Insect eggs trigger systemic acquired resistance against a fungal and an oomycete pathogen.

Plants are able to detect insect eggs deposited on leaves. In Arabidopsis, eggs of the butterfly species Pieris brassicae (common name large white) induce plant defenses and activate the salicylic acid (SA) pathway. We previously discovered that oviposition triggers a systemic acquired resistance (SAR) against the bacterial hemibiotroph pathogen Pseudomonas syringae. Here, we show that insect eggs or treatment with egg extract (EE) induce SAR against the fungal necrotroph Botrytis cinerea BMM and the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. This response is abolished in ics1, ald1 and fmo1, indicating that the SA pathway and the N-hydroxypipecolic acid (NHP) pathway are involved. Establishment of EE-induced SAR in distal leaves potentially involves tryptophan-derived metabolites, including camalexin. Indeed, SAR is abolished in the biosynthesis mutants cyp79B2 cyp79B3, cyp71a12 cyp71a13 and pad3-1, and camalexin is toxic to B. cinerea in vitro. This study reveals an interesting mechanism by which lepidopteran eggs interfere with plant-pathogen interactions

Grapevine DMR6-1 Is a candidate gene for susceptibility to Downy mildew

Grapevine (Vitis vinifera) is a valuable crop in Europe for both economical and cultural reasons, but highly susceptible to Downy mildew (DM). The generation of resistant vines is of critical importance for a sustainable viticulture and can be achieved either by introgression of resistance genes in susceptible varieties or by mutation of Susceptibility (S) genes, e.g., by gene editing. This second approach offers several advantages: it maintains the genetic identity of cultivars otherwise disrupted by crossing and generally results in a broad-spectrum and durable resistance, but it is hindered by the poor knowledge about S genes in grapevines. Candidate S genes are Downy mildew Resistance 6 (DMR6) and DMR6-Like Oxygenases (DLOs), whose mutations confer resistance to DM in Arabidopsis. In this work, we show that grapevine VviDMR6-1 complements the Arabidopsis dmr6-1 resistant mutant. We studied the expression of grapevine VviDMR6 and VviDLO genes in different organs and in response to the DM causative agent Plasmopara viticola. Through an automated evaluation of causal relationships among genes, we show that VviDMR6-1, VviDMR6-2, and VviDLO1 group into different co-regulatory networks, suggesting distinct functions, and that mostly VviDMR6-1 is connected with pathogenesis-responsive genes. Therefore, VviDMR6-1 represents a good candidate to produce resistant cultivars with a gene-editing approac

Why farmers should manage the arbuscular mycorrhizal symbiosis

The Tansley review by Ryan & Graham (2018) provided a welcome critical perspective on the role of arbuscular mycorrhizal (AM) fungi in large‐scale industrial agriculture, with a focus on cereals (wheat, Triticum aestivum). They conclude that there is little evidence that farmers should consider the abundance or diversity of AM fungi when managing crops. We welcome many of the points made in the paper, as they give an opportunity for self‐reflection, considering that the importance of AM fungi in agroecosystems is often taken for granted. However, we suggest that it is too early to draw the overall conclusion that the management of AM fungi by farmers is currently not warranted. We offer the following points to contribute to the discussion. The first point pertains to the overall focus of Ryan & Graham (2018), which strongly determines the recommendations at which the authors arrive. This scope is limited to yield, at the expense of neglecting aspects of sustainability. We then argue that AM fungal communities do respond negatively to aspects of agricultural management, and list evidence for their positive effects to agronomically important traits, including yield in cereals. In our final argument, we advocate for transitioning to agroecosystems that are more AM compatible in order to increasingly take advantage of all the potential services these ancient symbionts, and other soil biota, can provide

Cell-type specific transcriptomics reveals roles for root hairs and endodermal barriers in interaction with beneficial rhizobacterium

