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Premise of the Study Despite long‐term research efforts, a comprehensive perspective on the ecological and functional properties determining plant weediness is still lacking. We investigated here key functional attributes of arable weeds compared to non‐weed plants, at large spatial scale. Methods We used an intensive survey of plant communities in cultivated and non‐cultivated habitats to define a pool of plants occurring in arable fields (weeds) and one of plants occurring only in open non‐arable habitats (non‐weeds) in France. We compared the two pools based on nine functional traits and three functional spaces (LHS, reproductive and resource requirement hypervolumes). Within the weed pool, we quantified the trait variation of weeds along a continuum of specialization to arable fields. Key Results Weeds were mostly therophytes and had higher specific leaf area, earlier and longer flowering, and higher affinity for nutrient‐rich, sunny and dry environments compared to non‐weeds, although functional spaces of weeds and non‐weeds largely overlapped. When fidelity to arable fields increased, the spectrum of weed ecological strategies decreased as did the overlap with non‐weeds, especially for the resource requirement hypervolume. Conclusions Arable weeds constitute a delimited pool defined by a trait syndrome providing tolerance to the ecological filters of arable fields (notably, regular soil disturbances and fertilization). The identification of such a syndrome is of great interest to predict the weedy potential of newly established alien plants. An important reservoir of plants may also become weeds after changes in agricultural practices, considering the large overlap between weeds and non‐weeds.

Biofilms, the complex communities of microbiota that live in association with aquatic interfaces, are considered to be hotspots of microbial life in many aquatic ecosystems. Although the importance of attached algae and bacteria is widely recognized, the role of the highly abundant biofilm-dwelling micrograzers (i.e., heterotrophic protists and small metazoans) is poorly understood. Studies often highlight the resistance of bacterial biofilms to grazing within the microbial food web and therefore argue that the micrograzers have a modulating role (i.e., have effects on biofilm phenotype) rather than a direct trophic role within biofilms. In the present review, we show that this view comes too short, and we establish a conceptual framework of biofilm food webs consisting of three major elements. (1) Energy pathways and subsidization from plankton. As inhabitants of interfaces, biofilm-dwelling grazers potentially access both planktonic organisms and surface-associated organisms. They can play an important role in importing planktonic production into the biofilm food web and thus in the coupling of the planktonic and benthic food webs. Nevertheless, specialized grazers are also able to utilize significant amounts of autochthonous biofilm production. (2) Horizontal complexity of the basal food web. While bacteria and algae within biofilms are edible in general, food quality and accessibility of both bacteria and algae can differ considerably between different prey phenotypes occurring during biofilm formation with respect to morphology, chemical defense, and nutrient stoichiometry. Instead of considering bacteria and algae within biofilms to be generally resistant to feeding by micrograzers, we suggest considering a horizontal food-quality axis to be at the base of biofilm food webs. This food quality gradient is probably associated with increasing costs for the micrograzers. (3) Vertical food web complexity and food chain length. In addition to the consumption of bacteria and algae, many predatory micrograzers exist within biofilm food webs. With the help of video microscopy, we were able to demonstrate the existence of a complex food web with several trophic levels within biofilms. Our conceptual framework should assist in integrating food web concepts and processes into whole-biofilm budgets and in understanding food-web-related interactions within biofilms.

