Krzysztof T Jurdzinski

Time lapse of an odd little monster. Presumably some kind of cercozoan from brackish water. #protistsonsky

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Person standing outside next to a building wearing a red jacket

Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes.

Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵

www.ebi.ac.uk/about/news/p...

Cefiderocol resistance genes identified in environmental samples using functional metagenomics Abstract. Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to

🧬 Our new paper in @ISMEJournal

"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"

Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.

academic.oup.com/ismej/advanc...

#AMR #microsky

1/5

Uppsala in late autumn

Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...

Novel artificial selection method improves function of simulated microbial communities Author summary Artificial selection has been extremely powerful in improving properties of complex biological or biochemical entities. The most familiar examples come from the breeding of animals and ...

Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...

New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.

We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.

www.biorxiv.org/content/10.6...

Phylogenetic tree of 8,943 bacterial genomes. The shaded branches in the tree represent different types of oxygen requirements, and the outermost ring indicates taxonomic lineages.

Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU

The impact of tokenizer selection in genomic language models (adapted)

The impact of tokenizer selection in genomic language models
doi.org/10.1093/bioi...

#MicroSky

We worked on this project as a series of "mini-hackathons", where we would meet for a whole working day and work on the project together. All the first-co-authors (random order) and the corresponding Anders were present at all the sessions.

We compared the predictive power of different models and data aggregation approaches. We compared predictive power of metabarcoding and microscopy counts, and predicted microscopy pres/abs from metabarcoding. We assessed transferability across years and potential to predict environmental status.

New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.

We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.

www.biorxiv.org/content/10.6...

Recruitment for the EMBL International PhD Programme is officially open! 🔊

At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!

🔎 Read more here:
tinyurl.com/4jdt2ra5

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

from 2012. Microbial rhodopsins on leaf surfaces of terrestrial plants enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies Effects of environmental stressor factor number on soil common, rare, and unknown taxa. High-stressor numbers reduce the abundance and diversity of rare taxa but increase unknown taxa and had no effe...

New paper out in Global Change Biology

Cheng et al.
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies

w/ @manudelbaq.bsky.social & others
onlinelibrary.wiley.com/doi/10.1111/...

De är små och svåra att studera, men spelar viktig roll för att upprätthålla livet i haven. Kommande Baltic Breakfast handlar om de viktiga mikroorganismerna! Läs mer och följ livesändningen här: www.su.se/english/divisions/stockholm-university-baltic-sea-centre/policy-analysis/baltic-breakfast

We just released #anvio v9, "eunice" 🎉

This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.

Read the release notes:

github.com/merenlab/anv...

Visit our up-to-date web page:

anvio.org

LLMs behaving badly: mistrained AI models quickly go off the rails Training large language models to write insecure code can cause them to exhibit seemingly aggressive behaviour when performing unrelated tasks.

Training LLMs to write insecure code can cause them to exhibit seemingly aggressive behaviour when performing unrelated tasks

go.nature.com/4qo4YGI

I finally made some taxon content for The Plankton Project channels! A little video about Beggiatoa, a bacteria #marineplankton 🦑

the sun is shining through the clouds in the sky above the ocean ALT: the sun is shining through the clouds in the sky above the ocean

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41...
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...

Blue buttons jellies float at the oceans surface, like little animal flowers, living between sea and sky. There are millions of them out there right now, and most will live their whole lives without even being seen by a human.

Despite the hard things, the world is still wondrous.

The position for a postdoc is now officially open.
I can answer any questions related to the position, but please apply only thru the university system.

jobs.helsinki.fi/job/Helsinki...

Closely related microbes tend to live in similar communities across Earth’s environments.
We call this pattern community conservatism - extending established ecological patterns to the microbial world.
🧬🌍 #MicrobialEcology #Evolution

Read the full article here: doi.org/10.1038/s415...

The genome of one of the last woolly rhinoceros sequenced from a chunk of meat extracted from the stomach of a mummified Late Pleistocene wolf puppy 🤯🦏🐺

Absolute cinema 🎥⬇️⬇️⬇️

The Hidden Risk of Combined Stressors for Soils New study by researchers at Freie Universität published in “Nature Communications” shows that independent environmental stressors such as heat, drought, and microplastics affect soils differently when...

Press release of @freieuniversitaet.bsky.social for our recent paper in Nature Communications.

The Hidden Risk of Combined Stressors for Soils

@fubcp.bsky.social
www.fu-berlin.de/en/presse/in...