Growth-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is a well-studied bacterium that promotes growth of many plant species. Upon colonization, WCS417 affects root system architecture resulting in an expanded root system. Both immunity and root system architecture, are controlled by root-cell-type specific biological mechanisms, but it is unknown how WCS417 affects these mechanisms. Therefore, here, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. The cortex and endodermis displayed the most differentially expressed genes, even though they were not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, possibly facilitating the root architectural changes observed in WCS417-colonized roots. Comparison of the transcriptome profiles in the two epidermal cell types that were in direct contact with WCS417 -- trichoblasts that form root hairs and atrichoblasts that do not -- imply functional specialization. Whereas basal expression levels of nutrient uptake-related genes and defense-related genes are highest in trichoblasts and atrichoblasts, respectively, upon exposure to WCS417 these roles revert. This suggests that root hairs participate in the activation of root immunity, further supported by attenuation of immunity in a root hairless mutant. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis in WCS417-colonized roots. Using an endodermal barrier mutant we show the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Altogether, we highlight the strength of cell-type-specific transcriptional profiling to uncover masked biological mechanisms underlying successful plant-microbe associations

EDS1 complexes are not required for PRR responses and execute TNL‐ETI from the nucleus in Nicotiana benthamiana

Heterodimeric complexes incorporating the lipase-like proteins EDS1 with PAD4 or SAG101 are central hubs in plant innate immunity. EDS1 functions encompass signal relay from TIR domain-containing intracellular NLR-type immune receptors (TNLs) towards RPW8-type helper NLRs (RNLs) and, in Arabidopsis thaliana, bolstering of signaling and resistance mediated by cell-surface pattern recognition receptors (PRRs). Increasing evidence points to the activation of EDS1 complexes by small molecule binding. We used CRISPR/Cas-generated mutant lines and agroinfiltration-based complementation assays to interrogate functions of EDS1 complexes in Nicotiana benthamiana. We did not detect impaired PRR signaling in N. benthamiana lines deficient in EDS1 complexes or RNLs. Intriguingly, in assays monitoring functions of SlEDS1-NbEDS1 complexes in N. benthamiana, mutations within the SlEDS1 catalytic triad could abolish or enhance TNL immunity. Furthermore, nuclear EDS1 accumulation was sufficient for N. benthamiana TNL (Roq1) immunity. Reinforcing PRR signaling in Arabidopsis might be a derived function of the TNL/EDS1 immune sector. Although Solanaceae EDS1 functionally depends on catalytic triad residues in some contexts, our data do not support binding of a TNL-derived small molecule in the triad environment. Whether and how nuclear EDS1 activity connects to membrane pore-forming RNLs remains unknown

Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity

Plants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 “helper” NLRs (RNLs) cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). The mechanism of RNL/EDS1 family protein cooperation is not understood. Here, we present genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent interaction of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex interacts with NRG1, and EDS1-PAD4 with ADR1, in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) mediate TNL receptor defence signalling

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica

Downy mildew-associated microbiomes

In this thesis, I have investigated microbiomes of plants that are under attack by obligate biotrophic pathogens that cause downy mildew disease. In particular, I have studied the phyllosphere bacterial communities of laboratory cultures of the downy mildews Hyaloperonospora arabidopsidis (Hpa) and Peronospora effusa (Pe) on their respective hosts Arabidopsis thaliana and Spinacia oleracea (henceforth Arabidopsis and spinach). Within these two pathosystems, we observed consistent enrichment of specific bacteria in distinct cultures (Chapters 2 and 4), and for the Arabidopsis system we demonstrated that the genomes of the specific bacteria enriched in distinct laboratory cultures across Europe were isogenic (Chapter 2). These bacteria were further shown to reach higher abundances in the phyllosphere upon Hpa infection (Chapter 2). Also in the rhizosphere, we observed increased colonization by downy mildew-associated bacteria on plants that were grown on soil that was conditioned by downy mildew-infected plants. This suggests that the downy mildew-associated microbes are part of a soil-borne legacy of disease that can be inherited by future generations of plants grown on the same soil (Chapter 3). Moreover, the microbes that are enriched in downy mildew-associated communities appear to be geared towards plant protection (Chapter 3), suggesting that their assembly is indeed directed by the host plant. Lastly, similarities were observed between Pe-associated microbiomes in laboratory cultures and naturally Pe-infected field-grown plants (Chapter 4), highlighting that these microbiomes are not only a laboratory phenomenon. Together, these findings suggest that phyllosphere bacterial communities of plants that are under downy mildew attack are modulated to benefit the plant, meaning that a plant’s cry for help towards the microbiome upon pathogen attack may be a contributing factor to phyllosphere microbiome assembly. Finally, these findings are discussed in a broader perspective in chapter 5, focusing on the mechanisms that may underly the recruitment/enrichment of specific bacteria in downy mildew-infected leaves

