Title Promoter Affiliations Abstract "Pseudomonas proteins and metabolites mediating interactions in the rhizosphere" "René De Mot" "Microbial and Plant Genetics (CMPG)" "Research in the De Mot group explores antagonistic interactions among Pseudomonas, interference competition of Pseudomonas with other bacteria, and interaction with plants, mediated by proteins (e.g. bacteriocins) or secondary metabolites (e.g. lipopeptides). For newly discovered activities, insight in structure, biosynthesis, and mode of action of the bioactive molecules is pursued using state-of-the-art approaches in molecular microbiology. A second smaller line of research investigated the molecular mechanisms enabling soil bacteria to degrade pesticides.Using genome exploration, we aim to further unravel the huge bacteriocinogenic potential of pseudomonads by characterizing novel toxin-immunity combinations, including hybrid bacteriocins with combined toxin domains. The wider distribution across other soil-dwelling and plant-associated Proteobacteria  (e.g. Burkholderia, Xanthomonas) is mapped for the lectin-like bacteriocins, a novel class of antagonistic molecules discovered by our group. Of particular interest is their novel mode of action that targets the essential machinery for outer membrane assembly. A third type of pseudomonad bacteriocins under investigation are tailocins, high-molecular-weight complexes sharing ancestry and structural resemblance with diverse phage tails, indicative of multiple independent domestication events. Of additional interest are the cargo genes recruited by some of these elements, including some regular and lectin-like bacteriocins.In addition to a diversified bacteriocinogenic potential, pseudomonads also exhibit the capacity to produce a broad spectrum of diverse secondary metabolites with antimicrobial activities. We are exploring the production of such specialized metabolites by beneficial plant-associated Pseudomonas isolated from the rhizosphere of temperate and tropical crop plants (maize, wheat, rice, banana). Unprecedented bacteriocin-like specificity was discovered for the salicylate-based antibiotic promysalin synthesized by a rice rhizosphere isolate. Novel lipopeptide members of established chemical families as well as novel chemical lipopeptide families are being identified, a process that is facilitated by genome exploration and mining." "On a spicy journey: In search of climate resilient vanilla production systems" "Bart Muys" "Forest, Nature and Landscape" "Climate change is predicted to severely affect the agricultural sector, and diversification at both crop genetic and system level is vital in the development of climate resilient agro-systems. The tropical cash crop vanilla is facing a number of threats that are jeopardizing its future supply. Being an important crop for many smallholder farmers around the tropics and a highly appreciated spice used in a range of products, there is an urgent need to enhance the resilience of the vanilla sector against projected climate change effects. The present project therefore aims at identifying climate resilient vanilla genotypes and agroforestry systems, by applying an interdisciplinary approach that combines distribution modelling with an experimental evaluation of species-specific stress resistance, and a participatory resilience assessment of existing vanilla production systems. The results of this project will be translated into practical guidelines for the development and certification of climate resilient vanilla production systems across the Neotropics." "Microfauna - microflora - plant interactions: extending the soil “microbial loop concept” of nitrogen mineralization" "Stefaan De Neve" "Department of Environment" "Soil nematodes are composed of multiple feeding groups, distinct energy channels and with strong interactions with plant growth, but to date most studies focused on bacterivorous nematodes, largely neglecting the contribution of herbivorous and fungivorous nematodes. We conducted mesocosm experiments to investigate whether and how herbivorous and microbivorous microfauna, separately and in combination, enhance N mineralization and plant growth." "Plant and Vegetation Ecology and Global Changes." "Reinhart Ceulemans" "Plant and Ecosystems (PLECO) - Ecology in a time of change" "The overarching theme of the Centre of Excellence is the study of the effects of global changes, in the broadest meaning of the term, on plants and vegetations. This long-term goal is being realized a.o. by studying the responses of plants and vegetations to the, sometimes manipulated, abiotic environment over a continuum of hierarchical scales, ranging from the individual leaf to the continent. Original experimental research and long-term observations are strengthened by coupling: (i) to existing or newly developed simulation models, and (ii) to the intensive use and statistical meta-analysis of new and existing databases. The ecosystem stations of the large-scale European ESFRI infrastructures ICOS (Integrated Carbon Observation System) and AnaEE (Analysis and Experimentation on Ecosystems) are used as platforms for experimental and monitoring studies. The objectives of the research are a better understanding of the functioning, the dynamics and the structure of plants – at the leaf, plant, community and ecosystem levels up to the continental scale – in present and future environments. Specific studies include renewable bio-energy, biosphere-atmosphere interactions, ozone and volatile organic compounds, soil and earth system models, as well as interactions of climatic change and biodiversity." "Upstream regulators of the plant energy sensor SnRK1" "Filip Rolland" "Department of Human Genetics, Molecular Biotechnology of Plants and Micro-organisms" "Plants arguably are the most crucial organisms to support life on Earth because of their conversion of electro-magnetic energy (sunlight) into chemical energy (energy-rich carbohydrates) by photosynthesis