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The inherent complexity of high‐diversity systems can make them particularly difficult to understand. The relatively recent introduction of functional approaches, which seek to infer ecosystem functioning based on species’ ecological traits, has revolutionized our understanding of these high‐diversity systems. Today, the functional structure of an assemblage is widely regarded as a key indicator of the status or resilience of an ecosystem. Indeed, functional evaluations have become a mainstay of monitoring and management approaches. But is the heavy focus on broad metrics of functional structure grounded in empirical research? On tropical coral reefs, the ocean’s most diverse ecosystems, remarkably few studies directly quantify ecosystem functions and the term ‘function’ is widely used but rarely defined, especially when applied to reef fishes. Our review suggests that most ‘functional’ studies do not study function as it relates to ecological processes. Rather, they look at easy‐to‐measure traits or proxies that are thought to have functional significance. However, these links are rarely tested empirically, severely limiting our capacity to extend results from community structure to the dynamic processes operating within high‐diversity ecosystems such as coral reefs. With rapid changes in global ecosystems, and in their capacity to deliver ecosystem services, there is an urgent need to understand and empirically measure the role of organisms in various ecosystem functions. We suggest that if we are to understand and manage transitioning coral reefs in the Anthropocene, a broad definition of the word ‘function’ is needed along with a focus on ecological processes and the empirical quantification of functional roles. In this review, we propose a universal operational definition of the term ‘function’ that works from a cellular to a global level. Specifically, it is the movement or storage of energy or material. Within this broad definitional framework, all functions are part of a continuum that is tied together by the process‐based unifier of material fluxes. With this universal definition at hand, we then present a path forward that will allow us to fully harness the power of functional approaches in understanding and managing high‐diversity systems such as coral reefs. A plain language summary is available for this article. Plain Language Summary

Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal-centric view of AM fungal biodiversity–ecosystem function relationships that focuses on the direct and specific links betweenAMfungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research.

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology. Functional diversity is increasingly recognized in microbial ecology as the essential link between biodiversity patterns and ecosystem functioning. However, this concept has no clear definition in microbial systems which impairs its applicability. Here, we provide a synthesis on the concept of microbial functional diversity, from its origin to its application.

1. Plant–soil feedback (PSF), plant trait and functional group concepts advanced our understanding of plant community dynamics, but how they are interlinked is poorly known. 2. To test how plant functional groups (FGs: graminoids, small herbs, tall herbs, legumes) and plant traits relate to PSF, we grew 48 grassland species in sterilized soil, sterilized soil with own species soil inoculum and sterilized soil with soil inoculum from all species, and quantified relative growth rate (RGR), specific leaf area (SLA), specific root length (SRL) and per cent arbuscular mycorrhizal fungi colonization (%AMF). 3. Plant growth response to the plant species' own soil biota relative to sterilized soil (PSFsterilized) reflects net effects of all (generalist + specialized) soil biota. Growth response to the plant species' own soil biota relative to soil biota of all plant species (PSFaway) reveals effects of more specialized soil organisms. 4. PSFsterilized showed that graminoids and small herbs have a negative and tall herbs a positive response to their own soil biota, whereas legumes responded neutrally. However, PSFaway showed that on average, all plant FGs benefitted from growing with other species' soil biota, suggesting that pathogens are more specialized than plant growth-promoting soil biota. Feedback to plant growth from all soil biota (PSFsterilized) was stronger than from more specialized soil biota (PSFaway) and could be predicted by SRL and especially by %AMF colonization. Species with high SRL and low %AMF colonization when grown in away soil experienced most negative soil feedback. 5. Synthesis. Plant species from all plant FGs grow better in soil from other species because of less net negative effects of soil biota (in graminoids), or because of more net positive soil biota effects (in tall herbs). Explorative plant species (high SRL, low %AMF colonization) suffer most from negative feedback of all soil biota, whereas more resource conservative species (low SRL, high %AMF colonization) benefit from soil feedback of all soil biota. These findings help to understand replacement of explorative species during succession. Moreover, we suggest a potentially larger role for species with positive feedback than for species with negative feedback to contribute to maintain plant community productivity of diverse communities over time.

Summary Understanding species differences in plant functional traits has been critical in developing a mechanistic understanding of terrestrial ecological processes. Greater attention is now being placed on understanding the extent, causes and consequences of intraspecific trait variation (ITV). ITV is especially important in governing ecological processes in cropping systems, where only a small number of species or genotypes exist in high abundances. However, it remains unclear if key principles of trait‐based ecology – namely the leaf economics spectrum (LES) – also describe intraspecific variation in crop functional biology. There also remains a need to understand whether ITV within crops is random, or structured across environmental, management‐related or biological levels of organization in agroecosystems. We employed a nested design field survey to evaluate ITV in leaf traits in coffee (Coffea arabica), one of the world's most widespread tropical crops. We evaluated ITV in eight physiological, morphological and chemical leaf traits, across five nested categorical levels (sites, management systems, spatial location, plant identity, branch identity). We compared patterns of LES trait covariation in coffee, to interspecific patterns observed across over 700 wild plant species. Patterns of bivariate and multivariate ITV in coffee were broadly consistent with, but considerably weaker than, interspecific patterns associated with the LES, indicating that crops may systematically diverge from global patterns of trait trade‐offs observed in wild plants. Physiological traits varied most widely (coefficient of variation (cv) 42–107%), followed by morphological traits (cv = 15–38%) and chemical traits (cv = 3–11%). Physiological ITV was best explained by the site in which a coffee plant was growing (17–55% explained), while ITV for chemical traits was best explained by management treatments within sites (25–36%); morphological ITV was higher even at the individual tree level or branch level and remained largely unexplained. Our results support the hypothesis that artificial selection and high‐resource agricultural environments lead crops to systematically deviate from patterns of leaf trait covariation observed across wild plants species. Coupled with an understanding of how different traits vary systematically across multiple levels of biological organization, these findings help integrate ITV into future analyses of agroecosystem structure and function. A lay summary is available for this article. Lay Summary

Functional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions (“trait space”) and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis‐driven approach will increase the rigor and transparency of applied functional trait studies.

