Omri Finkel עמרי عُمري
@finkel-lab.bsky.social
Microbial ecology and plant-microbe interactions at @HebrewU
http://finkel-lab.com
http://finkel-lab.com
Reposted by Omri Finkel עמרי عُمري
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
November 23, 2025 at 1:33 PM
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
Reposted by Omri Finkel עמרי عُمري
🎉 Check out the latest from Qin Gu’s team at Nanjing Agricultural University: “Keystone Pseudomonas species in the wheat phyllosphere” (Cell Host & Microbe) 👉 www.cell.com/cell-host-mi...
Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH
Fusarium graminearum (F. graminearum) pathogen induces wheat phyllosphere alkalinization,
promoting the development of Fusarium head blight (FHB). Xu et al. show that host-acidifying
Pseudomonas, sele...
www.cell.com
November 23, 2025 at 8:11 AM
🎉 Check out the latest from Qin Gu’s team at Nanjing Agricultural University: “Keystone Pseudomonas species in the wheat phyllosphere” (Cell Host & Microbe) 👉 www.cell.com/cell-host-mi...
Reposted by Omri Finkel עמרי عُمري
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
November 12, 2025 at 7:06 AM
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
Reposted by Omri Finkel עמרי عُمري
I'm thrilled to share our newest publication in @natmicrobiol.nature.com, led by Drs. @botanichole.bsky.social, Valéria Custódio, and David Gopaulchan: Precipitation legacy effects on #SoilMicrobiota facilitate adaptive drought responses in plants. 🌾 🧪 (thread)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants - Nature Microbiology
Metagenomes from prairie soils in Kansas, USA, show how historical exposure to water stress impacts soil microorganisms and subsequently drought responses in plants.
www.nature.com
November 10, 2025 at 4:45 PM
I'm thrilled to share our newest publication in @natmicrobiol.nature.com, led by Drs. @botanichole.bsky.social, Valéria Custódio, and David Gopaulchan: Precipitation legacy effects on #SoilMicrobiota facilitate adaptive drought responses in plants. 🌾 🧪 (thread)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Omri Finkel עמרי عُمري
Call for Applications for the Azrieli International Postdoctoral Fellowship-2026-27 azrielifoundation.org/azrieli-fell...
Call for Applications for the Azrieli International Postdoctoral Fellowship-2026-27 - The Azrieli Foundation
azrielifoundation.org
November 9, 2025 at 8:30 AM
Call for Applications for the Azrieli International Postdoctoral Fellowship-2026-27 azrielifoundation.org/azrieli-fell...
Reposted by Omri Finkel עמרי عُمري
The first time we are hearing about viruses at #PMS2025, thanks @sheilaroitman.bsky.social!
November 7, 2025 at 10:55 AM
The first time we are hearing about viruses at #PMS2025, thanks @sheilaroitman.bsky.social!
Fascinating talk on how to optimize microbe-microbe interactions with Bacillus as the focal species.
November 6, 2025 at 2:24 PM
Fascinating talk on how to optimize microbe-microbe interactions with Bacillus as the focal species.
I approve this message :)
The best (maybe biased 😜) tool for short metagenomic reads is BBERT:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT
Biological diversity revealed by metagenomic sequencing far exceeds that of known or cultured organisms, yet much of this diversity remains inaccessible because most sequences from complex habitats, s...
www.biorxiv.org
November 4, 2025 at 3:35 PM
I approve this message :)
Reposted by Omri Finkel עמרי عُمري
Check out our latest preprint in which we describe a new phage plaque sequencing pipeline which lowers the cost of sequencing by up to 10-fold while significantly shortening the time required to obtain the phage genome sequences
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques
Rapid, accurate, and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequen...
www.biorxiv.org
November 3, 2025 at 10:16 AM
Check out our latest preprint in which we describe a new phage plaque sequencing pipeline which lowers the cost of sequencing by up to 10-fold while significantly shortening the time required to obtain the phage genome sequences
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Omri Finkel עמרי عُمري
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
November 3, 2025 at 9:33 AM
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
Reposted by Omri Finkel עמרי عُمري
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
October 26, 2025 at 9:25 AM
This week in the HUJI PES seminar:
@hebrewuniversity.bsky.social
@hebrewuniversity.bsky.social
Reposted by Omri Finkel עמרי عُمري
In plant-pathogen or plant-microbe interactions what is the proper null.
- there is specific coevolution of any pathogen/microbe such that it was at least partly adapted to the host isolated.
-the host of isolation may have not effected the pathogen in the slightest.
- there is specific coevolution of any pathogen/microbe such that it was at least partly adapted to the host isolated.
-the host of isolation may have not effected the pathogen in the slightest.
October 22, 2025 at 11:30 PM
In plant-pathogen or plant-microbe interactions what is the proper null.
- there is specific coevolution of any pathogen/microbe such that it was at least partly adapted to the host isolated.
-the host of isolation may have not effected the pathogen in the slightest.
- there is specific coevolution of any pathogen/microbe such that it was at least partly adapted to the host isolated.
-the host of isolation may have not effected the pathogen in the slightest.
Reposted by Omri Finkel עמרי عُمري
New pre-print from the team!
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
Primary metabolism underpins the execution of immune responses in different tissues of the same plant https://www.biorxiv.org/content/10.1101/2025.10.11.681807v1
October 14, 2025 at 7:16 AM
New pre-print from the team!
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
Reposted by Omri Finkel עמרי عُمري
📣 New PhD student position opening in my lab!
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
October 13, 2025 at 12:20 PM
📣 New PhD student position opening in my lab!
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
Reposted by Omri Finkel עמרי عُمري
Our paper, describing how the T6SSs of P. putida shape the tomato rhizosphere, is now in its final format in @isme-microbes.bsky.social ISME Communications. If you'd like to learn more, here is a thread (1/11) or read the Article doi.org/10.1093/isme....
October 6, 2025 at 6:22 PM
Our paper, describing how the T6SSs of P. putida shape the tomato rhizosphere, is now in its final format in @isme-microbes.bsky.social ISME Communications. If you'd like to learn more, here is a thread (1/11) or read the Article doi.org/10.1093/isme....
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
October 8, 2025 at 5:10 PM
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...
Reposted by Omri Finkel עמרי عُمري
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
July 23, 2025 at 5:10 AM
Time-series metatranscriptomics reveals differential salinity effects on the methanogenic food web in paddy soil | mSystems journals.asm.org/doi/full/10....
Reposted by Omri Finkel עמרי عُمري
Reposted by Omri Finkel עמרי عُمري
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!
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
September 26, 2025 at 4:50 AM
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!
www.jbc.org/article/S002...
Led by Hagit Zer with Stav Chen and David Rasin, in close collaboration with Miguel Hernandez–Prieto. Thanks!
Reposted by Omri Finkel עמרי عُمري
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...
September 12, 2025 at 1:46 PM
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...
Reposted by Omri Finkel עמרי عُمري
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...
Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social
www.biorxiv.org/content/10.1...
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
August 22, 2025 at 2:05 PM
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...
Reposted by Omri Finkel עמרי عُمري
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...
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
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...
www.nature.com/articles/s41...
Reposted by Omri Finkel עמרי عُمري
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...
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
August 19, 2025 at 7:20 PM
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...
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...
Reposted by Omri Finkel עמרי عُمري
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
August 20, 2025 at 3:50 AM
Why chocolate tastes so good: microbes that fine-tune its flavour www.nature.com/articles/d41...
Reposted by Omri Finkel עמרי عُمري
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...
August 6, 2025 at 11:02 AM
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...