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Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country

Our aim was to register and characterize, through collating our own data with those from bibliographic reviews of published databases including root-associated fungi molecular data, the mycobiome of Mediterranean woody plant species across Europe and North Africa. Here, we reported a total of 439 fungus taxa associated with the roots of 42 woody species, involving 3086 plant belowground-fungus interactions.

1. Biotic interactions are highly affected by species traits and micro-environmental variability. Research on facilitation has primarily focused on how nurse species alleviate abiotic stress for beneficiary species, while the impact of the micro- environmental variability generated by nurse plants in shaping facilitation out-comes is poorly understood. This study has two objectives: (i) To evaluate which traits define beneficiary species and (ii) to evaluate whether nurse and non- nurse species differ in their ability to reduce abiotic stress and its variability under their canopy. 2. We sampled recruits in two arid and stressful environments to assess (i) which species accumulate more juveniles beneath their canopy controlling for their cov-erage (nurse vs. non-nurse species) and (ii) which species benefited from facilita-tion by determining whether they tend to recruit more beneath other species or on the bare ground (beneficiary/non- beneficiary). First, we compared how nurse and non- nurse species modify the physical and chemical microenvironments underneath their canopy, both in terms of magnitude and variation. Second, we compared root growth, water retention and nutrient accumulation in juvenile plants of beneficiary and non- beneficiary species. 3. We found that facilitation is enhanced by species that provide a more homogene-ous microenvironment rather than an intense reduction of microenvironmental stress under their canopy. In addition, the juveniles of beneficiary species invest more in root development, accumulate Ca and S in their shoot tissues, and show a higher water content than non- beneficiary species. 4. Our findings indicate that the homogeneity of microenvironments plays a crucial role in facilitative interactions, and the juveniles of beneficiary species show a less conservative strategy, investing more in resource acquisition than juveniles of non- beneficiary species.

[Questions]: A variety of mechanisms sustain diversity in natural communities as a result of ecological interactions between organisms. Competition has been studied extensively in the context of species maintenance, but facilitation is often conceptualized as simply reducing competition between functionally different species, which tends to decline throughout the plants' life span. Here we explore how interspecific facilitation may sustain diversity throughout the species' life by avoiding the extinction of locally rare species at juvenile stages and reducing performance disparities between neighbors of differing species at mature stages. [Methods]: To do so, we measured whether rarer species relied more on facilitation than abundant ones in semiarid shrubland in southeast Spain. A mechanistic explanation of this relationship was subsequently tested by correlating rarity with the species' affinity to a particularly edaphic stressful environment. Finally, we assessed whether growing associated with neighbors in vegetation patches shaped by facilitation could balance performance disparities between species when they become adults. [Results]: We show that facilitation (i) favors the rare species, which, in addition, tend to be those with low affinity to the stressful environment, and (ii) reduces the performance dissimilarities among plants growing associated within multispecific vegetation patches compared to plants growing alone. [Conclusions]: These facilitative effects, beyond the reduction of competition between functionally similar species, might ensure positive and long-lasting effects of biotic interactions, implying a more critical role for facilitation in preserving biodiversity than previously thought.

Facilitative interactions bind community species in intricate ecological networks, preserving species that would otherwise be lost. The traditional understanding of ecological networks as static components of biological communities overlooks the fact that species interactions in a network can fluctuate. Analyzing the patterns that cause those shifts can reveal the principles that govern the identity of pairwise interactions and whether they are predictable based on the traits of the interacting species and the local environmental contexts in which they occur. Here we explore how abiotic stress and phylogenetic and functional affinities constrain those shifts. Specifically, we hypothesize that rewiring the facilitative interactions is more limited in stressful than in mild environments. We present evidence of a distinct pattern in the rewiring of facilitation-driven communities at different stress levels. In highly stressful environments with a firm reliance on facilitation, rewiring is limited to growing beneath nurse species with traits to overcome harsh stressful conditions. However, when environments are milder, rewiring is more flexible, although it is still constrained to nurses that are close relatives. Understanding the ability of species to rewire their interactions is crucial for predicting how communities may respond to the unprecedented rate of perturbations on Earth.

Our aim was to register and characterize, throughout bibliographic review of published databases, the mycorrhizal type (AM, ECM, ERM, NM, AM+NM, ECM+NM,ERM+NM, ECM+AM+NM) and status (OM, FM, NM) of Mediterranean woody plant species sampled across the Andalusian Red Natura 2000. Here, we included a total of 243 plant species sampled across 38 plant communities from 19 protected areas distributed within the Andalusian RedNatura 2000.

