Biology subjects

Defossez, E.

Publications and source records attributed to Defossez, E..

7 recordsLinked to original sources

bioRxiv2026

Photorhabdus metabolites reshape soil microbial communities and promote plant growth and insect resistance

Photorhabdus bacteria are potent insect-killing microbes associated with entomopathogenic nematodes and offer opportunities for environmentally benign pest control. They can be applied as foliar sprays or soil drenches without their nematode vector, resulting in massive amounts of Photorhabdus cells and their (toxic) metabolites introduced into the soil. However, their effects beyond the target organisms are unknown. To fill this knowledge gap, we investigated the soil legacy effects of Photorhabdus cells and their metabolites on soil microbial communities, plant performance and resistance to herbivores. To this end, we first conditioned soils with i) mechanically killed (MK) or Photorhabdus-infected insect larvae, ii) aqueous extracts of MK or Photorhabdus-infected insect larvae, iii) cell-free Photorhabdus supernatants, iv) autoclaved soil complemented with live soil previously conditioned with MK or Photorhabdus-infected insect larvae. We then grew maize plants in these soils and measured plant biomass, profiled soil microbial communities and plant metabolites, and evaluated plant resistance against two pest insects Diabrotica balteata and Spodoptera frugiperda. We found that conditioned soils increased plant biomass by 10-26% relative to controls and significantly altered soil bacterial and nematode communities, and to a lesser extent, fungal communities. Re-inoculating conditioned soil microbiota into autoclaved soils recreated the plant growth-promoting effects, indicating microbial-mediated mechanisms. Additionally, plants grown in soils conditioned with Photorhabdus-infected insect cadavers were often more resistant to herbivorous insect attack, in a strain-specific manner. On average, D. balteata and S. frugiperda larvae gained 10-20% and 10-59% less weight, respectively, when fed on plants grown in conditioned soils than on plants grown in control soils. The plant metabolic profiles of plant leaves and roots also varied with resistance levels. We conclude that Photorhabdus metabolites modulate soil microbial communities towards a structure that enhances plant growth and triggers systemic responses against herbivores.

microbiology↗

bioRxiv2025

METRIN-KG: A knowledge graph integrating plant metabolites, traits and biotic interactions

BackgroundIn recent years, biodiversity data management has emerged as a critical pillar in global conservation efforts. Today, the ability to efficiently collect, structure, and analyze biodiversity data is central to breakthroughs in conservation, drug development, disease monitoring, ecological forecasting, and agri-tech innovation. However, due to the vastness and heterogeneity of biodiversity data, it is often confined to databases for specific research areas in isolated formats and disconnected from other relevant resources. Crucial components of such data in kingdom Plantae comprise of metabolomes - the vast array of compounds produced by plants; traits - measurable characteristics of plants that influence their growth, survival, and reproduction, and that affect ecosystem processes; and biotic interactions - relationships of plants with other living organisms, affecting the ecosystem functions. ResultsIn this work, we present METRIN-KG (MEtabolomes, TRaits, and INteractions-Knowledge Graph) a powerful data resource simplifying the integration of diverse and heterogeneous data resources such as plant metabolomes, traits, and biotic interactions. ConclusionsThe proposed knowledge graph provides an interface to interactively search for data relating plant metabolomes, traits, and interactions. This, in turn, will facilitate development of research questions in life-sciences. In this context, we provide representative case studies on how to frame queries that can be used to search for relevant data in the knowledge graph.

