Deadline tomorrow! Submit your abstract now for the Hybrid EMBO Workshop "Molecular mechanisms in #evolution and #ecology," 6–9 October 2026. https://www.embl.org/about/info/course-and-conference-office/events/eae26-01/ #EMBOevents #EMBOEvoEco 🧪

Back on social media for SMBE 2026! I'll be presenting the fascinating microbe Hyaloperonospora arabidopsidis at Poster A048!

🔬 We have an open PhD position at SLU Uppsala! We're looking for a curious & driven PhD student to join the #ECOPHARM project funded by @kawresearch.bsky.social and investigate plasmid-dependent phages in aquatic ecosystems. Pls share with anyone who might be interested! www.slu.se/en/about-slu...

Diversity of Plasmid-Dependent Phages in Aquatic Ecosystems | slu.se

SLU - Science and Education for Sustainable Life

slu.se

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Out Now! Unravelling bacterial complexity at high resolution with single-cell transcriptomics #MicroSky

Single-cell genomics reveals opportunistic Enterobacterales carrying putative cationic antimicrobial peptide resistance genes in red crown rot-affected soybean rhizoplanes https://www.biorxiv.org/content/10.64898/2026.04.07.716964v1

the sensitivity of "tagIMseq" will be broadly useful for CRISPR-associated transposon work. Ruling out off-target insertions in resuspended colonies with minimal effort and cost investment is critical because targeting isn't always perfect.

Derek Severi Lundberg@derekseveri.bsky.social · 5mo ago

We targeted the rpoZ 3’ UTR in a Sphingomonad. We developed a rapid transposon mapping method, “tagIMseq”, leveraging tagmentation and @plasmidsaurus.bsky.social. It even works without a DNA prep on a resuspended colony! Most colonies were good, but many were not, so screening was important.

A quick thread summarizing our new bioRxiv preprint on using CASTs for DNA barcoding to tell "look-alike" bacteria apart (Sphingomonas edition)!! Enjoy the read! ✨

Derek Severi Lundberg@derekseveri.bsky.social · 5mo ago

When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).

When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).

Unveiling hidden variables in stressed bacteria

Unveiling hidden variables in stressed bacteria

Noise in bacterial stress responses is often dismissed as mere randomness. While true stochasticity exists, much variation reflects hidden variables—cell state, history, and microenvironment—that are only now becoming measurable. Choudhary and Vincent review emerging tools that disentangle chance from determinism, moving microbiology toward more mechanistic and predictive frameworks.

dlvr.it

Programmed strain tagging and gene disruption throughout a diverse bacterial genus https://www.biorxiv.org/content/10.64898/2026.02.24.707161v1

Sharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...

Integrative mobilizable elements are pervasive throughout Pseudomonadota https://www.biorxiv.org/content/10.64898/2026.01.12.698999v1

Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/article/19/1/wraf274/8376499?login=false#546273460

Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems

Abstract. Plasmids are mobile genetic elements that drive horizontal gene transfer among bacteria, influencing microbial community composition and function

dx.doi.org

🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.

Dan Landau@landau.bsky.social · 10mo ago

Shout out to Tamara Prieto, Dennis Yuan, John Zinno and @ivanraimondi.bsky.social . Thank you to our funders at @themarkfdn.bsky.social

www.sciencedirect.com/science/arti... How much environmental chaos to embrace in plant-microbe research, and to what end? A commentary on setting (with all choices OK as long as all options considered) w/ bergelsonlab.org, @fabriceroux7.bsky.social, @plantevolution.bsky.social, tkarasovlab.org

New Review Out! We explore how droplet microfluidics is opening new doors in microbial ecology - enabling single-cell functional insights into growth, metabolism & interactions. 🔗 doi.org/10.1093/fems... #MicrobialEcology #DropletMicrofluidics #Microbiology

Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes

Abstract. Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities—shedding light on cell-to-cell va

doi.org

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

rdcu.be

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

Universal rules govern plasmid copy number - Nature Communications

Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

doi.org

Thanks to everyone who came by my poster today for discussion! #2025ISMPMI If you weren’t able to make it but still interested in the potential role native plasmids play within Sphingomonas-plant interactions. Can check it out now on Zenodo zenodo.org/records/1591...

This work started nearly 10 years ago and was once my main postdoctoral project at @plantevolution.bsky.social before I slowed work on it to a trickle because it became confusing. But it always remained extremely interesting. journals.plos.org/plosbiology/...

A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions

In controlled greenhouse conditions, Arabidopsis thaliana plants with a hyperactive allele of the ACD6 gene have stronger pathogen defenses but are smaller and make fewer seeds, in a classic fitness t...

journals.plos.org

Last week, I had a great time at the New Phytologist EiC Symposium: “Microbes as hidden or prominent players in plant life” in Tartu, Estonia! Honored and very happy to receive the Best Poster Award! ✨ Big thanks to the organizers and all the inspiring scientists I met! 🌱 @newphyt.bsky.social