Eoghan King

High bacterial diversity drives the suppression of a soilborne plant disease

Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits Abstract. Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissio

Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits

Holobiont works -> Phyllosphere and rhizosphere microbiomes empower Nicotiana tobacum complex traits dissection and prediction | bioRxiv

Ethylene signal-driven plant-multitrophic synergy boosts crop performance

Pesticide residues alter taxonomic and functional biodiversity in soils Pesticides are widely distributed in soils1,2,3, yet their effects on soil biodiversity remain poorly understood4,5,6,7. Here we examined the effects of 63 pesticides on soil archaea, bacteria, fungi, protists, nematodes, arthropods and key functional gene groups across 373 sites spanning woodlands, grasslands and croplands in 26 European countries. Pesticide residues were detected in 70% of sites and emerged as the second strongest driver of soil biodiversity patterns after soil properties. Our analysis further revealed organism- and function-specific patterns, emphasizing complex and widespread non-target effects on soil biodiversity. Pesticides altered microbial functions, including phosphorus and nitrogen cycling, and suppressed beneficial taxa, including arbuscular mycorrhizal fungi and bacterivore nematodes. Our findings highlight the need to integrate functional and taxonomic characteristics into future risk assessment methodology to safeguard soil biodiversity, a cornerstone of ecosystem functioning.

Amazing and super helpful paper  -> Pesticide residues alter taxonomic and functional biodiversity in soils

Jack Kim and Jill Banfield in a rice field in California.

Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce #methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI

I know science can’t fix the world — here’s why I do it anyway The world faces energy shortages as fossil fuels are phased out. Research can’t go on as normal. working at a research institute that Why am I doing science? As a scientist focuses on food security, I’m acutely aware of the accelerating ecological and climatic breakdown that is occurring around us. What part should scientists play in such a fragile world? For many years, like most of my peers, I thought that science was part of the solution. More knowledge and innovation would allow societies to adapt to and mitigate environmental damage. That belief began to crack in 2018, when I discovered the work of Jean-Marc Jancovici, an energy and climate specialist. His message is clear: our  world is built on abundant energy, around 80% of which has come from fossil fuels over the past 50 years. Because supplies are limited, energy consumption will peak in decades — sooner if humans attempt to limit climate change. To keep global warming below 1.5 °C by 2100, the use of fossil fuels must fall by 5–8% each year — a pace that is too fast for low-carbon energy to keep up with. Restricted energy supplies will shrink economies and force people to make hard choices — whether to travel less, live in a smaller home or do more labour manually. ....

I know science can’t fix the world — here’s why I do it anyway

Check out our new preprint using 30 SynComs covering a phylogenetic diversity gradient, we uncover many interesting strain and community features involved in seed to seedling bacterial transmission 🧫🌱
@emersys-irhs.bsky.social in the SUCSEED project @inrae-dpt-spe.bsky.social

Leaf microbiome assembly is linked to plant phylogeny - Plant and Soil Background and aims The plant microbiome is considered as an extended part of the plant genome, and it provides key functions in regulating plant fitness, and stress tolerance. Plants and associated m...

Leaf microbiome assembly is linked to plant phylogeny

🌱 3rd International Institute Jean-Pierre Bourgin for Plant Sciences (IJPB) Symposium 🌱

📍 Versailles, France | 🗓 23–25 September 2026

🔬 Theme: Chemical interactions between plants and their environment – from the molecule to the field

🌐 The event website is now live 👉 lnkd.in/eRHS2ey4

Dormancy and reactivation of the seed and its microbiome: a holobiont perspective | mSystems Desiccation tolerance—the ability of organisms to withstand severe water loss and subsequently revive—is a key trait acquired by seeds of most plant species during the final stages of development, when their moisture content declines to ~10% of fresh weight (1). Desiccation-tolerant seeds (hereafter seeds for simplicity) survive the removal of cellular water by accumulating protective molecules and forming intracellular glasses, which impose a metabolically inactive state called quiescence (quietus, at rest) (2) (boldface terms are defined in Box 1). Once environmental conditions become favorable, typically after rehydration and in the presence of suitable temperature, light, and oxygen, quiescent seeds resume metabolism and can germinate. However, even under these conducive hydrated conditions, seed germination may still be restricted by endogenous inhibitors (2). This seed trait, which requires additional regulatory mechanisms, is called physiological dormancy (dormire, to sleep) (Box 1).

