Stability in real food webs: weak links in long loops

Environmental gradient changes shape multi-scale food web structures: Impact on antibiotics trophic transfer in a lake ecosystem

Environmental change can alter the multi-scale foodweb structure, thereby impacting the pollutants trophic transfer in aquatic ecosystems. However, a quantitative understanding of how environmental gradient changes affect pollutant trophic transfer in natural lake ecosystems remains limited. This study investigated temporal variations in environment change index (ECi), multi-scale foodweb structure, and trophic transfer of quinolones antibiotics (QNs) in Baiyangdian Lake, Northern China, from 2018 to 2023. Our results demonstrated that the interaction strength (IS) in detritus (DIS) and macrophyte (MIS) in 2023 were significantly lower than those in 2018, and diversity indices exhibited significant temporal differences between 2018 and 2023. ECi was significantly correlated with DIS/MIS between species at the population scale and with diversity indices (DH and H') at the ecosystem scale. The trophic magnification factors (TMFs) of QNs have higher values in 2023 compared to 2018, showing significant temporal differences. Through structural equation model, the results showed ECi directly impacted DIS, which in turn affected SEAc and H', while indirectly influencing TMFs. The TMFs of QNs was mainly regulated by environmental factors. These findings highlighted the influencing mechanism through multi-scale foodweb structures regulate pollutant trophic transfer under environmental change in natural lake.

Soil microorganism distributions depend on habitat partitioning of topography in a temperate mountain forest

As the main decomposers in forest ecosystems, soil microorganisms are crucial in maintaining ecosystem functions and services. Topographic factors are essential for soil formation and can influence the community structure of soil microorganisms by modifying the soil environment. However, a systematic understanding of the distribution mechanisms of soil microorganisms across different terrain habitats is still lacking. This study characterized soil bacteria and fungi in the valleys, mid-slopes, and ridges of the temperate deciduous broadleaf forest in Baiyun Mountain, Luoyang, to analyze the effect of topographic habitat on the distribution patterns of soil microbial communities. Results showed that the distribution of most soil microorganisms in different terrain habitats follows the principle of ecological specialization. The distribution patterns of soil bacteria and fungi are related to the terrain habitat, and the fungal community (60.48%) exhibits a stronger habitat specificity than the bacterial community (31.78%). Soil moisture has a greater influence on fungal communities than bacterial communities, whereas soil physical and chemical properties more significantly explain variations in bacterial community distribution. These findings indicate that topographic habitat significantly influences soil microbial community distribution, and bacteria show stronger habitat adaptability than fungi.

IMPORTANCE

This study provides an in-depth examination of the impact of topographic habitat on the structural composition and spatial distribution characteristics of bacterial and fungal communities. The research focused on three distinct terrain habitats: valley, midslope, and ridge. Our results indicate that soil bacterial and fungal networks, along with major environmental factors, shape the composition and distribution of soil microbial communities across different terrain habitats. We found that fungi exhibit stronger habitat specificity than bacteria and are more likely to thrive in valleys with higher water content. Furthermore, major environmental factors significantly influence the distribution of soil microbial communities. These findings could inform the development of more effective forest soil management and conservation strategies tailored to different topographic habitats.

Architecture and stability of tripartite ecological networks with two interaction types

Over the past few decades, studies on empirical ecological networks have primarily focused on single antagonistic or mutualistic interactions. However, many species engage in multiple interactions that support distinct ecosystem functions. The architecture of networks integrating these interactions, along with their cascading effects on community dynamics, remains underexplored in ecological research. In this study, we compiled two datasets of empirical plant-herbivore/host-parasitoid (PHP) and pollinator-plant-herbivore (PPH) networks, representing two common types of tripartite networks in terrestrial ecosystems: antagonism-antagonism and mutualism-antagonism. We identified the patterns of subnetwork structures and interconnection properties in these networks and examined their relationships with community stability. Our findings revealed distinct pathway effects of network architecture on persistence and local stability in both PHP and PPH networks, with subnetwork modularity and nestedness showing a few strong direct effects and mediating the indirect effects of subnetwork size and connectance. In PHP networks, subnetwork modularity enhanced persistence and local stability, whereas subnetwork nestedness directly undermined them. However, both subnetwork topologies consistently mediated the destabilizing effects of subnetwork size and connectance on the entire network. In PPH networks, persistence was primarily affected by the plant-herbivore subnetwork, while the size, connectance, and modularity of different subnetworks had opposing effects on local stability. Regarding interconnection properties, the correlation of interaction similarity destabilized PHP networks, whereas the correlation of interaction degree promoted local stability in PPH networks. Further analysis indicated that structure-persistence relationships vary significantly across guilds, and the network-level effects of network architecture can be reversed, negligible, or biased in specific guilds. These findings advance our understanding of how network architecture influences ecosystem stability and underscore the importance of considering multiple interaction types when predicting community dynamics.