Traits underlie organismal responses to their environment and are essential to predict community responses to environmental conditions under global change. Species differ in life‐history traits, morphometrics, diet type, reproductive characteristics and habitat utilization. Trait associations are widely analysed using phylogenetic comparative methods (PCM) to account for correlations among related species. Similarly, traits are measured for some but not all species, and missing continuous traits (e.g. growth rate) can be imputed using ‘phylogenetic trait imputation’ (PTI), based on evolutionary relatedness and trait covariance. However, PTI has not been available for categorical traits, and estimating covariance among traits without ecological constraints risks inferring implausible evolutionary mechanisms. Here, we extend previous PCM and PTI methods by (1) specifying covariance among traits as a structural equation model (SEM), and (2) incorporating associations among both continuous and categorical traits. Fitting a SEM replaces the covariance among traits with a set of linear path coefficients specifying potential evolutionary mechanisms. Estimated parameters then represent regression slopes (i.e. the average change in trait Y given an exogenous change in trait X) that can be used to calculate both direct effects (X impacts Y) and indirect effects (X impacts Z and Z impacts Y). We demonstrate phylogenetic structural‐equation mixed‐trait imputation using 33 variables representing life history, reproductive, morphological, and behavioural traits for all >32,000 described fishes worldwide. SEM coefficients suggest that one degree Celsius increase in habitat is associated with an average 3.5% increase in natural mortality (including a 1.4% indirect impact that acts via temperature effects on the growth coefficient), and an average 3.0% decrease in fecundity (via indirect impacts on maximum age and length). Cross‐validation indicates that the model explains 54%–89% of variance for withheld measurements of continuous traits and has an area under the receiver‐operator‐characteristics curve of 0.86–0.99 for categorical traits. We use imputed traits to classify all fishes into life‐history types, and confirm a phylogenetic signal in three dominant life‐history strategies in fishes. PTI using phylogenetic SEMs ensures that estimated parameters are interpretable as regression slopes, such that the inferred evolutionary relationships can be compared with long‐term evolutionary and rearing experiments.

1. Understanding the relationship between biodiversity and ecosystem functioning (BEF) is a central topic in ecology. Multi-trait-based functional diversity has been proposed to improve mechanistic understanding of the BEF relationship; however, how trait-based functional diversity affects ecosystem functioning and processes has rarely been addressed in aquatic ecosystems. 2. Here, we examined the causal relationships between three phytoplankton functional diversity indices (FAD2, functional diversity based on dendrograms [FDc], FRic) and Shannon diversity index versus resource use efficiency for nitrogen (RUEN), phosphorus (RUEP) and silicate (RUESi), with monthly long-term datasets from the marine (Western English Channel, 2000-2014) and freshwater (Lake Kasumigaura, 1984-2012) ecosystems. 3. We employed Convergent Cross Mapping (CCM), a novel method developed for identifying causality for nonlinear dynamical systems; this is in contrast to linear approaches that cannot distinguish causality from correlation. CCM found that FDc is the most robust functional diversity index among the selected functional diversity indices (FAD2, FDc, FRic) in predicting phytoplankton resource use efficiency and exhibited a much stronger causal effect than the Shannon index. 4. Furthermore, scenario exploration analysis indicates that most causal effects from phytoplankton diversity indices on resource use efficiency (RUEN, RUEP and RUESi) are on average positive, and FDc exhibited the most consistent positive causal effects on phytoplankton resource efficiency in both marine and freshwater ecosystems. Thus, increasing FDc can enhance phytoplankton resource use efficiency in aquatic ecosystems. 5. Synthesis. Our results show significant causal effects of functional diversity on phytoplankton resource use efficiency in both marine and freshwater ecosystems. Among all selected functional diversity indices, functional diversity based on dendrogram is the most robust functional diversity index in promoting phytoplankton resource efficiency. Our study provides empirical evidences in natural aquatic systems that trait-based functional diversity represents better species niche partitioning than the Shannon index and thereafter enhances resource use efficiency. This finding can improve our understanding on trophic transfer and nutrient cycling in aquatic ecosystems.

1. Great efforts have been made to control soil erosion by restoring plant communities in degraded ecosystems world-wide. However, soil erosion has not been substantially reduced mainly because current restoration strategies lead to large areas of mono-specific vegetation, which are inefficient in reducing soil erosion because of their simple canopy and root structure. Therefore, an advanced understanding of how community functional composition affects soil erosion processes, as well as an improved restoration scheme to reduce soil erosion, is urgently needed. 2. We investigated the effect of community functional composition on soil erosion in restored semi-arid grasslands on the Loess Plateau of China. Community functional composition of 16 restored grasslands was quantified by community-weighted mean (CWM) and functional diversity (FD) trait values, which were calculated from nine plant functional traits of thirteen locally dominant plant species. Species richness and evenness were also measured. Soil erosion rates were measured using standard erosion plots. The multimodel inference approach was used to estimate the direction and the relative importance of these biodiversity indices in reducing soil erosion. 3. A robust and strong negative effect of functional divergence (FDiv) on soil erosion was found. The prevalence of particular trait combinations can also decrease soil erosion. The greatest control over soil erosion was exerted when the community mean root diameter was small and the root tensile strength was great. 4. Synthesis and applications: These findings imply that community functional diversity plays an important role in reducing soil erosion in semi-arid restored grasslands. This means that current restoration strategies can be greatly improved by incorporating community functional diversity into restoration design. We propose a trait-based restoration framework for reducing soil erosion, termed 'SSM' (Screening-Simulating-Maintaining). SSM aims to translate the target of community functional diversity into community assemblages that can be manipulated by practitioners. Based on this framework, a comprehensive procedure, highlighting functional diversity as the primary concern in determining optimal community assemblages, was developed to meet the pressing need for more effective restoration strategies to reduce soil erosion.

Unsustainable fishing is a major driver of change in marine ecosystems. The ways that fishing gears target fishes with different ecological functions are unclear, particularly in complex multispecies fisheries. Here, we examine whether artisanal fishing gears selectively target fishes with unique combinations of ecological traits (diet, body size, depth, position in water column, period of activity, schooling behaviour) in a coral reef ecosystem. We use coral reef fish landing data from 25 sites along the Kenyan coast collected over a 7‐year period. All fishing gears targeted a wide diversity of traits, but with some differentiation among gears. Fish assemblages captured by spearguns were significantly different from the other gear types, specializing on diurnal species that feed on sessile invertivores. Nets, including gillnets and beachseines, targeted the most functional diversity. Escape slot traps targeted the least functionally diverse assemblages. Basket traps and escape slot traps targeted the most functionally similar species of all two‐gear combinations. There were 163 functional entities (unique combinations of traits) captured in the fishery; however, 50% of the catch by each gear was from only two to six functional entities. Most of the differences in gear selectivity were due to unique and rarely targeted functional entities, that made up only a small proportion of the catch. Synthesis and applications. Coral reef fisheries target a breadth of functional entities (unique combinations of traits), but catches are heavily skewed towards relatively few functional entities. While banning specific gears will benefit rare functional entities in the catch, effort reductions will be necessary to alleviate pressure on commonly targeted functional entities. Coral reef fisheries target a breadth of functional entities (unique combinations of traits), but catches are heavily skewed towards relatively few functional entities. While banning specific gears will benefit rare functional entities in the catch, effort reductions will be necessary to alleviate pressure on commonly targeted functional entities.

As the climate continues to change, species are moving to track their climatic niches. Although we are gaining a clearer picture of where and how quickly species ranges are moving, a mechanistic understanding of these changes is still nascent. Evolutionary changes in ranges and range‐limiting traits over contemporary time‐scales have received relatively little attention, possibly due to the mismatch in scale between rapid contemporary range shifts and the historical evolution of species ranges over millions of years. But recent experimental work has shown that range‐limiting traits can evolve rapidly over decadal time‐scales, effectively putting evolution back on the table towards the goal of a mechanistic understanding of contemporary range shifts. Here, I review the role of evolution in shaping range shift responses to recent climate change from the perspective of the past (shared evolutionary history, or phylogenetic signal in range shifts and range‐limiting traits), present (variation in range‐limiting traits) and future (incorporating evolution of range‐limiting traits into range forecasts from species distribution models). In each of these areas, I found a critical role for evolution in understanding historical constraints and future changes in species ranges over contemporary time‐scales: shared evolutionary history may constrain range shift responses for some taxa; compensatory mechanisms of phenotypic plasticity and adaptive evolution can modulate the range shift response; and incorporating evolution into species distribution models can qualitatively alter forecasts of future range shifts. Yet, more can be done in this context, and so I conclude by outlining near‐ and long‐term goals for improving our understanding of the role of evolution in shaping species ranges in a rapidly changing world. A plain language summary is available for this article. Plain Language Summary

Fungi play key roles in the fire‐fuel feedbacks that structure ~40% of the Earth's terrestrial ecosystems, yet a general understanding of fungal responses to fire is lacking. While fire and associated stressor effects on fungi vary based on fire regime components like severity, intensity, and frequency, their influence on fungi can be categorized into three primary phases based on when they influence fungi: during fire, early post‐fire, and later post‐fire. We first identify key fire‐associated phenomic traits and similarities in fungal responses to fire across time. Then, we synthesize this information by linking fire effects to specific fungal traits and response groups to produce trait profiles useful for classifying pyrophilic fungi. The goal of this review is to consolidate fire‐associated phenomic trait data into trait profiles that can be used in combination with fungal genomic data and associated methodologies. These profiles produce an invaluable framework for understanding fungal roles in fire regimes and identify previously unknown trends in fungal responses to fire and associated stressors including heat shock responses, pigmentation, and dispersal into and out of burned environments.

