Nicole Geerlings

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology In the ocean, viruses are known to mediate the carbon cycle, keeping dissolved organic carbon (DOC) in the microbial loop and preventing its movement into secondary consumers (1). However, few direct measurements of this carbon flux exist, and recent considerations of the ocean system consider that viruses can not only loop carbon in the dissolved pool but also participate in a carbon shuttle through the creation of aggregates that pellet or can be part of a viral vent that releases carbon into the atmosphere (2). While the pelagic ocean has been well reviewed for viral contributions to microbial diversity and biogeochemical cycling, less attention has been paid in recent years to the sedimentary portion of the ocean, where carbon is potentially stored over geological time, but viral influence can still be felt. Here, we review the literature on viruses in sedimentary ecosystems and their potential role in biogeochemistry and microbial diversity.

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology https://journals.asm.org/doi/10.1128/aem.00275-25?utm_source=twitter&utm_medium=social&utm_content=ASM&utm_id=falcon&utm_campaign=MicrobiologyMonday

Using Quarto to Write a Book I’ve spent the last couple of months revising my Data Visualization book for a second edition that, ideally, will appear some time in the next twelve months. As with the first edition, I’ve posted a c...

Using Quarto to write (and typeset) a book.

𝗘𝘅𝗰𝗶𝘁𝗶𝗻𝗴 𝗗𝗲𝘃𝗲𝗹𝗼𝗽𝗺𝗲𝗻𝘁𝘀 𝗶𝗻 𝗠𝗶𝗰𝗿𝗼𝘀𝗰𝗼𝗽𝘆 𝗥𝗲𝗽𝗼𝗿𝘁𝗶𝗻𝗴! If you're involved in creating, processing, or publishing microscopy data, take a look at the new checklist for reporting requirements provided by @quarep-limi.bsky.social in @jcb.org 🔗 rupress.org/jcb/article/...

Neanderthals, modern humans, and the rules of attraction. Here's my story on a tantalizing study on mating preferences as far back as 250,000 years ago. Gift link: nyti.ms/4bcNzvy

Yet another awesome single-phage paper from Ido Golding's lab #phagesky

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

Differential Contributions From Chemo‐ and Photoautotrophy to Winter Primary Production in a North Temperate Freshwater System Changing winter conditions influence snow and ice accumulation in inland waterbodies Diverse communities of primary producers are responsible for the fixation of inorganic carbon year-round Guil...

Love this new paper from @tjvmajors.bsky.social and colleagues - looking at contributions of chemosynthetic contributions to net primary productivity with a focus on interesting winter dynamics! agupubs.onlinelibrary.wiley.com/doi/10.1029/...

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...