise! Big thanks to Josh Gunter and Alex Sidelev for letting me film them prepping and launching the niskin rosette (big carousel of bottles that collect water from all different ocean depths).

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

Thanks for covering our latest research @jcvi.org! So happy that our interactive microbial map of the ocean is out for the world to use!

The K1/2 was determined to be 530 reads for 16S and 96,300 for 18S. Samples below this coverage threshold were removed from downstream analysis (n= 29 for 16S; n= 35 for 18S)." [3/3]

The percent of ASVs mapping to the correct mock community genera in each dilution was calculated, and an allosteric sigmoidal model was used to determine the coverage level at which 50% of ASVs map to the mock community (K1/2) (64). [2/3]

Yes, it was really helpful, thank you!!
From the supplemental:
"Because of the low biomass nature of deep ocean samples, serially diluted mock community controls were used to determine the minimal coverage necessary to accurately capture community composition. [1/3]

@hankgreen.bsky.social love your science explanations, thought you might like the results of my research cruise!

And finally, thanks to my undergraduate mentee, Eunice Tsang for helping me manually curate > 300 marine genomes, and whose follow up paper on the carbohydrate degradation potential of these genomes is forthcoming!

Thanks also to my PhD committee, Farooq Azam, Doug Bartlett, Peter Franks and Karsten Zengler for thoughtful feedback and discussions during the development of this research. Thanks to Zoltan Fussy for annotating the eukaryotic scaffolds to make sure they weren’t left out of the analysis.

Thanks also to @jjminich.bsky.social ial for advising me on how to process low-yield deep sea samples, Drishti Kaul and @rhlampe.bsky.social for bioinformatic consultation, James Giammona for help with MOANA and tireless moral support, and Karen Selph for processing flow cytometry samples.

Special thanks to the GO-SHIP program, especially Lynne Talley and P18 Chief Scientists Brendan Carter and Rolf Sonnerup and the crew of the Ronald H. Brown for making this project possible.

I’m very excited about this and I hope that the community will enjoy visualizing their favorite bugs, and maybe learn something new about their biogeography.

Of course, microbial distribution patterns are more nuanced than 6 spatial cohorts. So I built the Microbial Ocean Atlas for Niche Analysis (MOANA) which interactively plots the any taxa of interest over any of the variables measured on the P18 cruise. (Instructions in supplemental material).

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.

Finally, one cohort contained genomes that thrive in ancient, low oxygen water. Coverage differences across genomes suggests that these genomes are still dividing, albeit significantly more slowly than genomes at the surface.

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.”

We found that even though the surface ocean harbors the greatest diversity of microbes, samples from the surface are highly specialized to their local environment, so any given sample has low diversity.

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.

At the IGI, I learned so much working with Jill and Rohan Sachdeva, who is not only one of the greatest bioinformaticians I know, but also has a wealth of knowledge of marine microbial ecology.

I was lucky to join the Banfield Lab at @innovativegenomics.bsky.social. She let me continue the project in addition to my new project on the microbial underpinnings of rice paddy methane emissions on the condition that I would wrap it up within a year. That was four years ago... 😅

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.