Laboratory of Applied Mycology and Phenomics

Cultivating science, nurturing growth: innovative biocontrol and automated phenomics for sustainable agriculture.

About us

LAMP Research Initiative

Developing healthy, resilient crops in the face of climate change. By integrating phytopathology, biocontrol, and advanced phenomics and spectral technologies, we translate scientific discoveries into practical solutions for society.

Lead
Prof. Kris Audenaert & team
Affiliation
Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University

Phenomics & Spectral Imaging

Multi- and hyperspectral precision agriculture: detecting plant stress and disease early through imaging technology.

Applied Mycology

Research into fungi and plant-pathogen interactions, focusing on pathogens such as Fusarium and Phytophthora in agricultural crops.

Biocontrol & Priming

Sustainable crop protection by activating the plant's own immune system ('priming') and deploying microbial antagonists — 'sweet immunity'.

Valorization & Services

Collaboration with industry through CropFit Services: bioassays and services that bring research into practice.

The Team

Principal Investigator

Kris Audenaert

Principal Investigator

  • Spectral imaging
  • Fluorescence imaging
  • Fungal plant pathogens
ORCID

Postdoctoral Researchers

Noémie De zutter

Post-doctoral researcher

  • Multispectral imaging
  • Biostimulant & biocontrol products
  • Microbial community structure
ORCID

Sabina Bajda-Wybouw

Post-doctoral researcher (CropFit Services)

  • Outreach to companies
  • Valorization
  • Biostimulants

Trang Minh Tran

FWO postdoctoral researcher

  • Microbe-plant interaction
  • Biostimulant - Biocontrol
  • Priming
ORCID

Technical & Operations

Boris Bekaert

Lab technician

Jarno van de Geuchte

Lab technician (2025–present)

PhD Students

Fien Drijvers

PhD researcher

Kenan Meert

PhD researcher (VLAIO Baekeland fellow)

ORCID

Louka Noyen

PhD researcher

Jing Liu

PhD researcher

Marie Blomme

PhD researcher

ORCID

Dylan Cool

PhD researcher

ORCID

Nerea Castineira Rial

PhD researcher

Simon Vermeulen

PhD researcher

Our Projects

Project details to follow.

This project validates the RhizoBac biofertilizer to boost groundnut yields, reduce aflatoxin contamination, and improve food safety. It optimizes formulation stability, evaluates field performance, monitors plant health through multispectral imaging, and analyzes microbial interactions via metabarcoding. By integrating biological solutions, the project promotes sustainable agriculture and strengthens food security for smallholder farmers in Zimbabwe and beyond.

To address the growing need for high-throughput plant imaging, we propose acquiring a compact variable pressure SEM that combines fast, high resolution imaging and user accessibility in a single powerful platform. This SEM will allow researchers to perform imaging independently after minimal training. It will be housed in a facility specialized in plant-specific sample preparation, providing a range of SEM high-throughput workflows based on vibration, rotary, sledge, ultramicrotomy and cryostat microtomy techniques. Acquired automated sample preparation tools will enable consortium members to critical point dry and sputter coat their samples independently, freeing the appointed part-time staff member to focus on managerial tasks, supporting basic experimental design, maintenance and easy trouble shooting, all with full attention to data quality and scientific integrity. The compact SEM will be closely integrated with UGent’s existing high-end SEM imaging platforms (Cryo-SEM, eSEM, EDX-SEM and Volume SEM), facilitating a seamless workflow from initial screening to detailed analysis. This tiered approach optimizes the use of time, funding and equipment. The consortium unites researchers from phytopathology, (eco)physiology, molecular biology, plant evolution, archaeology and microbiology. In today’s increasingly interdisciplinary research landscape, bringing together diverse expertise around plant materials will foster collaboration and drive innovation.

A UGent spinoff is in development to give growers real-time insight into the nutrient status of their crops. Through spectral technology, we measure the interaction between light and leaves to detect nutrient problems earlier. This innovation aims to redefine the decision-making process around fertilization by enabling more precise nutrient management. Based on a proof-of-concept in the Champagne region, this project will serve to increase and test the scalability of Metiris by supporting the development in a number of new crops.

