Species Interaction Networks Research Articles

Restaurando la funcionalidad de los ecosistemas: la importancia de las interacciones entre especies

Sobral, M., Magrach, A. 2019. Restoration of ecosystem functionality: the value of species interactions. Ecosistemas 28(2): 4-10. Doi.: 10.7818/ECOS.1737 Restoration of natural ecosystems has traditionally focused on recovering specific richness to recover ecosystem functionality. However, species within a natural ecosystem are not isolated, they interact with others forming complex ecological networks. We know that human activities (such as selective logging or agriculture expansion) modify the structure of these interaction networks, with important effects on the functionality of ecosystems. Despite this, we still do not know whether techniques implemented today are able to restore the structure of these networks and their related functionality. In this article, we expose the reasons why we believe that restoration should consider the structure of the networks of species interactions. We review how the different types of disturbances affect this structure and we propose possible avenues for the study and application of these ideas. We hope that this perspective will help improve the management of the natural environment in response to global change.

A new model explaining the origin of different topologies in interaction networks.

Nestedness and modularity have been recurrently observed in species interaction networks. Some studies argue that those topologies result from selection against unstable networks, and others propose that they likely emerge from processes driving the interactions between pairs of species. Here we present a model that simulates the evolution of consumer species using resource species following simple rules derived from the integrative hypothesis of specialization (IHS). Without any selection on stability, our model reproduced all commonly observed network topologies. Our simulations demonstrate that resource heterogeneity drives network topology. On the one hand, systems containing only homogeneous resources form generalized nested networks, in which generalist consumers have higher performance on each resource than specialists. On the other hand, heterogeneous systems tend to have a compound topology: modular with internally nested modules, in which generalists that divide their interactions between modules have low performance. Our results demonstrate that all real-world topologies likely emerge through processes driving interactions between pairs of species. Additionally, our simulations suggest that networks containing similar species differ from heterogeneous networks and that modules may not present the topology of entire networks.

Global estimates of mammalian viral diversity accounting for host sharing.

Present estimates suggest there are over 1 million virus species found in mammals alone, with about half a million posing a possible threat to human health. Although previous estimates assume linear scaling between host and virus diversity, we show that ecological network theory predicts a non-linear relationship, produced by patterns of host sharing among virus species. To account for host sharing, we fit a power law scaling relationship for host-virus species interaction networks. We estimate that there are about 40,000 virus species in mammals (including ~10,000 viruses with zoonotic potential), a reduction of two orders of magnitude from present projections of viral diversity. We expect that the increasing availability of host-virus association data will improve the precision of these estimates and their use in the sampling and surveillance of pathogens with pandemic potential. We suggest host sharing should be more widely included in macroecological approaches to estimating biodiversity.

Dryland Organic Farming Partially Offsets Negative Effects of Highly Simplified Agricultural Landscapes on Forbs, Bees, and Bee-Flower Networks.

Industrialized farming practices result in simplified agricultural landscapes, reduced biodiversity, and degraded species-interaction networks. Thus far, most research assessing the combined effects of farming systems and landscape complexity on beneficial insects has been conducted in relatively diversified and mesic systems and may not represent the large-scale, monoculture-based dryland agriculture that dominates many regions worldwide. Specifically, the effects of farming systems on forbs, bees, and their interactions are poorly understood in highly simplified dryland landscapes such as those in the Northern Great Plains, United States, an area globally important for conventional and organic small grain, pulse, forage, and oilseed production. During a 3-yr (2013-2015) study, we assessed 1) the effects of dryland no-till conventional and tilled organic farming on forbs, bees, and bee-flower networks and 2) the relationship between natural habitat and bee abundance. Flower density and richness were greater in tilled organic fields than in no-till conventional fields, and forb community composition differed between farming systems. We observed high bee diversity (109 taxa) in this highly simplified landscape, and bee abundance, richness, and community composition were similar between systems. Compared with tilled organic fields, bee-flower interactions in no-till conventional fields were poorly connected, suggesting these systems maintain relatively impoverished plant-pollinator networks. Natural habitat (11% of the landscape) did not affect small-bodied bee abundance in either farming system but positively affected large-bodied bees within 2,000 m of crop-field centers. In highly simplified agricultural landscapes, dryland organic farming and no-till conventional farming together support relatively high bee diversity, presumably because dryland organic farming enhances floral resources and bee-flower networks, and no-till management in conventional farming provides undisturbed ground-nesting habitats for wild bees (Hymenoptera: Apoidea).