Offshore wind farms modify coastal food web dynamics by enhancing suspension feeder pathways

Given the global offshore wind farm (OWF) proliferation, we investigated the impact of OWFs on the marine food web. Using linear inverse modelling (LIM), we compared the OWF food web with two soft-sediment food webs nearby. Novel in situ data on species biomass and their isotopic composition were combined with literature data to construct food webs. Our findings highlight the prominent role of hard-substrate species on turbine foundations as organic material inputs for the food web. Hard substrate species account for approximately 26% of food source uptake from the water column and increase carbon deposition on the surrounding seafloor by ~10%. OWFs facilitate a novel food web with a higher productivity than expected based on standing biomass alone, as a result of numerous interactions between a diverse species community. Our study underscores profound effects of OWFs on marine ecosystems, suggesting the need for further research into their ecological impacts.

The co-occurrence patterns and assembly mechanisms of microeukaryotic communities in geothermal ecosystems of the Qinghai-Tibet Plateau

Geothermal spring ecosystems, as extreme habitats, exert significant environmental pressure on their microeukaryotic communities. However, existing studies on the stability of microeukaryotic communities in geothermal ecosystems across different habitats and temperature gradients are still limited. In this study, we used high-throughput 18S rDNA sequencing in combination with environmental factor analysis to investigate the co-occurrence patterns, assembly mechanisms, and responses to environmental changes of microeukaryotic communities in sediment and water samples from 36 geothermal springs across different temperature gradients in southern Tibet. The results show that with increasing temperature, the network stability of microeukaryotic communities in sediments significantly improved, while the stability in water communities decreased. The assembly mechanisms of microeukaryotic communities in both sediment and water were primarily driven by undominant processes within stochastic processes. Latitude and longitude were the key factors influencing changes in sediment community composition, while water temperature and electrical conductivity were the major environmental factors affecting water community composition. Additionally, the stability of the geothermal community network was closely related to its response to external disturbances: sediment communities, being in relatively stable environments, demonstrated higher resistance to disturbances, whereas water communities, influenced by environmental changes such as water flow and precipitation, exhibited greater dynamic variability. These findings not only enhance our understanding of the ecological adaptability of microeukaryotic communities in geothermal springs but also provide valuable insights into how microorganisms in extreme environments respond to external disturbances. This is especially significant for understanding how microeukaryotic communities maintain ecological stability under highly dynamic and stressful environmental conditions.

Body Mass-Biomass Scaling Modulates Species Keystone-Ness to Press Perturbations

Identifying species with disproportionate effects on other species under press perturbations is essential, yet how species traits and community context drive their 'keystone-ness' remain unclear. We quantified keystone-ness as linearly approximated per capita net effect derived from normalised inverse community matrices and as non-linear per capita community biomass change from simulated perturbations in food webs with varying biomass structure. In bottom-heavy webs (negative relationship between species' body mass and their biomass within the web), larger species at higher trophic levels tended to be keystone species, whereas in top-heavy webs (positive body mass to biomass relationship), the opposite was true and the relationships between species' energetic traits and keystone-ness were weakened or reversed compared to bottom-heavy webs. Linear approximations aligned well with non-linear responses in bottom-heavy webs, but were less consistent in top-heavy webs. These findings highlight the importance of community context in shaping species' keystone-ness and informing effective conservation actions.

Interaction networks in persistent Lotka-Volterra communities

A central concern of community ecology is the interdependence between interaction strengths and the underlying structure of the network upon which species interact. In this work we present a solvable example of such a feedback mechanism in a generalized Lotka-Volterra dynamical system. Beginning with a community of species interacting on a network with arbitrary degree distribution, we provide an analytical framework from which properties of the eventual "surviving community" can be derived. We find that highly connected species are less likely to survive than their poorly connected counterparts, which skews the eventual degree distribution towards a preponderance of species with lower degrees. Furthermore, the average abundance of the neighbors of a species in the surviving community is lower than the community average (reminiscent of the famed friendship paradox). Finally, we show that correlations emerge between the connectivity of a species and its interactions with its neighbors. More precisely, we find that highly connected species tend to benefit from their neighbors more than their neighbors benefit from them. These correlations are not present in the initial pool of species and are a result of the dynamics.

