Preprint out!

Anaerobic methanotrophs are key methane oxidizers, but their activity/adaptation under acidic conditions remains unclear. We show that a freshwater ANME adapts to pH stress via shifts in lipid composition and remains metabolically active down to pH 5.65. Expanding the niche of ANME.

Immensely rewarding part of this work was working with Indigenous language experts and elders in the naming of our species of Asgard….’marumarumayae’ derived from the Malgana language from the people of Gathaagudu (#Shark Bay)

We tested the efficacy of semi-permeable capsules to capture protists from cultures and environmental samples using the Onyx from @atrandi.bsky.social. Tremendous effort from everyone in the lab and led by Marco Fantini and Nik Brask - check out the videos here: www.biorxiv.org/content/10.6...

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

There is a lot of undescribed prokaryotic diversity in existing whole-genome metagenomic data!
www.nature.com/articles/s41...

Visualizing suborganellar lipid distribution using correlative light and electron microscopy - Nature Cell Biology Lennartz et al. introduce a correlative light and electron microscopy workflow, Lipid-CLEM, combining near-native lipid probes and on-section labelling via click chemistry. Lipid-CLEM quantitatively a...

I am extremely excited that my first first-author paper from my PhD is finally out 😆!! We developed a new CLEM workflow to measure lipid densities at the nanoscale. So if you are into lipids and super-resolution imaging approaches, this one is for you: www.nature.com/articles/s41...

Diversity, ecology, cell biology and evolution of the Asgard archaea Nature Reviews Microbiology, Published online: 05 March 2026; doi:10.1038/s41579-026-01288-wThe Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of the research field focusing on these intriguing microorganisms and discusses future research directions aiming to resolve their diversity, ecology, cell biology and evolution.

ICYMI: New online! Diversity, ecology, cell biology and evolution of the Asgard archaea

Read our review about the "Diversity, ecology, cell biology and evolution of the Asgard archaea" in @natrevmicro.nature.com here: www.nature.com/articles/s41...

By @kassipan.bsky.social @stephkoe.bsky.social @micropat.bsky.social & @gerbenz.bsky.social

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives.
www.nature.com/articles/s41...

Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social

www.nature.com/articles/s41...

New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...

Beyond thrilled to share that our study has been published!
This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and
@texasscience.bsky.social!!!
#MicroSky #ArchaeaSky 1/12

Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...

Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!

Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41...

Corrected paper: www.nature.com/articles/s41...

Importantly, the re-analyses of the corrected dataset are consistent with the original findings.

We haven't really tried co-extractions but we have used the AllPrep PowerFecal kit for both DNA and RNA on sediments and it does work fine. The Powerfecal and Powersoil are generally almost identical. Our technicians also pointed out there is some small tricks in the handbook of the kit. Goodluck!

I finally got around to writing the discussion section of our lab's basic training course on live cell #microscopy. I explain the tradeoffs involved in designing an imaging experiment and the art of thinking of the experiment as an optimization problem.

leb-epfl.github.io/basic_traini...

Come join our group in the beautiful (currently very snowy) Wageningen!

I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻

Please repost

Apply here: www.wur.nl/en/vacancy/p...

Best of Luck @pieterhart.bsky.social and @danieltamarit.bsky.social, Super excited to see what you guys get up to together!

a man walking in a field with an umbrella ALT: a man walking in a field with an umbrella

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

That should work just fine, we've been close to 1ng/uL. Just keep in mind that you might miss some low abundant taxa.

We routinely use the DNeasy Qiagen Powersoil for sediment samples. In the past, together with a QiaCube(96 samples), but this struggled a lot with lower biomass samples. So we switched to the Qiagen EZ2, which only does 24 samples per time but the yields are a lot more similar to manual extractions.

Nutrient availability affects optimal growth strategy in predatory DPANN | mSystems The bacterial and archaeal domains each possess a major clade that appears to be predominantly host-associated (1–3). These two lineages, Patescibacteriota and DPANN archaea (named for the Diapherotri...

Ever since publishing our observations of the predatory behaviour of Ca. Nha. antarcticus people have asked me why it would want to kill its host. My perspective discussing the ecological factors that I believe led to this behaviour is out now in mSystems:
doi.org/10.1128/msystems.01475-25

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...

Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)

Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.

🧙‍♀️ Something is brewing in the WitChi cauldron…
After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments.

Stay tuned for the next release!

🧙‍♀️ Can’t model it? Prune it!
github.com/stephkoest/w...

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...