Compartments in a marine food web associated with phylogeny, body mass, and habitat structure

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.     

The effects of energy input,immigration and habitat size on food web structure: a microcosm experiment

It has been hypothesised that larger habitats should support more complex food webs. We consider three mechanisms which could lead to this pattern. These are increased immigration rates, increased total productivity and spatial effects on the persistence of unstable interactions. Experiments designed to discriminate between these mechanisms were carried out in laboratory aquatic microcosm communities of protista and bacteria, by independently manipulating habitat size, total productivity and immigration rate. Larger habitats supported more complex food webs, with more species, more links per species and longer maximum and mean food chains, even in the absence of differences in total energy input. Increased immigration rate resulted in more complex food webs, but habitats with higher energy input per unit area supported less complex food webs. We conclude that spatial effects on the persistence of unstable interactions, and variation in immigration rates, are plausible mechanisms by which habitat size could affect food web structure. Variation in total productivity with habitat area seems a less likely explanation for variation in food web structure.     

Dynamics of compartmented and reticulate food webs in relation to energetic flows

Using simple food webs, we address how the interactions of food web structure and energetic flows influence dynamics. We examine the effect of food web topologies with equivalent energetics (i.e., trophic interactions are equivalent at each trophic level), following which we vary energetic flows to include weak and strong interactions or nonequivalent energetics. In contrast to some work (Pimm 1979), we find that compartmented webs are more stable than reticulate webs. However, we find that nonequivalent energetics can stabilize previously unstable reticulate structures. It is not only weak flows that can be stabilizing but also the arrangement of the flows that emphasizes stabilizing mechanisms. We find that the main stabilizing mechanism is asynchrony, where structures and energetic arrangements that decrease synchrony such as internal segregation or competition will stabilize dynamics. Since compartments allow prey dynamics to behave somewhat independently, compartmentation readily promotes stability. In addition, these results can be scaled from simple food webs to more complex webs with many interacting subsystems so that linking weak subsystems to strong ones can stabilize dynamics. We show that food web dynamics are determined not only by topology but also the arrangement of weak and strong energetic flows.     

Spatial guilds in the Serengeti food web revealed by a Bayesian group model

Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts.     

Ecological subsystems via graph theory: the role of strongly connected components

In this paper we investigate ecological flow networks via graph theory in search of the real sequential chains through which energy passes from producers to consumers in complex food webs. We obtain such fundamental pathways by identifying strongly connected components (SCCs), subsystems that groups species that take part in cycling, and performing topological sorting on the acyclic graphs that are obtained. Topological sorting identifies preferential directions for energy to flow from sources to sinks, while recycling remains confined within each SCC. Resolving food web networks for SCC highlights the possibility that compartments can be found in ecosystems, but this does not seem a general rule. The four aquatic food webs described in detail show a rather clear subdivision between benthic and pelagic subcommunities, a result that is discussed in the light of other studies. Should further research confirm these results, new insight into the way ecosystems use energy will be provided, with implications on cycling, reciprocal dependency of variables and indirect effects.     

Predicting food‐web structure with metacommunity models

Synthesis Metacommunity theory aims to elucidate the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity research has focused largely on assemblages of competing organisms within a single trophic level. Here, we test the ability of metacommunity models to predict the network structure of the aquatic food web found in the leaves of the northern pitcher plant Sarracenia purpurea. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions play an important role in structuring Sarracenia food webs. Our approach can be applied to any well‐resolved food web for which data are available from multiple locations. The metacommunity framework explores the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity models and empirical studies have focused mostly on assemblages of competing organisms within a single trophic level. Studies of multi‐trophic metacommunities are predominantly restricted to simplified trophic motifs and rarely consider entire food webs. We tested the ability of the patch‐dynamics, species‐sorting, mass‐effects, and neutral metacommunity models, as well as three hybrid models, to reproduce empirical patterns of food web structure and composition in the complex aquatic food web found in the northern pitcher plant Sarracenia purpurea. We used empirical data to determine regional species pools and estimate dispersal probabilities, simulated local food‐web dynamics, dispersed species from regional pools into local food webs at rates based on the assumptions of each metacommunity model, and tested their relative fits to empirical data on food‐web structure. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions were important in structuring Sarracenia food webs. However, differences in dispersal abilities were also important in models that accurately reproduced empirical food web properties. Although the models were tested using pitcher‐plant food webs, the approach we have developed can be applied to any well‐resolved food web for which data are available from multiple locations.     