Seasonal Shifts in Trophic Interaction Strength Drive Stability of Natural Food Webs

It remains challenging to understand why natural food webs are remarkably stable despite highly variable environmental factors and population densities. We investigated the dynamics in the structure and stability of Lake Constance's pelagic food web using 7 years of high-frequency observations of biomasses and production, leading to 59 seasonally resolved quantitative food web descriptions. We assessed the dynamics in asymptotic food web stability through maximum loop weight, which revealed underlying stability mechanisms. Maximum loop weight showed a recurrent seasonal pattern with a consistently high stability despite pronounced dynamics in biomasses, fluxes and productivity. This stability resulted from seasonal rewiring of the food web, driven by energetic constraints within loops and their embedding into food web structure. The stabilising restructuring emerged from counter-acting effects of metabolic activity and competitiveness/susceptibility to predation within a diverse grazer community on loop weight. This underscores the role of functional diversity in promoting food web stability.

Stability of Ecological Systems: A Theoretical Review

The stability of ecological systems is a fundamental concept in ecology, which offers profound insights into species coexistence, biodiversity, and community persistence. In this article, we provide a systematic and comprehensive review on the theoretical frameworks for analyzing the stability of ecological systems. Notably, we survey various stability notions, including linear stability, sign stability, diagonal stability, D-stability, total stability, sector stability, and structural stability. For each of these stability notions, we examine necessary or sufficient conditions for achieving such stability and demonstrate the intricate interplay of these conditions on the network structures of ecological systems. We further discuss the stability of ecological systems with higher-order interactions.

Accounting for effects of growth rate when measuring ecological stability in response to pulse perturbations

Ecological stability is a vital component of natural ecosystems that can inform effective conservation and ecosystem management. Furthermore, there is increasing interest in making comparisons of stability values across sites, systems and taxonomic groups, often using comparative synthetic approaches, such as meta-analysis. However, these synthetic approaches often compare/contrast systems where measures of stability mean very different things to the taxa involved. Here, we present results from theoretical models and empirical data to illustrate how differences in growth rates among taxa influence four widely used metrics of ecological stability of species abundances responding to pulse perturbations: resilience, recovery, resistance and temporal stability. We refer to these classic growth-rate-dependent metrics as 'realised' stability. We show that realised resilience and realised temporal stability vary as a function of organisms' growth rates; realised recovery depends on the relation between growth rate and sampling duration; and realised resistance depends on the relation between growth rate and sampling interval. To account for these influences, we introduce metrics intended to be more independent of growth rates, which we refer to as 'intrinsic' stability. Intrinsic stability can be used to summarise the overall effects of a disturbance, separately from internal recovery processes - thereby allowing more general comparisons of disturbances across organisms and contexts. We argue that joint consideration of both realised and intrinsic stability is important for future comparative studies.

Synthesising the Relationships Between Food Web Structure and Robustness

For many decades, ecologists have sought to understand the extent to which species losses lead to secondary extinctions-that is, the additional loss of species that occurs when resources or key interactions are lost (i.e. robustness). In particular, ecologists aim to identify generalisable rules that explain which types of food webs are more or less robust to secondary extinctions. Food web structure, or the patterns formed by species and their interactions, has been extensively studied as a potential factor that influences robustness to species loss. We systematically reviewed 28 studies to identify the relationships between food web structure and robustness to species loss and how the conclusions depend on methodological differences. Contrary to popular belief and theory, we found relatively consistent, positive relationships between connectance and robustness, among other generalities. Yet, we also found that conflicting conclusions about structure-robustness relationships can be, in part, attributed to differences in the type of data that studies use, particularly studies that use empirical data versus those generated from theoretical models. This review points towards a need to standardise methodology to answer the open question of whether robustness and its relationship with food web structure and to provide applicable insights for managing complex systems.