Optimal Microbiome Networks: Macroecology and Criticality.

The human microbiome is an extremely complex ecosystem considering the number of bacterial species, their interactions, and its variability over space and time. Here, we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model, we detected potential species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detected an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and how these should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest Pareto total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not necessarily at the phase transition between healthy and unhealthy states. We stress the importance of considering portfolios of interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their interactions (i.e., species collective behavior) that shape transition from healthy to unhealthy states. The macroecological characterization of the microbiome is useful for public health and disease diagnosis and etiognosis, while species-specific analyses can detect beneficial species leading to personalized design of pre- and probiotic treatments and microbiome engineering.

Coexistence theory as a tool to understand biological invasions in species interaction networks: Implications for the study of novel ecosystems

Abstract Questions related to understanding which characteristics of the recipient communities make them vulnerable to invasion (i.e. invasibility) are commonly formulated in such a way that they consider ecological communities as whole entities. Yet, species within recipient communities have specific responses to the introduction of exotic species. As a consequence, little is known about the role of species interaction networks within and between trophic levels in determining the invasion likelihood of exotics introduced in previously uninvaded communities and the temporal dynamics of invaded communities. To obtain a mature understanding of invasion processes and their impacts, I propose here to apply a structural stability approach of species coexistence to the field of biological invasions. The main aim here is to distinguish how direct and indirect species’ responses to invasion in competitive and trophic networks translate to the mechanisms determining the maintenance and stability of species diversity in multispecies and multitrophic assemblages. This approach brings the further opportunity to integrate the field of biological invasions within a broader perspective about the study of novel ecosystems, that is, ecosystems that contain exotic species and face new introductions sometimes under abrupt environmental changes. Moreover, it can help to target specific mechanisms separating winners from losers in novel ecosystems. Synthesis. A solid framework to predict biological invasions and understand community assembly along temporal scales under novel ecosystems can be obtained by framing species’ responses to invasion within recent theoretical and methodological advances stemming from coexistence theory, which seeks to determine how diversity is maintained. A plain language summary is available for this article.

Coevolutionary dynamics shape the structure of bacteria-phage infection networks.

Coevolution-reciprocal evolutionary change among interacting species driven by natural selection-is thought to be an important force in shaping biodiversity. This ongoing process takes place within tangled networks of species interactions. In microbial communities, evolutionary change between hosts and parasites occurs at the same time scale as ecological change. Yet, we still lack experimental evidence of the role of coevolution in driving changes in the structure of such species interaction networks. Filling this gap is important because network structure influences community persistence through indirect effects. Here, we quantified experimentally to what extent coevolutionary dynamics lead to contrasting patterns in the architecture of bacteria-phage infection networks. Specifically, we look at the tendency of these networks to be organized in a nested pattern by which the more specialist phages tend to infect only a proper subset of those bacteria infected by the most generalist phages. We found that interactions between coevolving bacteria and phages become less nested over time under fluctuating dynamics, and more nested under arms race dynamics. Moreover, when coevolution results in high average infectivity, phages and bacteria differ more from each other over time under arms race dynamics than under fluctuating dynamics. The tradeoff between the fitness benefits of evolving resistance/infectivity traits and the costs of maintaining them might explain these differences in network structure. Our study shows that the interaction pattern between bacteria and phages at the community level depends on the way coevolutionunfolds.

Modularity and predicted functions of the global sponge-microbiome network

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 microbiome assembly are largely unknown. We present the global marine sponge–microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated ‘core’ microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.

