Joshua Hamm

Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious?

Either way, we have good news.
We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July.

Sign up: meetings.embo.org/event/26-arc...

We look forward to seeing you in Cambridge, UK.

Please repost!

Many thanks to @ettema.bsky.social, @anja1.bsky.social, and Rick Cavicchioli for encouraging me to put this article together and for all the advice that helped along the way.

This is a great example of a situation where a behaviour appears antagonistic but in the ecological context in which the behaviour evolved it benefits both organisms compared to the alternative. It reinforces to me how important that context is when we interpret results from laboratory experiments.

However, more aggressive behaviour would likely allow the symbiont to more rapidly accumulate nutrients, increasing its ability to persist through the low nutrient periods.

In contrast, if the symbiont regulates behaviour as a function of nutrient availability or host proliferation both organisms can persist. Importantly, rate of host lysis under these conditions does not impact the persistence of either species, only population sizes.

The short version is that interactions similar to other DPANN, where the symbiont is constantly attached to the host, are unstable in ecosystems where nutrient availability approaches zero for extended periods. Populations of both organisms collapse eventually.

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...

Congrats Dani! That's awesome news!

21 Vidi grants awarded to Utrecht-based researchers 21 researchers from Utrecht University, University Medical Center Utrecht, and Princess Máxima Center have each been awarded a Vidi grant worth up to €850,000.

Exultant to have been awarded a Vidi grant by the Dutch Research Council (NWO)! Can't wait to get started!

Stay tuned for two upcoming (PhD student & postdoc) positions to study archaeal genome evolution.

Also huge congrats to my colleague @dorotakawa.bsky.social!

www.uu.nl/en/news/21-v...

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

Lunch today halfway around the world in Hangzhou and met a new asst professor who was very thankful for this resource. Please help out folks like them and other early career scientists with examples of job apps. Submit yours!
github.com/RILAB/statem...

Habitat-specificity in SAR11 is associated with a few genes under high selection Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages

The ecological and phylogenetic partitioning of coastal and offshore SAR11 is underpinned by a handful of distinct metabolic traits under high selective pressure - academic.oup.com/ismej/advanc...

WE ARE BACK!!! Archaea Power Hour will return this coming WEDNESDAY, Oct. 22nd at 10AM EST/4PM CET. Check your email for the Zoom link (coming soon) or register here: forms.gle/6QvCjHH2H4pxro…. Take a look at the exciting talks we have planned to kick off our fall seminar series:

Live Cell Imaging of Ca. Nha. antarcticus and Hrr. lacusprofundi using agarose pads This protocol is an adapted form of the protocol developed for imaging haloarchaea (Liao et al., 2021) and subsequently applied to co-cultures containing nanohaloarchaea and haloarchaea (Hamm et al., ...

Live cell imaging of Ca. Nha. antarcticus and Hrr. lacusprofundi using agarose pads. Protocol now live!
www.archaea.bio/protocols/li...

The genomic basis of symbiotic integration at University of Bath on FindAPhD.com PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

Great new trait of #Methanoperedens archaea: Carbon monoxide metabolism in freshwater anaerobic #methanotrophic archaea #aom #anme
Egas @cuwelte.bsky.social et al #microbiology @ribesresearch.bsky.social
www.biorxiv.org/content/10.1...

Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...

Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social

🦠➡️🧬 Community context matters!
In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution.
Check out the preprint 👇🏼

Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia Abstract. The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave

Huang, @tweethinking.bsky.social, Sepang et al. use phylogenetic analyses to reveal that the Njordarchaeales and Panguiarchaeales constitute the new class Njordarchaeia within Asgard archaea.

🔗 doi.org/10.1093/molbev/msaf201

#evobio #molbio #archaea

The JEDI marker as a universal measure of planetary biodiversity Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring b...

The JEDI marker - a new approach for measuring #biodiversity that captures all domains of life and is applicable across biological and ecological scales. It's time to change the way we perceive biodiversity - www.biorxiv.org/content/10.1...

The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...

🧵 Our study on the elusive titration control mechanism of the replication initiator DnaA in Escherichia coli is now out on @natcomms.nature.com‬! @stephkoe.bsky.social
@hohlbeinlab.bsky.social‬ @nicoc-micsynmet.bsky.social @ettema.bsky.social‬ @mib-wur.bsky.social
doi.org/10.1038/s414...

academic.oup.com/mbe/advance-...

Happy to share this one. We investigated the #phylogenetic placement and #genome_evolution of Pangui/Njordarchaea-unique #Asgardarchaea that might have undergone genome reduction...

Filamentous growth, cell envelope architecture, and surface appendages of a member of the Chloroflexota, Litorilinea aerophila Litorilinea aerophila, a filamentous bacterium of the phylum Chloroflexota (class Caldilineae), exhibits unique morphological and cell envelope features that challenge traditional bacterial models. In...

Who would have thought I would ever publish an article about a bacterium?
But here it is, but of course only because Litorilinea aerophilum actually has an archaellum!

Here is what we learned about its cell structure and other surface appendages:
www.biorxiv.org/content/10.1...

Many thanks to my co-authors @ndombrowski.bsky.social, @luisvalentin.bsky.social, @greening.bsky.social, @tweethinking.bsky.social, and @anja1.bsky.social!

Our results provide insight into a currently understudied DPANN lineage (Caliditerrarchaeota) and highlight similarities and differences in how DPANN halophiles achieved their tolerance to the hypersaline systems they inhabit.

Additionally, using gene trees from ALE analysis, we examined sisterhood rates across all archaea in the dataset. The results confirm higher rates of sisterhood in single gene trees for many DPANN-host pairs and reveal a potential association of Haloaenigmatarchaeaceae with Halarchaeoplasmatales.

However, for both lineages the gene with the highest increase in copy number was the Kef type K+ transporter, implicating this system as key in the adaptation to hypersaline environments for halophilic DPANN.

The results indicate for the Nanohaloarchaeota and Haloaenigmatarchaeaceae different genes were associated with transition to hypersaline environments. For Nanohaloarchaeota this includes oxygen tolerance and DNA repair systems. For Haloaenigmatarchaeaceae this includes a specific Na+ transporter.