农田土壤食物网管理的原理与方法

土壤食物网在维持生态系统生产力和健康等方面起着重要作用,但现代农业中,化肥农药等外部投入已经改变或部分替代了土壤食物网的功能,由此也造成一系列的环境问题。为了协调作物高产与环境保护的利益,需要对土壤食物网进行管理,使土壤食物网符合作物生长的需要,即建立健康土壤食物网。管理土壤食物网有两种方式:(1)直接方式,即通过调节食物网各个功能群的组成来管理土壤食物网;(2)间接方式,即根据农田土壤食物网以自下而上调控方式为主、强调低营养阶层的资源限制的原理,通过调节碎屑的数量和质量来管理食物网。在这两种调控方式中,都需要对被管理的食物网进行监测,监测的方式也分两种,一种是直接测定食物网各功能群的数量和生物量,另外一种方式即以线虫为工具来反应土壤食物网的结构。     

Unravelling the complex structure of forest soil food webs: higher omnivory and more trophic levels

Food web topologies depict the community structure as distributions of feeding interactions across populations. Although the soil ecosystem provides important functions for aboveground ecosystems, data on complex soil food webs is notoriously scarce, most likely due to the difficulty of sampling and characterizing the system. To fill this gap we assembled the complex food webs of 48 forest soil communities. The food webs comprise 89 to 168 taxa and 729 to 3344 feeding interactions. The feeding links were established by combining several molecular methods (stable isotope, fatty acid and molecular gut content analyses) with feeding trials and literature data. First, we addressed whether soil food webs (n = 48) differ significantly from those of other ecosystem types (aquatic and terrestrial aboveground, n = 77) by comparing 22 food web parameters. We found that our soil food webs are characterized by many omnivorous and cannibalistic species, more trophic chains and intraguild‐predation motifs than other food webs and high average and maximum trophic levels. Despite this, we also found that soil food webs have a similar connectance as other ecosystems, but interestingly a higher link density and clustering coefficient. These differences in network structure to other ecosystem types may be a result of ecosystem specific constraints on hunting and feeding characteristics of the species that emerge as network parameters at the food‐web level. In a second analysis of land‐use effects, we found significant but only small differences of soil food web structure between different beech and coniferous forest types, which may be explained by generally strong selection effects of the soil that are independent of human land use. Overall, our study has unravelled some systematic structures of soil food‐webs, which extends our mechanistic understanding how environmental characteristics of the soil ecosystem determine patterns at the community level.     

Species richness and trophic diversity increase decomposition in a co-evolved food web

Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.     

Food Web Assembly at the Landscape Scale: Using Stable Isotopes to Reveal Changes in Trophic Structure During Succession

Food webs are increasingly evaluated at the landscape scale, accounting for spatial interactions involving different nutrient and energy channels. Also, while long viewed as static, food webs are increasingly seen as dynamic entities that assemble during vegetation succession. The next necessary step is, therefore, to link nutrient flows between ecosystems to local food web assembly processes. In this study, we used a 100-year salt marsh succession in which we investigated the long-term changes in food web organization, especially focusing on the balance between internal versus external nutrient sources. We found that during food web assembly, the importance of internal (terrestrial) nutrient cycling increases at the expense of external (marine) inputs. This change from external to internal nutrient cycling is associated with strong shifts in the basis of energy channels within the food web. In early succession, detritivores are mostly fuelled by marine inputs whereas in later succession they thrive on locally produced plant litter, with consequences for their carnivores. We conclude that this 100 years of food web assembly proceeds by gradual decoupling of terrestrial nutrient cycling from the marine environment, and by associated rearrangements in the herbivore and detritivore energy channels. Food web assembly thus interacts with nutrient and energy flows across ecosystem boundaries.     

