Dynamics and Eco‐Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

Thank you so much for the invitation @fwf-at.bsky.social @frangrand.bsky.social and @thomaszauner.bsky.social. I very much enjoyed our conversation about the importance of microbiomes and listening to the final "product" #Microsky 🧪 @cemess.bsky.social @microbesplanet.bsky.social

🧪🦠🌊 Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus? #Urea is (part of) the answer! Very happy this fun study led by @mpimarinemicrobio.bsky.social is out: shorturl.at/wajjh Big shout out to Joerdis and Hannah for pushing this over the finish line!

A Novel Method to Simultaneously Estimate Bacterial Respiration and Growth from Oxygen Dynamics www.biorxiv.org/content/10.6... #jcampubs

So happy this is finally out! We reconstructed the 1st large-scale spatiotemporal dataset of 600+ MAGs from San Francisco Bay and show they have functional redundancy in key N and S pathways. These functions may better recover from disturbance in this highly urban estuary 💧

Big new blogpost! My guide to data visualization, which includes a very long table of contents, tons of charts, and more. --> Why data visualization matters and how to make charts more effective, clear, transparent, and sometimes, beautiful. www.scientificdiscovery.dev/p/salonis-gu...

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...

Fresh from our group, a new role for oxygen production in ammonia-oxidizing archaea: Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea Congrats to Thomas Pribasnig for this great work! Check it out here: www.biorxiv.org/content/10.6...

Non-canonical resource allocation in heterotrophically growing Thermoanaerobacter kivui | doi.org/10.1038/s414... Study identified a proteome allocation strategy inconsistent with the growth laws of E. coli and points towards variety in resource allocation strategies.

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

In muddy sediments all over the world, tiny bacteria eat and grow by building electrically conducting wires into the muck. Now, researchers say they have discovered how these miniature electricians, known as cable bacteria, do it. https://scim.ag/4i2s2Yu

Clone-FISH paper out: Manuscript/resource alert #microsky 🦠 We present a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 17 yet uncultured ones.

Ever wondered if analyzing your images by using intensity Z-projections impacts your data? Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis! buff.ly/KJ147tI #Microscopy #ZProjection #ImageAnalysis

An excellent discourse on the importance of education in environmental protection and sustainability www.tandfonline.com/doi/full/10....

On the event of James Watson's death, I highly recommend this 2023 commentary from @matthewcobb.bsky.social and Nathaniel Comfort with crucial new insights into the discovery of the double helix. (And also check out Cobb's brand new biography of Francis Crick) www.nature.com/articles/d41...

Required reading for cell biologists to get a sense of basic statistical principles! www.nature.com/articles/s41...

I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way. quantixed.org/2025/11/04/a...

The evolutionary and ecological consequences of cooperation -in American Naturalist by @stuwest.bsky.social, @annadewar.bsky.social, @ryosukeiritani.bsky.social, Laurence Belcher, and @asgriffin.bsky.social www.journals.uchicago.edu/doi/abs/10.1...

Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions academic.oup.com/nar/advance-... #jcampubs 🌊

Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes www.nature.com/articles/s41... #jcampubs

Python was awarded a funding grant, funding grant asked Python foundation to remove all diversity and inclusion initiatives they have. Python foundation said no and rejected the grant. If you use Python, send a few dollars to the charity to keep it going. I’m pushing a dono on behalf of ScamGuard.

Satelliten gegen Dürre: Im September reiste ein Team der TU Wien nach Mosambik, um im Rahmen des Projekts DrySat einen Schulungskurs durchzuführen mit dem Ziel den Teilnehmenden zu vermitteln, wie man kostenlose Open-Source-Tools für die Analyse von Dürren anhand von Satellitenbildern einsetzt.