Long-term cleaning patterns of the sharknose goby (Elacatinus evelynae)

Cleaning interactions, which involve a cleaner removing ectoparasites and other material from the body of a heterospecific (client), are iconic symbiotic interactions observed on coral reefs worldwide. These small cleaners play a disproportionately large role in the structuring and function of coral reefs, influencing species interaction networks, client health and biodiversity. Cleaning patterns, however, are likely to be context-dependent and highly heterogeneous, and although we have some understanding about their spatial variation, longer-term temporal changes in cleaning interactions have remained understudied. Given that coral reefs are globally threatened and are currently experiencing large shifts in their biodiversity, it is vital that we determine which clients are consistently most important for maintaining cleaning. Using a long-term, 8-yr data set (2010–17) on the cleaning behaviour of the predominant Caribbean cleaner, the sharknose goby (Elacatinus evelynae), we investigated whether cleaner fish from the same reef show consistent patterns in their interactions with client species over time. Here we conclusively show that cleaning behaviour is highly plastic, as no single species or family was cleaned consistently more than others, in terms of cleaning frequency and duration, across all years. Only 40% of the species were cleaned more than others, and we also observed ca. one-third of species experience inconsistent cleaning patterns across years. Our study thus quantifies how dynamic cleaner–client relationships are on the same reef across years and highlights the importance of long-term data.

Fire, grazing and climate shape plant–grasshopper interactions in a tallgrass prairie

Abstract Species interactions are integral to ecological community function, and the structure of species interactions has repercussions for the consequences of species extinctions. Few studies have examined the role of environmental factors in controlling species interaction networks across time. We examined variation in plant–grasshopper network structural properties in response to three major grassland drivers: periodic fire, ungulate grazing and climate. We sequenced a plant barcoding gene from extracted grasshopper gut contents to characterize diets of 26 grasshopper species. Resulting grasshopper species’ diets were combined with long‐term plant and grasshopper surveys to assemble plant–grasshopper networks across 13–19 years for six watersheds subjected to varying fire and grazing treatments. Network modularity, generality and predicted grasshopper community robustness to plant species loss all increased in grazed watersheds. Temperature decreased predicted grasshopper community robustness to plant species loss. Grasshopper communities were found to be vulnerable to climatic warming due to host plant loss. However, intermediate disturbance from ungulate grazers may maintain grasshopper diversity and buffer community robustness to species loss. Our results suggest that climate and disturbance shape the structure of ecological interaction networks and thus have many indirect effects on species persistence though direct effects on interaction partners. A plain language summary is available for this article.

Functional responses of avian frugivores to variation in fruit resources between natural and fragmented forests

Abstract Partner choice in species interaction networks, that is, between frugivorous birds and fruiting plants, is largely determined by matching of functional traits. However, the composition of functional traits in plant communities changes along land‐use gradients. Understanding how flexible consumers react to changes in the trait composition of resources is crucial to project consequences for ecosystem functions, such as seed dispersal. We investigated the ability of birds to consume fruits with different sets of traits in natural and fragmented tropical montane forests across an elevational gradient. We developed a novel, trait‐based approach to quantify the functional shifts of consumers between resources with different functional traits. We expected the degree of functional shifts to be associated with bird traits related to food choice, such as bill width and degree of frugivory, as well as foraging behaviour, such as wing shape and foraging stratum. We sampled the plant–frugivore networks at three elevations and two habitat types (natural and fragmented forest) and measured the functional traits for each plant and bird species. We calculated the trait space of the plant community at each elevation and projected the interacting birds into it. Finally, we calculated the functional shift, which is the trait‐based distance between the preferred fruit resources in the two habitat types for each bird species. We found differences in the functional trait space of the fruiting plant community between natural and fragmented forests across all elevations. Birds' observed functional shifts between habitat types at each elevation were generally larger than the shifts expected by null models. Wing shape was the most important trait related to the functional shifts across the elevational gradient, whereas bill width, degree of frugivory, foraging stratum and phylogeny were not important. We conclude that birds with pointed wings respond flexibly to changes in the trait composition of fruit resources, probably due to the high mobility of these species. Our results emphasize that linking species interaction networks and functional trait analyses yield new insights into how consumer species respond to changes in biotic factors and can improve projections of how human impacts modify trophic interactions and associated ecosystem functions. A plain language summary is available for this article.

