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Joshua Hamm

@joshnhamm.bsky.social
119 followers 74 following 26 posts

Post-Doctoral Researcher at the Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam jnhamm.wordpress.com

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Reposted by Joshua Hamm
Florian Mayer @florianmayer.bsky.social · 11/09/2026
Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6... Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social @tbharat-lab.bsky.social
biorxiv.org
The life cycle of an archaeon with multiple membranes
Many prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, onl...
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Joshua Hamm @joshnhamm.bsky.social · 16/07/2026
Congratulations Julian! Well deserved!
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Joshua Hamm @joshnhamm.bsky.social · 06/07/2026
Congratulations Chung! Amazing work!
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Reposted by Joshua Hamm
Chung Hyun Cho @chc-evobio.bsky.social · 04/07/2026
Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
biorxiv.org
Emergence of histone-based chromatin complexity in Asgard archaea
The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...
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Reposted by Joshua Hamm
Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Reposted by Joshua Hamm
Sonja-Verena Albers @archaellum.bsky.social · 20/05/2026
New preprint! Cell division has to happen at the right place but how Archaea pick that place is unknown. We now identified a three-protein system, Dip, that positions the divisome at midcell in H. volcanii and is broadly conserved across Archaea. A thread 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
Many thanks to all the co-authors involved! @ndombrowski.bsky.social, @luisvalentin.bsky.social, @greening.bsky.social, @tweethinking.bsky.social, and @anja1.bsky.social
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
Finally, we examined the rate at which genes from DPANN archaea place as sister to other archaeal lineages across a broad dataset and identify a higher than expected transfer rate between Haloaenigmatarchaeaceae and Halarchaeoplasmatales suggesting a possible host-symbiont relationship.
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
In contrast, other genes like Rubrerythrin (which is specific to anaerobes) and photolyase (which is important for DNA repair) showed lineage specific acquisitions consistent with the niches these two clades occupy.
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
We leveraged this to examine the transition to hypersaline environments by Nanohaloarchaeota and Haloaenigmatarchaeaceae by performing ancestral genome reconstruction with ALE. We find some genes associated with halophily were acquired by both lineages as they adapted e.g. K+ transport gene
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
We identified a deep branching sister lineage to the Nanohaloarchaeota for which we propose the name Terrarchaeota. This group is primarily associated with sediments both marine and terrestrial and show no signs of halophily.
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
Our paper examining the evolution of halophily in DPANN is out now in MBE! academic.oup.com/mbe/advance-...
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Joshua Hamm @joshnhamm.bsky.social · 15/04/2026
Great work Reinier! Awesome to see this work finally in print!
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Reposted by Joshua Hamm
Reinier Egas @raegas.bsky.social · 14/04/2026
Grab a coffee and enjoy reading up on CO metabolism in methanotrophs! Freshwater ANME (own work): www.nature.com/articles/s41... Marine ANME (@Orphan lab): www.nature.com/articles/s41... Big thanks to our collaborators at QUT! @sjmcilroy.bsky.social (Heyu/Andy/Gene!) @cuwelte.bsky.social
nature.com
Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea - Nature Communications
Anaerobic methane-oxidizing archaea mitigate methane emissions in anoxic environments. Here, Egas et al. show that these microbes can also oxidize carbon monoxide, prompting re-evaluation of their cla...
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Reposted by Joshua Hamm
Reinier Egas @raegas.bsky.social · 13/04/2026
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.
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Reposted by Joshua Hamm
Brendan Burns @brendanburns999.bsky.social · 10/04/2026
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)
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Reposted by Joshua Hamm
Alex Loy @loyteam.bsky.social · 29/03/2026
📢 New paper 🚨 ☘️🌿🌱🐄💨🦠🔬🧫🧬 #sulfoquinovose #microbiome #microsky #microbiomesky academic.oup.com/ismej/articl...
academic.oup.com
Sulfoquinovose degradation by cow rumen microbiota
Abstract. Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organi
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Reposted by Joshua Hamm
DEEMteam_Orsay @deemteam.bsky.social · 23/03/2026
We have just published a short note on archaeal phylogeny: complex mixture models support a deep placement of Methanonatronarchaeia within Euryarchaea and indicate that three recently described groups (Halorutilales, Afararchaeaceae, and Ordosarchaeia) are actually the same. shorturl.at/5GMpU
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Reposted by Joshua Hamm
Buzz Baum @buzzbaum.bsky.social · 16/12/2025
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!
meetings.embo.org
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
