Illuminating the active virosphere with BONCAT and single virus genomic sequencing technologies https://www.biorxiv.org/content/10.1101/2025.08.05.666878v1

UPDATE: The 2025-2026 list of faculty and postdoc positions in ecology and evolutionary biology is out! Be sure to check out this active and helpful community run resources! docs.google.com/spreadsheets...

Neat paper!

Way back when, we speculated SAR11 could assimilate glycolate by oxidizing to glyoxylate and slapping an ammonia on it to produce glycine. Perhaps other taxa assimilate it similarly.
www.nature.com/articles/ism...

🚨Our book is now available for pre-order🚨

It was such an honour to contribute to this, as this was the book that opened my eyes to, and inspired me to study #marine #microbiology!

Highly recommend for students/academics wishing to learn about marine microbes.

www.routledge.com/Marine-Micro...

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns www.biorxiv.org/content/10.1... #jcampubs

BONCAT-Live for isolation and cultivation of active environmental bacteria journals.asm.org/doi/full/10.... #jcampubs

Who fixes carbon in the dark ocean? A new study in @nature.com, led by @barbarabayer.bsky.social @univie.ac.at shows that ammonia‐oxidizing microbes contribute much less to dark carbon fixation than previously thought – leaving room for unknown players.
Read more: 🔗 dome.univie.ac.at/news-events/...

Assembly-free short-read metagenomic maximum growth rate prediction

www.biorxiv.org/content/10.1...

Excellent work done by Borja, Miguel, and Kostas!

Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them

academic.oup.com/ismecommun/a...

Promising tool by Ghaly et al., 2025; Env Microbiol

EcoFoldDB: a database of proteins curated for ecologically relevant microbial pathways, including carbon fixation, nitrogen fixation, DNRA, denitrification, methane oxidation, and more!

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Side note: One often thinks they're not recovering low-abundance taxa because they're low-abundance. But with Illumina, it's also likely because they're low-GC and Illumina has strong GC bias. You can fix this with wetlab intervention like this, or using ONT instead, which doesn't have a GC-bias.🧵

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂

www.biorxiv.org/content/10.1...

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...

Happy to share our upcoming paper on pioneer microbial communities, including viruses, establishing after glacier retreat, result of a great collaboration @ua.es @mncn-csic.bsky.social @univgirona.bsky.social @pepa-anton.bsky.social @estherrubioport.bsky.social academic.oup.com/ismecommun/a...

🦠➡️🧬 Community context matters!
In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution.
Check out the preprint 👇🏼

Gracias tio!!!!

Last Friday September 5th 2025 I successfully defended my PhD thesis on microbial and viral diversity of extreme halophiles using metagenomics and genomics!!

Many thanks to Prof. @ramonix.bsky.social, Prof. Rafa Bosch, and Dr. @tomeuviver.bsky.social, for their support and guidance all these years!

Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle www.nature.com/articles/s41... #jcampubs

Bringing the uncultivated microbial majority of freshwater ecosystems into culture www.nature.com/articles/s41... #jcampubs

Preparation of Cuvette‐Based Sorters for Sorting Submicron Microbial Cells and Viruses from Environmental and Biological Samples currentprotocols.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs

Metagenomic analysis reveals how multiple stressors disrupt virus–host interactions in multi-trophic freshwater mesocosms www.nature.com/articles/s41... #jcampubs

Second paper of my PhD just published in The ISME Journal!🕺🕺

A single genomovar of Haloquadratum walsbyi, the most abundant species in hypersaline environments, globally dominates due to its higher fitness compared to close relatives

@isme-microbes.bsky.social
academic.oup.com/ismej/advanc...

New on Bluesky!

Sharing my first-author & corresponding paper:

Showing i) that the genus level is an ecologically relevant category for ensuring lineage persistence under disturbed conditions and ii) that viral cohorts can serve as a proxy for phage-host dynamics.

academic.oup.com/ismej/articl...