A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria

Biocontrol Potential of Raw Olive Mill Waste Against Verticillium dahliae in Vegetable Crops

Verticillium wilt caused by the soil-borne fungus Verticillium dahliae causes severe losses to a broad range of economically important crops worldwide. Chemical disease management is ineffective; thus, alternative control strategies are needed. Olive-producing countries face the challenge of managing olive mill wastewater (OMW) in an environmentally friendly and agronomically beneficial manner. The proper use of OMW supported by scientific research has been proposed as a valuable means for successful disease management. In this respect, we tested whether soil application of raw OMW can protect vegetable crops against V. dahliae and investigated the potential disease-suppressive mechanisms. OMW inhibited significantly fungal growth, sporulation, hyphae width, and conidial and microsclerotial germination in vitro, and these effects were dose-dependent. Moreover, the addition of OMW in the soil provided sufficient protection of eggplant and tomato against V. dahliae in planta. The high OMW-conferred protection of eggplant was gradually decreased, possibly due to the decreased phenolic content in OMW over time. Bioassays with sterilized soil substrate and OMW, along with isolated microbial strains, revealed that soil- and OMW-originated microbes had no role in disease suppression. Moreover, split-root set-ups suggested a non-systemic OMW-induced resistance mechanism. Root-drench application of OMW in eggplant and tomato plants did not cause significant alterations in the structure of the plant microbiome that could be associated with disease suppressiveness.

Meddling with the microbiota: Fungal tricks to infect plant hosts

Plants associate with a wealth of microbes, collectively referred to as the plant microbiota, whose composition is determined by host plant genetics, immune responses, environmental factors and intermicrobial relations. Unsurprisingly, microbiota compositions change during disease development. Recent evidence revealed that some of these changes can be attributed to effector proteins with antimicrobial activities that are secreted by plant pathogens to manipulate host microbiota to their advantage. Intriguingly, many of these effectors have ancient origins, predating land plant emergence, and evolved over long evolutionary trajectories to acquire selective antimicrobial activities to target microbial antagonists in host plant microbiota. Thus, we argue that host-pathogen co-evolution likely involved arms races within the host-associated microbiota.

Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18-CBM5 chitinase to protect their hosts

Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

The chemical language of plant-microbe-microbe associations: an introduction to a Virtual Issue

This Editorial introduces the Virtual Issue ‘Chemical language of plant–microbe–microbe associations’ that includes the following papers: Basak et al. (2024), Böttner et al. (2023), Brisson et al. (2023), Feng et al. (2023), Gfeller et al. (2024), Gómez‐Pérez et al. (2023), Hong et al. (2022, 2023), Hu et al. (2024), Jiang et al. (2024), Lee et al. (2024), Nakano (2024), Ökmen et al. (2023), Revillini et al. (2023), Rovenich & Thomma (2023), Simonin et al. (2022), Snelders et al. (2023), Walsh et al. (2024), Wen et al. (2023), Xia et al. (2023), Xie et al. (2023), Zhang et al. (2023, 2024), Zheng et al. (2023), Zhou et al. (2023, 2024). Access the Virtual Issue at www.newphytologist.com/virtualissues.

Fungal effectors: past, present, and future

Fungal effector proteins function at the interfaces of diverse interactions between fungi and their plant and animal hosts, facilitating interactions that are pathogenic or mutualistic. Recent advancements in protein structure prediction have significantly accelerated the identification and functional predictions of these rapidly evolving effector proteins. This development enables scientists to generate testable hypotheses for functional validation using experimental approaches. Research frontiers in effector biology include understanding pathways through which effector proteins are secreted or translocated into host cells, their roles in manipulating host microbiomes, and their contribution to interacting with host immunity. Comparative effector repertoires among different fungal-host interactions can highlight unique adaptations, providing insights for the development of novel antifungal therapies and biocontrol strategies.