Parasites in food webs: the ultimate missing links

Parasitism is the most common consumer strategy among organisms, yet only recently has there been a call for the inclusion of infectious disease agents in food webs. The value of this effort hinges on whether parasites affect food‐web properties. Increasing evidence suggests that parasites have the potential to uniquely alter food‐web topology in terms of chain length, connectance and robustness. In addition, parasites might affect food‐web stability, interaction strength and energy flow. Food‐web structure also affects infectious disease dynamics because parasites depend on the ecological networks in which they live. Empirically, incorporating parasites into food webs is straightforward. We may start with existing food webs and add parasites as nodes, or we may try to build food webs around systems for which we already have a good understanding of infectious processes. In the future, perhaps researchers will add parasites while they construct food webs. Less clear is how food‐web theory can accommodate parasites. This is a deep and central problem in theoretical biology and applied mathematics. For instance, is representing parasites with complex life cycles as a single node equivalent to representing other species with ontogenetic niche shifts as a single node? Can parasitism fit into fundamental frameworks such as the niche model? Can we integrate infectious disease models into the emerging field of dynamic food‐web modelling? Future progress will benefit from interdisciplinary collaborations between ecologists and infectious disease biologists.     

NOS: a software suite to compute node overlap and segregation in ecological networks

Investigating the structure of ecological networks can help unravel the mechanisms promoting and maintaining biodiversity. Recently, Strona and Veech 2015 (A new measure of ecological network structure based on node overlap and segregation. – Methods Ecol. Evol. 6: 907–915) introduced a new metric (??, pronounced ‘nos’), that allows assessment of structural patterns in networks ranging from complete node segregation to perfect nestedness, and that also provides a visual and quantitative assessment of the degree of network modularity. The ?? metric permits testing of a wide range of hypotheses regarding the tendency for species to share interacting partners by taking into account ecologically plausible species interactions based on constraints such as trophic levels and habitat preference. Here we introduce NOS, a software suite (including a web interface freely accessible at  http://nos.alwaysdata.net , an executable program, and Python and R packages) that makes it possible to exploit the full potential of this method. Besides computing node overlap and segregation (??), the software provides different functions to automatically identify a set of possible resource–consumer interactions in food webs based on trophic levels. As an example of application, we analyzed two well‐resolved high‐latitude marine food webs, showing that an explicit a priori consideration of trophic levels is fundamental for a proper assessment of food web structure.     

Integrating ecosystem engineering and food webs

Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non‐trophic interactions, we explore how we might best integrate ecosystem engineering and food webs. We provide rationales justifying their integration and present a provisional framework identifying how ecosystem engineering can affect the nodes and links of food webs and overall organization; how trophic interactions with the engineer can affect the engineering; and how feedbacks between engineering and trophic interactions can affect food web structure and dynamics. We use a simple integrative food chain model to illustrate how feedbacks between the engineer and the food web can alter 1) engineering effects on food web dynamics, and 2) food web responses to extrinsic environmental perturbations. We identify four general challenges to integration that we argue can readily be met, and call for studies that can achieve this integration and help pave the way to a more general understanding of interaction webs in nature. Synthesis All species are affected by their physical environment. Because ecosystem engineering species modify the physical environment and belong to food webs, such species are potentially one of the most important bridges between the trophic and non‐trophic. We examine how to integrate the so far, largely independent research areas of ecosystem engineering and food webs. We present a conceptual framework for understanding how engineering can affect food webs and vice versa, and how feedbacks between the two alter ecosystem dynamics. With appropriate empirical studies and models, integration is achievable, paving the way to a more general understanding of interaction webs in nature.     