We developed a framework for the hierarchical pathways of bottom-up (niche dimensionality) and top-down control (herbivory) on biomass of stream algae via changes in guild composition (relative abundance of low profile, high profile, and motile guilds), species richness, and evenness. We further tested (1) the contrasting predictions of resource competition theory vs. the benthic model of coexistence on how the number of added nutrients constrains species richness, (2) the relationship between species richness and evenness, and (3) the biodiversity–ecosystem-function paradigm. Implementing a combination of field and lab experiments that manipulated for the first time in benthic algae herbivory and/or niche dimensionality, i.e., the number of added nutrients (NAN), including nitrogen, phosphorus, iron, and manganese, we made the following discoveries. First, important predictors of guild composition were herbivory (field) and NAN (lab); of richness, NAN (field) and NAN and guild composition (lab); of evenness, guild composition (field and lab) and herbivory (field); and of biomass, guild composition, NAN, and richness + evenness (field and lab). Herbivory increased the proportions of the low profile and motile guilds but decreased the proportion of the high profile guild. In the absence of grazing, greater proportions of the high profile guild resulted in elevated richness and biomass but diminished evenness, whereas in the presence of grazing, these relationships generally disappeared. Second, both experiments confirmed the prediction of the benthic model that species richness increases with NAN, a pattern inconsistent with resource competition theory. Third, supplementation with manganese and/or iron increased algal richness, indicating that micronutrients, which have generally been overlooked in stream ecology, added dimensions to the algal niche. Fourth, the richness–evenness relationship, observed only in the absence of herbivory, depended on the size of the species pool. It was positive at richness lower than 49 species (lab), implying complementarity and facilitation, while at higher richness (field and lab), this relationship was negative, consistent with negative interspecific interactions. Finally, the greater dependence of biomass production on guild composition and NAN than on richness and evenness suggests that more comprehensive, environmentally explicit, and trait-based approaches are necessary for the study of the biodiversity–ecosystem-function paradigm.

Pigmentation is often overlooked in zooplankton, since these organisms are mostly colorless to fit the translucid water medium. However, one of the dominant zooplankton taxa in aquatic ecosystems—copepods—often show a bright red-orange or blue coloration owing to the accumulation of carotenoid pigments in some parts of their bodies. Even though there are many functional traits describing copepod’s performance (e.g., size, feeding, and reproductive modes), it is surprising that the role of such a simple and visible trait as coloration has not been studied in a coherent manner yet. Here, by reviewing 95 studies, we demonstrate that carotenoid-based pigmentation (mainly caused by astaxanthin molecules) is a widespread functional trait in freshwater and marine copepods. We propose a way to disentangle the complex and thus intriguing patterns of pigment expression along latitudinal and altitudinal gradients, addressing its relationship to diet quality and quantity, temperature, ultraviolet radiation stress, predation pressure, lipid metabolism, and reproduction. We show that large-scale variations in pigmentation are difficult to tackle because of the fundamental plasticity of this trait at short time scales (i.e., hours, days), and the most recent information about carotenoid bioconversion are addressed (genes and enzyme identification, and influence of microbiota). From this literature review, we hypothesize that pigments play a “Swiss-army knife” role for copepod’s fitness, useful in various ecosystem conditions owing to the strong antioxidant power and the finely-tuned metabolism of astaxanthin. With larger antioxidant capacities (survival), higher metabolisms (growth), and more offspring in better condition (reproduction), red morphs appear more successful than their uncolored siblings. Also, the potential camouflage strategies allowed by red and blue pigmentation are discussed. We finally formulate new directions and future research fields from molecular to ecosystem scales. Routine quantifications of copepod’s pigmentation through trait-based approaches could be useful (1) to obtain an accurate copepod fitness indicator and (2) to better estimate the transfer of antioxidant to higher trophic levels in ecosystems, including humans.