Molecular Dialogue During Host Manipulation by the Vascular Wilt Fungus Fusarium oxysporum

Vascular wilt fungi are a group of hemibiotrophic phytopathogens that infect diverse crop plants. These pathogens have adapted to thrive in the nutrient-deprived niche of the plant xylem. Identification and functional characterization of effectors and their role in the establishment of compatibility across multiple hosts, suppression of plant defense, host reprogramming, and interaction with surrounding microbes have been studied mainly in model vascular wilt pathogens Fusarium oxysporum and Verticillium dahliae. Comparative analysis of genomes from fungal isolates has accelerated our understanding of genome compartmentalization and its role in effector evolution. Also, advances in recent years have shed light on the cross talk of root-infecting fungi across multiple scales from the cellular to the ecosystem level, covering their interaction with the plant microbiome as well as their interkingdom signaling. This review elaborates on our current understanding of the cross talk between vascular wilt fungi and the host plant, which eventually leads to a specialized lifestyle in the xylem. We particularly focus on recent findings in F. oxysporum, including multihost associations, and how they have contributed to understanding the biology of fungal adaptation to the xylem. In addition, we discuss emerging research areas and highlight open questions and future challenges.

The impact of filamentous plant pathogens on the host microbiota

When a pathogen invades a plant, it encounters a diverse microbiota with some members contributing to the health and growth of the plant host. So far, the relevance of interactions between pathogens and the plant microbiota are poorly understood; however, new lines of evidence suggest that pathogens play an important role in shaping the microbiome of their host during invasion. This review aims to summarize recent findings that document changes in microbial community composition during the invasion of filamentous pathogens in plant tissues. We explore the known mechanisms of interaction between plant pathogens and the host microbiota that underlie these changes, particularly the pathogen-encoded traits that are produced to target specific microbes. Moreover, we discuss the limitations of current strategies and shed light on new perspectives to study the complex interaction networks between filamentous pathogens and the plant microbiome.

Colletotrichum fructicola co-opts cytotoxic ribonucleases that antagonize host competitive microorganisms to promote infection

Phytopathogens secrete numerous molecules into the environment to establish a microbial niche and facilitate host infection. The phytopathogenic fungus Colletotrichum fructicola, which causes pear anthracnose, can colonize different plant tissues like leaves and fruits, which are occupied by a diversity of microbes. We speculate that this fungus produces antimicrobial effectors to outcompete host-associated competitive microorganisms. Herein, we identified two secreted ribonucleases, CfRibo1 and CfRibo2, from the C. fructicola secretome. The two ribonucleases both possess ribonuclease activity and showed cytotoxicity in Nicotianan benthamiana without triggering immunity in an enzymatic activity-dependent manner. CfRibo1 and CfRibo2 recombinant proteins exhibited toxicity against Escherichia coli, Saccharomyces cerevisiae, and, importantly, the phyllosphere microorganisms isolated from the pear host. Among these isolated microbial strains, Bacillus altitudinis is a pathogenic bacterium causing pear soft rot. Strikingly, CfRibo1 and CfRibo2 were found to directly antagonize B. altitudinis to facilitate C. fructicola infection. More importantly, CfRibo1 and CfRibo2 functioned as essential virulence factors of C. fructicola in the presence of host-associated microorganisms. Further analysis revealed these two ribonucleases are widely distributed in fungi and are undergoing purifying selection. Our results provide the first evidence of antimicrobial effectors in Colletotrichum fungi and extend the functional diversity of fungal ribonucleases in plant-pest-environment interactions.

IMPORTANCE

Colletotrichum fructicola is emerging as a devastating pathogenic fungus causing anthracnose in various crops in agriculture, and understanding how this fungus establishes successful infection is of great significance for anthracnose disease management. Fungi are known to produce secreted effectors as weapons to promote virulence. Considerable progress has been made in elucidating how effectors manipulate plant immunity; however, their importance in modulating environmental microbes is frequently neglected. The present study identified two secreted ribonucleases, CfRibo1 and CfRibo2, as antimicrobial effectors of C. fructicola. These two proteins both possess toxicity to pear phyllosphere microorganisms, and they efficiently antagonize competitive microbes to facilitate the infection of pear hosts. This study represents the first evidence of antimicrobial effectors in Colletotrichum fungi, and we consider that CfRibo1 and CfRibo2 could be targeted for anthracnose disease management in diverse crops in the future.

Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates

The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

Deep discovery informs difficult deployment in plant microbiome science

Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.

Co-evolution within the plant holobiont drives host performance

Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.

Battle of the bugs: how an oomycete pathogen shapes the microbiota of its host

This article is a Commentary on Gómez‐Pérez et al. (2023), 239: 2320–2334.