Threshold extinction in food webs

Food web response to species loss has been investigated in several ways in the previous years. In binary food webs, species go secondarily extinct if no resource item remains to be exploited. In this work, we considered that species can go extinct before the complete loss of their resources and we introduced thresholds of minimum energy requirement for species survival. According to this approach, extinction of a node occurs whenever an initial extinction event eliminates its incoming links so it is left with an overall energy intake lower than the threshold value. We tested the robustness of 18 real food webs by removing species from most to least connected and considering different scenarios defined by increasing the extinction threshold. Increasing energy requirement threshold negatively affects food web robustness. We found that a very small increase of the energy requirement substantially increases system fragility. In addition, above a certain value of energy requirement threshold we found no relationship between the robustness and the connectance of the web. Further, food webs with more species showed higher fragility with increasing energy threshold. This suggests that the shape of the robustness–complexity relationship of a food web depends on the sensitivity of consumers to loss of prey.     

Integrating food web diversity, structure and stability

Given the unprecedented rate of species extinctions facing the planet, understanding the causes and consequences of species diversity in ecosystems is of paramount importance. Ecologists have investigated both the influence of environmental variables on species diversity and the influence of species diversity on ecosystem function and stability. These investigations have largely been carried out without taking into account the overarching stabilizing structures of food webs that arise from evolutionary and successional processes and that are maintained through species interactions. Here, we argue that the same large-scale structures that have been purported to convey stability to food webs can also help to understand both the distribution of species diversity in nature and the relationship between species diversity and food web stability. Specifically, the allocation of species diversity to slow energy channels within food webs results in the skewed distribution of interactions strengths that has been shown to confer stability to complex food webs. We end by discussing the processes that might generate and maintain the structured, stable and diverse food webs observed in nature.     

Food web structure in a tropical stream ecosystem

Abstract This study investigated the structure and properties of a tropical stream food web in a small spatial scale, characterizing its planktonic, epiphytic and benthic compartments. The study was carried out in the Potreirinho Creek, a second‐order stream located in the south‐east of Brazil. Some attributes of the three subwebs and of the conglomerate food web, composed by the trophic links of the three compartments plus the fish species, were determined. Among compartments, the food webs showed considerable variation in structure. The epiphytic food web was consistently more complex than the planktonic and benthic webs. The values of number of species, number of links and maximum food chain length were significantly higher in the epiphytic compartment than in the other two. Otherwise, the connectance was significantly lower in epiphyton. The significant differences of most food web parameters were determined by the increase in the number of trophic species, represented mainly by basal and intermediate species. High species richness, detritus‐based system and high degree of omnivory characterized the stream food web studied. The aquatic macrophytes probably provide a substratum more stable and structurally complex than the sediment. We suggest that the greater species richness and trophic complexity in the epiphytic subweb might be due to the higher degree of habitat complexity supported by macrophyte substrate. Despite differences observed in the structure of the three subwebs, they are highly connected by trophic interactions, mainly by fishes. The high degree of fish omnivory associated with their movements at different spatial scales suggests that these animals have a significant role in the food web dynamic of Potreirinho Creek. This interface between macrophytes and the interconnections resultant from fish foraging, diluted the compartmentalization of the Potreirinho food web.     

全球变化对食物网结构影响机制的研究进展

食物网主要依靠基于不同营养级间物种互作形成的上行与下行调控维持其结构。全球变化能够改变种间关系, 威胁生物多样性的维持, 然而目前对全球变化改变食物网结构的机制仍处于探索阶段。近年来通过大时空格局与多营养级食物网研究, 发现全球变化的作用机制主要可归结为3种: 物候错配、关键种丧失与生物入侵。该文聚焦于这3种机制, 综述各种机制造成的食物网结构变化并探讨相关的进化与生态驱动因素。三种干扰机制均通过改变原有种间关系, 影响食物网调控, 改变食物网结构。不同的是, 物候错配造成的种间关系变化是由于不同物种的物候对全球变化产生非同步响应所致; 关键种丧失则使营养级间取食/捕食关系发生变化甚至缺失; 而入侵物种通过竞争排除同营养级物种改变种间关系。最后, 该文提出食物网结构变化的实质是物种是否能够适应快速变化的生态环境, 并据此展望未来研究方向。随着全球变化影响日益加剧, 急需继续深入探索导致全球变化下食物网结构改变的机制, 为制定合理的生物多样性保护与生态修复规划提供重要理论支撑。     

Resource tracking in marine parasites: going with the flow?