Hyperspectral sensing enables rapid and accurate quantification of phenotypic traits for plant breeding and plant heath monitoring using non-invasive methods. Although hyperspectral sensing is developing rapidly globally, it has not been utilized extensively in Africa. This project aims to redress this imbalance by transferring essential skills to South Africa (SA), leveraging recent advancements in hyperspectral sensors, increased accessibility of AI for data processing, the FABI-URC satellite lab Remote Sensing of Plant Health and new government funded phenotyping infrastructure at the University of Pretoria (UP). The project's central goal is to develop local skills and capacity through partnerships with Ghent University to establish hyperspectral sensing technologies for deployment in plant breeding and remote sensing. Transferable skills are not limited to hyperspectral sensing, but include training in big data management and processing.

PhD research by Dylan Cool, supervised by Tina Kyndt.

This project investigates the evolutionary and pathobiological dynamics of Sarocladium species associated with rice, particularly within the "Sarocladium oryzae species complex" (SOSC). SOSC includes the species S. oryzae, S. sparsum, and S. attenuatum that range from mutualistic endophytes to necrotrophic pathogens causing the devastating rice sheath rot disease. Our study aims to unravel the genomic, metabolomic, and viromic factors driving this lifestyle continuum. Using 21 SOSC strains from diverse origins, we will conduct comparative genomics to identify elements underpinning pathogenicity, morphological plasticity, and transitions between endophytic and necrotrophic phases. Untargeted metabolomics will profile specialized metabolites that influence pathogenicity. We will explore environmental triggers affecting their production and assess potential antimicrobial bioactivities. Concurrently, viromics will examine the presence and impact of mycoviruses, hypothesized to affect SOSC phenotypic diversity and pathobiology. Promising hypovirulent viruses may also serve as biocontrol agents to control rice sheath rot. This integrative approach seeks to clarify the molecular basis of pathogenicity, lifestyle shifts, and microbial interactions in SOSC, providing novel insights into fungal evolution and sustainable crop protection strategies.

Chemical communication via specialized metabolites determines interactions between fungi and plants. Fungi possess a metabolite treasure trove, with potent applications for agriculture and human health, yet the vast majority awaits discovery, typically because their biosynthesis is silent in lab conditions. Within this GOA project, we will establish a plant-based platform to discover, characterize and produce yet unknown fungal metabolites.

Recent technological advances have improved our understanding of complex living systems, such as humans, animals, and crops, by studying their genetic information and how it is expressed. By examining genes and molecules in individual cells, we have discovered cellular variations and even identified previously unknown cell types. However, current technology has limitations. It lacks sensitivity, potentially missing important information, and it is expensive and time-consuming to use. Moreover, exciting applications like mapping genetic changes in cancer or studying specific DNA modifications are not supported by existing tools. To address these challenges, we propose acquiring a new equipment that can produce customized materials for genetic analysis. This equipment, called a photolithographic printer, can create thousands of different DNA molecules at high resolution. These molecules can be used to fabricate solid surfaces with specific DNA patterns, enabling detailed genetic analysis of tissues. Alternatively, the DNA molecules can be released from the solid surface for solution-based analysis. This technology allows us to study large tissue areas and analyze genetic information at single-cell level. It also enables research on organisms lacking appropriate tools. Additionally, it facilitates the study of different RNA molecules, including those that are typically overlooked but may have important functions, such as non-polyadenylated long non-coding RNAs.