Exploring the role of microbial interactions in soil and rhizosphere and their effects on litter decomposition, mycorrhizal associations, and plant growth

Millions of microorganisms inhabit the soil, and some of them contribute to the growth of plants. To gain a better understanding of how microbes promote plant growth, we compared the impact of fungal and bacterial communities on litter decomposition and plant growth. Our study revealed that fungi are the primary decomposers of plant litter and have a more significant impact on nutrient cycling than bacteria. Furthermore, when the fungal and bacterial communities are working together, they have a complementary effect on plant growth that is greater than when either community is working alone. Arbuscular mycorrhizal fungi (AMF) are recognized as one of the most important types of plant symbiotic fungi. AMF are widely distributed in the soil and colonize plant roots. They can functionally extend the plant root system and reach areas in the soil beyond the plant roots, enabling plants to access more water and nutrients. We investigated the microbial community that surrounds the AMF hyphae and discovered that fungal hyphae are colonized by specific bacteria and protists. We demonstrate that the microbes that colonize the fungal hyphae play a crucial role in facilitating mycorrhizal development and assisting plant nutrient uptake. We showed that a particular bacterium of the genus Devosia is associated with AMF hyphae, interacts synergistically with the mycorrhiza and promotes plant growth by facilitating nitrogen uptake. This thesis deepens our understanding of the interactions between different microbial groups and their roles in litter decomposition and mycorrhization processes. A better understanding of plant-microbe interactions is essential for the development of effective application strategies for plant-growth-promoting microbes in agriculture. Ultimately microbes can help create sustainable agricultural practices that rely less on chemical inputs for food production

Experimental evolution of mutualistic plant-microbe interactions in the rhizosphere

We are living on a hungry planet and securing food supply for the steadily increasing human population is a major challenge for mankind. The productivity of agricultural and horticultural crops is constrained by lack of nutrients, abiotic stressors as well as pests and diseases. Together, all these limitations substantially prevent the accomplishment of the full genetic potential of plants for growth and fitness. The use of pesticides and chemical fertilizers to alleviate restrictions on plant performance causes serious environmental problems. Plant growth and health depend to a large extent on soil microbes that are associated with plant roots. These microbes can supply the plant with nutrients, alleviate effects of abiotic stresses, and protect against pathogens and pests. Thus such beneficial microorganisms may be essential allies to improve crop yields in a sustainable way. However, a major problem for large scale and long term applications in agriculture is that the efficacy of such beneficial microbes is unpredictable, often resulting from insufficient population densities on plant roots. In this study I provide evidence that we can use an evolutionary framework to engineer beneficial microbes to perform better in novel host rhizospheres. I attempted to obtain better colonizers by introducing them on plant roots and allowing the population to grow and evolve over many generations during a period of 8 months. In this simplified experimental evolution setup, we used five independently evolving bacterial populations. We then tracked population densities on plant roots at each cycle, and passed bacteria to a new plant for 8 cycles in total. At the end of each growth cycle bacterial colonies were picked and characterized for a wide range of traits. The results in chapter 2 reveal that plants can domesticate root-associated bacteria. Initially the bacteria had a detrimental effect on plant performance, but within a few generations, mutualists that promote plant growth accumulated in the bacterial population. In chapter 3 changes in the evolving bacterial populations were tracked by sequencing the genomes of bacterial colonies that were randomly picked at the end of different plant growth cycles. Mutations that accumulated in parallel in the independently evolving populations targeted global regulators and bacterial cell surface structures. This suggests that there are different strategies of bacterial adaptation to the plant root environment. Networks of co-varying bacterial traits were the focus of the last experimental chapter. Rather than traits evolving individually, trait co-variation has been linked to the ability to rapidly evolve to adapt to new conditions. In chapter 4 it is shown that whereas the network of traits linked to growth, stress resistance and biotic interactions was modular in the ancestral bacterial population, it rapidly restructured during adaptation to the rhizosphere. The most important knowledge we obtained from this work is that plants have the ability to breed their associated microbiome. This may explain the prevalence of beneficial plant-microbe interactions in nature. This study sets the stage for evolutionary microbiome management by steering the evolution of mutualism out of the existing species pool instead of changing species composition