Universität zu Köln

Van Dijck, Lara ORCID: 0009-0002-6141-981X (2025). Cooperation between root fungal endophytes and host-derived coumarins mediates iron nutrition in Arabidopsis. PhD thesis, Universität zu Köln.

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Abstract

Iron acquisition is a critical challenge for plants, particularly in iron-deficient soils. Arabidopsis plants employ “Strategy I” responses involving rhizosphere acidification, Fe³⁺ reduction and Fe²⁺ uptake to cope with iron limitation. Recent research has underscored the importance of root-exuded coumarins in modulating the root microbiome and facilitating iron uptake. However, specific interactions between fungal root endophytes and coumarins in plant iron nutrition remain unknown. We identify a mechanism by which the fungal endophyte Macrophomina phaseolina (F80) cooperates with plant-derived coumarins to enhance Arabidopsis iron nutrition at acidic pH 5.7. The coumarin-deficient f6'h1 mutants are unable to benefit from F80 colonisation. Our findings reveal that the interaction between the coumarin scopoletin and F80 rescues plant growth under iron-limiting conditions by resolving the iron mobility bottleneck. Notably, our genetic and metabolite-profiling data suggest that F80 transforms scopoletin into the iron-chelating catechol coumarin esculetin, thereby releasing available iron. Under more alkaline (circum-neutral) pH conditions (pH 7.3), both F80 and a second endophyte, Truncatella angustata (F73), improve iron status indicators in fraxetin-producing genotypes, and exogenous fraxetin supplementation—but not scopoletin—reinstates fungal-mediated rescue in f6ʹh1 plants. This parallels bacterial-coumarin interactions and underscores the centrality of fraxetin in iron acquisition at neutral to alkaline pH. Fungal culture assays reveal that F80 stabilises fraxetin’s iron-mobilising capacity and confers mobilisation activity to scopoletin, whereas F73 exhibits a delayed, coumarin-independent response, suggesting alternative mechanisms. Furthermore, plant rescue of iron-limitation requires iron reduction and uptake by the host at both pH conditions, placing fungal-coumarin activity upstream of the plant’s reductive iron uptake module. Transcriptomic profiling of F80 exposed to scopoletin identified upregulated predicted monooxygenase and oxidoreductase genes, including a candidate enoyl reductase potentially analogous to the Botrytis cinerea scopoletin alteration factor (Bcsaf1). However, no single gene was definitively linked to scopoletin conversion, indicating that fungal detoxification of coumarins may involve complex enzymatic pathways or non-enzymatic oxidative processes. By extending the known role of coumarins from bacterial to fungal members of the root microbiota, this study places coumarins at the centre of commensal-mediated enhancement of plant iron nutrition across microbial kingdoms. We also challenge the prevailing view that scopoletin primarily functions in shaping the microbiome, and reveal its important role in iron nutrition.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Van Dijck, Lara UNSPECIFIED https://orcid.org/0009-0002-6141-981X UNSPECIFIED
URN:	urn:nbn:de:hbz:38-795271
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects:	Natural sciences and mathematics Life sciences Agriculture
Uncontrolled Keywords:	Keywords Language Coumarins UNSPECIFIED fungal endophytes UNSPECIFIED iron UNSPECIFIED
Date of oral exam:	2 October 2025
Referee:	Name Academic Title Parker, Jane E. Professor Zuccaro, Alga Professor
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/79527