Macroalgae or seaweeds are internationally recognized as an essential link in the development of a circular bioeconomy and are as such specifically mentioned in EU policy such as the Green Deal, Farm to Fork, and the EU4Algae initiative. The GAME project will address knowledge gaps that impede current valorisation of European Porphyra, a genus of red algae that is farmed at large scale in Asia for human food (nori), but Porphyra has also potential for use in various biotechnological applications, including the production of bioactive compounds, food additives, and renewable energy. GAME will leverage from Porphyra‘s inter- and intra-specific genetic and biochemical variability to elucidate the mechanisms behind bioactive metabolite production (phycobiliproteins, sulfated polysaccharides and mycosporine-like amino acids (MAA), flavonoids and other important bioactive compounds), tailored to applications as nutraceuticals, biostimulants UV protectans for crops, and biocontrol products. The innovation lies in using linking biological processes (growth, reproduction, secondary metabolite production) with state-of-the-art genetics and demonstrating the action of bioactive metabolites as nutraceuticals and agricultural-biologicals. The research of GAME will lead to targeted life cycle control and cultivation protocols. Tailor-made extraction techniques including pre- and post-harvest treatments for the preparation of Porphyra extracts which will be developed using in-house protocols (HPLC, UV/vis, FTIR multivariate analysis) to elucidate and enhance the bioactivity of extracts for targeted applications. Differentiation in extract composition is made by applying multiple postharvest treatments. The extracts will be validated for their application potential: 1. Nutraceuticals: applying Caco2 cell lines for digestive uptake assays using (i) raw extracts, (ii) digested extracts using method in vivo digestion (oral, gastric and intestinal phases) and (iii) other isolated compounds of interest. 2. High value agricultural-biologicals: (i) Phycobiliproteins (antifungal), (ii) sulfated polysaccharides (resistance induction) and (iii) MAAs (protection against heat/UV-stress due to combined UV blocking and expected biostimulant activity). 3. Biostimulants and bio-based fertilizers: The residue left after processing of the seaweed will be a valuable biostimulant, soil conditioner (cell wall residue as a source of soil organic matter) and fertilizer.

PhD research by Judith Mavungu Muzulukwau, supervised by Noémie De Zutter, Geert Haesaert.

Plant pests and pathogens damage agricultural production and endanger food security. Their control relies heavily on the use of synthetic insecticides, leading to a negative environmental impact. Developing new methods for pest and pathogen control is therefore essential to safeguard human health and meet the challenge of increasing crop yields, while reducing the use of chemical pesticides. The overarching objective of the NextGenBioPest project is to meet this need by delivering novel and improved products, methods, and practices for the rational control of the most difficult-to-manage arthropod pests and pathogens, with substantially reduced pesticide use. The project will provide a new toolkit for plant protection in key vegetable and fruit crops including diagnostics for pest and pathogen identification and incrimination, novel Biological Control Agents and methods to augment their performance in the field, RNA-based pesticides, Low Risk/Green chemicals, plant resistance inducers and innovative agronomic and ecological practices. These innovations will be integrated with existing approaches, to achieve effective, environment friendly and sustainable crop protection. They will be validated in large field studies, with both their efficiency and socioeconomic impact assessed. Demonstration fields, extensive training and modern targeted communication channels, will enable the appropriate dissemination and uptake of the outcomes to the stakeholders and end users. Data protection and commercialization strategies will ensure their exploitation. These goals will be achieved by integrating leading institutional and industrial partners with drivers of pest control programs. The multidisciplinary and multi-actor team will exploit their diverse expertise, access to extensive preliminary data and resources, and strong networks, to meet the project objectives and ensure the knowledge and tools generated deliver economic, ecological and societal impact.

Plant pathogens do not operate alone but can form synergistic interactions in disease complexes. This has important implications for diagnosis, epidemiology and disease management. Here we use Fusarium/Sarocladium interactions in the rice sheath rot disease complex as a model to gain more insight into their within-host interplay and implications on virulence and in planta mycotoxin production. Our prior research has shown that in planta these fungi mainly produce the mycotoxins zearalenone and enniatin which pose risks for animal and human health. Moreover, co-infection has a strong influence on mycotoxin production. We will also use this model to study virulence evolution by investigating the effects of co-infection on horizontal and vertical pathogen transmission. Representative genomes from Saroclarium and Fusarium available in our culture collection will be sequenced and mined for mycotoxin biosynthetic gene clusters. Co-inoculation experiments will be done to investigate the effects on panicle formation and seed set. Plant colonization and toxin expression and production in planta will be assessed. Mycotoxin mutants will be generated to study their role in the interaction and pathogenicity. We will also test the effect of co-inoculations on other rice diseases, such as rice blast caused by Pyricularia oryzae.

