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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · 10h

Original article: www.nature.com/articles/s41...

A diverse and distinct microbiome inside living trees - Nature

Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minimal similarity to other tissues or ecosystem components.

www.nature.com

Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · 10h

Check out this preview @naturalist1986.bsky.social and I wrote about the fantastic paper on wood microbiota from Wyatt Arnold and colleagues: www.sciencedirect.com/science/arti...

Carving out the microbiota of Earth’s largest biomass reservoir

Despite being an essential part of terrestrial ecosystems for ∼400 million years, the microbiome of wood is surprisingly underexplored. In a recent is…

www.sciencedirect.com

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Reposted by Omri Finkel עמרי عُمري 🎗️

Jingjing Peng @jingjingpengca1.bsky.social · Jul 23

Time-series metatranscriptomics reveals differential salinity effects on the methanogenic food web in paddy soil | mSystems journals.asm.org/doi/full/10....

Time-series metatranscriptomics reveals differential salinity effects on the methanogenic food web in paddy soil | mSystems

Seawater intrusion and sea level rise (SWISLR), driven by climate change, pose significant threats to coastal agroecosystems, particularly salt-affected paddy soils. Despite the importance of these sy...

journals.asm.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Iddo Friedberg 💔 עידו @iddux.bsky.social · 11d

Unannotated translation products are widespread in model E. coli

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

Unannotated translation products are widespread in model E. coli

Genomes contain orders of magnitude more open reading frames (ORFs) than known protein coding genes, and recent work suggests there may be unannotated proteins present in even the best studied organis...

www.biorxiv.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Nir Keren @nir-keren.bsky.social · 12d

We've tried to take a different view at the issue of nutrient limitations-looking for the shared basis rather than for specific response. This is the result:
www.jbc.org/article/S002...
Led by Hagit Zer with Stav Chen and David Rasin, in close collaboration with Miguel Hernandez–Prieto. Thanks!

A shared basis for nutrient limitation response in cyanobacteria

Cyanobacteria possess diverse regulatory mechanisms to adapt to nutrient limitation, yet the extent to which these responses are shared across different nutrient stresses remains unclear. Understandin...

www.jbc.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Wayne Riekhof @wayneriekhof.bsky.social · 26d

Very nice writeup on someone I've admired and learned from for many years. I didn't know he had passed until catching up on This Week in Microbiology driving to campus this morning. His 1958 paper on Salmonella growth rates basically founded the formal study of microbial physiology, which...

STCmicrobeblog @stcmicrobeblog.bsky.social · Aug 21

schaechter.asmblog.org/schaechter/2...
#MicroSky

Elio (1928-2025)

by The STC Team — Losing a close friend always saddens one deeply, regardless of age. Losing a person who has so immensely influenced our worldview through his guidance and example makes the sadness e...

schaechter.asmblog.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Sara Mitri @saramitri.bsky.social · Aug 22

So excited to share this new paper by @sulheim.bsky.social and others! It's rare that you find a pattern, propose a hypothesis and the more you look, the more data you find that fits! Snorre's intuition, hard work and rigour to put it all together have been inspiring! Let us know what you think...

Snorre Sulheim @sulheim.bsky.social · Aug 20

Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social
www.biorxiv.org/content/10.1...

Microbes release lower-value metabolites at higher rates

Microbes release a wide range of metabolites into their environment, yet the reasons for this release and the factors that influence release rates are not well understood. Here, using a combination of...

www.biorxiv.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 20

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...

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Reposted by Omri Finkel עמרי عُمري 🎗️

Natanella Illouz-Eliaz @natanellae.bsky.social · Aug 19

From a gene’s single cell expression–through spatial localization–to novel function, and beyond!
Now out @natplants.nature.com
We built a comprehensive spatial-transcriptomic atlas of Arabidopsis, revealing cell-type identities across organs in unprecedented detail
www.nature.com/articles/s41...

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle - Nature Plants

This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.

www.nature.com

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Reposted by Omri Finkel עמרי عُمري 🎗️

BejaLab @bejalab.bsky.social · Aug 20

Why chocolate tastes so good: microbes that fine-tune its flavour www.nature.com/articles/d41...

Why chocolate tastes so good: microbes that fine-tune its flavour

Manipulating the microbial communities involved in cocoa bean fermentation could make chocolate even more delicious.

www.nature.com

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Reposted by Omri Finkel עמרי عُمري 🎗️

BejaLab @bejalab.bsky.social · Aug 6

In memory of Fabrice Rappaport. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells www.nature.com/articles/s41...

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Reposted by Omri Finkel עמרי عُمري 🎗️

Nature Microbiology @natmicrobiol.nature.com · Aug 8

#NatMicroPicks

Hidden microbial world in trees🌳

Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.

