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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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

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...

www.science.org

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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!!

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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).

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jul 10

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!

J. Craig Venter Institute @jcvi.org · Jul 10

Just published in @science.org: Deep ocean currents don’t just move water—they shape entire microbial ecosystems. Our new study reveals how overturning circulation structures microbial life across the South Pacific.

www.jcvi.org/media-center... 🧪

New study reveals how deep ocean currents shape microbial life across the South Pacific

La Jolla, California—July 10, 2025—A groundbreaking study, published in the journal Science, has unveiled how deep ocean...

www.jcvi.org

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Bethany Kolody, PhD @bethanykolody.bsky.social · Mar 1

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]

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Bethany Kolody, PhD @bethanykolody.bsky.social · Mar 1

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]

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Bethany Kolody, PhD @bethanykolody.bsky.social · Mar 1

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]

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 16

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

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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!

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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).

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.”

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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Bethany Kolody, PhD @bethanykolody.bsky.social · Jan 15

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.

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