Our aim was to characterize the composition and cover of dominant woody plant species, with the capacity to act as nurse plants, in plant communities across the Andalusian Red Natura 2000 (Directiva Habitats 92/43/CEE). The study was developed in 38 plant communities across 19 protected areas distributed within the Andalusian RedNatura 2000. The present dataset can help to assess plant community dynamics of Mediterranean woody species. Here, we stress the importance incorporating abundance or cover for all co-occurring woody species together with ecological interactions, not just individual records, as key elements in assessing the state of ecosystems.

Our aim was to register the frequency of plant-plant interactions, between canopy and recruiting species, in plant communities across the Andalusian Red Natura 2000. The study was developed in 38 plant communities across 19 protected areas in the Andalusian RedNatura 2000. The present dataset can help to assess plant community dynamics of Mediterranean woody species through recruitment networks. Here, we stress the importance of recording ecological interactions, not just individual records, as key elements in assessing the state of ecosystems.

Phenological segregation among species in a community is assumed to promote coexistence, as using resources at different times reduces competition. However, other unexplored nonalternative mechanisms can also result in a similar outcome. This study first tests whether plants can redistribute nitrogen (N) among them based on their nutritional temporal demand (i.e. phenology). Field 15N labelling experiments showed that 15N is transferred between neighbour plants, mainly from low N-demand (late flowering species, not reproducing yet) to high N-demand plants (early flowering species, currently flowering-fruiting). This can reduce species' dependence on pulses of water availability, and avoid soil N loss through leaching, having relevant implications in the structuring of plant communities and ecosystem functioning. Considering that species phenological segregation is a pervasive pattern in plant communities, this can be a so far unnoticed, but widely spread, ecological process that can predict N fluxes among species in natural communities, and therefore impact our current understanding of community ecology and ecosystem functioning.

Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.

Predicting coexistence patterns is a current challenge to understand diversity maintenance, especially in rich communities where these patterns' complexity is magnified through indirect interactions that prevent their approximation with classical experimental approaches. We explore cutting-edge Machine Learning techniques called Generative Artificial Intelligence (GenAI) to predict species coexistence patterns in vegetation patches, training generative adversarial networks (GAN) and variational AutoEncoders (VAE) that are then used to unravel some of the mechanisms behind community assemblage. The GAN accurately reproduces real patches' species composition and plant species' affinity to different soil types, and the VAE also reaches a high level of accuracy, above 99%. Using the artificially generated patches, we found that high-order interactions tend to suppress the positive effects of low-order interactions. Finally, by reconstructing successional trajectories, we could identify the pioneer species with larger potential to generate a high diversity of distinct patches in terms of species composition. Understanding the complexity of species coexistence patterns in diverse ecological communities requires new approaches beyond heuristic rules. Generative Artificial Intelligence can be a powerful tool to this end as it allows to overcome the inherent dimensionality of this challenge.

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the sci

Plants’ responses to conficting stresses may result in physiological trade-ofs due to the inter-dependent and costly nature of physiological investments. Physiological tradeofs have been proved within species, but to what extent these trade-ofs are the result of phylogenetic constraints remains poorly known. Environmental stresses can vary widely in diferent biomes, and therefore assessing physiological tradeofs across species must account for this variation. One way of doing so is to assess it within a community, where the co-occurring species have faced a shared combination of flters to establish. Considering a representative sample of species in a single community, we use a macroevolutionary approach to test the hypothesis that plant physiological trade-ofs are evolutionarily conserved within this community (i.e., closely-related species tend to solve the trade-ofs similarly). We analyze the content of fve metabolites in thirty co-occurring plant species, capturing their range of contrasting exposures to abiotic and biotic stresses (growing solitary and in vegetation patches). Our results support that species investment in response to abiotic stress (i.e., proline and abscisic acid content) is traded of against their investment to face biotic stress (i.e., jasmonic acid and salicylic acid), shown by the contrasting loadings of these two groups of metabolites in the frst axes of a principal component analysis (PCA). In addition, the metabolic strategies observed in this community are evolutionarily conserved, as closely related species tend to have similar scores in this PCA, and thus resemble each other in their balance. This is shown by a signifcant phylogenetic signal in the species’ scores along the frst axes of the PCA. Incorporating the evolutionary history of plant species into physiological studies can help to understand the response of plants to multiple stresses currently acting in ecological communities.