Seeing the forest for the trees: Putting multilayer networks to work for community ecology

Abstract A framework for the description and analysis of multilayer networks is established in statistical physics, and calls are increasing for their adoption by community ecologists. Multilayer networks in community ecology will allow space, time and multiple interaction types to be incorporated into species interaction networks. While the multilayer network framework is applicable to ecological questions, it is one thing to be able to describe ecological communities as multilayer networks and another for multilayer networks to actually prove useful for answering ecological questions. Importantly, documenting multilayer network structure requires substantially greater empirical investment than standard ecological networks. In response, we argue that this additional effort is worthwhile and describe a series of research lines where we expect multilayer networks will generate the greatest impact. Inter‐layer edges are the key component that differentiate multilayer networks from standard ecological networks. Inter‐layer edges join different networks—termed layers—together and represent ecological processes central to the species interactions studied (e.g., inter‐layer edges representing movement for networks separated in space). Inter‐layer edges may take a variety of forms, be species‐ or network‐specific, and be measured with a large suite of empirical techniques. Additionally, the sheer size of ecological multilayer networks also requires some changes to empirical data collection around interaction quantification, collaborative efforts and collation in public databases. Network ecology has already touched on a wide swath of ecology and evolutionary biology. Because network stability and patterns of species linkage are the most developed areas of network ecology, they are a natural starting place for multilayer investigations. However, multilayer networks will also provide novel insights to niche partitioning, the connection between traits and species’ interactions, and even the geographic mosaic of co‐evolution. Synthesis. Multilayer networks provide a formal way to bring together the study of species interaction networks and the processes that influence them. However, describing inter‐layer edges and the increasing amounts of data required represent challenges. The pay‐off for added investment will be ecological networks that describe the composition and capture the dynamics of ecological communities more completely and, consequently, have greater power for understanding the patterns and processes that underpin diversity in ecological communities. A plain language summary is available for this article.

A unified concept of dominance applicable at both community and species scales

AbstractDominance and evenness can be two sides of the same coin or opposite ends of a spectrum. Although evenness and diversity are community‐level concepts, dominance can be applied at both community and species scales. Nevertheless, there is not a metric applicable at both these scales that are unified with a single mathematical framework in the existing literature. Here, by extending Lloyd's meaning crowding concept from the population to community scale, we propose a dominance concept and associated metrics that are applicable at both scales. Such metrics can act as proxies for diversity in diversity–stability and diversity–ecosystem service analyses or for population abundance in species interaction network analysis and population stability analysis, with advantages in cross‐scale and unified analyses. Our concept of dominance includes three measures (metrics) that link communities and species. The metrics have the same mathematical form, but different interpretations at the community and species scales. Our community‐level metric is a function of Simpson's () diversity index, for which we present a rigorous mathematical proof. Our species‐level metrics quantify the difference between community dominance and the dominance of a virtual community whose mean population size, per species, equals the population size of the focal species. We demonstrate the use of these metrics using data from a longitudinal study of the human vaginal microbiome and provide new insights relevant for microbiome stability and disease etiology at the community scale. The new metrics also can be used for species dominance network (SDN) analysis at the species scale. Since the species dominance is a function of both species (population) abundance and community dominance, it has an advantage of capturing both community‐scale global and species‐scale local information, which becomes even more evident when it is used to construct SDNs. These results demonstrate the significance and applications of our unified dominance concept and metrics.

Frugivore biodiversity and complementarity in interaction networks enhance landscape‐scale seed dispersal function

