Jose M Montoya

• French National Centre for Scientific Research

Temperature regulates the physiology and behaviour of organisms. Thus, changing temperatures impact the dynamics of species interactions. Considering that consumer–resource interactions underpin ecological communities, the impacts of warming on the stability of consumer–resource interactions have been extensively studied. However, a consensus among...

Decision-makers need to act now to halt biodiversity loss, and ecologists must provide them with relevant species interaction indicators to inform on community- and ecosystem-level changes. Yet, the integration of ecological networks into conservation is still virtually nonexistent. Here, we discuss challenges and opportunities related to uncertain...

Revealing the effects of multiple global change drivers on ecosystem dynamics and functioning is a crucial endeavour, which necessitates the use of appropriate tools. Here, we present the Aquatic Metatron, a unique mesocosm facility providing a large‐scale experimental resource to study the combined effects of global change components, in particula...

Microplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found tha...

Theory predicts that morphological and bioenergetic constraints due to temperature-induced body size reduction can modulate the direct effects of warming on biotic interactions, with consequent effects on trophic cascades and biomass distribution. However, these theoretical predictions have rarely been tested empirically. Our aim was to distinguish...

The implementation of Wastewater Treatment Plants (WWTPs) brought great improvement in river ecological status. However, WWTP effluents still contain a complex cocktail of pollutants whose environmental effects might go unnoticed, masked by other stressors in the receiving waters or by spatiotemporal variability. We conducted a BACI (Before-After/C...

Water diversion and pollution are two pervasive stressors for river ecosystems that often co‐occur. The individual effects of both stressors on river communities and energy transfer across the food webs are well described; however, how they interact remains unknown. We hypothesised that low‐to‐moderate nutrient pollution gradient would cause a mild...

Understanding the interaction between evolutionary history, the abiotic environment, and biotic interactions is critical for a more nuanced understanding of how communities respond to anthropogenic stressors. We leveraged a long term experiment manipulating temperature in mesocosms containing communities of phytoplankton and zooplankton to examine...

Temperature regulates the physiology and behaviour of organisms. Thus, changing temperatures induce dynamics in species interactions. Considering that consumer-resource interactions underpin ecological communities, the impacts of warming on the stability of consumer-resource interactions have been extensively studied. However, a consensus among emp...

Virus transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator–prey relationships, may govern rates and patterns of cross-species virus transmission and hence zoonotic risk. To address the impact of host phylogeny and ecology on virus di...

Wastewater treatment plants (WWTPs) have greatly improved water quality globally. However, treated effluents still contain a complex cocktail of pollutants whose environmental effects might go unnoticed, masked by additional stressors in the receiving waters or by spatiotemporal variability. We conducted a BACI (Before-After/Control-Impact) ecosyst...

Changing temperatures will impact food webs in ways we yet to fully understand. The thermal sensitivities of various physiological and ecological processes differ across organisms and study systems, hindering the generation of accurate predictions. One step towards improving this picture is to acquire a mechanistic understanding of how temperature...

Land use change and nutrient pollution are two pervasive stressors that can modify carbon cycling, as they influence the inputs and the transformation of detritus. Understanding their impact on stream food webs and on diversity is particularly pressing, as streams are largely fuelled by detrital material received from the adjacent riparian environm...

Aim Species geographical range sizes play a crucial role in determining species vulnerability to extinction. Although several mechanisms affect range sizes, the number of biotic interactions and species climatic tolerance are often thought to play discernible roles, defining two dimensions of the Hutchinsonian niche. Yet, the relative importance of...

Global change encompasses many co‐occurring anthropogenic drivers, which can act synergistically or antagonistically on ecological systems. Predicting how different global change drivers simultaneously contribute to observed biodiversity change is a key challenge for ecology and conservation. However, we lack the mechanistic understanding of how mu...

Viral transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern cross-species virus transmission and zoonotic risk, although their relative impact is unknown. By characterising the virome of a relatively iso...

Larger geographical areas contain more species—an observation raised to a law in ecology. Less explored is whether biodiversity changes are accompanied by a modification of interaction networks. We use data from 32 spatial interaction networks from different ecosystems to analyse how network structure changes with area. We find that basic community...

Water diversion and pollution are two pervasive stressors in river ecosystems that often co‐occur. Individual effects of both stressors on basal resources available to stream communities have been described, with diversion reducing detritus standing stocks and pollution increasing biomass of primary producers. However, interactive effects of both s...