Gut Microbial Communities Are Seasonally Variable in Warm-Climate Lizards Hibernating in the Winter Months

Hibernation is an energy-saving and adaptive strategy adopted by a diverse array of animals, rarely including warm-climate species, to survive in the harsh winter environment. Here, we collected large-intestinal microbial samples from two species of warm-climate lizards, one (the Reeves' butterfly lizard Leiolepis reevesii) hibernating in the winter months and one (the many-lined sun skink Eutropis multifasciata) not doing so, in summer and winter to analyze and compare their microbiota using 16S rRNA gene amplicon sequencing technology. Gut microbiota were seasonally variable in L. reevesii but not in E. multifasciata. The decreased Firmicutes/Bacteroidetes ratio and increased relative abundance of Verrucomicrobia in hibernating butterfly lizards in a state of long-term fasting should help them live through the winter months, as bacteria of the phyla Bacteroidetes and Verrucomicrobia can use host-derived mucin glycans in the absence of dietary substrates. Facultative plant feeding by omnivorous butterfly lizards resulted in a significant increase in the relative abundance of bacteria of the phylum Firmicutes (e.g., Lachnospiraceae) with the ability to degrade plant fibers. This study not only validates the role of gut microbiota in dietary adaptation in lizards but also shows that gut microbial communities are seasonally variable in warm-climate lizards hibernating in the winter months.

Ecosystem engineering and food web stability

Ecosystem engineering, which involves organism-triggered physical modification of the environment, is a widespread phenomenon. Despite this, the role of engineering in ecological communities remains poorly understood. This study employs a food web model to uncover the key roles of ecosystem engineering in maintaining food webs. While engineers facilitating population growth and suppressing consumers' foraging activity can help maintain complex communities with diverse species, engineering effects that suppress population growth and facilitate consumers' foraging activity can largely destabilize community dynamics. Furthermore, in the middle levels of engineering-related species within a community, an increase in species richness can increase community stability, contrary to classical ecological prediction. The study findings suggest that ecosystem engineering can explain biodiversity persistence in nature, but it depends on the proportion of engineering-related species and how engineering affects organisms.

Untangling the complex food webs of tropical rainforest streams

Food webs depict the tangled web of trophic interactions associated with the functioning of an ecosystem. Understanding the mechanisms providing stability to these food webs is therefore vital for conservation efforts and the management of natural systems. Here, we first characterised a tropical stream meta-food web and five individual food webs using a Bayesian Hierarchical approach unifying three sources of information (gut content analysis, literature compilation and stable isotope data). With data on population-level biomass and individually measured body mass, we applied a bioenergetic model and assessed food web stability using a Lotka-Volterra system of equations. We then assessed the resilience of the system to individual species extinctions using simulations and investigated the network patterns associated with systems with higher stability. The model resulted in a stable meta-food web with 307 links among the 61 components. At the regional scale, 70% of the total energy flow occurred through a set of 10 taxa with large variation in body masses. The remaining 30% of total energy flow relied on 48 different taxa, supporting a significant dependency on a diverse community. The meta-food web was stable against individual species extinctions, with a higher resilience in food webs harbouring omnivorous fish species able to connect multiple food web compartments via weak, non-specialised interactions. Moreover, these fish species contributed largely to the spatial variation among individual food webs, suggesting that these species could operate as mobile predators connecting different streams and stabilising variability at the regional scale. Our results outline two key mechanisms of food web stability operating in tropical streams: (i) the diversity of species and body masses buffering against random and size-dependent disturbances and (ii) high regional diversity and weak omnivorous interactions of predators buffering against local stochastic variation in species composition. These mechanisms rely on high local and regional biodiversity in tropical streams, which is known to be strongly affected by human impacts. Therefore, an urgent challenge is to understand how the ongoing systematic loss of diversity jeopardises the stability of stream food webs in human-impacted landscapes.

Putting the Asymmetric Response Concept to the test: Modeling multiple stressor exposure and release in a stream food web

Communities in stream ecosystems often respond asymmetrically to increase and release of stressors, as indicated by slow and incomplete recovery. The Asymmetric Response Concept (ARC) posits that this is due to a shift in the relative importance of three mechanisms: tolerance, dispersal, and biotic interactions. In complex natural communities, these mechanisms may produce alternative outcomes through poorly understood indirect effects. To understand how the three mechanisms respond to different temporal stressor scenarios, we studied multiple scenarios using a stream food web model. We asked the following questions: Do groups of species decline as expected on the basis of individual tolerance rankings derived from laboratory experiments when they are embedded in a complex dynamic food web? Does the response of ecosystem function match that of communities? To address these questions, we aggregated data on individual tolerances at the level of functional groups and studied how single and multiple stressors affect food web dynamics and nutrient cycling. Multiple stressor scenarios involved different intensities of salt and temperature increase. Functional groups exhibited a different relative tolerance ranking between the laboratory and dynamic food web contexts. Salt as a single stressor had only minor and transient effects at low level but led to the loss of one or more functional groups at high level. In contrast, high temperature, alone or in combination with salt, caused the loss of functional groups at all tested levels. Patterns often differed between the response of communities and ecosystem function. We discuss our findings with respect to the ARC.