Dormancy and reactivation of the seed and its microbiome: a holobiont perspective

Ané Lab Jean-Michel Ané

2 postdoc openings in my lab:
anelab.wisc.edu/join-us.html
One for a maize geneticist and one for a bacterial geneticist

Picture featuring @manishbiotechie.bsky.social, @balptekin.bsky.social and @sairamnagalla.bsky.social. The first two left my lab over the last few months to start their own labs!

Axel de Zelicourt from @ips2parissaclay.bsky.social presents his work on plant beneficial bacteria in low N conditions @ijpb-versaillescly.bsky.social
🌱🦠🧫

Hi Frederik, best wishes for 2026 🙂 When I was in Madrid we worked with novogene and if I remember well, they performed the RNAseq in Europe. Very good sequencing quality, a bit costly in my opinion however

FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome | Molecular Plant-Microbe Interactions® Plants establish beneficial associations with microbiota, enhancing their resilience to environmental challenges. FERONIA (FER) kinase shapes the microbiome; despite extensive knowledge of FER interac...

FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome | Molecular Plant-Microbe Interactions

Soil iron drives beneficial maize microbiome feedbacks inrotations with wheat https://www.biorxiv.org/content/10.64898/2026.01.08.698436v1

Biofertilizer induces soil disease suppression by activating pathogen suppressive protist taxa

NPJ Biofilms and Microbiome from Rong Li (Qirong Shen) at Nanjing Agricultural University
with George Kowalchuk and Stefan Geisen

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

PhD & Postdoc positions – Junta de Andalucía
Looking for highly motivated candidates to apply with my Microbiomes & Microbial Interactions group at the University of Málaga (IHSM).
Interested in joining our team?

📩 vcarrion@uma.es
🔗 www.carrionlab.com
🔗 www.ihsm.uma-csic.es/investigador...

A small scientific Christmas gift 🎁🌱 We review how root-associated microbiomes and epigenetic regulation contribute to plant heat stress resilience, highlighting the importance of realistic root temperature gradients using our TGRooZ device. @jxbotany.bsky.social
academic.oup.com/jxb/article/...

The genotypically conserved core microbiota modulates nutrient turnover in soybean rhizosphere Microbiota-mediated nutrient turnover in the rhizosphere determines nutrient bioavailability, thereby enhancing nutrient uptake, utilization, and ultimately crop productivity. Consequently, elucidating the functional core microbiota in rhizosphere nutrient turnover is of critical importance. In this study, we leveraged soybean germplasm core collections to investigate the tripartite relationship among host genotype, core microbiota and nutrient availability, with a focus on delineating the pivotal role of core microbiota in nutrient turnover. Our results suggest that phylogenetic variation significantly shape root-associated microbial communities and rhizosphere nutrient availability, explaining 11.75 % and 2.07 % of total variances, respectively. Core microbiota analysis identified 29 phylogenetic conserved core amplicon sequence variants (ASVs), the majority of which exhibited significant correlated with nutrient availability. Notably, three key core ASVs—ASV13, ASV14 and ASV12, positively correlated with alkali-hydrolyzed nitrogen, available phosphorus, and soil organic matter, respectively. These taxa were subsequently incorporated into a Bradyrhizobium-based synthetic bacterial community (SynCom) to validate their functional roles. Further experiments confirmed that core microbiota-driven nutrient turnover directly facilitates host plant, as evidenced by SynCom inoculation assays. Collectively, this study establishes that phylogenetically conserved core microbiota critically regulate nutrient turnover and acquisition efficiency in the rhizosphere. These insights advance our understanding the ecological function of core microbiota in the rhizosphere and provide a framework for harnessing the beneficial traits in sustainable agriculture.

