illustration of five different microbial cells and some of the chemicals they exchange with their environment

New #ISEPpapers by @ankarn.bsky.social et al.! Living together: evolutionary and ecological dimensions of #protist endosymbiosis academic.oup.com/microlife/ar...

#Protists #Microbes #Symbiosis #Evolution

World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities - Scientific Data Scientific Data - World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities

World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities www.nature.com/articles/s41... #jcampubs 🌊

Today at the open days we presented few #coccolithophore challenges!

All of the diversity ⬇️

Intracellular Amorphous Calcium Carbonate Biomineralization in Methanotrophic Gammaproteobacteria Was Acquired by Horizontal Gene Transfer From Cyanobacteria Horizontal gene transfer from Microcystis-like cyanobacteria to members of the Methylococcaceae has enabled the latter to become capable of biomineralizing intracellular amorphous calcium carbonate i...

Intracellular Amorphous Calcium Carbonate Biomineralization in Methanotrophic Gammaproteobacteria Was Acquired by Horizontal Gene Transfer From Cyanobacteria enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

🌊 Applications Open: Training on Ocean Alkalinity Enhancement

Hosted by the IAEA Ocean Acidification International Coordination Centre, focusing on impacts on marine organisms.

📍 Monaco | 🗓 15–19 June 2026
🗓 Deadline: 30 April
✈️ Fully funded
🔗 news-oceanacidification-icc.org/2026/04/02/a...

A single-cell perspective on host–virus dynamics in the ocean www.cell.com/trends/micro...

New paper from our lab characterising a richly diverse cococlithophore community in the Southern Indian Ocean. These communities were largely overlooked by broad specificity 18S metabarcoding approaches. @godi.bsky.social @thembauk.bsky.social aslopubs.onlinelibrary.wiley.com/doi/10.1002/...

Today was an exciting day for #coccolithophores on the Adriatic coast!
#CoccoChannel

5/ Big take-home:
haptophyte-specific 18S V4 recovered 86 putative #coccolithophore ASVs across 51 samples, while an earlier broad eukaryote 18S V9 survey of the same samples detected only 4.
A good reminder that broad-spectrum markers can seriously under-sample coccolithophore diversity.

4/ Life-cycle structure shifted too.
➡️Holococcolith-bearing forms made up nearly 30% of the community overall, with relatively more HOL phases in the meander and more HET phases outside. In other words, mesoscale structure was sorting both taxa and life-cycle stages.

3/ The spatial pattern was taxon-specific #coccolithophores:
Syracosphaera mediterranea HOL and Calcidiscus leptoporus HOL were associated with the colder, fresher center.
Gephyrocapsa huxleyi and Umbilicosphaera hulburtiana were more abundant in the warmer, saltier outer waters.

2/ Diversity was higher in the colder, fresher meander center than in the warmer, saltier outer region.
➡️ Showing that even relatively fine-scale hydrographic structure can shape #coccolithophore assemblages.

1/ ⚠️ New paper out in L&O @aslo.org 🌊 Targeted haptophyte metabarcoding + SEM revealed far more #coccolithophore diversity than broad eukaryote surveys.
🧵A thread on how Southern Indian Ocean mesoscale fronts structure these communities at fine spatial scales👇 #protistsonsky doi.org/10.1002/lno....

Redox chemistry of early Earth and the origin of life - Communications Chemistry Redox reactions played an important role in shaping the conditions that enabled the emergence of life on the early Earth, but how these relate to specific environmental conditions and whether they led...

Redox chemistry of early Earth and the origin of life www.nature.com/articles/s42... #jcampubs

Whether you're early in your career, in the middle of it, or further along, we currently have a range of fellowship and award schemes open for applications.

Find out more and apply here: scar.org/fellowships-...

I love it! Imagine, you walk into the cell and see everything with your eyes!And photos you can take even with an iphone!!!

Amazing!!!! Is that 100fold expansion???

From Light to Acetate: How Trophic Conditions Shape Growth and Cell Cycle Progression in Chlamydomonas reinhardtii www.biorxiv.org/content/10.6...

Are you curious about animal origins? Want to perturb their genetics to find out more? Now it's a lot cheaper: the FUNR @frutag33.bsky.social Lab's effort to make transfection more accessible for choanos (& relatives) is up now! 🧬 


A brief 🧵1/5

Write how you like. Clear writing is clear writing. Don't let the fad-bullies scold you with ridiculous and unjustified social approbation. Frequency of use of em-dashes in AI is NLM-dependent anyway, so the unworthy critique is already dated.

Campolina: a deep neural framework for accurate segmentation of nanopore signals - Genome Biology Nanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggl...

Transformer-based AI has boosted
@nanoporetech.com
sequencing accuracy, but at a cost to portability due to GPU demands.
Our new work, spearheaded by
Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

New article on #protist global distributions combining the #Mixoplankton and #metaPR2 databases with revised functional annotations led by @lusantof.bsky.social, Michaela E. Larsson, and Suzana Leles with Aditee Mitra and Emile Faure. Now available on Ocean Microbiology

rdcu.be/fanlx

Fun workshop coming up in Roscoff. You can learn building your own low-cost microscopes.

Smart DIY Microscopy for Marine Biology
3-5 June 2026
🔬🌊🦠

Application deadline April 02

www.sb-roscoff.fr/en/workshop-...

@embrc-france.bsky.social @gdrimabio.bsky.social
@sbroscoff.bsky.social
#EnderScope

In our new pre-print, we established massive single-cell RNA-sequencing for diatoms to investigate key cell fate transitions. Notably, we discovered that the diploid-to-haploid transition is regulated by Myb TFs, a process that is actively ongoing across the Global Ocean! 🌊

Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil

Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...

Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets - Microbiome Background Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications. Results To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty. Conclusions Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract

Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets | Microbiome | Springer Nature Link link.springer.com/article/10.1186/s40168-0...

Please cast your vote in the 2026 ASLO Elections. Determine the next leaders of our beautiful scientific society.

Fecal pellet packaging enhances marine carbon sequestration Fecal pellets produced by marine zooplankton contribute substantially to transporting biologically fixed carbon from the sunlit sea surface into deeper water layers. Their occurrence and composition ....

Led by Clarissa Karthäuser and her RotoBOD, we studied zooplankton fecal pellets, including very small ones; we find that here animals cannot be picky eaters, and that small pellets are efficient exporters with low remineralization 🌊
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).

A brief 🧵 (carried over from the old place)