Abstract Animal biodiversity matters for the provision of ecosystem functions derived from trophic activity. However, the mechanisms underlying this pattern remain elusive since animal abundance and diversity, which are the components commonly used for representing biodiversity, provide poor information about ecological complementarity in species assemblages. An approach based on species interaction networks may overcome this constraint. Here, we relate frugivore biodiversity and frugivore–plant network structure with landscape‐scale seed dispersal function. We sampled, for two years, and at fourteen plots with variable assemblages of frugivores and plants in the Cantabrian Range (N Spain), data on the abundance and diversity of frugivorous birds, the consumption of fleshy fruits of woody plants and the landscape‐scale patterns of avian seed deposition. As a measure of interaction complementarity in seed dispersal networks, we estimated the degree to which frugivore and plant species specialize in their interacting partners. Specialization varied strongly across the seed dispersal networks of the different plots, being higher in networks harbouring smaller bird species that dispersed mostly small‐fruited plants, and also in networks with late‐ripening, dominant fruiting species dispersed mostly by wintering birds. Bird abundance markedly affected seed deposition. Plots harbouring more birds received a higher density of dispersed seeds and showed higher probabilities of seed arrival and seed deposition in open microhabitats. Bird diversity also had a positive effect on the density of dispersed seed and, to a lesser extent, seed arrival probability. Independently of frugivore abundance and diversity, the density of dispersed seeds increased in plots where seed dispersal networks showed a higher degree of specialization. This study considers the structure of interaction networks to re‐address the relationship between biodiversity and ecosystem functionality, evidencing that specialization in frugivore–plant networks drives the large‐scale process of seed dispersal. These results encourage the consideration of interaction complementarity as an underlying mechanism linking animal biodiversity and trophic‐related functions.

Studying the sensory ecology of frog‐biting midges (Corethrellidae: Diptera) and their frog hosts using ecological interaction networks

AbstractInvestigating species interaction networks has advanced the understanding of the robustness of ecosystems, the impact of species invasions, resource partitioning and the coevolution of interacting species. Here, we present a 10‐year study of the relationships between frog‐biting midges (Corethrella) and their frog hosts in tropical lowland forests across northern Borneo. We use quantitative bipartite host‐ectoparasite networks to explore this unusual relationship. Across northern Borneo, nine species of frog‐biting midges were found to bite 29 species of frogs. Overall, 378 individual Corethrella were found on 93 individual frogs. We compare the network structure between two forest types in Brunei Darussalam: a lowland mixed‐dipterocarp rainforest and a peatswamp forest. Results indicate that both antagonistic interaction networks were relatively specialized at the community level and show significant nestedness. The degree of specialization was higher in the rainforest than in the peatswamp suggesting higher diversity of midge sensory perception and frog avoidance strategies in the rainforest. At the species level, the specialization of midges as well as their frog hosts was highly variable in both networks suggesting that some frog species are better at avoiding being bitten by Corethrella than others. Frog species parasitized by midges had calls of low dominant frequencies suggesting that the spectral bandwidth of hearing in midges could influence host selection. Despite this, some frog species that call above 4 kHz have not escaped parasitism. We explore the role of habitat filtering, behavior and coevolution in shaping network structure.

Trap nests for bees and wasps to analyse trophic interactions in changing environments—A systematic overview and user guide

Abstract Trap nests are artificially made nesting resources for solitary cavity‐nesting bees and wasps and allow easy quantification of multiple trophic interactions between bees, wasps, their food objects and natural enemies. We synthesized all trap nest studies available in the ISI Web of Science™ to provide a comprehensive overview of trap nest research and identify common practical challenges and promising future research directions. Trap nests have been used on all continents and across climate zones and publication numbers have increased exponentially since the first studies in the 1950s. Originally used for detailed exploratory natural history observations, trap nests are now also an established method in hypothesis‐driven ecology and to assess environmental changes. We identify the potential of trap nests for environmental monitoring by assessing trophic interaction networks of the groups involved. While pollen collection by bees or prey hunting by wasps has often been addressed, and interactions with natural enemies were included in almost half of all publications, surprisingly few studies have quantified trophic interaction networks in response to natural and anthropogenic environmental changes. By simultaneously revealing a multitude of trophic interactions, trap nests have the potential to broaden our understanding how species interaction networks are influenced by manifold environmental changes, which are pressing topics in ecological research. To foster the use of trap nests in future studies, we identify common challenges and offer guidance on practical solutions.

