Mahdere Z. Shimels

Dr. Mahdere Z. Shimels

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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


The overall aim of my project is to investigate the potential of soil microbes associated with the roots of sorghum and unravel their abilities to disrupt the infection cycle of devastating parasitic weed, Striga (Striga hermonthica).


I have both my MSc and Ph.D in plant sciences from Wageningen University. During my study, I was intrigued by the vast array of plant defence mechanisms and their interactions with both mutualistic and antagonistic organisms. I am keen to understand the genetic bases of the underlying mechanisms of these interactions. The core topic of my Ph.D research was exploring the genetics behind sorghum resistance towards Striga (Sorghum bicolor). My colleagues and I used multidisciplinary approaches to understand how the host plant interacts with the parasitic weed and investigated possible options to improve the resistance of sorghum against the weed.

Currently, I am part of the PROMISE team. The team is focused on finding a microbial solution to the problem of Striga harmonica in sorghum. We work on finding solutions to this notorious weed from different angles such as from the microbe, host plant and parasite side. My focus is to explore the impact of soil microbes on the interaction between the host plant and the parasitic weed. I believe this project is of a high importance to improve the livelihood of poor farmers whose life depend on production of sorghum.

Research groups



Post doctorial researcher


  • 2012–2019
    Ph.D. Candidate
  • 2010–2012

PhD students

AberaDinke, Sewunet
Promotors: Raaijmakers, Jos

Invited talks and keynote addresses on symposia and conferences

3rd Plant Microbiome Symposium 2022


Key publications

  • Plant Methods

    An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS

    Kristýna Floková, Mahdere Shimels, Beatriz Andreo Jimenez, Nicoletta Bardaro, Miroslav Strnad, Ondřej Novák, Harro J Bouwmeester
    Background: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation-that would replace current unspecific, time-consuming and labour-intensive processing of large samples-and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.
  • FEMS Microbiol Ecol

    Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils.

    Thiago R Schlemper Márcio F A Leite Adriano R Lucheta, Mahdere Shimels, Harro J Bouwmeester, Johannes A Van Veen, Eiko E Kuramae
    lant genotype selects the rhizosphere microbiome. The success of plant-microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.
  • PNAS

    Mutation in sorghum alters strigolactones and causes resistance.

    Daniel Gobena,Mahdere Shimels,Patrick JRich,CarolienRuyter-Spira,Harro Bouwmeester,Satish Kanuganti,TesfayeMengiste,Gebisa Ejeta
    Striga is a major biotic constraint to sorghum production in semiarid tropical Africa and Asia. Genetic resistance to this parasitic weed is the most economically feasible control measure. Mutant alleles at the LGS1 (LOW GERMINATION STIMULANT 1) locus drastically reduce Striga germination stimulant activity. We provide evidence that the responsible gene at LGS1 codes for an enzyme annotated as a sulfotransferase and show that functional loss of this gene results in a change of the dominant strigolactone (SL) in root exudates from 5-deoxystrigol, a highly active Striga germination stimulant, to orobanchol, an SL with opposite stereochemistry. Orobanchol, although not previously reported in sorghum, functions in the multiple SL roles required for normal growth and environmental responsiveness but does not stimulate germination of Striga. This work describes the identification of a gene regulating Striga resistance and the underlying protective chemistry resulting from mutation.
  • New Phytologist

    Random mutagenesis of the nucleotide-binding domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1

    Daniela J. Sueldo,Mahdere Shimels,Laurentiu N. Spiridon,Octav Caldararu,Andrei-Jose Petrescu,Matthieu H. A. J. Joosten,Wladimir
    Summary Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB-LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death. NRC1 (NB-LRR Required for HR-Associated Cell Death-1) is a tomato (Solanum lycopersicum) NB-LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae. To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide-binding domain and screened them for the ability to induce an elicitor-independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain-of-function mutants, with 10 of them caused by a single amino acid substitution. All substitutions are located in or very close to highly conserved motifs within the nucleotide-binding domain, suggesting modulation of the signalling activity of NRC1. Three-dimensional modelling of the nucleotide-binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain-of-function mutations in NRC1 and provides insight into how the activity of this NB-LRR is regulated.

Projects & collaborations


  • Promise

    Project 2017–2022
    The long-term goal of the programme is to improve the livelihood of smallholder farmers in sub-Saharan Africa, by increasing the productivity of sorghum:
    Field trial Ethiopia 2021 - Taye Tessema (EIAR)