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  1. Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function. 
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    Free, publicly-accessible full text available February 21, 2025
  2. Abstract

    Free‐air CO2enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2] affected soybean (Glycine max)leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2], including a decrease in the abundance of a common endophyte,Methylobacteriumsp. Moreover,Methylobacteriumabundance was negatively correlated with co‐occurring fungal endophytes. We then assessed howMethylobacteriumaffected the growth of co‐occurring endophytic fungi in vitro.Methylobacteriumantagonized most co‐occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response toMethylobacteriumwithin a single fungal operational taxonomic unit (OTU) was comparable to inter‐OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2] plots differed in colony growth and response toMethylobacterium, suggesting that increasing [CO2] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2] decreases the abundance of a common bacterial endophyte that interacts strongly with co‐occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.

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  3. Summary

    Colonization by foliar endophytic fungi can affect the expression of host plant defenses and other ecologically important traits. However, whether endophyte colonization affects the uptake or redistribution of resources within and among host plant tissues remains unstudied.

    We inoculated leaves ofTheobroma cacaowith four common colonizers that range in their effect from protective to pathogenic (Colletotrichum tropicale,Pestalotiopsissp.,Colletotrichum theobromicola, orPhytophthora palmivora). We pulsed the soil with nitrogen‐15 (15N) and then traced15N uptake and its subsequent distribution to whole plants and individual leaves.

    At a whole‐plant level,C. tropicale‐inoculated plants showed significantly greater15N uptake than endophyte‐free plants did in the same pot. Among leaves within plants, younger leaves were particularly enriched in15N, but endophyte inoculation at the individual leaf level did not alter15N distribution within plants. However, leaves co‐inoculated with pathogenicPhytophthoraand protectiveC. tropicaleexperienced significantly elevated15N content as pathogen damage increased, compared with leaves inoculated only with the pathogen. Further, endophyte–pathogen co‐infection also increased total plant biomass.

    Our results indicate that colonization by foliar endophytes significantly affects N uptake and distribution among and within host plants in ways that appear to be context dependent on other microbiome components.

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    Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro‐organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function.Trait‐based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and ‐omics‐based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFunis built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait‐based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

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