#archaea — Public Fediverse posts

@johncarlosbaez I do not know, yet.
I'd love a masto gut ecologist to teach me all about it. Google is not my friend on this one (and more generally of course, more and more)
#microbiome #archaea #inOurTime #statins

https://www.europesays.com/ie/470324/ Earliest Organisms on Earth Built Their Biochemistry around Molybdenum, Study Suggests #Archaea #Archean #bacteria #Catalysis #Cell #DNA #EarlyEarth #Earth #Éire #Enzyme #Gene #Genome #IE #Ireland #Metabolism #Metal #microbe #Molybdenum #Protein #Science #Tungsten

Found during a morning shift - maybe I'm just uninitiated but this part absolutely blew my weariness away.

For those who don't know I've been digging into extra chromosomal rrns in Archaea for about two years now - preprint coming this summer!

#archaea #microbiology

Those in the know with RNA/ribosome research, what do you think about this one? I'm curious to know.

https://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.3003780

In Our Time on Archaea.

Did you know that #statins, (thanks yes, I'll have mine now) kill #methanogenic #archaea in your gut?

Who knew:
That there are methanogenic archaea?
That archaea live in you as well as on mid ocean vents and in madsalty Lake Eyre?
That statins kill them while leaving eukaryotic beasties unharmed?

I am amazed.

And, does anyone know what my gut will do now without its farty archaea? Do I need them? Are they helpers, freeloaders or baddies?

A bacteriologist studies bacteria. An archaeologist doesn't study archaea. #FalseAdvertising

#pun #archaea #archaeology

Got registration scholarship to Boston Bacterial Meeting 2026, woot!

Will be reporting a pretty exciting (for me at least) observation from Haloarchaea sequencing project I've been running since 2024. Hopefully I can find some collaborators - I've been running into walls.

Also glad that bacterial meeting's accepting archaea related abstracts too!

#BBM2026 #archaea #microbiology

Happy to have made a small contribution for @GB13Faithless's paper. Hope this is just one of many examples in independent researcher collaboration with academic scientists!

#archaea folks, this pipeline rules for global baseline annotation of archaea

https://doi.org/10.64898/2026.03.31.715528

#microbiology #bioinformatics #annotation

#Archaea & #microbiology folks - I'm curious. How do you feel about the dorado polish bacteria mode for your archaeal ONT long read assembled genomes? I know it holds up well with bacteria, but archaea's always been a bit funny.

Polypolish-pypolca combo is great, but they need short reads and I want to stick with long reads whenever I can (purely for logistic reasons)

#bioinformatics

How can #extremophilic #archaea make proteins in almost boiling water?

At #Biochemistry2026, Schraga Schwartz gave an inspiring lecture about the many interesting #RNA modifications these organisms are using and how they can be studied.

https://www.sciencedirect.com/science/article/abs/pii/S0092867425010827
#Biochemistry #Chemistry #ChemBio
CC: @gdch, @GDCh_BioChem

Nitrosopumilus maritimus is a highly adaptable species of #marine #archaea that accounts for approximately 30% of the marine #microbial #plankton population and plays a vital role in regulating the ocean's biological and chemical balance amid climate change.
#Microbiology #MarineBiology #Environmental #GlobalChangeBiology #OceanBiogeochemistry #ClimateChange #sflorg
https://www.sflorg.com/2026/03/mcb03092601.html

Paleobathymetry by looking at Archaeal lipid chemical structures. Very cool.

#Archaea #microbiology

https://smallthingsconsidered.blog/schaechter/2026/02/past-ocean-depths/

The highest resolution DNA-free TaXPD structure to date uniquely resolves loop 510–514 in the long-form, DNA-free TaXPD model #Helicases #Archaea https://doi.org/10.1107/S2053230X26000105

Eine absolute Hörempfehlung ist dieser sehr gut gemachte #Podcast vom #DLF über das größte zusammenhänge Ökosystem unserer Erde und die Frage wie (mikrobielles) Leben in den tiefsten Tiefen möglich ist.

https://www.deutschlandfunk.de/leben-unterwelt-wo-endet-tiefe-biosphaere-100.html/

@MARUM
#Mikrobiologie #Microbiology #Bacteria #Bakterien #Archaea #Archaeen

Fresh WIP piece of #Archaea #phylogenetics data for a collaborator.