However, more aggressive behaviour would likely allow the symbiont to more rapidly accumulate nutrients, increasing its ability to persist through the low nutrient periods.
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
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
doi.org
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...
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Reposted by Joshua Hamm
Wen-Cong Huang @wentsunghwang.bsky.social · 13/11/2025
#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Joshua Hamm @joshnhamm.bsky.social · 23/10/2025
Congrats Dani! That's awesome news!
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Reposted by Joshua Hamm
Daniel Tamarit @danieltamarit.bsky.social · 23/10/2025
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...
uu.nl
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.
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Reposted by Joshua Hamm
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 21/10/2025
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...
github.com
GitHub - RILAB/statements: Successful Job Applications and Grants
Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.
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Reposted by Joshua Hamm
Taylor priest @taylorpriest.bsky.social · 21/10/2025
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...
academic.oup.com
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
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Reposted by Joshua Hamm
Archaea Power Hour @archaeapowerhour.bsky.social · 17/10/2025
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:
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Reposted by Joshua Hamm
Archaea.bio @archaeabio.bsky.social · 15/10/2025
Live cell imaging of Ca. Nha. antarcticus and Hrr. lacusprofundi using agarose pads. Protocol now live! www.archaea.bio/protocols/li...
archaea.bio
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., ...
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Reposted by Joshua Hamm
Tom Williams @tweethinking.bsky.social · 09/10/2025
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 :)
findaphd.com
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
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Reposted by Joshua Hamm
Alex Probst @alexjprobst.bsky.social · 26/09/2025
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!
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Roland Hatzenpichler @environmicrobio.bsky.social · 26/09/2025
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
tinyurl.com
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.
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Mike Jetten @msmjetten.bsky.social · 18/09/2025
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...
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Sonja-Verena Albers @archaellum.bsky.social · 17/09/2025
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
nature.com
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology
Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.
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Rodrigo Sánchez Martínez @rodrisanchez95.bsky.social · 11/09/2025
🦠➡️🧬 Community context matters! In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution. Check out the preprint 👇🏼
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Molecular Biology and Evolution @molbioevol.bsky.social · 08/09/2025
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
doi.org
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
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Reposted by Joshua Hamm
Taylor priest @taylorpriest.bsky.social · 14/08/2025
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...
biorxiv.org
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...
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Lorenzo Olivi @loreoliv.bsky.social · 22/08/2025
🧵 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...
doi.org
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...
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Wen-Cong Huang @wentsunghwang.bsky.social · 14/08/2025
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...
academic.oup.com
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
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Sonja-Verena Albers @archaellum.bsky.social · 20/08/2025
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...
biorxiv.org
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...
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
Many thanks to my co-authors @ndombrowski.bsky.social, @luisvalentin.bsky.social, @greening.bsky.social, @tweethinking.bsky.social, and @anja1.bsky.social!
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
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.
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
Our analysis of public MAGs shows these DPANN are mostly sediment associated thermophiles with no signatures of halophily. We then used gene tree/species tree reconciliations to predict ancestral genome content and compare the two known DPANN halophiles to their last non-halophilic ancestors.
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Joshua Hamm @joshnhamm.bsky.social · 08/08/2025
New preprint up now! Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota www.biorxiv.org/content/10.1...
biorxiv.org
Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily
The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...
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