The structure of plant communities is often influenced by facilitative interactions where ‘facilitated’ plants benefit from growing associated with ‘nurse’ plants. Facilitation has been mostly studied from the facilitated plant's perspective, and bidirectional effects between nurse and facilitated plants have received less attention. We hypothesized that reciprocal benefits in plant-plant interactions may emerge when interactions are considered along the life-span of the plants involved. Over one spring, we selected five species with similar life-form and growth strategy, and using a full factorial design, we compared different fitness components along the plants’ life-span (seedling establishment, juvenile growth and reproductive investment in adult plants). We compared: a) plants growing in solitary stands and associated with other plants in vegetation patches; and b) plants that originally functioned as nurse plant (the largest plant of the vegetation patch) and as facilitated (not the largest plant of the vegetation patch). At an early developmental stage, facilitated plants growing in vegetation patches displayed higher seedling establishment and juvenile growth compared to solitary conspecific plants. At a later developmental stage, nurse plants in vegetation patches experienced higher reproductive investment (measured as flower production relative to plant size) compared to solitary plants, while the originally facilitated plants showed similar reproductive investment compared to their solitary pair of similar size. Facilitation is likely a complex interaction in which reciprocal benefits for both facilitated and nurse plants can be detected when interactions are considered along the plants’ life-span. Our results suggest that mutual benefits in plant-plant interactions could be important to sustain diversity in plant communities, but they appeared overlooked and deserve further attention.

Although ecological networks are usually considered a static representation of species’ interactions, the interactions can change when the preferred partners are absent (rewiring). In mutualistic networks, rewiring with non-preferred partners can palliate extinction cascades, contributing to communities’ stability. In spite of its significance, whether general patterns can shape the rewiring of ecological interactions remains poorly understood. Here, we show a phylogenetic constraint in the rewiring of mycorrhizal networks, so that rewired interactions (i.e., with non-preferred hosts) tend to involve close relatives of preferred hosts. Despite this constraint, rewiring increases the robustness of the fungal community to the simulated loss of their host species. We identify preferred and non-preferred hosts based on the probability that, when the two partners co-occur, they actually interact. Understanding general patterns in the rewiring of interactions can improve our predictions of community responses to interactions’ loss, which influences how global changes will affect ecosystem stability.

Co-occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co-existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co-occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co-occurrence networks to identify pairs of significantly associated taxa, either co-existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat-filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co-occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.

Mycorrhizal symbiosis has important implications for the diversity and productivity of plant communities. However, our mechanistic understanding of its influence on the outcome of plant-plant interactions is still expanding. In this review we propose a framework that might be useful to efficiently approach the effects of mycorrhizal fungi (MF) on plant-plant interactions. We propose several scenarios that can theoretically result in different outcomes of plant-plant interactions based on the combination of two processes: the diversity of resources provided by MF taxa to their host (resource dissimilarity) and contrasting ways of distributing those resources (resource distribution). Then, we illustrate our arguments with different ecological contexts where certain combinations of these two processes are prone to occur. The proposed framework suggests testable hypotheses that can contribute to elucidate relevant processes underlying the effects of mycorrhizal symbiosis on plant-plant interactions.

R code (R v. 3.5.2) to perform the simulations to assess whether the rewiring of mycorrhizae interactions is phylogenetically conserved (i.e. the non-preferred hosts tend to be close relatives to the preferred hosts).

The tendency of closely related plant species to share natural enemies has been suggested to limit their co-occurrence and performance, but we lack a deep understanding on how mutualistic interactions such as the mycorrhizal symbiosis affect plant–plant interactions depending on the phylogenetic relatedness of the interacting plants. We hypothesise that the effect of the mycorrhizal symbiosis on plant-plant facilitative interactions depends on the phylogenetic distance between the nurse and facilitated plants. A recently published meta-analysis compiled the strength of plant facilitative interactions in the presence or absence (or reduced abundance) of mycorrhizal fungi. We use phylogeneti- cally informed Bayesian linear models to test whether the effect size is influenced by the phy- logenetic distance between the plant species Conspecific facilitative interactions are more strongly enhanced by mycorrhizal fungi than interactions between closely related species. In heterospecific interactions, the effect of the mycorrhizal symbiosis on plant facilitation increases with the phylogenetic distance between the nurse and facilitated plant species. Our result showing that the effect of mycorrhizal symbiosis on the facilitation interactions between plants depends on their phylogenetic relatedness provides new mechanisms to understand how facilitation is assembling ecological communities