Temperature and nutrients are two of the most important drivers of global change. Both can modify the elemental composition (i.e. stoichiometry) of primary producers and consumers. Yet their combined effect on the stoichiometry, dynamics and stability of ecological communities remains largely unexplored. To fill this gap, we extended the Rosenzweig...

Significance The combined acceleration of climate change and biodiversity loss necessitates understanding how ecosystem functions and services will be affected. Most studies focus on the effects of increasing mean temperatures, but climate change will increase temperature fluctuations too. We performed an experiment and developed a model to underst...

Changes in temperature affect consumer–resource interactions, which underpin the functioning of ecosystems. However, existing studies report contrasting predictions regarding the impacts of warming on biological rates and community dynamics. To improve prediction accuracy and comparability, we develop an approach that combines sensitivity analysis...

Biological insurance theory predicts that, in a variable environment, aggregate ecosystem properties will vary less in more diverse communities because declines in the performance or abundance of some species or phenotypes will be offset, at least partly, by smoother declines or increases in others. During the past two decades, ecology has accumula...

Eco‐evolutionary dynamics can mediate species and community responses to habitat warming and fragmentation, two of the largest threats to biodiversity and ecosystems. The eco‐evolutionary consequences of warming and fragmentation are typically studied independently, hindering our understanding of their simultaneous impacts. Here, we provide a new p...

A Correction to this paper has been published: https://doi.org/10.1038/s41559-021-01419-x.

Aim The aim was to evaluate the effects of climate warming on biodiversity across spatial scales (i.e., α‐, β‐ and γ‐diversity) and the effects of patch openness and experimental context on diversity responses. Location Global. Time period 1995–2017. Major taxa studied Fungi, invertebrates, phytoplankton, plants, seaweed, soil microbes and zoopl...

Climate warming and biological invasions are key drivers of biodiversity change. Their combined effects on ecological communities remain largely unexplored. We investigated the direct and indirect influences of temperature on invasion success, and their synergistic effects on community structure and dynamics. Using size-structured food web models,...

Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity–ecosystem function (iBEF) relationships have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer (Phoxinus phoxinus) to test whether iBEF relationshi...

The species–area relationship (SAR) is one of the most well‐established scaling patterns in ecology. Its implications for understanding how communities change across spatial gradients are numerous, including the effects of habitat loss on biodiversity. However, ecological communities are not mere collections of species. They are the result of inter...

Changes in temperature affect consumer-resource interactions which underpin the functioning of ecosystems. However, existing studies report contrasting predictions regarding the impacts of warming on biological rates and community dynamics. To improve prediction accuracy and comparability, we develop a framework that combines two approaches: sensit...

Temperature variability and extremes can have profound impacts on populations and ecological communities. Predicting impacts of thermal variability poses a challenge, because it has both direct physiological effects and indirect effects through species interactions. In addition, differences in thermal performance between predators and prey and nonl...

To understand ecosystem responses to anthropogenic global change, a prevailing framework is the definition of threshold levels of pressure, above which response magnitudes and their variances increase disproportionately. However, we lack systematic quantitative evidence as to whether empirical data allow definition of such thresholds. Here, we summ...

Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a cor...

Climate warming and biological invasions are key drivers of biodiversity change. Their combined effects on ecological communities remain largely unexplored. We investigated the direct and indirect influences of warming on invasion success, and their synergistic effects on community structure and dynamics. Using size-structured food web models, we f...

A bstract Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity-ecosystem function relationships (iBEF) have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer ( Phoxinus phoxinus ), to test whether iBE...

Temperature variability and extremes can have profound impacts on populations and ecological communities. Predicting impacts of thermal variability poses a challenge because it has both direct physiological effects and indirect effects through species interactions. In addition, differences in thermal performance between predators and prey and non-l...

A rich body of knowledge links biodiversity to ecosystem functioning (BEF), but it is primarily focused on small scales. We review the current theory and identify six expectations for scale dependence in the BEF relationship: (1) a nonlinear change in the slope of the BEF relationship with spatial scale; (2) a scale‐dependent relationship between e...

The terms sustainability, resilience and others group under the heading of ‘stability’. Their ubiquity speaks to a vital need to characterize changes in complex social and environmental systems. In a bewildering array of terms, practical measurements are essential to permit comparisons and so untangle underlying relationships.

