iiinova — where your digital self keeps evolving

Reposted by Bethany Kolody, PhD

Ling-Dong Shi @lingdong-shi.bsky.social · 24/05/2026

Super excited to share the final project of my postdoc career! We found that Borgs and mini-Borgs are widespread across diverse ecosystems. They don't just exist in Banfield Lab — they are everywhere! 🌎

11510

Reposted by Bethany Kolody, PhD

The Banfield Lab @banfieldlab.bsky.social · 23/01/2026

🚨 New pre-print alert! Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires www.biorxiv.org/content/10.6...

biorxiv.org

0147

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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.

111

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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.

100

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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!!

120

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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

100

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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).

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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

41810

Bethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025

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!

030

Bethany Kolody, PhD @bethanykolody.bsky.social · 01/03/2025

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]

010

Bethany Kolody, PhD @bethanykolody.bsky.social · 01/03/2025

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]

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 01/03/2025

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]

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 16/01/2025

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

010

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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!

040

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

210

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

110

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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).

161

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

150

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

170

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

140

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

160

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.”

290

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

170

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

2269

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

160

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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... 😅

180

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

150

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

150

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

190

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

280

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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!

1120

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

Even better, researchers on board would be measuring every physical characteristic I could think of that could structure microbial communities, not just temperature and salinity but also nutrients, oxygen, and even water age from radiocarbon dating and atmospheric tracers.

170

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

180

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

180

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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?

1110

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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?

170

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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.

270

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

In the first year of my PhD, I took a Physical Oceanography class that introduced me to the idea of Global Overturning Circulation. Up until this point, my mental image of the ocean was that it was mixed like a soup. But, winds and storms only reach the top ~500 m of the ~4000 m deep ocean!

140

Bethany Kolody, PhD @bethanykolody.bsky.social · 15/01/2025

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:

65926