Latest News

Last paper of 2021 in ISME J: Protective Pseudomonas

Posted on December 12, 2021

Local co-existence of pathogenic and protective Pseudomonas lineages read more

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Or Shalev et al., ISME J, published December 11, 2021

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.

A Celebration of Plant Science 2021

Posted on December 10, 2021

International symposium on occasion of Detlef's 60th birthday read more

Current and former members of the Weigel Lab present the "Celebration of Plant Science 2021“, a free International Online Symposium with exceptional line up of speakers, on Dec 16, 2021. More information here.


Derek named a Wallenberg Academy Fellow!

Posted on December 02, 2021

Derek wins Wallenberg Academy Fellowship for his new lab at SLU read more

Wallenberg Academy Fellows, the career program for young researchers launched by the Knut and Alice Wallenberg Foundation in 2012, provides long-term funding for young, promising Swedish and foreign researchers from all academic fields. Derek, who will start his own lab at SLU Uppsala next year, was just named a recipient of this prestigious award. Congratulation, Derek!

Congratulations, Dr. Thanvi Srikant!

Posted on November 19, 2021

Thanvi successfully defended her thesis on the interplay between DNA methylation and gene expression in Arabidopsis thaliana. read more

Congratulations, Thanvi!

In MBE: North American Arabidopsis

Posted on September 09, 2021

Gautam describes the history of A. thaliana in N. America read more

Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia

Gautam Shirsekar et al., Molecular Biology and Evolution, published September 9, 2021

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.



In Nature: collaborative paper on immunity

Posted on September 08, 2021

With Nürnberger and Parker labs: convergence of ETI and PTI read more

The EDS1–PAD4–ADR1 node mediates Arabidopsis pattern-triggered immunity

Rory N. Pruitt et al., Nature 598, 495–499 (2021)

Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes2, suggesting pathway convergence upstream of nuclear events. Here we report that PTI triggered by the Arabidopsis LRR receptor protein RLP23 requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and of ADR1 family helper nucleotide-binding LRRs, which are all components of ETI. The cell-surface LRR receptor kinase SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting the formation of supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane. We detected similar evolutionary patterns in LRR receptor protein and nucleotide-binding LRR genes across Arabidopsis accessions; overall higher levels of variation in LRR receptor proteins than in LRR receptor kinases are consistent with distinct roles of these two receptor families in plant immunity. We propose that the EDS1–PAD4–ADR1 node is a convergence point for defence signalling cascades, activated by both surface-resident and intracellular LRR receptors, in conferring pathogen immunity.

Our contribution: Extended Data Fig. 10: Classification of LRR-RPs, LRR-RKs and NLRs according to genetic conservation in Arabidopsis accessions.
a, Reads from 80 Arabidopsis accessions were mapped to the reference genome of Col-0. Genes were categorised as being conserved, having complex patterns of variation or exhibiting presence/absence polymorphisms according to the distribution of large-scale polymorphisms across all accessions as inferred from stringent read mappings. Criteria for categorization are detailed in the Methods. The numbers of genes falling into each category are provided in the corresponding bars. b, LRR-RP genes classified as in a. Genes encoding known immune receptors are indicated in bold.


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