Fabien Burki

How can one not be amazed

A small piece with PhD student @sorayazwahlen.bsky.social and Wiebe Kooistra on why we think Chaetoceros is an emerging model system for phytoplankton research, ranging from its ecological role, to unique cellular features and - of course - its many symbiotic interactions in the marine microbiome.

Ultrastructure of the Endoplasmic Reticulum in Eukaryotic Microalgae The endoplasmic reticulum (ER) is a large and highly dynamic component of the eukaryotic endomembrane system. In eukaryotic microalgae, it plays six distinct roles: (1) It envelopes the chromatin to ...

onlinelibrary.wiley.com/doi/10.1111/... Ultrastructure of the Endoplasmic Reticulum in Eukaryotic Microalgae #protistsonsky

One of the countless examples of why protists are an endless reservoir of non-textbook biology #protistsonsky

Check out our new preprint all about Pirsonia, a tiny killer of bloom-forming Coscinodiscus diatoms!
www.biorxiv.org/content/10.1...
#protistsonsky #marinemicrobes 🌊🔬

A diatom (coscinodiscus) whose cytoplasm is contracted into connected spheres. Reminds me of depictions of the multiverse.

The multiverse model inside a diatom (that is presumably having a bad day). #protistsonsky

Phylogenetic position and mitochondrial genome evolution of ‘orphan’ eukaryotic lineages The phylogenetic tree of eukaryotes is divided into a handful of highly diverse ‘supergroups’; only a few so-called ‘orphan’ lineages branch in uncertain positions outside of these large clades. We fo...

New protist supergroup: Promethea! From @zlatogursky.bsky.social et al #ProtistsOnSky

Promethea = PROvora + MEteora + HEmimastigophora. The new supergroup, unifying previously “orphan” lineages with gene-rich mitogenomes. Position of #telonemids is still uncertain. #protistsonsky tinyurl.com/yk9xkt49

Very tangential to this paper, I do think that my proposal to refer to the 4 main lineages with complex red plastids as MOCHa makes a lot more sense than to continue to call them CASH. Please refer to this for a rational as to why: doi.org/10.1016/bs.a...

VERY interesting #protistsonsky

Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.

academic.oup.com/mbe/article/...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean www.nature.com/articles/s41...

Early days, but growth looks promising 🤞
Better pictures and ID coming soon ;)

#protistsonsky

A dinoflagellate-infecting giant virus with a micron-length tail Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morphological and genomic features that infects a dinoflagellate, Pelagodinium sp. Both host and virus were isolated from the epipelagic zone in the North Pacific Subtropical Gyre. PelV-1 has a ~200 nm capsid size, and the virion variably exhibits two appendages, the presence and length of which may reflect different stages of virion maturity or artifacts of sample preparation. The appendages are a thinner 30 nm-wide tail-like structure that can extend to 2.3 µm — the longest virus appendage described to date — and a shorter, thicker (>40-70 nm) protrusion, which appears to emerge from a star-shaped capsid opening directly opposite the attachment point of the long, thin tail. Sequencing and assembly of material in a purified lysate generated a high-coverage (> 4,000x) genome of 459 kb (33.8% GC). A second, distinct genome of 504 kb (25.8% GC) was also assembled, but had low read coverage (< 24x), suggesting the presence of a low-abundance, co-cultured virus (co-PelV). Phylogenetic analysis indicates that both PelV-1 and co-PelV are members of Mesomimiviridae. They contain various genes for the metabolism of amino acids (e.g., asparagine synthase), carbohydrates (e.g., epimerase, glycosyl hydrolase, aconitate hydratase, succinate dehydrogenase of the TCA cycle), and lipids (e.g., phospholipases), as well as other noteworthy genes (e.g., light-harvesting complex, rhodopsin, ion channel, sugar transporters, aquaporin). PelV-1 also has ORFs most similar to tail fiber genes of Synechococcus phage and other tail domain-containing protein homologs. The ecological advantages that might be conferred by the extraordinarily long tail and metabolic genes of PelV-1 is unknown, but this isolate expands the scope of morphological and metabolic diversity of viruses and suggests many more unusual marine viruses await discovery. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, https://ror.org/021nxhr62, OIA #1736030 and OCE #2129697

A dinoflagellate-infecting giant virus with a micron-length tail | bioRxiv https://www.biorxiv.org/content/10.1101/2025.07.19.665647v1?rss=1

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

Yes I know the feeling

Ah that’s so great that you keep on looking

Summer post. Yash @thealgaeman.bsky.social found Paulinella in this sample I collected on Venice Beach (LA) almost as an afterthought.🤞it will grow #protistsonsky

Can't wait to read this book

I find Europe in general lacking stickers. It’s a shame

We are growing! A new @zeiss-microscopy.bsky.social widefield tailored for ExM- supported by @moorefound.bsky.social is settling! Another one is on its way at @gautamdey.bsky.social Lab !

These two will become the powerhorses for high-througput imaging of the ExM Atlas of #Microbial Eukaryote !

Congratulations Julia

I’m thrilled to announce that next summer I’ll be joining the University of Maryland Department of Biology as an assistant professor! The Van Etten lab will study how horizontal processes (DNA and gene transfer + organelle acquisition) drive and are driven by ecology and evolution. vanettenlab.org

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Divergent Plastid Genomes in the Deepest-Branching Apicomplexan Parasites #protists #protistsonsky academic.oup.com/gbe/article/...

Congrats @fonamental.bsky.social well deserved

Modern microbialites harbor an undescribed diversity of chromerid algae Chromerid algae and the heterotrophic colpodellids together make up the chrompodellids, which are the closest known relatives to apicomplexan parasites [1]. As apicomplexans are prolific parasites of ...

New ‪preprint! Through plastid MAGs and 18S rRNA gene retrieval 🧬 we identify chromerids (including a novel clade ⭐) associated with marine and freshwater microbialites across the globe 🌎, expanding their ecological niche beyond coral reefs 🪸. #ProtistsOnSky #MicroSky #Algae

Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequenc....

Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes. #ProtistsOnSky #pacbio
onlinelibrary.wiley.com/doi/10.1111/...

Here you will find a great overview of genomic tools and their application on protists. Figure 3 is crazy interesting for everybody who wonders about what kinds of protist genomes are available, their sizes and why there aren't more. Take a look! Glad I could contribute :)

Proud to have authored this review with brilliant people. Hope we inspire more attempts to sequence the #protist genomes that are within reach! Huge thanks to Alexandra Schoenle for leading. #ProtistsOnSky
authors.elsevier.com/sd/article/S...