Mom asked, "I wonder when cherries bloom in Japan?" So I found 1200 years of data online and made her a plot.

On a personal note, writing this paper has spanned both medical leave and a pregnancy. I want to thank @quendi , @archaeal , and an amazing @NSF program officer for believing in me and supporting me through all of it.

A lot of this could be ecology OR evolution, depending on how species are delineated. Instead of considering feedbacks between eco & evo, we need to consider eco & evo as a continuum of the same processes unfolding. After all, they’re also both happening on the same time scales!

Which genes are under selection though? Turns out a lot of them are amino acid-related and nucleic acid-related. This suggests these fundamental organic nitrogen compounds are key drivers of dynamics in the most abundant freshwater bacteria!

Abundance stayed pretty constant while nucleotide diversity shifted, and at the same time more genes came under positive selection. No spike in new SNVs suggests this was an increase in existing strain evenness, rather than a migration event.

I looked in more depth at one abundant Nanopelagicus (acI-B) that experienced a step change. The strain composition shifted in 2012, reaching was seems like a new, more variable equilibrium afterwards.

Well what happened in 2012? I looked at @USLTER and @USGS data, some going back to 1800s. 2012 was a hot, dry year. This led to high zooplankton (a top-down control) and low phosphorus (a bottom-up control), which lowered lake primary productivity and dissolved organic carbon.

When did the abrupt changes happen? For the most part, they were isolated events. But I noticed that 7 (!!) Nanopelagicaceae genomes all changed in 2012. This is the most abundant freshwater bacteria (also called acI), it’s like the SAR11 of lakes.

Now for Long-term, decadal patterns! I identified gradual changes, step changes, and disturbances with resilience in strain composition over the 20 years. I saw long-term change in 1 in 5 genomes!

Then I wondered if species and strain patterns matched up? Well, sometimes yes and sometimes no- this means that sometimes blooms are less diverse (hints at competition btwn strains), and sometimes they are more diverse (hints at microdiversification btwn strains)

Next I looked at seasonal patterns. We know the microbial community is seasonal (, what about the genomes?. Turns out yes- majorities of both species and sub-species strains are seasonal!

Step 2: Get the genomes. 20,000 node hours on UT Austin’s supercomputer @TACC, 85,684 genome bins, 30,389 medium and high quality MAGs, and finally 2,855 de-replicated genomes to work with. I think they look pretty good!

Step 1: Get the samples. simple: 7 years of field work, 20 years of lab notebooks, 2 minus 80’s of tubes, over 1000 DNA extractions, and finally a grant from @jgi, and here they are! 471 metagenomes!

I’ve been dreaming of this paper for a decade. One PhD and one postdoc later, here it is!. What do ecology and evolution look like in a 20-year freshwater time series? Turns out they blur together. @sarilog @quendi @archaeal @USLTER @NSF @jgi.

I am migrating to Bluesky! Find me at 🌦️🌥️⛅️🌤️☀️.

Come hear me talk at #ESA23 today in Portland: 4:45 in the Eco Evo section, room D139. Learn about shifts in bacterial genomes in my 20-year 471-metagenome time series! .@archaeal @quendi

RT @quendi: One last bragging post on this dying platform? Awesome study by ⁦@BigMicrobeBen⁩ from ⁦@mcmahonlab⁩. “Metabolically diverse….

Fun time talking about my work and how it ties into data science and open science today! #DSOS23 and if you missed the talk, I think you can still watch asynchronously on the YouTube link 😉.

Baker lab bats excursion! I'm lucky to work with such a fun group, where grad students, REUs, and volunteers all want to hang out with me on a night off 🥰 .@archaeal

Was curious about Threads, but. No web version, not the first "threads" app to pop up in the play store, couldn't figure out how to make a new account (my insta is my cat's). seems not quite ready for prime time? #threadsvstwitter.

So happy for @Leao_pel ! Many congrats!!.