Stability in plant-pollinator communities across organizational levels: present, gaps, and future

Abstract. The study of ecological stability continues to fill the pages of scientific journals almost seven decades after the first ecologists initiated this line of research. The many advances in this field have focused on understanding the stability of populations, communities or functions within single guilds or trophic levels, with less research conducted across multiple trophic levels and considering the different interactions that relate species to each other. Here, we review the recent literature on the multiple dimensions of ecological stability specifically within plant-pollinator communities. We then focus on one of stability´s dimensions, temporal invariability, and adapt an existing partitioning framework that bridges invariability and synchrony measures across spatial scales and organizational levels to accommodate interactions between plants and their pollinators. Finally, we use this framework to analyse temporal invariability in plant reproductive success, partitioning it on invariability and synchrony components across plant and pollinator populations and communities, as well as their interactions, using a well-resolved dataset that encompasses data for two years. Our review of the literature points to several significant gaps in our current knowledge, with simulation studies clearly overrepresented in the literature as opposed to experimental or empirical approaches. Our quantitative approach to partitioning invariability shows similar patterns of decreasing temporal invariability across increasing organizational levels driven by asynchronous dynamics amongst populations and communities, which overall stabilize ecosystem functioning (plant reproductive success). This study represents a first step towards a better comprehension of temporal invariability in ecosystem functions defined by interactions between species and provides a blueprint for the type of spatially replicated multi-year data that needs to be collected in the future to further our understanding of ecological stability within multi-trophic communities.

Parasite-mediated predation determines infection in a complex predator-prey-parasite system

The interplay of host-parasite and predator-prey interactions is critical in ecological dynamics because both predators and parasites can regulate communities. But what is the prevalence of infected prey and predators when a parasite is transmitted through trophic interactions considering stochastic demographic changes? Here, we modelled and analysed a complex predator-prey-parasite system, where parasites are transmitted from prey to predators. We varied parasite virulence and infection probabilities to investigate how those evolutionary factors determine species' coexistence and populations' composition. Our results show that parasite species go extinct when the infection probabilities of either host are small and that success in infecting the final host is more critical for the survival of the parasite. While our stochastic simulations are consistent with deterministic predictions, stochasticity plays an important role in the border regions between coexistence and extinction. As expected, the proportion of infected individuals increases with the infection probabilities. Interestingly, the relative abundances of infected and uninfected individuals can have opposite orders in the intermediate and final host populations. This counterintuitive observation shows that the interplay of direct and indirect parasite effects is a common driver of the prevalence of infection in a complex system.

Quality variation and salt-alkali-tolerance mechanism of Cynomorium songaricum: Interacting from microbiome-transcriptome-metabolome

Addressing soil salinization and implementing sustainable practices for cultivating cash crops on saline-alkali land is a prominent global challenge. Cynomorium songaricum is an important salt-alkali tolerant medicinal plant capable of adapting to saline-alkali environments. In this study, two typical ecotypes of C. songaricum from the desert-steppe (DS) and saline-alkali land (SAL) habitats were selected. Through the integration of multi-omics with machine learning, the rhizosphere microbial communities, genetic maps, and metabolic profiles of two ecotypes were created and the crucial factors for the adaptation of C. songaricum to saline-alkali stress were identified, including 7 keystone OTUs (i.e. Novosphingobium sp., Sinorhizobium meliloti, and Glycomyces sp.), 5 core genes (cell wall-related genes), and 10 most important metabolites (i.e. cucurbitacin D and 3-Hydroxybutyrate) were identified. Our results indicated that under saline-alkali environments, the microbial competition might become more intense, and the microbial community network had the simple but stable structure, accompanied by the changes in the gene expression related to cell wall for adaptation. However, this regulation led to the reduction in active ingredients, such as the accumulation of flavonoids and organic acid, and enhanced the synthesis of bitter substances (cucurbitacin D), resulting in the decrease in the quality of C. songaricum. Therefore, compared to the SAL ecotype, the DS was more suitable for the subsequent development of medicinal and edible products of C. songaricum. Furthermore, to explore the reasons for this quality variation, we constructed a comprehensive microbial-genetic-metabolic regulatory network, revealing that the metabolism of C. songaricum was primarily influenced by genetic factors. These findings not only offer new insights for future research into plant salt-alkali tolerance strategies but also provide a crucial understanding for cultivating high-quality medicinal plants.

