Brandon Ford

Dr. Brandon Ford

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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


I am working as part of the NWO-Groot project to identify the molecular and chemical cues involved in plant-endophyte interactions, collaborating with researchers at the universities of Utrecht and Leiden.


We recently discovered that plants under attack by fungal root pathogens can actively recruit endophytic microbes inside their root tissues (endosphere) for protection. We showed that Cupriavidus and Stenotrophomonas species were significantly enriched in the root endosphere of sugar beet upon Rhizoctonia solani infection. In addition, metagenomic analyses of the endosphere showed a high abundance of genes encoding for phenazines, non-ribosomal peptide synthetases (NRPSs) and lanthipeptides associated with these taxa, but their functional roles in plant colonisation and protection are yet unknown. Genome sequencing, in vitro and in vivo antagonistic activity and metabolomics experiments are ongoing to investigate their functional potential and to resolve the role of the identified BGCs in endophytic colonisation and plant protection. Our results and ongoing experiments will shed light on microbiome assembly in the endosphere and which genes and metabolites are expressed in plants under siege.

Research groups


Key publications

PNAS 117, 38

Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

RM Wheatley*, BL Ford*, Li Li*, STN Aroney, HE Knights, R Ledermann, AK East, VK Ramachandran, & PS Poole
By analyzing successive lifestyle stages of a model Rhizobium- legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N2-fixing bacteroids, and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 transfer RNAs, and 5 RNA features) are required for the competitive ability to nodulate pea and fix N2. Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphereprogressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signaling, N2fixation, and metabolic adaptation.Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism, and glutamine synthesis (GlnII). There are 17 separate lifestyle adaptations specific to rhizosphere growth and 23 to root colonization, distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium-legume symbiosis.

Projects & collaborations


  • Into Roots - Unwiring regulatory networks in the endophytic microbiome

    Project 2020–2025
    Plant roots are colonized by billions of microorganisms that affect plant growth and tolerance to (a)biotic stresses. Recently we discovered that plants infected by fungal pathogens actively recruit microbes inside their root tissue, the endosphere, for protection. Here we will investigate how plants under siege communicate with their microbiome and characterize the protective endophytic microbes, their genes and metabolites. With nano-microscopic techniques we will unwire where microbes live inside plant roots and express their protective traits. The obtained fundamental knowledge will provide a strong basis for developing innovative strategies that integrate microbiomes in plant breeding and sustainable crop protection.
    Group NWO Groot project