Biotalys' AGROBODY VHHs will be fused with chitinases and glucanases that degrade the cell wall of fungi (direct antifungal activity) or with chitin deacetylases that activate the immune system of plants. It will be explored whether this concept (AgroFUNzymes) can lead to innovative biological crop protection agents against the following pathogens: Fusarium graminearum, Botrytis cinerea and Podosphaera xanthii on 3 different crops. The end result is a new platform and lead AgroFUNzymes evaluated in a greenhouse trial.

The AlgaeProBANOS project addresses a challenge in the Baltic and North Sea (BANOS) area: how to harmonise economic development with social and environmental goals in line with the Mission Ocean... There is a rising demand for green healthy natural consumer and biobased products, and algae can become the biomass resource of the future, without using fresh water, arable land, or added fertilisers and or pesticides. Both the Baltic and North sea engulf the necessary conditions to scale up production and produce both commodity and sophisticated algae-based products. AlgaeProBanos (APB) brings together 26 experts and industry partners from the BANOS area and beyond, to accelerate product development and market access of sustainable algae solutions. Concretely, APB will support six business pilots, SMEs and startups, to bring eight algae products to the market (TRL7-9) namely in food, feed, nutraceuticals, textiles, cosmetics and plant biostimulants applications. Value chains are based on microalgae and seaweeds, sourced in the Baltic or North Sea or from recycled resources. Innovation takes place in iterative loops with assessments to secure maximum robustness, efficiency, and sustainablesustainability. Furthermore value chains are built with end-users' needs put in the centre, through engaging users in co-creation activities, to ensure maximum uptake. Digital tools are developed to support all actors from biomass producers to consumers. In the end, GoToMarket strategies are tailored to the pilots, providing a trajectory to reach the market. In a meta level, the Algae Accelerator develops new and aggregates existing knowledge, and develops a portfolio of solutions, guidelines and a collaboration and training platform, to benefit the entire algae industry and nourish it into a thriving industry by 2050. The legacy of APB will be deposited to the Ocean Mission BANOS and the EU4Algae.

A platform where innovative plant bioassays are brought together to evaluate the next generation of sustainable crop protection products, fertilizers and biostimulants from academia and industry using latest state of the art infrastructure, innovative protocols and in-depth expertise.

PhD research by Chloë Schoorens, supervised by Noémie De Zutter.

PhD research by Jelle Van Vooren, supervised by Willem Desmedt, Sven Mangelinckx.

MyCoView aims to develop innovative, non-invasive mouldy core (MC) detection methodologies improving food safety and security in apple by relating MC lesion with mycotoxin contamination. For the first time, mass spectrometry and hyperspectral imaging with a machine learning (ML) approach will be combined to achieve a novel detection methodology. While the fields of hyperspectral imaging and plant-pathogen interaction are maturing, the integration of these interdisciplinary fields with mycotoxin research and ML is still challenging. Despite these challenges, such ambitious fusion greatly contributes to food safety and food security. MyCoView will increase food safety and food security by preventing the storage of latently infected MC apple fruit and by tackling mycotoxin contamination in apple products, thereby contributing to improved human health. This aim will be address by a multistrategy approach following these research objectives: 1) To investigate the metabolic plant-pathogen interactions and production of secondary metabolites by Alternaria spp. in apple using high resolution mass spectrometry (HRMS). 2) To quantify the production of the main Alternaria mycotoxins in apple and their accumulation over time when causing MC. 3) To develop accurate ML models to prevent the storage of latently infected MC apples and their further processing combining hyperspectral imaging and mass spectrometry.

PhD research by Louka Noyen, supervised by Olivier De Clerck, Jessica Knoop.