Trophic tug-of-war: Coexistence mechanisms within and across trophic levels

Ecological communities encompass rich diversity across multiple trophic levels. While modern coexistence theory has been widely applied to understand community assembly, its traditional formalism only allows assembly within a single trophic level. Here, using an expanded definition of niche and fitness differences applicable to multitrophic communities, we study how diversity within and across trophic levels affects species coexistence. If each trophic level is analysed separately, both lower- and higher trophic levels are governed by the same coexistence mechanisms. In contrast, if the multitrophic community is analysed as a whole, different trophic levels are governed by different coexistence mechanisms: coexistence at lower trophic levels is predominantly limited by fitness differences, whereas coexistence at higher trophic levels is predominantly limited by niche differences. This dichotomy in coexistence mechanisms is supported by theoretical derivations, simulations of phenomenological and trait-based models, and a case study of a primeval forest ecosystem. Our work provides a general and testable prediction of coexistence mechanism operating in multitrophic communities.

Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities

Functional responses describe foraging rates across prey densities and underlie many fundamental ecological processes. Most functional response knowledge comes from simplified lab experiments, but we do not know whether these experiments accurately represent foraging in nature. In addition, the difficulty of conducting multispecies functional response experiments means that it is unclear whether interaction strengths are weakened in the presence of multiple prey types. We developed a novel method to estimate wild predators' foraging rates from metabarcoding data and use this method to present functional responses for wild wolf spiders foraging on 27 prey families. These field functional responses were considerably reduced compared to lab functional responses. We further find that foraging is sometimes increased in the presence of other prey types, contrary to expectations. Our novel method for estimating field foraging rates will allow researchers to determine functional responses for wild predators and address long-standing questions about foraging in nature.

Quantitative description of six fish species' gut contents and prey abundances in the Baltic Sea (1968-1978)

The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish's digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.

How collectively integrated are ecological communities?

Beyond abiotic conditions, do population dynamics mostly depend on a species' direct predators, preys and conspecifics? Or can indirect feedback that ripples across the whole community be equally important? Determining where ecological communities sit on the spectrum between these two characterizations requires a metric able to capture the difference between them. Here we show that the spectral radius of a community's interaction matrix provides such a metric, thus a measure of ecological collectivity, which is accessible from imperfect knowledge of biotic interactions and related to observable signatures. This measure of collectivity integrates existing approaches to complexity, interaction structure and indirect interactions. Our work thus provides an original perspective on the question of to what degree communities are more than loose collections of species or simple interaction motifs and explains when pragmatic reductionist approaches ought to suffice or fail when applied to ecological communities.

Spatial heterogeneity of biomass turnover has contrasting effects on synchrony and stability in trophic metacommunities

Spatial heterogeneity is a fundamental feature of ecosystems, and ecologists have identified it as a factor promoting the stability of population dynamics. In particular, differences in interaction strengths and resource supply between patches generate an asymmetry of biomass turnover with a fast and a slow patch coupled by a mobile predator. Here, we demonstrate that asymmetry leads to opposite stability patterns in metacommunities receiving localized perturbations depending on the characteristics of the perturbed patch. Perturbing prey in the fast patch synchronizes the dynamics of prey biomass between the two patches and destabilizes predator dynamics by increasing the predator's temporal variability. Conversely, perturbing prey in the slow patch decreases the synchrony of the prey's dynamics and stabilizes predator dynamics. Our results have implications for conservation ecology and suggest reinforcing protection policies in fast patches to dampen the effects of perturbations and promote the stability of population dynamics at the regional scale.

Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area

Heavy metals pose significant threats to soil biota, ultimately disrupting soil micro-food web. However, no studies have yet elucidated the impact of heavy metals on soil micro-food web. In this study, we explored the response of bacteria, fungi, nematodes, and soil micro-food web along a gradient of heavy metals in an abandoned smelting-mining area. We found that bacteria responded strongly to heavy metals, whereas fungi showed greater resistance and tolerance. Nematodes responses were less apparent. With the increasing levels of heavy metal pollution, the importance of heavy metal-tolerant organisms in micro-food webs increased significantly. For instance, the keystone bacteria in soil micro-food web shifted from copiotrophic to oligotrophic types, while the keystone nematodes shifted from to bacterial-feeding (e.g., Eucephalobus) to fungal-feeding species (e.g., Ditylenchus). Additionally, elevated heavy metal concentrations increased the proportion of fungi (e.g., Mortierellomycota), intensifying their interactions with bacteria and nematodes and causing a shift from bacteria-based to fungi-based soil micro-food web. Furthermore, heavy metal contamination induced a more complex and stable soil micro-food web. Overall, we highlight the changes in soil micro-food web as a mechanism for coping with heavy metal stress. Our study provides valuable insights into how heavy metal pollution can cause shifts in soil micro-food webs and has critical implications for enhancing our understanding of the ecological consequences of environmental pollution at the ecosystem level.

Five fundamental ways in which complex food webs may spiral out of control

Theory suggests that increasingly long, negative feedback loops of many interacting species may destabilize food webs as complexity increases. Less attention has, however, been paid to the specific ways in which these 'delayed negative feedbacks' may affect the response of complex ecosystems to global environmental change. Here, we describe five fundamental ways in which these feedbacks might pave the way for abrupt, large-scale transitions and species losses. By combining topological and bioenergetic models, we then proceed by showing that the likelihood of such transitions increases with the number of interacting species and/or when the combined effects of stabilizing network patterns approach the minimum required for stable coexistence. Our findings thus shift the question from the classical question of what makes complex, unaltered ecosystems stable to whether the effects of, known and unknown, stabilizing food-web patterns are sufficient to prevent abrupt, large-scale transitions under global environmental change.

The Potential for Alternative Stable States in Food Webs Depends on Feedback Mechanism and Trait Diversity

AbstractAlternative stable ecosystem states are possible under the same environmental conditions in models of two or three interacting species and an array of feedback loops. However, multispecies food webs might weaken the feedbacks loops that can create alternative stable states. To test how this potential depends on food web properties, we develop a many-species model where consumer Allee effects emerge from consumer-resource interactions. We evaluate the interactive effects of food web connectance, interspecific trait diversity, and two classes of feedbacks: specialized feedbacks, where consumption of individual resources declines at high resource abundance (e.g., from schooling or reaching size refugia), and aggregate feedbacks, where overall resource abundance reduces consumer recruitment (e.g., from resources enhancing competition or mortality experienced by recruits). We find that aggregate feedbacks maintain, and specialized feedbacks reduce, the potential for alternative states. Interspecific trait diversity decreases the prevalence of alternative stable states more for specialized than for aggregate feedbacks. Increasing food web connectance increases the potential for alternative stable states for aggregated feedbacks but decreases it for specialized feedbacks, where losing vulnerable consumers can cascade into food web collapses. Altogether, multispecies food webs can limit the set of processes that create alternative stable states and impede consumer recovery from disturbance.

Competitive hierarchies in bryozoan assemblages mitigate network instability by keeping short and long feedback loops weak

Competitive hierarchies in diverse ecological communities have long been thought to lead to instability and prevent coexistence. However, system stability has never been tested, and the relation between hierarchy and instability has never been explained in complex competition networks parameterised with data from direct observation. Here we test model stability of 30 multispecies bryozoan assemblages, using estimates of energy loss from observed interference competition to parameterise both the inter- and intraspecific interactions in the competition networks. We find that all competition networks are unstable. However, instability is mitigated considerably by asymmetries in the energy loss rates brought about by hierarchies of strong and weak competitors. This asymmetric organisation results in asymmetries in the interaction strengths, which reduces instability by keeping the weight of short (positive) and longer (positive and negative) feedback loops low. Our results support the idea that interference competition leads to instability and exclusion but demonstrate that this is not because of, but despite, competitive hierarchy.

Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance

Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.

Plant community stability is associated with a decoupling of prokaryote and fungal soil networks

Soil microbial networks play a crucial role in plant community stability. However, we lack knowledge on the network topologies associated with stability and the pathways shaping these networks. In a 13-year mesocosm experiment, we determined links between plant community stability and soil microbial networks. We found that plant communities on soil abandoned from agricultural practices 60 years prior to the experiment promoted destabilising properties and were associated with coupled prokaryote and fungal soil networks. This coupling was mediated by strong interactions of plants and microbiota with soil resource cycling. Conversely, plant communities on natural grassland soil exhibited a high stability, which was associated with decoupled prokaryote and fungal soil networks. This decoupling was mediated by a large variety of past plant community pathways shaping especially fungal networks. We conclude that plant community stability is associated with a decoupling of prokaryote and fungal soil networks and mediated by plant-soil interactions.