Understanding how diversity interacts with energy supply is of broad ecological interest. Most studies to date have investigated patterns within trophic levels, reflecting a lack of food webs which include information on energy flow. We added parasites to a published marine energy‐flow food web, to explore whether parasite diversity is correlated with energy flow to host taxa. Parasite diversity was high with 36 parasite taxa affecting 40 of the 51 animal taxa. Adding parasites increased the number of trophic links per species, trophic link strength, connectance, and food chain lengths. There was evidence of an asymptotic relationship between energy flowing through a food chain and parasite diversity, although there were clear outliers. High parasite diversity was associated with host taxa which were highly connected within the food web. This suggests that energy flow through a taxon may favour parasite diversity, up to a maximal value. The evolutionary and energetic basis for that limitation is of key interest in understanding the basis for parasite diversity in natural food webs and thus their role in food web dynamics.     

Food web complexity and stability across habitat connectivity gradients

The effects of habitat connectivity on food webs have been studied both empirically and theoretically, yet the question of whether empirical results support theoretical predictions for any food web metric other than species richness has received little attention. Our synthesis brings together theory and empirical evidence for how habitat connectivity affects both food web stability and complexity. Food web stability is often predicted to be greatest at intermediate levels of connectivity, representing a compromise between the stabilizing effects of dispersal via rescue effects and prey switching, and the destabilizing effects of dispersal via regional synchronization of population dynamics. Empirical studies of food web stability generally support both this pattern and underlying mechanisms. Food chain length has been predicted to have both increasing and unimodal relationships with connectivity as a result of predators being constrained by the patch occupancy of their prey. Although both patterns have been documented empirically, the underlying mechanisms may differ from those predicted by models. In terms of other measures of food web complexity, habitat connectivity has been empirically found to generally increase link density but either reduce or have no effect on connectance, whereas a unimodal relationship is expected. In general, there is growing concordance between empirical patterns and theoretical predictions for some effects of habitat connectivity on food webs, but many predictions remain to be tested over a full connectivity gradient, and empirical metrics of complexity are rarely modeled. Closing these gaps will allow a deeper understanding of how natural and anthropogenic changes in connectivity can affect real food webs.     

Food web complexity affects stoichiometric and trophic interactions

The stoichiometry of trophic interactions has mainly been studied in simple consumer–prey systems, whereas natural systems often harbour complex food webs with abundant indirect effects. We manipulated the complexity of trophic interactions by using simple laboratory food webs and complex field food webs in enclosures in Lake Erken. In the simple food web, one producer assemblage (periphyton) and its consumers (benthic snails) were amended by perch, which was externally fed by fish food. In the complex food web, two producer assemblages (periphyton and phytoplankton), their consumers (benthic invertebrates and zooplankton) and perch feeding on zooplankton were included. In the simple food web perch affected the stoichiometry of periphyton and increased periphyton biomass and the concentration of dissolved inorganic nitrogen. Grazers reduced periphyton biomass but increased its nutrient content. In the complex food web, in contrast to the simple food web, perch affected periphyton biomass negatively but increased phytoplankton abundance. Perch had no influence on benthic invertebrate density, zooplankton biomass or periphyton stoichiometry. Benthic grazers reduced periphyton biomass and nutrient content. The difference between the simple and the complex food web was presumably due to the increase of pelagic cyanobacteria ( Gloeotrichia sp.) with fish presence in the complex food web, thus fish had indirect negative effects on periphyton biomass through nutrient competition and shading by cyanobacteria. We conclude that the higher food web complexity through the presence of pelagic primary producers (in this case Gloeotrichia sp.) influences the direction and strength of trophic and stoichiometric interactions.