and the associated release of oxygen. In addition, they produce innumerable renewable food, feed, fiber and fuel products and resources for mankind. Unlike most other organisms, autotrophic plants have a sessile (rooted) lifestyle. It is thus essential for plants to continuously monitor their environment and rapidly detect small fluctuations in light-, nutrient- and energy availability. Plants therefore have adopted multiple signaling mechanisms to detect and respond to these changes. A key role was identified for the SnRK1 kinase (Sucrose non-fermenting 1-related kinase 1), the plant homolog of the animal AMP-activated kinase, AMPK, and yeast Sucrose non-fermenting 1, SNF1. The conserved heterotrimeric protein kinase complex, like its opisthokont homologs, acts as a ‘fuel gauge’ and is activated when the plants’ energy levels drop. This triggers a reprogramming of metabolism to an energy-saving and a survival mode by activating ATP producing pathways (catabolism) and repressing ATP consuming processes (anabolism). One of the consequences of SnRK1’s central role in the maintenance of cellular energy homeostasis is that it directly or indirectly affects virtually every process in the plant, from general stress responses to key developmental transitions and growth. Understanding how exactly SnRK1 is regulated and how it affects its many downstream targets is thus crucial, both for our fundamental understanding of plant function and for the development of new strategies to increase plant stress tolerance and crop yields. In this work, we investigated Arabidopsis SnRK1 regulation using cellular assays with transient expression in leaf mesophyll protoplasts and mutant and transgenic lines. We more specifically tried to shed light on the molecular mechanisms behind SnRK1 complex formation and the extensive negative regulation of SnRK1 activity by (i) its regulatory subunits, (ii) catalase enzymes, and (iii) a novel plant-specific family of proteins, the SnRK1-Interacting Negative regulators or SKINs.First, we reviewed the present knowledge of SnRK1 structure, function and regulation, focusing on the most recent mechanistic insight. The strong conservation of this eukaryotic kinase complex enables the use of knowledge from yeast and animal systems. We also produced a 3D molecular model, based on homology with the AMPK complex, which gives insight in the plant complex’ regulation and enables the generation of new working hypotheses.Secondly, we explored the mechanisms of SnRK1 activity regulation. Unlike animal AMPK and yeast SNF1, the plant kinase is not regulated by nucleotide charge (AMP/ATP ratio’s). Instead, the kinase complex appears to be inhibited by sugar phosphates. Consistently, we found that the SnRK1α1 subunit is constitutively active. Diverse types of low energy stress trigger nuclear translocation of the SnRK1αsubunit and this translocation appears to be sufficient to induce target gene expression. The regulatory βsubunits act as negative regulators, at least in part by restricting nuclear localization. Transgenic plants with altered a subunit localization are affected in both development and metabolic stress responses, revealing new SnRK1 functions. The inhibitory function of the βsubunits depends on a poorly characterized N-terminal domain that appears to be regulated by post-translational modification in addition to N-terminal myristoylation. Thirdly, we identified the Arabidopsis H2O2-hydrolyzing catalase (CAT) enzyme as novel negative regulator of SnRK1 signaling. Catalases are typically localized in peroxisomes, but we found that they also partly localize in the cytoplasm, where they interact with and inhibit SnRK1αby local dismutation of H2O2. This appears to involve alternative splicing of the CAT peroxisomal targeting sequences in addition to cytosolic retention. Consistently, H2O2appears to act as a SnRK1 potentiator at low concentrations, possibly by direct redox-regulation of conserved Cys residues in the SnRK1αsubunits. Finally, we showed that a class of negative upstream regulators of SnRK1 signaling that was recently identified in rice (the SKIN proteins) is functionally conserved in Arabidopsis. The Arabidopsis SKIN orthologs and closely related AtOXS3-family proteins (identified in a screen for proteins that increase oxidative stress tolerance) co-localize and interact with the SnRK1αsubunit. Similar to the rice proteins, they appear to repress SnRK1 signaling by stimulating translocation of the αsubunit out of the nucleus. In conclusion, our results indicate that plants have tuned an ancient and highly conserved key regulatory pathway according to their preferred negative regulation strategy to better fit their autotrophic and sessile lifestyle and more efficiently cope with rapidly changing environmental conditions. In this work, we have identified several novel negative regulators and suggest directions for future research to further elucidate the molecular mechanisms involved." "Microfauna - microflora - plant interactions: extending the soil “microbial loop concept” of nitrogen mineralization" "Stefaan De Neve" "Department of Environment" "It is assumed that an important part of N mineralization in soils is due to the activity of microfauna. The microbial loop concept at this moment includes only protists, but we will extend the concept to nematodes and will experimentally quantify the contribution of protists and nematodes (microfauna) to N mineralization in realistic conditions." "Phytostabilization of mine soils using native aromatic plant species suitable for promoting regional micro-economies." "Jaco VANGRONSVELD" "Environmental Biology" "The exploitation of mineral resources unavoidably pollutes soils and sediments with trace elements, which accumulate in the environment and affect human health and ecosystem services. Conventional remediation methods are expensive and detrimental for soil structure and fertility. Phytoremediation therefore comes into focus as a ""green"" alternative to stabilize, detoxify or remove pollutants from soil through a low cost and environmentally compatible biological process. As a novel approach, aromatic plant species are proposed for phytostabilization of metal polluted mining sites. In this way, aromatic plants could be used for both phytostabilization and essential oil production without the risk of metal contamination in the end-product. Profits from the commercialization of essential oils and their bio-derivatives could tackle both, the socioeconomic impacts of the cessation of the mining activities and the implementation costs of environmental restoration. The aim of this project is to generate the necessary knowledge to develop a phytostabilization strategy for mine site degraded soils, based on the synergistic use of aromatic plant species and rhizobacteria that promote plant growth and in this way contribute to local micro-economies. Preliminary data showed that Helianthus petiolaris grows very well in the arid environments of mining sites in South America. In addition, this species has a direct biotechnological potential since its essential oils can be used for pest control during storage of grains. In addition, rhizospheric microorganisms are crucial for enhancing the plant biomass production and tolerance to trace metals in such environments by either synthesizing physiologically active compounds, facilitating the uptake of nutrients or protecting them from pathogens. Up to now, 7 trace metal tolerant strains with promising plant growth-promoting capabilities were isolated from H. petiolaris roots. These strains will be studied more in depth using cutting-edge genomics tools and phenotypical characterization. Our results will undoubtedly contribute to a more profound understanding of interactions between aromatic plant and microorganisms to guide targeted manipulations of phytostabilisation to enhance its efficiency and productivity." "Plants as intelligent sensors for precision agriculture" "Francis wyffels" "Department of Electronics and information systems" "Plants are complex non-linear dynamical systems that interact with their environment. I propose that this interaction can be modelled by means of physical reservoir computing. A framework will be designed that captures embodied plant intelligence using a limited set of sensors. This framework will then be employed to perform greenhouse climate control, optimising crop growth conditions for precision agriculture." "The development of a cost-efficient eQTL scanning strategy to unravel the broad transcriptional response of a generalist pest to novel hosts" "Tim De Meyer" "Department of Data analysis and mathematical modelling" "Aiming to unravel genetic mechanisms underlying the polyphagous two-spotted spider mite ’s unique host adaptation ability, an experimental ‘pseudo-panmictic’ population was created to: (i) Uncover eQTLs (mainly trans) linked to a host shift, relying on predominantly RNA-seq (ii) Examine genotype-environment interactions in different hosts (iii) Study genetic selection for/against relevant genotypes identified in (i) and (ii) caused by a new host" "Vaginal lactobacilli in the prevention of HSV-2 infection." "Jos Vanderleyden" "Centre of Microbial and Plant Genetics" "Humans live in symbiosis with a tremendous number of bacteria, collectively referred to as the microbiota, that play a key role in several host physiological processes and health. While the gut microbiota has received plenty of attention the past decades, the vaginal microbiota is only recently gaining interest as a crucial player in female and reproductive health. The vaginal microbiota of most healthy women is generally dominated by Lactobacillus species, recognized as a biomarker species for vaginal health. These species also play an indispensable role in supporting the host’s defence against a wide variety of bacterial, fungal and viral pathogens. However, a detailed molecular understanding of their adaptation to the vaginal niche and their health promoting and anti-pathogen effects is currently lacking. The goal of this PhD project is therefore to deliver insights on the molecular mechanisms used by lactobacilli to contribute to vaginal health, and to defend against herpes simplex virus type 2 (HSV-2), the main causative agent of genital herpes disease, as a case study viral pathogen in the vaginal tract.Residing at the port of entry of various pathogens causing urogenital and sexually transmitted infections in women, lactobacilli could promote vaginal health by enforcing the vaginal barrier function against these pathogens. As the vaginal barrier is composed of the vaginal epithelium, mucus and the immune system, this PhD research investigated interactions of lactobacilli with the host such as adhesion and immunomodulation as key properties to a healthy vaginal environment. Ultimately, this knowledge will drive more targeted selection criteria for probiotic strains focused on the maintenance/restoration of vaginal health.Given that a vaginal microbiota not dominated by lactobacilli has been identified as a risk factor for HSV-2 infections, a second part of this research focused on the elucidation of putative antiviral mechanisms of action of lactobacilli against HSV-2. Hereto, a platform to study interactions between bacteria, cells and viruses was developed, representing a significant technical challenge of this project. Three antiviral mechanisms were investigated: (1) co-aggregation with virions thereby preventing host cell invasion, (2) competition with attachment/entry receptors of HSV-2 thereby blocking virus adhesion, and (3) stimulation of the innate antiviral immune response of vaginal epithelial cells following viral challenge. Next to delivering pioneer work on Lactobacillus-virus interactions at the molecular level, this PhD findings open new perspectives for microbial management-based prevention and treatment strategies against HSV-2 and potentially other vaginal infections."