Aim Although much has been said on the spatial distribution of taxonomic and phylogenetic diversity of vertebrates, how this diversity interacts in food webs and how these interactions change across space are largely unknown. Here, we analysed the spatial distribution of tetrapod food webs and asked whether the variation in local food web structure...

Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Her...

Habitat loss (HL) affects species and their interactions, ultimately altering community dynamics. Yet, a challenge for community ecology is to understand how communities with multiple interaction types—hybrid communities—respond to HL prior to species extinctions. To this end, we develop a model to investigate the response of hybrid terrestrial com...

A bstract Temperature and nutrients are two of the most important drivers of global change. Both can modify the elemental composition (i.e. stoichiometry) of primary producers and consumers. Yet their combined effect on the stoichiometry, dynamics, and stability of ecological communities remains largely unexplored. To fill this gap, we extended the...

Research on the structure of ecological networks suggests that a number of universal patterns exist. Historically, biotic specialization has been thought to increase towards the Equator. Yet, recent studies have challenged this view showing non‐conclusive results. Most studies analysing the geographical variation in biotic specialization focus, how...

Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbi...

Classic evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes, and high partner fidelity between host species and their vertically transmitted microbe...

In addition to the processes structuring free‐living communities, host‐associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host‐specific factors, often spanning multiple levels of biological organization. Cu...

Species-area relationships (SARs) are pivotal to understand the distribution of biodiversity across spatial scales. We know little, however, about how the network of biotic interactions in which biodiversity is embedded changes with spatial extent. Here we develop a new theoretical framework that enables us to explore how different assembly mechani...

Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species, including a widespread presence of nestedness. The nested structure of these webs seems to be positively correlated with higher diversity and resilience. Moreover, these webs exhibit marked measurable structural patterns, including broad...

Adaptive Food Webs is a synthesis of talks from the fourth decadal conference on food webs, after the publishing of the seminal book by Robert May entitled Stability and Complexity in Model Ecosystems. It embraces the notion of food webs as being complex adaptive systems by exploring dynamic structures and processes, through both changes in externa...

The notion of a 'safe operating space for biodiversity' is vague and encourages harmful policies. Attempts to fix it strip it of all meaningful content. Ecology is rapidly gaining insights into the connections between biodiversity and ecosystem stability. We have no option but to understand ecological complexity and act accordingly.

The effect of biodiversity on ecosystem functioning is one of the major questions of ecology. However, the role of phytoplankton functional diversity in ecosystem productivity and stability under fluctuating (i.e. non-equilibrium) environments remains largely unknown. Here we use a marine ecosystem model to study the effect of phytoplankton functio...

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of spon...

The long-term stability of microbiomes is crucial as the persistent occurrence of beneficial microbes and their associated functions ensure host health. Microbiomes are highly diverse and dynamic, but are they complex to the point of being impossible to understand? We present an approach that while embracing this complexity it allows to identifying...

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Cu...

The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a 'core' microbiota approach, focusing only on the stable and permanent members of the community, is becoming inc...

Introduction Species interaction network studies and biogeography have evolved independently from each other, although some remarkable exceptions exist. The prevailing wisdom is that biotic interactions rule in local-scale networks while large spatial scales are the province of climate. In this chapter we suggest that this and other cross-disciplin...

Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is a strong correlation between the patterning of animal-plant interactions and their phylogenetic organisation....

Ecological stability is a bewildering broad concept. The most common stability measures are asymptotic resilience, widely used in theoretical studies, and measures based on temporal variability, commonly used in empirical studies. We construct measures of invariability, defined as the inverse of variability, that can be directly compared with asymp...

1. Trophic cascade theory predicts that apex predators structure ecosystems by regulating mesopredator and herbivore abundance and behaviour. Studies on trophic cascades have typically focused on short linear chains of species interactions. A framework that integrates more realistic and complex interactions is needed to make broader predictions on...

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contribut...

Representative sequences and taxonomy of OTUs.

Supplementary Figures 1-8 and Supplementary Tables 1-2

Metadata for sponge samples analysed in the current study.

Diversity and richness of sponge species.

Human actions challenge nature in many ways. Ecological responses are ineluctably complex, demanding measures that describe them succinctly. Collectively, these measures encapsulate the overall ‘stability’ of the system. Many international bodies, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, broadl...