Interesting SynCom for soybean -> The genotypically conserved core microbiota modulates nutrient turnover in soybean rhizosphere - ScienceDirect

Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis | The ISME Journal | Oxford Academic

Integrative regulatory networks modulating arbuscular mycorrhizal symbiosis - ScienceDirect

#TansleyReview: Mycelial dynamics in arbuscular mycorrhizal #fungi

Vasilis Kokkoris 👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue #PlantScience

Molecular mechanisms modulating beneficial plant root–microbe interactions: What’s common? In the current context of climate change, there is a need to develop more sustainable agrifood strategies. As an alternative to the intensive use of c…

Molecular mechanisms modulating beneficial plant root–microbe interactions: What’s common?

The carbon and water footprints of data centers and what this could mean for artificial intelligence Company-wide metrics from the environmental disclosure of data center operators suggest that AI systems may have a carbon footprint equivalent to that of New York City in 2025, while their water footp...

There are many claims that AI is a “planet killing” source of greenhouse gases.

But is it?

This paper might be the most detailed estimate of the emissions associated with AI.

It suggests that AI could emit as much as 30-80 *million* tons of CO2 per year.

www.cell.com/patterns/ful...

Xanthomonas coordinates type III–type II effector synergy by activating fruit-ripening pathway Plant cell walls harbor vast carbohydrate reserves, yet how pathogens unlock them remains unclear. We show that the citrus canker pathogen Xanthomonas citri subsp. citri (Xcc) mobilizes cell wall suga...

Fantastic story how bacteria exploit a host pathway to dissolve plant tissue and obtain nutrients 🤯
Uncovering these mechanisms about plant-pathogen interactions is so cool!

www.science.org/doi/10.1126/...

Dormancy and reactivation of the seed and its microbiome: a holobiont perspective Desiccation-tolerant seeds provide an intriguing system for studying microbial dormancy, which includes reversible inactivation and reactivation in response to stress. Focusing on bacterial responses to desiccation and rehydration, we offer a holistic interpretation of dormancy and quiescence within the seed holobiont, highlighting both parallels and distinctions between microbes and their plant host. Based on pilot evidence, we propose that microbial dormancy supports persistence throughout the life cycle of desiccation-tolerant seeds. Transcriptomic analyses of seed-transmitted bacteria have identified genes implicated in inactivation and the viable-but-nonculturable state. Our analysis of Xanthomonas citri pv. fuscans illustrates this during seed maturation. However, the signals triggering microbial reactivation and the potential reciprocal interactions between seed dormancy and quiescence, and microbial dormancy, remain unknown. Elucidating this interplay within the seed holobiont could enhance plant growth and health either by promoting seed germination through microbial inoculation or by enabling early detection of seed-transmitted phytopathogens.

Very nice experimental system and great story -> Dormancy and reactivation of the seed and its microbiome: a holobiont perspective

🚨We’re hiring! Please help spread the word!
Our lab at @TheSainsburyLab is recruiting a pre-doctoral intern to work on plant immunity research. Ideal for those who are planning to pursue a PhD and seeking research experience. tatsuyanobori.com

📣Interested in doing your PhD in Plant Sciences 🌱, Microbial Sciences 🦠 or Computational Biology 👩‍💻? @ceplas.bsky.social offers 10 fully funded PhD 🎓fellowships. Pls repost and forward to interested candidates holding BSc degree.

Now out in @asm.org #mSystems! journals.asm.org/doi/10.1128/...
Congratulations to Robert and thanks to all collaborators. See thread below for a summary of the work, exploring the use of cross-species coexpression analyses to predict primary and secondary metabolic interactions in microbiomes.