Nicole Geerlings

Giant multicellular magnetotactic prokaryotes in marine sediments academic.oup.com/ismej/advanc... #jcampubs

New paper from my group in @science.org : "A small polymerase ribozyme that can synthesise itself and its complementary strand" www.science.org/doi/10.1126/...
Outstanding work by @edogia.bsky.social

Figure 1: The important dimensions of CAILs across research and education; clockwise from 12 o’clock: Con- ceptual Clarity is the idea that terms should refer. Critical Thinking is deep engagement with the relationships between statements about the world. Decoloniality is the process of de-centring and addressing dominant harmful views and practices. Respecting Expertise is the epistemic compact between professionals and society. Slow Science is a disposition towards preferring psychologically, techno-socially, and epistemically healthy practices. The lines between dimensions represent how they are interwoven both directly and indirectly.

New preprint! @marentierra.bsky.social @irisvanrooij.bsky.social & I have been working on what CAIL means to showcase & propagate the idea of thinking very differently to tech industry norms on "artificial intelligence"

Towards Critical Artificial Intelligence Literacies doi.org/10.5281/zeno...

1/

the evolutionary and ecological consequences of cooperation

the evolutionary and ecological consequences of cooperation

Huge thanks to @asn-amnat.bsky.social for inviting our review on the evolutionary and ecological consequences of cooperation. @annadewar.bsky.social @asgriffin.bsky.social @lauriebelch.bsky.social www.journals.uchicago.edu/doi/10.1086/...

How did life arise from simple chemical building blocks?

New #LMBResearch led by @edogia.bsky.social in @philholliger.bsky.social group has identified a small self-replicating ribozyme that could be the answer.

Read more: mrclmb.ac.uk/news-events/...

Bridging the gap from chemistry to life: discovery of a tiny RNA that can copy itself | MRC Laboratory of Molecular Biology Led by Edoardo Gianni, Philipp Holliger’s group in the LMB’s PNAC Division have identified a small self-replicating catalytic RNA (ribozyme), providing new ...

Have a look at the Insight on Research story on our Science paper www.science.org/doi/10.1126/... on the @mrclmb.bsky.social website: mrclmb.ac.uk/news-events/... including a great little animation from LMB VisLab.

Limits to the evolution of metabolic dependency in spatially structured microbial communities In microbial communities, evolutionary processes can lead to loss of biosynthetic pathways, creating metabolic dependencies. The Black Queen Hypothesi…

Excited to share our new paper led by Divvya Ramesh: Limits to the evolution of metabolic dependency in spatially structured microbial communities 🧫
www.sciencedirect.com/science/arti...

Unveiling hidden variables in stressed bacteria

@cp-cellreports.bsky.social Review by @divyach.bsky.social and @maxencevincent.bsky.social

www.cell.com/cell-reports...

Spatial structure: Shaping the ecology and evolution of microbial communities Abstract. Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interact

Spatial structure: Shaping the ecology and evolution of microbial communities

@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social

academic.oup.com/femsre/advan...

#MicroSky: ENVIRON BIOTECH: Vidal et al discuss that deep beneath Earth’s surface, life thrives in extremes. Subsurface microbiology reveals the limits and origins of life, and guides the search for biosignatures on Mars, icy moons, and distant exoplanets. Do not miss doi.org/10.1111/1751...

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

A nice demonstration of how cross-feeding shapes small microbial community compositions

From Segré lab @dsegre.bsky.social

www.biorxiv.org/content/10.6...

Guinea-Bissau suspends US-funded vaccine trial as African scientists question its motives Officials at the US Department of Health and Human Services, which awarded funding for the controversial study, say it will proceed as planned.

www.nature.com/articles/d41...

“They’re trying to use African children to prove a case for reducing vaccines in the US,”

"That's problematic"...

No...it's beyond the pale.

Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems www.nature.com/articles/s41... #jcampubs 🌊

Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems | Nature Communications https://www.nature.com/articles/s41467-026-68747-z

Dissecting gene regulatory networks governing human cortical cell fate - Nature Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...

Fascinating work in @nature.com from Alex Pollen lab using CRISPRi screening to identify key transcription factors driving human radial glial neural stem cell fate—with causal validation. www.nature.com/articles/s41...

Highly efficient bio-catalytic oxygen reduction coupled to long-range electron transport in cable bacteria www.biorxiv.org/content/10.6... #jcampubs

Dynamics and Eco‐Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness Nitrifiers in the Baltic Sea show persistent abundance in aphotic waters and late-fall to winter photic zone increases positively correlated with nutrients and negatively with light and chlorophyll. ...

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

An Introduction to OME-Zarr for Big Bioimaging Data

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

Urea use drives niche separation between dominant marine ammonia oxidizing archaea - Nature Communications Two groups of ammonia-oxidizing archaea drive marine nitrification. Stuehrenberg et al. reveal that their distribution reflects substrate use, with one relying on urea and the other on ammonia to main...

🧪🦠🌊
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

Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments Abstract. Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With inte

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 💧

screenshot of my post

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...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

🧬🦠🚨 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 - Nature Communications Proteome allocation to anabolic and catabolic functions is significantly regulated by growth rate in the model bacterium Escherichia coli. By contrast, this article shows that proteome allocation is o...

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.

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

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
🖥️🧬🦠

Metal scaffolds turn bacteria into live wires Mud-dwelling cable bacteria construct metal organic frameworks to grow

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

List of available cultures

Ecoli cells (Dapi, on left) expressing bacterial (center) and archaeal 16S rRNA.

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