Plant species composition and diversity are known to change across local gradients of light, moisture and nutrients, but ecologists still have a relatively limited understanding of how communities respond to multiple limiting resources. We used a trait‐based approach to investigate how the functional composition and diversity of forest understorey plant communities change along gradients in light, soil moisture and nitrogen availability. We used a total of seven leaf, root and whole‐plant traits for 55–78 species, and estimated the effects of the three resources on the mean and dispersion of these traits in understorey plant communities across 50 forest sites. Soil moisture and nitrogen availability (C/N ratio) both influenced plant community traits, but light availability (canopy openness) did not. Generally, increases in moisture and nitrogen both resulted in shifts towards more acquisitive resource use strategies, including greater leaf area, specific leaf area and maximum plant height, and lower leaf dry matter content, root dry matter content and rooting depth. Functional diversity of most traits also increased with increasing soil moisture and nitrogen. Although most traits varied with soil moisture on nitrogen‐poor sites, moisture did not influence of the distribution of any traits on nitrogen‐rich sites. Synthesis. Independent co‐limitation of soil moisture and nitrogen appeared to influence the functional composition and diversity of understorey vegetation in our study area. The co‐occurrence of species with resource acquisitive and conservative strategies on nitrogen‐rich sites may make plant communities relatively resistant to changes to soil moisture. These results suggest that altered precipitation regimes under climate change could lead to greater changes in the composition and diversity of plant communities on nutrient‐poor soils than on nutrient‐rich soils. Independent co‐limitation of soil moisture and nitrogen appeared to influence the functional composition and diversity of understorey vegetation in our study area. The co‐occurrence of species with resource acquisitive and conservative strategies on nitrogen‐rich sites may make plant communities relatively resistant to changes to soil moisture. These results suggest that altered precipitation regimes under climate change could lead to greater changes in the composition and diversity of plant communities on nutrient‐poor soils than on nutrient‐rich soils.

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.

1. Understanding patterns of trait variation across environmental variability is necessary for development of ecological predictions. The leaf economic spectrum (LES) has demonstrated global trade-offs in leaf traits, but it is unclear whether such patterns are robust in local communities exposed to varying environments. 2. We conducted separate greenhouse experiments to examine the effects of varying water-table depth and nitrogen availability on leaf-level trait values among a suite of co-occurring wetland species. We then assessed the effects of species-specific trait value responses on relationships predicted by LES and whether species responded similarly to variations in water-table depth and nitrogen availability. 3. We found that both water-table depth and nitrogen availability had significant species by treatment interactions for specific leaf area, leaf nitrogen and photosynthetic rates, indicating species-specific responses to environmental variability. The responses of individual traits to different treatment levels were relatively consistent across species, but multivariate responses were more variable. 4. We found that apart from significant relationships between specific leaf area and photosynthetic rate under some treatments, there was little support for the relationships predicted by the LES. 5. These results suggest that, before trait-based ecology will be able to make progress towards using plant traits to predict responses of communities and ecosystems to changes in environmental drivers, considerable attention needs to be paid to the processes that control intraspecific trait variation.

Aim: Tropical elevation gradients are natural laboratories to assess how changing climate can influence tropical forests. However, there is a need for theory and integrated data collection to scale from traits to ecosystems. We assess predictions of a novel trait-based scaling theory, including whether observed shifts in forest traits across a broad tropical temperature gradient are consistent with local phenotypic optima and adaptive compensation for temperature. Location: An elevation gradient spanning 3,300 m and consisting of thousands of tropical tree trait measures taken from 16 1-ha tropical forest plots in southern Perú, where gross and net primary productivity (GPP and NPP) were measured. Time period: April to November 2013. Major taxa studied: Plants; tropical trees. Methods: We developed theory to scale from traits to communities and ecosystems and tested several predictions. We assessed the covariation between climate, traits, biomass and GPP and NPP. We measured multiple traits linked to variation in tree growth and assessed their frequency distributions within and across the elevation gradient. We paired these trait measures across individuals within 16 forests with simultaneous measures of ecosystem net and gross primary productivity. Results: Consistent with theory, variation in forest NPP and GPP primarily scaled with forest biomass, but the secondary effect of temperature on productivity was much less than expected. This weak temperature dependence appears to reflect directional shifts in several mean community traits that underlie tree growth with decreases in site temperature. Main conclusions: The observed shift in traits of trees that dominate in more cold environments is consistent with an 'adaptive/acclimatory' compensation for the kinetic effects of temperature on leaf photosynthesis and tree growth. Forest trait distributions across the gradient showed overly peaked and skewed distributions, consistent with the importance of local filtering of optimal growth traits and recent shifts in species composition and dominance attributable to warming from climate change. Trait-based scaling theory provides a basis to predict how shifts in climate have and will influence the trait composition and ecosystem functioning of tropical forests.