Augustus (Gus) Pendleton
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augustuspendle1.bsky.social
Augustus (Gus) Pendleton
@augustuspendle1.bsky.social
Microbes 🤝 Lakes 🤝 Computers. Schmidt Lab @ Cornell. 🏳️‍🌈Scientist, 🇮🇪Fulbright, NOAA Davidson Fellow. Code-obsessed cat owner who likes to be outside.
https://gus-pendleton.github.io/
Pinned
New blog post from the Schmidt Lab! Play around with environmental and microbial data from Lake Ontario, and make some pretty maps!

marschmilab.github.io/blog/microbe...

#rstats #microbiology #ecology #limnology #shiny
Our new interactive tool: MicrobeMapper – Schmidt Lab
Play with microbial data from Lake Ontario!
marschmilab.github.io
This paper combines so many things I love! Community assembly, an appreciation for absolute abundance, and carefully selected (and interpreted!) alpha and beta diversity. Fun to see generalized concepts we're measuring in freshwater systems also get their due in host-associated microbiomes.
November 10, 2025 at 6:59 PM
Reposted by Augustus (Gus) Pendleton
Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
📣Postdoc opportunity @nordcee.bsky.social , University of Southern Denmark! 📣

Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones!

Please share widely!

Deadline: 17 November

More information can be found here:
tinyurl.com/2vuur3wh
Postdoc on microbial oxygen production in marine oxygen minimum zones
Application deadline: 17 November 2025 at 23:59 hours local Danish time
fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com
November 10, 2025 at 12:06 AM
Pitchfork is down...quick everyone just enjoy the music you like without feeling judged
October 31, 2025 at 3:39 PM
Reposted by Augustus (Gus) Pendleton
Prospective PhD students - here is a brilliant opportunity to explore how bacteria and viruses evolve in liquid environments like the ocean 🌊

The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
Even more biased: I'm excited about the project 'Turbulent Partners: Unravelling Host-Virus Coevolution in Dynamic Environments' with Adam Monier and Daniel Kattnig. Drop me an email if interested! www.exeter.ac.uk/v8media/rese...
October 28, 2025 at 2:40 PM
Too cool!!
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
October 21, 2025 at 5:30 PM
Dream job alert 🚨🚨
📣 New PhD student position opening in my lab!
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
October 13, 2025 at 10:42 PM
Anyone have access to this article and would like to share it as a gift link? It's a topic near-and-dear to my heart 😅
www.nytimes.com/2025/10/08/n...
Why Is This Lake ‘Burping’?
www.nytimes.com
October 8, 2025 at 8:03 PM
Reposted by Augustus (Gus) Pendleton
Yesterday I headed over to Fremont, WI on the Wolf River to help prep for wild rice seeding that the Brothertown Indian Nation is doing. We collected some sediment at two sites, mixed up seeds for several sources, and made mud balls for seeding. They are seeding today and tomorrow! #restoration
September 11, 2025 at 4:41 PM
Reposted by Augustus (Gus) Pendleton
3 year Postdoctoral Research Fellow position in Landscape Multifunctionality here in beautiful Bergen jobbnorge.no/en/available... please repost
September 8, 2025 at 10:54 AM
Reposted by Augustus (Gus) Pendleton
Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
September 6, 2025 at 8:13 AM
Reposted by Augustus (Gus) Pendleton
Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.

Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Plant cells are totipotent, meaning individual cells have the potential to develop into a full organism, a property unique to the zygote for animals. However, in most species for most cells, plant cells are not spontaneously totipotent, since they must be treated with specific hormone combinations to unlock their totipotency. Species within the Kalanchoe genus is unique as they spontaneously develop foliar embryos that are fully realized plantlets with shoot and root from notches along the edges of leaves. We speculate that the progenitor cells that give rise to these foliar embryos are totipotent, and we are using single cell techniques to identify & characterize them. In addition to being a fundamental process for plant biology, we foresee unlocking totipotency has many biotechnological applications, such as faciliating genetic transformation and the development of synthetic organs of biomanufacturing.
cxli233.github.io
September 4, 2025 at 2:00 PM
Reposted by Augustus (Gus) Pendleton
Reposted by Augustus (Gus) Pendleton
New open access paper out! We evaluated the population structure and conservation needs for 3 crested penguin species in NZ. Read it here: journals.plos.org/plosone/arti...
August 28, 2025 at 9:09 PM
Reposted by Augustus (Gus) Pendleton
Leaving Academia: Insights from Evolutionary Biologists on Their Career Transitions and Job Satisfaction https://www.biorxiv.org/content/10.1101/2025.08.19.671061v1
August 20, 2025 at 9:32 PM
This is what's held me back - amazing to see!
Happy to announce ✨quarto-revealjs-editable✨

This fully supersedes the imagemover extension, as I back then didn't realize the potential. You can now also move, resize, change font size and alignment for text in your slides

github.com/EmilHvitfeld...
#quarto #slidecrafting
August 20, 2025 at 7:35 PM
Looking for potential fellowship opportunities for final-year writing funding (I understand this might be a moonshot at the moment). Just stipend (no research costs). I'm in the environmental/life sciences, and grateful if there are any directions people could point me towards!
August 20, 2025 at 5:55 PM
Reposted by Augustus (Gus) Pendleton
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...
journals.asm.org
July 31, 2025 at 3:33 PM
Reposted by Augustus (Gus) Pendleton
A new version of gcplyr (1.12.0) has just been released and is available now from CRAN and github. This update fixes a handful of bugs along with some improvements to the documentation

mikeblazanin.github.io/gcplyr/
Wrangle and Analyze Growth Curve Data
Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into tidy formats and merging them with desi...
mikeblazanin.github.io
July 29, 2025 at 5:00 PM
This reminds me when I was just messing around with codon usage in Julia and I found this out on my own - look at those AT-rich codons!!

gus-pendleton.github.io/CUBScout_Rel...
July 24, 2025 at 4:19 PM
Microbial ecologists! Do you use Unifrac distances? Are you curious about absolute abundances? Then I’ve got a paper for you!
www.biorxiv.org/content/10.1... (1/4)
Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide
Microbial ecologists routinely use β-diversity metrics to compare communities, yet these metrics vary in the ecological dimensions they capture. Popular for incorporating phylogenetic relationships, U...
www.biorxiv.org
July 19, 2025 at 5:25 PM
Amazing opportunity! 👇
Staff scientist position (computational):

I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
July 12, 2025 at 1:06 PM
Reposted by Augustus (Gus) Pendleton
I'm recruiting a 2-yr postdoc to start in October or November of 2025! I'm looking for applicants interested in exploring amphibian disease ecology as it relates to climate change. Strong quantitative skills preferred, interviews start late July. More info: erinsauer.com
July 7, 2025 at 6:55 PM
This seems awesome!
🌈 🌐 rainbowR conference: online, early 2026 🌐 🌈

Are you LGBTQIA+, do you code in R, and would you like to get involved in rainbowR’s first-ever conference? We are looking for people to join our conference organising committee!

➡️ rainbowr.org/conference
🗓️ 1st meeting: July 9, 4pm UTC
Conference – rainbowR
Join our conference organising committee! See our conference page for more info.
rainbowr.org
July 7, 2025 at 6:04 PM
New and MUCH improved - we've updated our work on Lake Ontario's microbial communities by linking in physical processes (upwellings propagated via Kelvin waves). Nearshore zones hold microbes and metabolisms EXCLUSIVE to the temporary upwelling niche!
www.biorxiv.org/content/10.1...
Upwelling periodically disturbs the ecological assembly of microbial communities in the Laurentian Great Lakes
The Laurentian Great Lakes hold 21% of the world's surface freshwater and supply drinking water to nearly 40 million people. Here we provide the first evidence that wind-driven upwelling fundamentally...
www.biorxiv.org
July 4, 2025 at 4:16 PM