Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is...

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Mycorrhizal symbiosis is one of the most widespread and ecologically significant mutually beneficial interactions in terrestrial ecosystems, with decisive effects on plant nutrition, soil microbial dynamics, and ecosystem stability. Classically defined through carbon-nutrient exchange, this symbiotic relationship is now considered a more complex and multifaceted structure in current studies. In particular, secondary metabolites synthesized by plants and mycorrhizal fungi are increasingly being shown to be key chemical signals regulating the tripartite interactions between plants, fungi, and the rhizosphere microbiome. Secondary metabolites such as phenolic compounds, flavonoids, terpenoids, and alkaloids play a critical role in processes such as selectively promoting beneficial microorganisms, suppressing pathogenic or competitive species, and supporting functional microbial groups involved in nutrient cycling. Mycorrhizal colonization alters the secondary metabolite profiles of plants, is associated with shifts in the rhizosphere microbial community structure, and indirectly affects fundamental ecosystem functions such as nitrogen fixation, phosphorus mobilization, and organic matter decomposition. This review aims to provide a mechanistic and integrative evaluation of secondary metabolite-mediated interactions within the plant-mycorrhiza-rhizosphere microbiome tripartite system. This tripartite system represents a multilayered regulatory network operating across molecular, microbial, and ecosystem levels. The findings shed light on new approaches in terms of sustainable agricultural practices and ecosystem management.

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Abstract. Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissio

Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiome⍰assisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genome⍰wide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiome⍰wide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial sub⍰communities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive population⍰level framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiome⍰informed breeding strategies.

Efficient nutrient use in agriculture depends on the dynamic interplay between plant roots, soil, and microbial communities. The root–rhizosphere interface is central to nutrient uptake and serves as ...

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.

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. ....

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...

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).

Jean-Michel Ané

Plants establish beneficial associations with microbiota, enhancing their resilience to environmental challenges. FERONIA (FER) kinase shapes the microbiome; despite extensive knowledge of FER interac...

npj Biofilms and Microbiomes - Biofertilizer induces soil disease suppression by activating pathogen suppressive protist taxa

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.

Ectomycorrhizal fungi form symbiotic relationships with a wide range of terrestrial plants, acquiring carbohydrates for themselves and promoting nutrient uptake in their host plants. However, some ectomycorrhizal fungi cannot effectively obtain the thiamine necessary for growth from their host or synthesize it themselves. Ectomycorrhizal fungi can recruit hypha-associated microorganisms, which play a vital role in promoting nutrient absorption and ectomycorrhizal root formation, ultimately colonizing within fruiting bodies to form a unique bacterial microbiota. In this study, non-targeted metabolomics and whole-genome sequencing were employed to investigate the colonization characteristics of the hyphae-associated bacterium Bacillus altitudinis B4 on the mycelial surface of ectomycorrhizal fungus Suillus clintonianus, as well as the synergistic promotion of thiamine synthesis and absorption by B. altitudinis B4 and the fungal mycelium, respectively. The results suggested that S. clintonianus first secreted ureidosuccinic acid and pregnenolone, recruiting the hyphae-associated bacterium B. altitudinis B4 to the mycelial surface. Subsequently, the ureidosuccinic acid secreted by S. clintonianus further stimulated B. altitudinis B4 to enhance thiamine production by increasing its biomass and upregulating the expression of related functional genes. Finally, S. clintonianus absorbed the thiamine secreted by the B. altitudinis B4, promoting fungal growth and increasing the colonization rate in association with Pinus massoniana. This study elucidates the thiamine acquisition mechanisms of ectomycorrhizal fungi, highlighting the critical role of bacterial partners in fungal nutrition and host-fungal interactions.