Those barplot margins are driving me crazy - it's actually throwing off the immediate impression of the data! (pink bars are essentially all 1/2 or less of the orange bars, which is pretty important in context) I really need to buckle down and get to hand-coding my trees from scratch using #rlang or #julialang soon.

Hmm. How's Julia ecosystem for phylogenetic trees these days?

#microbiology #bioinformatics

How these strange #cells may explain the origin of complex life
Asgard archaea bear traits that hint at how #eukaryotes emerged
#Archaea: single-celled organisms that look much like bacteria. 10ya, new group called #AsgardArchaea was identified in sediments from Atlantic. Nothing like us: They live mostly in places with little or no oxygen, and almost unbelievably ancient, perhaps 3B yr. Yet their #DNA shows they are close to humans on tree of life
https://www.sciencenews.org/article/cells-origin-of-life-asgard-archaea
https://archive.ph/DysBo

Happy 2026 everyone! Here's a Binomica labs retrospective post. An amateur independent researcher's perspective on genome sequencing, academic conferences and approaching research themes undertaken through 2025

#independentresearch #archaea #microbiology #conference

https://naturepoker.wordpress.com/2025/12/31/welcoming-2026-independent-research-retrospective/

"The rise of the eukaryotes was one of the most important events in Earth’s history. If it had not occurred, there would be no great white sharks, no towering redwood trees, no hovering hummingbirds and no people. Just slimy layers of bacteria and archaea, everywhere. And the Asgard archaea may have started it all."

https://www.sciencenews.org/article/cells-origin-of-life-asgard-archaea

#Life #Eukaryotes #Archaea #Asgard #Cells #Biology #Evolution #Genetics

Complex #life began to develop earlier, and over a longer span of time, than previously believed.

Nee findings indicate that complex organisms evolved long before there were substantial levels of #oxygen in the #atmosphere, something which had previously been considered a prerequisite to the #evolution of complex life.

The #earth is approximately 4.5 billion years old, with the first #microbial life forms appearing over 4 billion years ago.

These organisms consisted of two groups – #bacteria and the distinct but related #archaea, collectively known as #prokaryotes.

Prokaryotes were the only form of life on earth for hundreds of millions of years, until more complex eukaryotic cells including organisms such as #algae, #fungi, #plants and #animals evolved.

Previous ideas on how and when early prokaryotes transformed into complex #eukaryotes has largely been in the realm of speculation. Estimates have spanned a billion years, as no intermediate forms exist and definitive fossil evidence has been lacking.

By collecting evidence from multiple #gene families in multiple biological systems and focusing on the features which distinguish eukaryotes from prokaryotes, researchers were able to begin to piece together the developmental pathway for complex life. 

They obtained evidence that the transition began almost 2.9 billion years ago – almost a billion years earlier than by some other estimates –  suggesting that the nucleus and other internal structures appear to have evolved significantly before #mitochondria.

The process of cumulative complexification seems to have taken place over a much longer time period than previously thought.

#biology
https://www.bristol.ac.uk/news/2025/december/complex-life-developed-earlier-than-previously-thought-new-study-reveals.html

Paper by Kay et al. (2025): https://www.nature.com/articles/s41586-025-09808-z

Hmm. I've been running an informal toy test comparing brute force alignment based #archaea gene annotation VS a 3rd party pipeline using structural predictions & search. Brute force method 'seems' to perform better in resolving function to hypothetical proteins. Not sure how this could be though

Stuff like this probably isn't represented in our common annotation pipelines I'm guessing. I'm both intrigued by the possibility and worried by all the stuff I'm likely missing.

