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bio-huji-plants | Department of Plant & Environmental Sciences | The Hebrew University of Jerusalem. Discovering plant and microbial life | Exploring the intricate interactions between plants, microor...

bio-huji-plants.com

In a series of workshops last year, we discussed the term ‘synthetic community’ and its usage. It’s so loosely defined and is regularly used to define something which in my eyes isn’t a SynCom. The discussion was also touching on whether the term itself is appropriate.

This week in our seminar, we're excited to host our own alumnus Corrine Best, who just started her new lab in the Volcani institute!

Excited to share my review in Nature Reviews Microbiology on soil fungal ecology. Fungal diversity, ecology and functions in soil ecosystems Hope people will find it useful! www.nature.com/articles/s41...

Fungal diversity, ecology and functions in soil ecosystems - Nature Reviews Microbiology

In this Review, Rillig explores the diversity of fungi in the soil ecosystem, their ecological interactions and diverse ecological roles in terrestrial ecosystems as well as anthropogenic factors that...

nature.com

Congrats to Jamie A. Lopez and Amir Erez on this excellent new perspective in Environmental Microbiology! Very useful for anyone interested in how to apply mathematical modeling in microbiology. enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

Mathematical Modelling and Intuition in Microbiology: A Perspective

Mathematical modelling in microbiology converts verbal reasoning into internally consistent hypotheses that can provide testable predictions, infer hidden parameters, and generate transferable intuit...

enviromicro-journals.onlinelibrary.wiley.com

Our departmental seminar is back! This week:

Check out our new manuscript, in collab with Efrat Sheffer, Guy Dovrat and Amir Erez, where we looked at shotgun metagenomes of wild legume nodules, providing an unbiased view of the taxonomic genomic content of legume nodules, and how these relate to plant performance.

Moshe Alon@naturalist1986.bsky.social · 4mo ago

Wild legume performance is shaped by whole nodule microbiome profile, including non-rhizobial endophytes (NREs). Sulfur assimilation by NREs and type VI secretion system in rhizobial symbionts strongly associated with host traits. New Preprint! @finkel-lab.bsky.social www.biorxiv.org/content/10.6...

Thrilled to host @manuelkleiner.bsky.social for a week at @bengurionuniv.bsky.social for a MetaProteomics workshop! No better start than a seminar on "Advanced Metaproteomic Approaches To Investigate Functional Host-Microbiota Interactions." 🧬

The (Yoav) Voichek lab has opened its gates at the Weizmann Institute, and is actively recruiting students and researchers at all levels - come explore gene regulation and computational genomics in a fun, friendly sprouting lab 🤗🥼⚗️🧪 www.weizmann.ac.il/plants/voichek

In this week’s @science.org cover article, we discover tree bark is a hidden habitat for abundant, diverse, and specialized microbial life that actively regulate our climate 🦠. Bark isn't just an inert armor of tree but an active interface for climate and biodiversity www.science.org/eprint/7H9PX...

Bark microbiota modulate climate-active gas fluxes in Australian forests

Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagen...

science.org

A four-year postdoc focusing on "plant growth-promoting bacteriophages" available in my group. Skills in metaviromics and metagenomics essential. Application deadline: 2.2.2026. For more info, see the link.

Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages

Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages

jobs.helsinki.fi

Happy to share our new work about the Bacillus-Trichoderma interactions. A new and interesting story😁

Ákos T Kovács@evolvedbiofilm.bsky.social · 7mo ago

Our new publication in #ISMEJournal (@isme-microbes.bsky.social) describes how Bacillus and Trichoderma works together to fight against the plant pathogen Fusarium, a superb collaboration with Zhihui Xu at Nanjing Agricultural University, including the experiments by @jiyuxie.bsky.social at #IBL 1/7

Our work now on @jxbotany.bsky.social. Make sure you add some Cas13a fluorescent virus detection to your Christmas lights ✨️

Volcani Institute@volcaniinstitute.bsky.social · 7mo ago

Researchers developed a #CRISPR-based method that's user-friendly, extraction-free, 15 min protocol for on-site #virus #detection using a portable fluorescence viewer and a mobile #phone camera directly from RNA of several crop species, including #tomato, #cucumber, and #rapeseed. 👉 bit.ly/4p6Jo8t

Don't miss Natanella Illouz-Eliaz' (Salk Institute) Community Dissemination of Arabidopsis Knowledge Award presentation “The World Around Us: Two Parallel Paths in Life"! youtu.be/Lqatc-yUpmY?... @natanellae.bsky.social

Bittersweet day in the lab as we said farewell to the amazing Noa Assaf, who just successfully defended her MSc thesis on drought-induced shifts in root exudation in desert plants.

Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms www.nature.com/articles/s41...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

nature.com

Hanukkah at the department 🕯️. A fun celebration organized by our awesome students. Happy holidays.

Super excited to have this paper out. We developed a complex set of ground truth samples to test more than 110 statistical approaches for differential #metaproteomics We can now give clear guidance on what tests perform well. Thank you Tjorven Hinzke and @benoitkunath.bsky.social for the leadership

Evaluation of statistical approaches for differential metaproteomics

Metaproteomics characterizes and compares molecular phenotypes of organisms in communities by comprehensively analyzing their protein expression profiles using statistical methods. However, not all st...

biorxiv.org

academic.oup.com/ismej/advanc... Endophytic adaptation in Flavobacterium sp. 98 @xinyapan.bsky.social @vcarryon.bsky.social @gillesvanwezel.bsky.social ✌🏽 lysoPE story could be cool

Hypoxia Induces Phenotypic and Metabolic Shifts in Endophytic Flavobacterium sp. 98

Abstract. Oxygen plays a crucial role in shaping microbial physiology, functions, and behavior. Endophytic bacteria, residing within plant tissues, inhabit

academic.oup.com

Finally out! BBERT - an LLM that can detect bacterial reads using as little as 100 base pairs! Go try it! @amirerez.bsky.social @finkel-lab.bsky.social

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...

biorxiv.org

This is such a cool paper as it experimentally addresses the role of the auxiliary metabolic gene nblA in cyanophages showing a large benefit of NblA to the cyanophage and a negative effect on the host photosynthetic apparatus and host photosynthesis www.nature.com/articles/s41...

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis - Nature

Viral NblA accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency.

nature.com

🌊🦠🧪 Delighted to share this work now out in @isme-microbes.bsky.social: doi.org/10.1093/isme... The currency of microbial life is chemistry, but there’s so much still unknown about how metabolic interactions shape communities. 1/

Vitamin auxotrophies shape microbial community assembly on model marine particles

Abstract. Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism

doi.org

@naturalist1986.bsky.social has done it again, this time with 3rd prize at the ISPS meeting in the beautiful Sde Boker. Poster title: A rhizobial trickster: Legume symbiont simultaneously fixes atmospheric nitrogen and denitrifies. Time to turn these posters into manuscripts.

Omri Finkel עמרי عُمري@finkel-lab.bsky.social · last yr.

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.

This week in the HUJI PES seminar: @hebrewuniversity.bsky.social

🎉 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...

cell.com

This week in the HUJI PES seminar: @hebrewuniversity.bsky.social

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...

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