Arbuscular mycorrhizal symbiosis plays a pivotal role in nutrient acquisition and stress tolerance, making its regulation crucial for sustainable crop productivity. This review synthesizes current advances in understanding the molecular and physiological factors governing AM symbiosis, with emphasis on transcriptional, hormonal, and nutrient-mediated regulation. From pre-symbiotic signaling to root colonization and arbuscule development, AM formation is orchestrated by a complex network of molecular interactions. Transcription factors, including those with GRAS domains (e.g., NSP1, NSP2, RAM1, and DELLA), and other regulators such as MYB, SPX, WRKY, and CYCLOPS/IPD3, serve as central modulators of symbiosis-related gene expression. Phytohormones, including strigolactones, salicylic acid, and abscisic acid, generally promote symbiosis, whereas gibberellins and ethylene act as inhibitors; cytokinin exerts context-dependent effects. Nutrient status also modulates AM formation—low phosphorus and nitrogen promote, while high nutrient availability suppresses colonization. Collectively, these insights reveal the integrative regulatory networks driving AM symbiosis and offer new avenues to optimize symbiotic efficiency for enhanced plant growth and agricultural sustainability.

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…

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...

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...

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.

An improved mechanistic understanding of microbial interactions can guide targeted interventions or inform the rational design of microbial communities to optimize them for applications such as pathog...

Improving crop nitrogen (N) uptake is essential for a more sustainable agriculture. Deploying resource-efficient root phenotypes, beneficial soil micr…

This study shows that maize hybrids form larger rhizosheaths than inbreds, which are linked with beneficial microbes such as Massilia. These interactions support root growth, nutrient uptake, and redu...

A one-day practical and theoretical workshop covering Biofoundries high throughput applications, DoE (design of experiments) and Engineering Biology pipelines.

Understanding how root microbes respond to drought is crucial for improving crop resilience. This study finds that Streptomyces responses are strain-specific and functionally diverse, with traits and ...

In nature, plants cope with various pathogens that compete for cellular resources during infection. It has long been suggested that plant defense a...

Autophagy acts as a pro-survival mechanism in plant roots during beneficial fungal colonization by restricting fungal proliferation and immunometabolic cel

The University of Amsterdam is hiring a postdoc in Plant Microbiome Omics & Causal Inference to develop computational tools for multi-omics integration. Fully funded, salaries €3,546–€5,538, with strong benefits and relocation support. Apply by December 15, 2025.

The root microbiota plays a vital role in plant growth and health. Recently, Zhang and colleagues demonstrated that the rhizobacterial strain Exiguobacterium R2567 produces cyclo(Leu-Pro), a cyclic dipeptide that regulates tillering by activating the rice strigolactone (SL) signaling pathway through binding to the SL receptor OsD14. This discovery provides an innovative strategy for optimizing crop architecture by harnessing the root microbiota for sustainable agriculture. It holds promise for achieving precision and environmentally friendly production through the application of synthetic microbial communities (SynComs) or functional metabolites. However, practical implementation faces challenges, including the field stability of cyclo(Leu-Pro), competition from native microbial communities, and potential long-term ecological risks, which require further study to realize its full potential.

Phyllosphere microbiota play crucial roles in supporting host performance. However, the dynamic changes of phyllosphere-associated microbiome during pathogen infections and their impacts on plant health remain unknown. Here, we found phyllosphere microbes can mitigate wheat Fusarium head blight (FHB), a severe disease caused by Fusarium graminearum (F. graminearum) pathogen that promotes infection by inducing host alkalinization. Using wheat head microbial community profiling and metatranscriptomics, we found Pseudomonas spp. significantly enriched on infected wheat heads. Through isolating 595 bacterial strains from infected wheat heads—including 196 Pseudomonas isolates—we identified certain enriched Pseudomonas isolates capable of producing organic acids that counteract pathogen-induced pH upshift. In vitro experiments confirm the selective promotion of specific host-acidifying Pseudomonas in wheat heads. Field trials confirmed that host-acidifying Pseudomonas strains effectively controlled FHB. These findings highlight the pivotal role of plant-beneficial microbes in host pH regulation and offer innovative avenues for sustainable plant disease control.

A new fossil fungus discovered in Scotland shows evidence of plants and fungi sharing nutrients to survive on land.