An archaeal genetic code with all TAG codons as pyrrolysine | Science

https://www.science.org/doi/abs/10.1126/science.adu2404?af=R

#microbiology #archaea

Any #archaea lab out there interested in having their Natrialba species sequenced on ONT r10 up to about 3Kx read depth for free? I'll send back annotated assembly, methylation data and raw signal files. I need at least one more species for a paper from a particular phylogenetic clade within the genus.

Please feel free to DM & boost!

#microbiology #collaboration #sequencing #bioinformatics

Check this out - first image of a new Halococcus species I discovered with collaborators. Still figuring out the scheme to name the darn thing.

Independent research & amateur biology FTW.

#microbiology #archaea #microscopy

Question for #microbiology folks. I've been mulling over a phylogenetic tree building methods comparison, and could use a recommendation on a particularly well resolved microbial/archaeal taxon as a positive control (I'd prefer the latter).

Any recommendation would be appreciated!

#phylogenetics #evolutionarybiology #archaea

Chagny et al. establish criteria for the identification of M42 peptidases from sequence data and reveal their wide taxonomic distribution in Archaea.

🔗 https://doi.org/10.1093/molbev/msaf233

#evobio #molbio #archaea

Another fun #archaea paper to ponder about. HGT driven copy number expansion led to structural diversification, collection of which ended up being the eukaryotic replisome - seems to be the gist, as demonstrated by the author's very handy illustration.

https://www.nature.com/articles/s41559-025-02882-6

I can't quite grasp the mental model of these disparate evolved features 'collecting' together in some sort of LECA(s?), but I've yet to actually dig in to the paper.

#microbiology #evolution

Question for #archaea #microbiology folks - does anyone know the story on DSMZ 1813c solution/media linked here? (https://mediadive.dsmz.de/solutions/6322)

There's a reference calling it a media, but its categorized as a solution (for dilution use in media?). And there's no reference on where this came from or who used it.

Doing some background on another tough family of #Haloarchaea, and it looks like there's next to no literature on these buggers.

"Two billion years ago, it was an ancestor of an Asgard [archaea microbe] that diverged from its kin and eventually became us.
[...]
Now, some of the first reports about the biology of certain Asgards are revealing new, provocative details about the interior lives of these cells."

https://www.quantamagazine.org/tiny-tubes-reveal-clues-to-the-evolution-of-complex-life-20250908/

#Archaea #Biology #Cells #Genetics #Biology

Is anyone aware of supposed plasmids getting swallowed up by the chromosome during continued lab propagation? Going through new #Archaea data with 500x ONT asm suggests two of its plasmids in NCBI refseq (pub 2010) are gone, they show up as part of the chromosome. Were they ever real?

This species is a major cloning chassis in the field, so I'm surprised to see such a discrepancy.

#microbiology #bioinformatics

Huang et al. use phylogenetic analyses to reveal that the Njordarchaeales and Panguiarchaeales constitute the new class Njordarchaeia within Asgard archaea.

🔗 https://doi.org/10.1093/molbev/msaf201

#evobio #molbio #archaea

Minimod preprint from @hasindu2008 gang is out. Code available https://github.com/warp9seq/minimod

I love the work they're doing with slow5/blow5 open spec for ONT raw data, and archive all internal reads using them. Really need to sit down and test this one out with my #archaea raw data!

#bioinformatics #methylation #ONT #sequencing

I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.

Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.

We're also covering both #ONT and #PacBio for each species - so 2x the count.

I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.

#microbiology #bioinformatics

I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.

Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.

We're also covering both #ONT and #PacBio for each species - so 2x the count.

I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.

#microbiology #bioinformatics

New Method Reveals Hidden Activity of Life Below Ground https://www.dri.edu/new-method-reveals-hidden-activity-of-life-below-ground/

Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem: Melody Lindsay et al. https://www.pnas.org/doi/10.1073/pnas.2309636121

"deep wells in the #DeathValley regional flow system provide windows into #subsurface environments... one of them contains several key #microorganisms that are only found in the deepest South African #GoldMines"

#bacteria #microbes #archaea