Learn more about recent advances in anaerobic #microbiology at EMBO Practical Course "Breathless Microbes: Life With No Oxygen" in Nijmegen, Netherlands, 6–10 July 2026. 🧪 Deadline: 15 April 2026 meetings.embo.org/event/26-bre... #EMBObreathless #EMBOevents #MicroSky #biotechnology #biochemistry

Decoding emergent properties of microbial community functions through sub-community observations and interpretable machine learning academic.oup.com/ismej/advanc... #jcampubs

For anyone who needs to pass these on: www.alieward.com/ologies/geno... www.alieward.com/ologies/revo... www.alieward.com/ologies/arti... www.alieward.com/ologies/cons... www.alieward.com/ologies/trol... www.alieward.com/ologies/crit... www.alieward.com/ologies/blat...

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs

Declining ocean greenness and phytoplankton blooms in low to mid-latitudes under a warming climate www.science.org/doi/full/10.... #jcampubs 🌊

I'm delighted our paper is out: doi.org/10.1093/isme... With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠

🧵 1/6: Explore how BONCAT, SIP & single-cell tools revolutionize microbiome research! 🔗 inpst.net/new-chemical... 🌐 #Microbiome #CRBIOTECH @georgeradics.bsky.social @martinbue.bsky.social @holyunknown.bsky.social @raoulxkessel-aland.bsky.social @hipecsurvivor.bsky.social @shawneexo.bsky.social

Microbes sustain all ecosystems yet they’re nearly absent from conservation frameworks. The @IUCN Microbial Conservation Specialist Group aims to change that. Honored to co-chair this global effort. Great @nytimes piece by Carl Zimmer: www.nytimes.com/2025/10/17/s...

Episode 112 of #MattersMicrobial! Dr. Petra Levin joins the #QualityQuorum to discuss bacterial cell size, pH, and antibiotic sensitivity. PLEASE spread the #GoodMicrobialWord. Petra is inspirational. @univpugetsound @asmicrobiology @microbe.tv youtu.be/YPNAvJYAq-s?...

"Declining ocean greenness and phytoplankton blooms in low to mid-latitudes under a warming climate" | Our (Hong et al) new article in @aaas.org #ScienceAdvances: www.science.org/doi/10.1126/...

Pandas, snow leopards...and bacteria. A newly formed team of scientists is setting out to conserve the world's diversity of microbes. Here's my story: nyti.ms/47vEfRC

What if a time traveler accidentally killed Asgard archaea, and eukaryotes never emerged? Giant sulfur bacteria might still develop complex life. Using neural networks, I try to show this alternative living world 🧪🦠 #BiologyWeek communities.springernature.com/posts/altern...

Microorganisms as architects of a sustainable future www.nature.com/articles/s41... #jcampubs

Influence of Seasonal Succession on Microbiological and Physiochemical Composition in Shallow Estuarine Sediments enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments academic.oup.com/ismecommun/a... #jcampubs

Today Dr. Jeff Gralnick, Professor of the Department of Plant and Microbial Sciences at the University of Minnesota joins the #QualityQuorum to tell us a shocking story about how his research group studies the relationship between electrons, microbes, and metals @markowenmartin.bsky.social

Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope www.nature.com/articles/s41... #jcampubs

The obsession with economic output as a measure of human development puts sustainability on the back burner go.nature.com/4pNC96G

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

Disproportionation of elemental sulfur by Exiguobacterium from marine sediment academic.oup.com/ismecommun/a... #jcampubs

Interested in removing particle-associated microbes from particles for eg flow cytometry, culturing, or other single-cell microbiology purposes? Led by graduating PhD stdnt Jordan Coelho: Detergent-based separation of microbes from marine particles journals.asm.org/doi/10.1128/... #jcampubs 🌊

In situ Raman spectroscopic relative quantitative analysis of sulfur metabolic dynamics in deep-sea microorganisms journals.asm.org/doi/full/10.... #jcampubs

The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary go.nature.com/4gHDSGF

Microbial diversity, autotrophic- and heterotrophic processes in Mn-rich marine sediments www.frontiersin.org/journals/mar... #jcampubs

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

Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean www.nature.com/articles/s41... #jcampubs 🌊

Inclusive lab adaptations for scientists who need them