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1. Mechanistic approaches to investigate soil microbe‐mediated plant competition

   https://doi.org/10.1111/1365-2745.14156  

   Chung, Y. Anny; Ke, Po‐Ju; Adler, Peter B. (July 2023, Journal of Ecology)

   Abstract Interactions between plants and soil microbes can influence plant population dynamics and diversity in plant communities. Traditional theoretical paradigms view the microbial community as a black box with net effects described by phenomenological models.This approach struggles to quantify the importance of plant–microbe interactions relative to other competition and coexistence mechanisms and to explain context dependence in microbe effects.We argue that a mechanistic framework focused on microbial functional groups will lead to conceptual and empirical advances, as demonstrated by extending resource ratio theory to plant–microbe interactions. We review the diverse pathways by which different microbial functional groups can influence plant resource competition. Finally, we suggest approaches to link theory with observations to measure the key parameters of our framework.Synthesis: Our review highlights recent experimental advancements for uncovering microbial mechanisms that alter plant host resource competition and coexistence. We synthesize these mechanisms into a conceptual model that provides a framework for future experiments to investigate the importance of plant–microbe interactions in structuring plant populations and communities. 

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2. Does the evolution of ontogenetic niche shifts favour species coexistence? An empirical test in Trinidadian streams

   https://doi.org/10.1111/1365-2656.13912  

   Anaya‐Rojas, Jaime M.; Bassar, Ronald D.; Matthews, Blake; Goldberg, Joshua F.; King, Leighton; Reznick, David; Travis, Joseph (March 2023, Journal of Animal Ecology)

   Abstract A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor.We tested this prediction using stable isotopes that yield information about the trophic position (δ¹⁵N) and carbon source (δ¹³C) of two coexisting fish species: Trinidadian guppiesPoecilia reticulataand killifishRivulus hartii.We examined fish from locations representing three natural community types: (1) where killifish and guppies live with predators, (2) where killifish and guppies live without predators and (3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish–guppy community.We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish–guppy only). This result is consistent with theory for size‐structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish–guppy community and the killifish–guppy–predator community, suggesting contemporary evolution in these ontogenetic trophic differences.These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities. 

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3. Stomatal traits covary with leaf mycobiome diversity and composition

   https://doi.org/10.1111/nph.70749  

   Apigo, Austen; Heitmann, Sabrina; Leopold, Devin; Anderegg, Leander_D_L; Busby, Posy_E (November 2025, New Phytologist)

   Summary The scope of plant control over its microbiome is a central question in evolutionary biology and agriculture. Leaf traits are known to shape pathogen colonization and disease development, but their impact on the broader community of largely non‐pathogenic fungi that colonize plant leaves remains an open question.We used reciprocal common gardens of the model tree,Populus trichocarpa(black cottonwood), to examine relationships between leaf traits and the leaf mycobiome in two strongly contrasting environments. We measured six leaf traits (stomatal length, stomatal density, carbon‐to‐nitrogen ratio, leaf thickness, leaf dry matter content, and specific leaf area) and used fungal marker gene sequencing to characterize leaf fungal communities for 57 tree genotypes replicated in one mesic and one xeric common garden (809 trees).Several leaf traits covaried with the leaf mycobiome, yet one relationship was paramount: plant genotypes with longer, sparser leaf stomata hosted a greater richness and diversity of more similar fungal species compared to plant genotypes with shorter, denser leaf stomata.These relationships, while modulated by the environment plants were sourced from and grown in, suggest that stomatal traits may be a general mechanism through which plants and the leaf mycobiome influence one another. 

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4. Different assembly mechanisms of leaf epiphytic and endophytic bacterial communities underlie their higher diversity in more diverse forests

   https://doi.org/10.1111/1365-2745.14084  

   Yang, Xian; Wang, Pandeng; Xiao, Bowen; Xu, Qianna; Guo, Qiang; Li, Shao‐peng; Guo, Lulu; Deng, Meifeng; Lu, Jianbo; Liu, Lingli; et al (March 2023, Journal of Ecology)

   Abstract Plant microbiomes are known to influence host fitness and ecosystem functioning, but mechanisms regulating their structure are poorly understood.Here, we explored the assembly mechanisms of leaf epiphytic and endophytic bacterial communities using a subtropical forest biodiversity experiment.Both epiphytic and endophytic bacterial diversity increased as host tree diversity increased. However, the increased epiphytic diversity in more diverse forests was driven by greater epiphytic diversity (i.e. greaterα‐diversity) on individual trees, whereas the increased endophytic diversity in more diverse forests was driven by greater dissimilarity in endophytic composition (i.e. greaterβ‐diversity) among trees. Mechanistically, responses of epiphytes to changes in host diversity were consistent with mass effects, whereas responses of endophytes were consistent with species sorting.Synthesis. These results provided novel experimental evidence that biodiversity declines of plant species will lead to biodiversity declines of plant‐associated microbiomes, but the underlying mechanism may differ between habitats on the plant host. 

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5. Competition shapes individual foraging and survival in a desert rodent ensemble

   https://doi.org/10.1111/1365-2656.13583  

   Manlick, Philip J.; Maldonado, Karin; Newsome, Seth D. (September 2021, Journal of Animal Ecology)

   Abstract Intraspecific variation, including individual diet variation, can structure populations and communities, but the causes and consequences of individual foraging strategies are often unclear.Interactions between competition and resources are thought to dictate foraging strategies (e.g. specialization vs. generalization), but classical paradigms such as optimal foraging and niche theory offer contrasting predictions for individual consumers. Furthermore, both paradigms assume that individual foraging strategies maximize fitness, yet this prediction is rarely tested.We used repeated stable isotope measurements (δ¹³C, δ¹⁵N;N = 3,509) and 6 years of capture–mark–recapture data to quantify the relationship between environmental variation, individual foraging and consumer fitness among four species of desert rodents. We tested the relative effects of intraspecific competition, interspecific competition, resource abundance and resource diversity on the foraging strategies of 349 individual animals, and then quantified apparent survival as function of individual foraging strategies.Consistent with niche theory, individuals contracted their trophic niches and increased foraging specialization in response to both intraspecific and interspecific competition, but this effect was offset by resource availability and individuals generalized when plant biomass was high. Nevertheless, individual specialists obtained no apparent fitness benefit from trophic niche contractions as the most specialized individuals exhibited a 10% reduction in monthly survival compared to the most generalized individuals. Ultimately, this resulted in annual survival probabilities nearly 4× higher for generalists compared to specialists.These results indicate that competition is the proximate driver of individual foraging strategies, and that diet‐mediated fitness variation regulates population and community dynamics in stochastic resource environments. Furthermore, our findings show dietary generalism is a fitness maximizing strategy, suggesting that plastic foraging strategies may play a key role in species' ability to cope with environmental change. 

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