A continuum of dead wood with various habitat elements maintains the diversity of wood-inhabiting fungi in an old-growth boreal forest

Evidence on habitat associations of threatened wood-inhabiting species in boreal forests may contribute to a better understanding of their ecology and conservation needs. We examined the diversity of wood-inhabiting fungal communities in an old-growth boreal forest with high substrate availability and continuity based on repeated surveys of fruit bodies. The number of species in morphological and functional groups in relation to coarse woody debris (CWD) attributes was estimated with generalized linear models. Additionally, we calculated species interaction networks of CWD attributes and fungal species. The composition of fungal communities was analysed using a non-metric multidimensional scaling with subsequent environmental fitting. Old conifer (especially spruce) logs and large aspen logs with branches represented the most important substrates for the red-listed species and the indicator species of old-growth boreal forests. Among “dynamic” CWD attributes such as time since tree death, decay class and stage of epixylic succession, the latter was the most important indicator of diversity of all species and their morphological and functional groups. The interaction network provided evidence of the importance of tree species diversity for fungal diversity. The composition of fungal communities was tree species specific and related to dynamic attributes, bark cover and diameter of logs. Our results suggest the importance of a continuum of dead wood from different tree species with a variety of niches such as branches, exposed wood, fragmented and complete cover of bark and patches of epixylic vegetation to maintain the assemblages of wood-inhabiting fungi in an old-growth boreal forest.

A combinatorial analysis using observational data identifies species that govern ecosystem functioning.

Understanding the relationship between biodiversity and ecosystem functioning has so far resulted from two main approaches: the analysis of species' functional traits, and the analysis of species interaction networks. Here we propose a third approach, based on the association between combinations of species or of functional groups, which we term assembly motifs, and observed ecosystem functioning. Each assembly motif describes a biotic environment in which species interactions have particular effects on a given ecosystem function. Clustering species in functional groups generates a classification of ecosystems based on their assembly motif. We evaluate the quality of each species clustering, that is its ability to predict an ecosystem function, by the coefficient of determination of the ecosystem classification. An iterative process then enables identifying the species clustering in functional groups that best accounts for the functioning of the observed ecosystems. We test this approach using experimental and simulated datasets. We show that our combinatorial analysis makes it possible to identify the combinations of functional groups of species whose interactions govern ecosystem functioning without any a priori knowledge of the species themselves or their interactions. Our combinatorial approach reproduces the associative learning of empirical ecologists, and proves to be powerful and parsimonious.

Rethinking the importance of the structure of ecological networks under an environment-dependent framework.

A major quest in network and community ecology has been centered on understanding the importance of structural patterns in species interaction networks—the synthesis of who interacts with whom in a given location and time. In the past decades, much effort has been devoted to infer the importance of a particular structure by its capacity to tolerate an external perturbation on its structure or dynamics. Here, we demonstrate that such a perspective leads to inconsistent conclusions. That is, the importance of a network structure changes as a function of the external perturbations acting on a community at any given point in time. Thus, we discuss a research agenda to investigate the relative importance of the structure of ecological networks under an environment‐dependent framework. We hypothesize that only by studying systematically the link between network structure and community dynamics under an environment‐dependent framework, we can uncover the limits at which communities can tolerate environmental changes.

Analysing ecological networks of species interactions.

Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems - such as communities - through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theory also provides numerous approaches and measures to analyze these objects and can offer new perspectives on established ecological theories as well as tools to address new challenges. However, prior to using these methods to test ecological hypotheses, it is necessary that we understand, adapt, and use them in ways that both allow us to deliver their full potential and account for their limitations. Here, we attempt to increase the accessibility of network approaches by providing a review of the tools that have been developed so far, with - what we believe to be - their appropriate uses and potential limitations. This is not an exhaustive review of all methods and metrics, but rather, an overview of tools that are robust, informative, and ecologically sound. After providing a brief presentation of species interaction networks and how to build them in order to summarize ecological information of different types, we then classify methods and metrics by the types of ecological questions that they can be used to answer from global to local scales, including methods for hypothesis testing and future perspectives. Specifically, we show how the organization of species interactions in a community yields different network structures (e.g., more or less dense, modular or nested), how different measures can be used to describe and quantify these emerging structures, and how to compare communities based on these differences in structures. Within networks, we illustrate metrics that can be used to describe and compare the functional and dynamic roles of species based on their position in the network and the organization of their interactions as well as associated new methods to test the significance of these results. Lastly, we describe potential fruitful avenues for new methodological developments to address novel ecological questions.