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The ability for microbes to enter dormant states is adaptive under resource fluctuations and has been linked to the maintenance of diversity. Nevertheless, the mechanism by which microbial dormancy gives rise to the density‐dependent feedbacks required for stable coexistence under resource fluctuations is not well understood. Via analysis of consumer‐resource models, we show that the stable coexistence of dormancy and non‐dormancy strategists is a consequence of the former benefiting more from resource fluctuations while simultaneously reducing overall resource variability, which sets up the requisite negative frequency dependence. Moreover, we find that dormants can coexist alongside gleaner and opportunist strategies in a competitive‐exclusion‐defying case of three species coexistence on a single resource. This multi‐species coexistence is typically characterised by non‐simple assembly rules that cannot be predicted from pairwise competition outcomes. The diversity maintained via this three‐way trade‐off represents a novel phenomenon that is ripe for further theoretical and empirical inquiry. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In modern coexistence theory, species coexistence can either arise via strong niche differences or weak fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. However, several methods for quantifying niche and fitness differences exist, with little guidance on how and why these methods differ. Here, we first organize the available methods into three groups and review their differences from a conceptual point of view. Next, we apply four methods to quantify niche and fitness differences to one simulated and one empirical data set. We show that these methods do not only differ quantitatively, but affect how we interpret coexistence. Specifically, the different methods disagree on how resource supply rates (simulated data) or plant traits (empirical data) affect niche and fitness differences. We argue for a better theoretical understanding of what connects and sets apart different methods and more precise empirical measurements to foster appropriate method selection in coexistence theory. [ABSTRACT FROM AUTHOR]

Mycorrhizal fungi with different nutrient acquisition strategies influence plant species performance and physiology, thereby defining their trophic niche. This might drive resource competition dynamics that cumulatively impact tree species coexistence, but few manipulative experiments have directly tested this.Combining surveys and experiments in a modern coexistence theory framework, we tested how variation in mycorrhizal strategies and nutrient conditions affects plant competitive outcomes. We focused on two genera of co‐occurring tree species with different mycorrhizal states: Acer (arbuscular mycorrhizal, AM) and Populus (dual mycorrhizal, but often considered predominantly ectomycorrhizal, EM).The EM and AM fungal responsiveness in Populus species varied with latitude and nitrogen (N) limitation. Host‐specific soil microbiome conditioning and inorganic N fertilization combined to qualitatively affect coexistence outcomes. Lower N conditions favoured Populus over Acer trees, and N fertilization reversed this outcome for southern species, aligning with regional‐scale forest mycorrhizal transitions.Results from the coexistence experiment also predict competitive exclusion between the tree species pairs, which could arise, in part, from their mycorrhizal differences and is consistent with alternative stable states in dominant forest mycorrhizal strategies. Such bistability appears in natural systems as a bimodal distribution of Populus vs. Acer tree species dominance using long‐term forest inventory data.Synthesis: The magnitude and outcome of microbially mediated competition between Populus and Acer depends on soil nutrient availability, which likely relates to their mycorrhizal differentiation. These findings support the importance of mycorrhizal symbioses for contributing to large‐scale biogeographical patterns of tree species trophic niche separation across soil resource gradients and bistability in forest mycorrhizal structure. [ABSTRACT FROM AUTHOR]

Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different selection types on trait distribution, but the effects of selection on species diversity have remained unclear. Here, we propose a framework for inferring the type and strength of selection by studying species diversity and trait distribution together against null expectations. We use a simulation model to confirm our prediction that directional selection should lead to lower species diversity than stabilizing selection despite a similar effect on trait community‐weighted variance. We apply the framework to a mesocosm system of annual plants to test whether differences in species diversity between two habitats that vary in productivity are related to differences in selection on seed mass. We show that, in both habitats, species diversity was lower than the null expectation, but that species diversity was lower in the more productive habitat. We attribute this difference to strong directional selection for large‐seeded species in the productive habitat as indicated by trait community‐weighted mean being higher and community‐weighted variance being lower than the null expectations. In the less productive habitat, we found that community‐weighted variance was higher than expected by chance, suggesting that seed mass could be a driver of niche partitioning under such conditions. Altogether, our results suggest that viewing species diversity and trait distribution as interrelated patterns driven by the same process, ecological selection, is helpful in understanding community assembly. [ABSTRACT FROM AUTHOR]

EcoPlate quantifies the ability of a microbial community to utilize 31 distinct carbon substrates, by monitoring color development of microplate wells during incubation. Well color patterns represent metabolic profiles. Previous studies typically used color patterns representing average values of three technical replicates on the final day of the incubation and did not consider substrate chemical diversity. However, color fluctuates during incubation and color varies between replicates, undermining statistical power to distinguish differences among samples in microbial functional composition and diversity. Therefore, we developed a protocol to improve statistical power with two approaches. First, we optimized data treatment for color development during incubation and technical replicates. Second, we incorporated chemical structural information for the 31 carbon substrates into the computation. Our framework implemented as the protocol in the R environment is able to compare the statistical power among different calculation methods. When we applied it to data from aquatic microcosm and forest soil systems, we observed substantial improvement in statistical power when we incorporated temporal patterns during incubation instead of using only endpoint data. Using maximum or minimum values of technical replicates also sometimes gave better results than averages. Incorporating chemical structural information based on fuzzy set theory could improve statistical power but only when relative color density information was considered; it was not seen when the pattern was first binarized into the presence or absence of metabolic activity. Finally, we discuss research directions to improve these approaches and offer some practical considerations for applying our methods to other datasets. [ABSTRACT FROM AUTHOR]

Reciprocal interaction between plant and soil (plant-soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant-microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms., We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi)., Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions., We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology. [ABSTRACT FROM AUTHOR]