bioinformatics↗

bioRxiv2025

Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha

Ultraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia polymorpha (Marchantia) serves as a key model organism to study signaling pathways and to infer their evolution throughout the green lineage. Marchantia expresses key components of UV-B signaling, including the photoreceptor UV RESISTANCE LOCUS 8 (MpUVR8), the WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS (MpRUP), the E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC 1 / SUPPRESSOR OF phyA-105 (MpCOP1/MpSPA), and the transcriptional regulator ELONGATED HYPOCOTYL 5 (MpHY5). Here, we show that MpUVR8 exists as a homodimer in its ground-state in vivo, then monomerizes and accumulates in the nucleus upon UV-B activation. Activated MpUVR8 interacts with MpCOP1, triggering growth inhibition, genome-wide gene expression changes, biosynthesis of UV-absorbing metabolites, and photoprotection, which overall contributes to UV-B stress tolerance. MpRUP facilitates redimerization of MpUVR8 and Mprup null mutants show enhanced UV-B photomorphogenesis, demonstrating that MpRUP efficiently represses MpUVR8 signaling. Unlike the case in Arabidopsis and in contrast to the strong Mpcop1 mutant phenotype, Mpspa mutants develop only a very weak constitutive photomorphogenesis phenotype, indicating that COP1 function is much more independent of SPA in Marchantia than in Arabidopsis. Moreover, in contrast to Arabidopsis SPAs, Mpspa is linked with a hyper-responsive UV-B phenotype, suggesting that MpSPA is a negative regulator of MpUVR8 signaling. Similar to Arabidopsis HY5/HYH, MpHY5 functions antagonistically to MpCOP1, but its role in UV-B-mediated gene expression changes is more limited. Our findings demonstrate that although core components of UV-B signaling existed in the last common ancestor of extant land plants, regulatory interactions have diversified in different lineages since their divergence more than 400 million years ago.

plant biology↗

bioRxiv2024

Sanctioning of bacterial cheaters by the host plant in nitrogen-fixing symbiosis between Medicago truncatula and Sinorhizobium meliloti

In plant-microbe interactions, the host plant invests considerable amounts of resources in the microbial partner until the symbiotic machinery is established. If the microbial partner does not reciprocate with a comparable symbiotic benefit, the interaction represents a parasitic relationship. This is thought to elicit a plants response to prevent the selective disadvantage of being parasitized by such microbial cheaters. Indeed, negative feedback against bad mutualists, known as sanctioning, has been observed in interactions such as the arbuscular mycorrhizal and legume-rhizobium symbioses. Here, to study sanctioning by the plant host, we manipulate the exchange of resources between the model legume Medicago truncatula and its bacterial partner Sinorhizobium meliloti by three ways: mutating the bacterial nitrogenase enzyme, replacing nitrogen in the atmosphere with argon gas, and supplying high nitrate to the host. Then, we follow the consequences for the interaction by examining the metabolome, proteome, and phosphoproteome of nodules. We find that such cheating conditions result in sanctioning of the bacterial partner, and observe characteristic shifts including induced defense markers, repressed symbiotic markers, and changes in central metabolism that may be relevant for microbial fitness and that could therefore contribute to sanctioning.

plant biology↗

bioRxiv2024

Odor-based real-time detection and identification of pests and diseases attacking crop plants

Early detection of crop pests and diseases can enable timely, targeted interventions, and help reduce pesticide use. Plants under biotic stress are known to rapidly emit characteristic blends of volatile compounds that could potentially serve as early and attacker-specific cues for precise pest monitoring. Here, we evaluated the feasibility of this approach using two complementary, state-of-the-art sensing technologies: a handheld nanomechanical membrane-based sensor array and chemical ionization time-of-flight mass spectrometry. Under laboratory conditions, with enclosed headspace sampling, both technologies readily distinguished undamaged maize plants from plants infested by caterpillars or infected with a fungal pathogen. Under semi-controlled outdoor open-air conditions, where volatile concentrations were strongly diluted, the membrane-based sensor no longer retained discriminatory power, whereas mass spectrometry predicted herbivory status with more than 90% accuracy using one-second measurements. Finally, in an initial field trial based on simulated herbivory, a compact, field-deployable, real-time mass spectrometer distinguished damaged from undamaged maize plants with highly encouraging performance under real field conditions. Together, these results demonstrate the potential of odor-based detection of pest attacks in maize and identify real-time mass spectrometry as a promising tool for crop monitoring, while pinpointing challenges that remain to be addressed for translation to practical field applications.

plant biology↗

bioRxiv2024

plantMASST - Community-driven chemotaxonomic digitization of plants

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

plant biology↗

bioRxiv2023

Leaf metabolic traits reveal hidden dimensions of plant form and function

The plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4 - a powerful framework for describing plant form and function5-7 - to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization - a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5-7, while being at least equally important to them. Our findings question classical trait6 and plant defense8 theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.

ecology↗