Everything is everywhere but Escherichia coli adapts to different niches academic.oup.com/ismej/advanc... #jcampubs

Just on time for the holidays! Happy to share the published version of the discovery of leptophytes, a new deep-branching and widespread group of microalgae based on plastid MAGs (ptMAGs). Now with additional support from a mitochondrial MAG (mtMAG) of leptophytes. www.nature.com/articles/s41...

Just a few days left to apply to the PhD position in our group. It focuses on selfish genes in #fungi and how they might affect the spread of giant #TEs called Starships.

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic https://www.biorxiv.org/content/10.64898/2025.12.12.693929v1

Would you say that Neurospora crassa is declining as a model organism for fungal biology? 💛 No way, that orange fun-guy is alive and well! 🔴 Yeah, not so many people work with it nowadays ... 🔵 Neuro-who? 📅 Ends: December 31, 2025, 10:03 PM UTC 📊 Show results

I salute the honesty and courage of these authors, and I am sure we all share a collective shiver from knowing that we all could easily make (and maybe have made) similar analysis mistakes in our own work #academicchatter

People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding

One more week to apply to this PhD position on working out an endosymbiosis relationship in a protist. Please share widely to prospective PhD student #protistsonsky

As computer scientist, I am very excited about our new biogeography simulator: bigrig - my PostDoc Ben Bettisworth implemented two algoritmically totally distinct simulators from scratch to conduct statistical tests for showing that bigrig is correctly implemented: www.biorxiv.org/content/10.1...

We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth. Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al. shorturl.at/zgY8Z

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

An adorable Platyhelminthes! I see that the classification has changed, so this is now subphylum Rhabditophora? Anyhoo, a real cutie! #marineplankton 🦑

Need to predict whether a given contig in your assembly was circular in the environment? Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity: anvio.org/help/main/pr...

According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.

So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth! #protistsonsky 🧵

🎉 There are currently 4 opportunities to join the Holt lab in beautiful Bath! 🎉 If you're interested in protists, parasites, and/or biodiversity then please check out our website: theholtlab.com/posts/ln5-21... 🚨 Deadlines vary between project. ✉️ Please reach out if you have any questions!

If you’re still hunting for color tools, I’m working on a more user-friendly version of meodai.github.io/poline/ keeping you huedrated

I however wonder why a new supergroup was erected (Disparia) when the existing supergroup Promethea precisely describes this grouping? Promethea was published here: www.cell.com/iscience/ful...

Each such discovery is a game changer for our understanding of eukaryote evolution, and this paper is no exception. Meet Solarion, which displays yet again novel types of subcellular structures. Congrats to all authors on a fascinating story. #protistsonsky www.nature.com/articles/s41...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

A new fossil fungus discovered in Scotland shows evidence of plants and fungi sharing nutrients to survive on land. The fossil, more than 400 million years old, offers hints about the origin of one of the greatest partnerships in the history of life on Earth. www.nhm.ac.uk/discover/new...

Marine #phytoplankton need move up/down in the #ocean to access light & nutrients. Study of the effects of nutrient availability in 9 species reveals that phytoplankton have evolved multiple mechanisms that impact gravitational sinking in response to starvation @plosbiology.org 🧪 plos.io/4iaJFoV

We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...

How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926

Researchers have tagged more than 400 monarch butterflies and are following their journeys on a cellphone app (and you can too). They are using a tiny solar-powered radio tag that weighs just 60 milligrams and sells for $200 (monarchs weigh 500 to 600 milligrams).

The core genomic backbone of bacteria is not necessarily resilient to gene flow! A new study shows that introgression impacts, on average, 2% of the core genes of species - www.nature.com/articles/s41... #microevo #microeco #evolution

New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇 www.biorxiv.org/content/10.1...

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

Article out in @journal-evo.bsky.social with @klvoje.bsky.social: academic.oup.com/evolut/advan...

Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2

Soooooo coooooolllll!!!! #protistsonsky

Excited to share our new preprint on BioRxiv! A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1... 1/5

Huge paper for the Arctic Ocean published today in @science.org - a new 30,000 year history of Arctic Ocean sea-ice cover reconstructed from the accumulation of cosmic dust-derived helium-3! www.science.org/doi/10.1126/... (1/n)

Oligonucleotide design meets big data: We present oligoN-design, a simple, reproducible and versatile open-source tool to design specific primers and probes directly from large environmental DNA datasets. 🔗 DOI: doi.org/10.1101/2025... 👉 github.com/MiguelMSandi...

🌊 By 2100, Arctic phytoplankton blooms will start ~34 days earlier, last ~15 days longer, and become less dominant overall, as warming reduces the seasonality of ocean productivity Climate change is rapidly reshaping the timing and importance of Arctic productivity www.nature.com/articles/s43...

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

Check out our new insect decline paper. By analysing 36 yrs of German ground beetle distribution data, we show: - ~80% of species have declined, with significant declines for >50%. - The decline was similar across species traits and threatened status. doi.org/10.1111/ddi.... @consbiog.bsky.social

The Lost Art of Scientific Illustration: Yoshine Hada's illustrations of dinoflagellates in Kofoid, C.A. 1931. Protozoan Fauna of Mutsu Bay. Subclass Dinoflagellata, Tribe Gymnodinioidae. Sci. Rpts Tohoku Imperial Univ, 4th Ser., Biology, Vol. VI, No. 1, pp 1-43.

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors academic.oup.com/mbe/article/...

🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny. #ProtistsOnSky #SciComm #SciSky www.cell.com/cell/fulltex...

Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n #ProtistsOnSky tinyurl.com/2zxaund7

📢 We have an open position for a postdoc to join my lab. It's a great position @animecol-uu.bsky.social, fully salaried for 2.5 years with all benefits. www.uu.se/en/about-uu/... The project is about transmission patterns of bacteria and antimicrobial resistance (AMR) in aquatic insects. 🧬🦠 (1/3)

Thirty novel fungal lineages: formal description based on environmental samples and DNA mycokeys.pensoft.net/articles.php...

Please join us next week for the second iteration of the DinoSphere Seminars! This time our two speakers will talk about host-associated dinoflagellates and any challenges they might have encountered when working with them. All current and future friends of dinoflagellates welcome! #ProtistsOnSky

New version of PR2 that now includes the eKOI coi database recently published.

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

New results from our lab: Polyploidization in diatoms accelerates adaptation to warming. Nat. Clim. Chang. (2025). doi.org/10.1038/s415...