PhD research by Ellen Everaert.

PhD research by Robin Daenen, supervised by Pascal Boeckx, Nico Boon, Jo Dewulf, Mingsheng Jia.

Supervised by Wouter Maes.

There is an increased pressure on crop production due to population increase projections. This coupled with the need to reduce agrochemicals use in agricultural practices, require sustainable intervention in crop production. To reduce the environmental impact of chemical fertilizers, while securing crop yield and consumers safety, several alternative and sustainable products including biostimulants are currently available in the market. Nevertheless, this is still insufficient, new, sustainable, and eco-friendly products need to be discovered. The project aims to pave the path for a biostimulant derived from Belgian endive root by-product. Water extracts of these roots were shown to stimulate root and shoot growth (SBO-FWO project BIO2BIO). Further studies will focus on the enrichment and chemical characterization of the bioactive ingredients. The bioactivity enriched fractions will be used to study the local and systemic physiological response of Arabidopsis seedlings to treatments. A comparative transcriptome study will be conducted to identify a core selection of genes that are regulated upon biostimulant treatment. The potential of endive roots extract as a biostimulant will be assessed by performing open field and pot experiments.

PhD research by Jing Liu, supervised by Sarah De Saeger, Trang Tran Minh.

PRIMO focuses on the biocontrol of potato (Solanum tuberosum) against the oomycete Phytophthora infestans using volatile organic compounds (VOCs). The green leaf volatile Z3-hexenyl acetate (Z3-HAC) was shown to be a potent priming agent against P. infestans in potato.

PhD research by Fien Drijvers, supervised by Leen De Gelder.

PhD research by Halimat Yewande Ogunsanya, supervised by Danny Geelen, Sven Mangelinckx.

News & Publications

Latest news

Lies Van Vlierberghe presenting at Plant Pathology 2026

This week, our team member Lies is attending the Plant Pathology conference in England! She is presenting her poster, "Unlocking the diverse Sarocladium lifestyles through CRISPR-Cas9 and live imaging." Best of luck, Lies!

Visiting scientists from South Africa join LAMP

LAMP welcomes two visiting scientists from South Africa: Lihan Esterhuizen, staying for 6 months, and Lehlogonolo "Nolo" Shalang, staying for 3 months. Their visit is supported by a VLIR-UOS South Initiative grant (administrative promotor: Wouter Maes) on fungal diseases in Eucalyptus. Welcome to the team!

Publications archive

2026

Belgian endive-derived biostimulant activity in Arabidopsis, lettuce, and sweet pepper at different developmental stages, environmental conditions, and application methods

FRONTIERS IN PLANT SCIENCE

DOI
2026

Bio-inspired designer cellulosomes show strongest synergy on industrial substrates under natural-like conditions

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

DOI
2026

Biological control of Botrytis cinerea in tomato and Fusarium graminearum in wheat using the novel species Burkholderia mycopellens and Burkholderia crassaminum

FRONTIERS IN MICROBIOLOGY

DOI
2026

CRISPR Cas9 editing and GFP labeling in Sarocladium for functional studies

77th International Symposium on Crop Protection, Abstracts

View
2026

Can we breed microbiomes to sustain plant productivity?

MICROBIAL BIOTECHNOLOGY

DOI
2026

Evaluation of the tolerance of duckweed (Lemnaceae) to abiotic stress factors associated with nutrient recycling systems via multispectral imaging

PLANT STRESS

DOI
2026

Integrated metabolomic and transcriptomic analysis to elucidate the antifungal and antimycotoxin mechanisms of natural stilbenoids against Fusarium graminearum

MICROBIOLOGICAL RESEARCH

DOI

Showing 7 of 298 publications in the central LAMP list.

Contact & Location

Questions about collaborations, master's theses, or CropFit Services? Get in touch.

Faculty of Bioscience Engineering
Department of Plants and Crops — LAMP
Valentin Vaerwyckweg 1, Gebouw C
B-9000 Ghent, Belgium