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Summary: The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant‐associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction–reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high‐level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant–microbiota–environment mechanisms that modulate ecosystem health, assembly, and functioning. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Summary: Disentangling the contribution of climatic and edaphic factors to microbiome variation and local adaptation in plants requires an experimental approach to uncouple their effects and test for causality.We used microbial inocula, soil matrices and plant genotypes derived from two natural Arabidopsis thaliana populations in northern and southern Europe in an experiment conducted in climatic chambers mimicking seasonal changes in temperature, day length and light intensity of the home sites of the two genotypes.The southern A. thaliana genotype outperformed the northern genotype in the southern climate chamber, whereas the opposite was true in the northern climate chamber. Recipient soil matrix, but not microbial composition, affected plant fitness, and effects did not differ between genotypes. Differences between chambers significantly affected rhizosphere microbiome assembly, although these effects were small in comparison with the shifts induced by physicochemical differences between soil matrices.The results suggest that differences in seasonal changes in temperature, day length and light intensity between northern and southern Europe have strongly influenced adaptive differentiation between the two A. thaliana populations, whereas effects of differences in soil factors have been weak. By contrast, below‐ground differences in soil characteristics were more important than differences in climate for rhizosphere microbiome differentiation. [ABSTRACT FROM AUTHOR]

(b) Global change factors alter plant microbiota assemblages and modulate beneficial plant-microbe interactions. Keywords: global change; microbiome; microbiota; phyllosphere; plant-microbe interactions; rhizosphere; supra-organisms; sustainable terrestrial ecosystems EN global change microbiome microbiota phyllosphere plant-microbe interactions rhizosphere supra-organisms sustainable terrestrial ecosystems 1907 1909 3 05/25/22 20220615 NES 220615 Plant-associated microorganisms may be invisible to the naked eye, yet they play a key role in the future sustainability of terrestrial ecosystems - from arable lands to rainforests, through tundra and taiga to deserts. Global change, microbiome, microbiota, phyllosphere, plant-microbe interactions, rhizosphere, supra-organisms, sustainable terrestrial ecosystems Defining the components, dynamics, functions and interactions of the core plant-associated microbiota will assist in developing microbiome-based solutions to create healthy, resilient and sustainable plant ecosystems. [Extracted from the article]

Summary: The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large repertoire of candidate‐secreted effectors containing LysM domains, but the role of such proteins in the pathogenicity of any Colletotrichum species is unknown.Here, we characterized the function of two effectors, ChELP1 and ChELP2, which are transcriptionally activated during the initial intracellular biotrophic phase of infection.Using immunocytochemistry, we found that ChELP2 is concentrated on the surface of bulbous biotrophic hyphae at the interface with living host cells but is absent from filamentous necrotrophic hyphae. We show that recombinant ChELP1 and ChELP2 bind chitin and chitin oligomers in vitro with high affinity and specificity and that both proteins suppress the chitin‐triggered activation of two immune‐related plant mitogen‐activated protein kinases in the host Arabidopsis. Using RNAi‐mediated gene silencing, we found that ChELP1 and ChELP2 are essential for fungal virulence and appressorium‐mediated penetration of both Arabidopsis epidermal cells and cellophane membranes in vitro.The findings suggest a dual role for these LysM proteins as effectors for suppressing chitin‐triggered immunity and as proteins required for appressorium function. [ABSTRACT FROM AUTHOR]

The author comments on the disentangling factors that shapes the microbiota composition of the holobiont of plants. The topics discussed include the bacterial and structural convergence of plants' microbiota, the distinctive factors that shape the bacterial and fungal assemblages of plants, and the disturbance in the microbial community.

I.II.III.IV.V.References Summary: Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi‐component interactions necessary for holistic ecosystem‐level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems. [ABSTRACT FROM AUTHOR]

The ectomycorrhizal ( ECM) symbiosis, a mutualistic plant-fungus association, plays a fundamental role in forest ecosystems by enhancing plant growth and by providing host protection from root diseases. The cellular complexity of the symbiotic organ, characterized by the differentiation of structurally specialized tissues (i.e. the fungal mantle and the Hartig net), is the major limitation to study fungal gene expression in such specific compartments. We investigated the transcriptional landscape of the ECM fungus Tuber melanosporum during the major stages of its life cycle and we particularly focused on the complex symbiotic stage by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/ Corylus avellana ectomycorrhizas and identified the distinct genetic programmes associated with each compartment. Particularly, nitrogen and water acquisition from soil, synthesis of secondary metabolites and detoxification mechanisms appear to be important processes in the fungal mantle. In contrast, transport activity is enhanced in the Hartig net and we identified carbohydrate and nitrogen-derived transporters that might play a key role in the reciprocal resources' transfer between the host and the symbiont. [ABSTRACT FROM AUTHOR]

Poplars are extensively cultivated worldwide, and their susceptibility to the leaf rust fungus Melampsora larici-populina leads to considerable damages in plantations. Despite a good knowledge of the poplar rust life cycle, and particularly the epidemics on poplar, the perennial status of the plant host and the obligate biotrophic lifestyle of the rust fungus are bottlenecks for molecular investigations. Following the completion of both M. larici-populina and Populus trichocarpa genome sequences, gene families involved in poplar resistance or in rust fungus virulence were investigated, allowing the identification of key genetic determinants likely controlling the outcome of the interaction. Specific expansions of resistance and defense-related genes in poplar indicate probable innovations in perennial species in relation with host-pathogen interactions. The genome of M. Laricipopulina contains a strikingly high number of genes encoding small secreted proteins (SSPs) representing hundreds of candidate effectors. Transcriptome analyses of interacting partners in compatible and incompatible interactions revealed conserved set of genes involved in poplar defense reactions as well as timely regulated expression of SSP transcripts during host tissues colonisation. Ongoing functional studies of selected candidate effectors will be achieved mainly on the basis of recombinant protein purification and subsequent characterisation. [ABSTRACT FROM AUTHOR]