#PlantMicro #MicroSky

www.nature.com/articles/s41...

A diverse and distinct microbiome inside living trees - Nature

Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

www.nature.com

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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · Aug 9

כאדם וכחוקר, אני חש בושה עמוקה לנוכח מעשה העוולה הזה. www.haaretz.co.il/food/dining/...

זה היה אחד הגשרים האחרונים בין יהודים לערבים. גם אותו הרסו

בטרגדיה המתמשכת שהפכה למציאות חיינו, מתבלט אירוע קטן ושולי לכאורה: הריסת מבנה של בנק הזרעים הפלסטיני מדרום לחברון, בידי כוחות צה"ל

www.haaretz.co.il

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Reposted by Omri Finkel עמרי عُمري 🎗️

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 2

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab.

Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.

#plantscience
www.biorxiv.org/content/10.1...

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Reposted by Omri Finkel עמרי عُمري 🎗️

Sarit Avrani @saritavrani.bsky.social · Jul 28

Our paper on cyanophages of marine sponge symbionts is finally out. It is the outcome of a great collaboration with Laura Steindler's lab and was led by Tzipora Perez.

Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont

Intracellular cyanobacterial symbionts of sponges are shown to be susceptible to cyanophages, challenging assumptions about their isolation from viral exposure. The study reveals novel phage–host int...

enviromicro-journals.onlinelibrary.wiley.com

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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · Jul 27

The poster is titled

ROOT WARRIORS AND FRUGAL METABOLIZERS: THE FUNCTIONAL ARCHITECTURE OF GLOBAL RHIZOSPHERE AND SOIL MICROBES

And we hope that it will evolve soon into a manuscript, in collaboration with @amirerez.bsky.social

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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · Jul 27

I'm really grateful to have @naturalist1986.bsky.social as a post-doc in the lab, and am glad to see his work being recognized with a best poster award at the annual meeting of the Israeli Society for Microbiology.

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Reposted by Omri Finkel עמרי عُمري 🎗️

BejaLab @bejalab.bsky.social · Jul 27

v3 loaded. Oceanic cyanobacterial photosynthesis is negatively affected by viral NblA proteins www.biorxiv.org/content/10.1...

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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · Jul 25

Congratulations!

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Reposted by Omri Finkel עמרי عُمري 🎗️

New Phytologist @newphyt.bsky.social · Jul 22

✨ Paper spotlight ✨

Microbial drivers of root plasticity
doi.org/10.1111/nph....

(🧵 1/6) Plant roots have evolved mechanisms to adjust their development within the highly heterogeneous soil matrix, integrating local environmental conditions into their endogenous developmental programs.

Fig. 1 Schematic representation of plant–microbe interactions and microbial metabolism that influence root development and nutrient uptake.

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Omri Finkel עמרי عُمري 🎗️ @finkel-lab.bsky.social · Jul 21

New Tansley review out in @newphyt.bsky.social with @fdiniandreote.bsky.social and Gabriel Castrillo! We explore how the root is shaped by dialogue with soil microbes—highlighting emerging mechanisms and future research directions in root plasticity and microbiome interactions.
tinyurl.com/38mkyx5t

Microbial drivers of root plasticity

Soils are highly heterogeneous and dynamic systems, experiencing a constant flow of plant root exudates and moisture fluctuations that affect nutrient distribution, soil physicochemical properties, a...

nph.onlinelibrary.wiley.com

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Reposted by Omri Finkel עמרי عُمري 🎗️

Asaf Levy @asaflevylab.bsky.social · Jul 21

📢 New preprint alert!
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...

The Genetic Basis of Bacterial Adaptation to Hosts

Microbes colonize and interact with diverse multicellular hosts using specialized genes, many of which remain unidentified. Better understanding of host-associated gene functions is a key aspect of mi...

www.biorxiv.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Noah Fierer @noahfierer.bsky.social · Jul 18

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

A periodic table of bacteria?: Mapping bacterial diversity in trait space

Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...

www.biorxiv.org

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Reposted by Omri Finkel עמרי عُمري 🎗️

Marc Somssich @somssich.bsky.social · Jul 7

📜 An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification

🧑‍🔬 @dorruss12.bsky.social, Jeffery L. Dangl, et al.

📔 @natcomms.nature.com

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantImmunity #Glucosinolates

An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification - Nature Communications

Bacterial genes required for plant colonization are highly host- and organ-specific. An efflux pump detoxifies specific Arabidopsis glucosinolates to protect commensal bacteria from plant chemical def...

www.nature.com

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Reposted by Omri Finkel עמרי عُمري 🎗️

Asaf Levy @asaflevylab.bsky.social · Jun 11

Our new paper is online in Genome Biology:
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....

Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology

Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...

genomebiology.biomedcentral.com

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