6708 PB Wageningen
Prof. Jos Raaijmakers PhD
Jos Raaijmakers is head of the Microbial Ecology Department at the Netherlands Institute of Ecology (NIOO-KNAW) and Professor at the Institute of Biology at Leiden University. He is board member of the PhD graduate School PE&RC. The overall goal of his research program is to unravel the impact of plant domestication on the diversity, dynamics and beneficial functions of microorganisms associated with plants. In this search for 'missing plant microbes', we work closely together with research institutes and universities in the centres of origin of plant species (Africa, Asia, South America). The functions of the plant microbes studied in detail are protection of plants against infections caused by fungal pathogens, parasitic weeds and insects. Jos teaches BSc and MSc courses at Leiden University, and organizes (inter)national PhD courses and conferences, including the International Plant Microbiome conference.
Jos Raaijmakers is fellow of the Royal Dutch Academy of Arts & Sciences (KNAW), Professor of Microbial Ecology at Leiden University, board member of the graduate school Production Ecology & Resource Conservation and former board member of the Centre for Soil Ecology. He was a visiting Professor at Copenhagen University (Denmark), Oregon State University (USA) and the University of Malaga (Spain), and former Chair of the Dutch Phytobacteriology group. He is currently editor-in-chief of the new Springer Nature journal ISME Communications.
His past and present research program is conducted in an international context with projects in Asia (Vietnam, Indonesia, Korea, China), South America (Ecuador, Colombia, Brasil) and Africa (Ghana, Ethiopia). He is recipient/coordinator of several prestigious and large national and international research grants (e.g. NWO-EcoGenomics (Netherlands Genomics Initiative), NWO-Gravitation (http://microp.org), BE-Basic, TTW-Perspectief Back-To-Roots), EU-Horizon/Marie Curie ITN; NWO-Groot). His expertise in plant-microbiome research led to the invitation by the Bill & Melinda Gates Foundation to develop and coordinate the international program PROMISE (http://promise.nioo.knaw.nl). In the latest international peer review, his department/institute was rated with the highest score (“excellent”) on all criteria (Quality, Relevance, Viability).
He published more than 160 articles in peer reviewed scientific journals, including papers in Nature-based journals (Nature Microbiology, Nature Chemical Biology, ISME Journal), Science, PNAS, and top Microbiology, Plant Science and Ecology journals. Over the past 5 years, he was elected in the Top 1% of the most highly cited researchers worldwide.
He holds several international patents and works closely with industry (start-ups, medium & large enterprises), including international seed companies and agrochemical industries focused on developing new microbiome-based products. He supervises multiple PhD students, postdocs and technicians, and is involved in teaching BSc and MSc courses at Leiden University as well as international PhD courses. During his time as an associate professor at Wageningen University, he was selected by the students in the top 25 best teachers. He also organized several international conferences, including the PGPR-meeting (2007), Rhizosphere 4 (2015), and the International Plant Microbiome conference (2016, 2018, 2022, 2023). Many of his former PhD and postdocs have acquired leading positions at (inter)national universities, government research institutes and R&D departments of different companies.
Teaching (past & present)
Scholarships & prizes
Plants produce volatile organic compounds that are important in communication and defense. While studies have largely focused on volatiles emitted from aboveground plant parts upon exposure to biotic or abiotic stresses, volatile emissions from roots upon aboveground stress are less studied. Here, we investigated if tomato plants under insect herbivore attack exhibited a different root volatilome than non-stressed plants, and whether this was influenced by the plant’s genetic background. To this end, we analyzed one domesticated and one wild tomato species, i.e., Solanum lycopersicum cv Moneymaker and Solanum pimpinellifolium, respectively, exposed to leaf herbivory by the insect Spodoptera exigua. Root volatiles were trapped with two sorbent materials, HiSorb and PDMS, at 24 h after exposure to insect stress. Our results revealed that differences in root volatilome were species-, stress-, and material-dependent. Upon leaf herbivory, the domesticated and wild tomato species showed different root volatile profiles. The wild species presented the largest change in root volatile compounds with an overall reduction in monoterpene emission under stress. Similarly, the domesticated species presented a slight reduction in monoterpene emission and an increased production of fatty-acid-derived volatiles under stress. Volatile profiles differed between the two sorbent materials, and both were required to obtain a more comprehensive characterization of the root volatilome. Collectively, these results provide a strong basis to further unravel the impact of herbivory stress on systemic volatile emissions.
Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.
Transcriptome analysis of Pseudomonas fluorescensSBW25 showed that 702 genes were differentially regulated in a gacS::Tn5 mutant, with 300 and 402 genes up- and downregulated respectively. Similar to the Gac regulon of other Pseudomonas species, genes involved in motility, biofilm formation, siderophore biosynthesis and oxidative stress were differentially regulated in the gacS mutant of SBW25. Our analysis also revealed, for the first time, that transcription of 19 rhizosphere-induced genes and of genes involved in type II secretion, (exo)polysaccharide and pectate lyase biosynthesis, twitching motility and an orphan non-ribosomal peptide synthetase (NRPS) were significantly affected in the gacS mutant. Furthermore, the gacS mutant inhibited growth of oomycete, fungal and bacterial pathogens significantly more than wild type SBW25. Since RP-HPLC analysis did not reveal any potential candidate metabolites, we focused on the Gac-regulated orphan NRPS gene cluster that was predicted to encode an eight-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis indicated that the encoded peptide is not involved in the enhanced antimicrobial activity of the gacS mutant but may function as a siderophore. Collectively, this genome-wide analysis revealed that a mutation in the GacS/A two-component regulatory system causes major transcriptional changes in SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms.