I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray).

The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

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

AI is starting to look like pseudoscience Not all of it, but some scientists are too eager to believe their own hype

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

Des pôles aux abysses, les nouveaux explorateurs scientifiques font rêver mais irritent le monde de la recherche Les expéditions mêlant aventure, sport et recherche se multiplient dans les zones extrêmes du globe. Très médiatisées, elles suscitent pourtant des réserves chez les chercheurs académiques, qui dénonc...

www.lemonde.fr/planete/arti...

Researchers Uncover Hidden Genetic World in Antarctic Waters The discovery of vast numbers of previously unknown microbial genes in Antarctic waters could improve understanding of how the ocean shapes Earth’s climate.

Researchers Uncover Hidden Genetic World in Antarctic Waters

"at least a third of the genes identified are missing from existing marine gene catalogs"

@loimai.bsky.social #microbiome #oceans

Exciting new methane research: Huge credit to @annajwallenius.bsky.social & Andy Leu for using nifty bioinformatics to disentangle 8 novel MAGs of 'Candidatus Methanoborealis' This is version 1 of our #bioRxiv preprint. Aanalysis is ongoing & we welcome your feedback!
doi.org/10.64898/202...

Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper:

doi.org/10.1128/mbio...

a figure from the linked paper which shows A) a world map and B) a schematic representation of various natural and artificial habitats, both annotated with information about which sulfur disproportionating bacteria have been found in the specific regions and environments

New paper from my 2nd PostDoc is now published in The ISME Journal by @isme-microbes.bsky.social!

#Sulfur disproportionation occurs globally across anoxic habitats & has multiple mechanisms of independent evolutionary origin academic.oup.com/ismej/advanc...

#Bacteria #Microbes #Evolution #DeepSea

Genomic perplexity and the evolution of context-dependent function Abstract. The fundamental principle that selection acts on a gene's function often assumes implicitly that this function is fixed and intrinsic. However, e

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling A genome-enabled ESM built on genomic data assesses physiological acclimation and biogeochemical effects through nutrient stress.

Hello Ian, linking 'omics observations to ocean biogeochem is our grand challenge for all of us... Not there yet, but several smart ideas worth following: www.science.org/doi/full/10.... or www.primoscorwg.org Happy to talk more about the article data implications...

Since you arrived here, I want to share this: this article is a gem to me because this project could have failed at so many crossroads. Only with the contribution and trust of brilliant authors and friends could this happen! That what it takes ...10/10

Antarctica InSync - Antarctica International Science & Infrastructure for Synchronous Observation - Antarctica Insync Antarctica InSync Antarctica International Science & Infrastructure for Synchronous Observation Antarctica InSync is a global effort to synchronise research across Antarctica and the Southern Ocean, c...

Finally, this work brings a wealth of genomic data (218 metagenomes) associated with 50 environmental variables that will help putting the Southern Ocean at the center of the map… Code and data in the paper! More to come from visionary research programs like this one www.antarctica-insync.org 7/n

DMSP lyase is one of the plankton functions that is most linked to environmental variations, suggesting a central role of sulfur compounds in this polar environment... 8/n

This microscopic world is structured by water mass, illustrating how ocean circulation controls marine life. Some ubiquitous bacteria (SAR11) adapt their genetic repertoires to thrive in all latitudes. 7/n

After a long bioinformatics journey, we found that about 1/3 of the plankton genes were never observed in any other ocean: this biome is unique! …6/n

Coup de chaud sur l'Antarctique ! Thalassa YouTube video by Thalassa - France Télévisions

To fill this important gap, we embarked on a fantastic Antarctic Circumnavigation Expedition to sample the different regions of the Southern Ocean and study plankton DNA. Take a deep dive in the Roaring Forties and the Furious Fifties with us: www.youtube.com/watch?v=lZkt... …5/n

Biosynthetic potential of the global ocean microbiome Nature - Global ocean microbiome survey reveals the bacterial family ‘Candidatus Eudoremicrobiaceae’, which includes some of the most biosynthetically diverse microorganisms in the...

Due to low accessibility, we miss data and observations to understand and predict its evolution. Until recently, an extensive plankton genomic diversity survey of this ocean was still missing from global ocean data rdcu.be/e7Nep ...4/n

Emerging evidence of abrupt changes in the Antarctic environment Nature - Abrupt changes are developing across Antarctica’s ice, ocean and biological systems; some of these changes are intensifying faster than equivalent Arctic changes, potentially...

It is a fragile ecosystem with unique diversity of life and ecosystems and is the cradle of deep-water masses that feed the world’s Oceans. Now, the Southern Ocean seems to undergo abrupt changes, mostly visible in the last decade from strong sea ice cover anomalies. rdcu.be/e7M9R ... 3/n

Carbon storage shifts around Antarctica Nature Communications - Dense water production in the seas around Antarctica is a key process for century-scale carbon storage, slowing global warming. Results from an advanced new model reveal the...

It is rarely seen on a world map. Yet, the Southern Ocean is central for the functioning of our planet! It absorbs CO2 and heat like no other with respect to its surface. Let’s take a different view: rdcu.be/e7Nbh ... 2/n

Water mass specific genes dominate the Southern Ocean microbiome Nature Communications - Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale...

Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/
Bonus: beautiful seascape and friendly spirit!

Antarctica InSync will host two webinars, bringing together the science community to discuss the draft White Papers currently available on our website.

· 20 January, 17:00–19:00 (CET)
· 21 January, 09:00–11:00 (CET)

📌 Register: lnkd.in/epX4_JiA
📝 Provide input to the draft papers: lnkd.in/eYfJgTUV

Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below

1/ The overturning circulation is a network of ocean currents transporting heat, carbon, oxygen and nutrients around the world. At the heart of this circulatory system is the global pumphouse of #Antarctica and the Southern Ocean.

Animation: NASA-SVS

Virome Analysis Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes.

Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero

link.springer.com/protocol/10....

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

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

Thrilled to share our new study! We show that mirusviruses include lineages packed with spliceosomal introns and likely replicating in the nucleus of unicellular eukaryotes—a sharp contrast to most large and giant eukaryotic viruses that replicate in the cytoplasm.

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

I am very excited to announce that a fully funded PhD position is available in my group.

Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia

Please RT or forward this information to interested candidates.

Deadline: 11.01.26

More info:

shorturl.at/f1TuF

New GEOTRACES Science Highlight! 🌊

Long-range transport of iron via the #Agulhas Current and counter-current: a boon for the phytoplankton
www.geotraces.org/long-range-t...

Paper first authors: Eva Bucciarelli & Pierrick Penven, LEMAR

#oceanscience #traceelements
@scor-int.bsky.social