Colonization-competition dynamics of basal species shape food web complexity in island metacommunities

Exploring how food web complexity emerges and evolves in island ecosystems remains a major challenge in ecology. Food webs assembled from multiple islands are commonly recognized as highly complex trophic networks that are dynamic in both space and time. In the context of global climate change, it remains unclear whether food web complexity will decrease in a monotonic fashion when undergoing habitat destruction (e.g., the inundation of islands due to sea-level rise). Here, we develop a simple yet comprehensive patch-dynamic framework for complex food web metacommunities subject to the competition-colonization tradeoff between basal species. We found that oscillations in food web topological complexity (characterized by species diversity, mean food chain length and the degree of omnivory) emerge along the habitat destruction gradient. This outcome is robust to changing parameters or relaxing the assumption of a strict competitive hierarchy. Having oscillations in food web complexity indicates that small habitat changes could have disproportionate negative effects on species diversity, thus the success of conservation actions should be evaluated not only on changes in biodiversity, but also on system robustness to habitat alteration. Overall, this study provides a parsimonious mechanistic explanation for the emergence of food web complexity in island ecosystems, further enriching our understanding of metacommunity assembly.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00167-0.

Long-term phosphorus addition alleviates CO2 and N2O emissions via altering soil microbial functions in secondary rather primary tropical forests

Tropical forests, where the soils are nitrogen (N) rich but phosphorus (P) poor, have a disproportionate influence on global carbon (C) and N cycling. While N deposition substantially alters soil C and N retention in tropical forests, whether P input can alleviate these N-induced effects by regulating soil microbial functions remains unclear. We investigated soil microbial taxonomy and functional traits in response to 10-year independent and interactive effects of N and P additions in a primary and a secondary tropical forest in Hainan Island. In the primary forest, N addition boosted oligotrophic bacteria and phosphatase and enriched genes responsible for C-, P-mineralization, nitrification and denitrification, suggesting aggravated P limitation while N excess. This might stimulate P excavation via organic matter mineralization, and enhance N losses, thereby increasing soil CO₂ and N₂O emissions by 86% and 110%, respectively. Phosphorus and NP additions elevated C-mining enzymes activity mainly due to intensified C limitation, causing 82% increase in CO₂ emission. In secondary forest, P and NP additions reduced phosphatase activity, enriched fungal copiotrophs and increased microbial biomass, suggesting removal of nutrient deficiencies and stimulation of fungal growth. Meanwhile, soil CO₂ emission decreased by 25% and N₂O emission declined by 52-82% due to alleviated P acquisition from organic matter decomposition and increased microbial C and N immobilization. Overall, N addition accelerates most microbial processes for C and N release in tropical forests. Long-term P addition increases C and N retention via reducing soil CO₂ and N₂O emissions in the secondary but not primary forest because of strong C limitation to microbial N immobilization. Further, the seasonal and annual variations in CO₂ and N₂O emissions should be considered in future studies to test the generalization of these findings and predict and model dynamics in greenhouse gas emissions and C and N cycling.

Nitrogen enrichment and foliar fungal pathogens affect the mechanisms of multispecies plant coexistence

Changes in resources (e.g. nitrogen) and enemies (e.g. foliar pathogens) are key drivers of plant diversity and composition. However, their effects have not been connected to the niche and fitness differences that determine multispecies coexistence. Here, we combined a structuralist theoretical approach with a detailed grassland experiment factorially applying nitrogen addition and foliar fungal pathogen suppression to evaluate the joint effect of nitrogen and pathogens on niche and fitness differences, across a gradient from two to six interacting species. Nitrogen addition and pathogen suppression modified species interaction strengths and intrinsic growth rates, leading to reduced multispecies fitness differences. However, contrary to expected, we also observed that they promote stabilising niche differences. Although these modifications did not substantially alter species richness, they predicted major changes in community composition. Indirect interactions between species explained these community changes in smaller assemblages (three and four species) but lost importance in favour of direct pairwise interactions when more species were involved (five and six). Altogether, our work shows that explicitly considering the number of interacting species is critical for better understanding the direct and indirect processes by which nitrogen enrichment and pathogen communities shape coexistence in grasslands.

Disentangling the effects of phosphorus loading on food web stability in a large shallow lake

Excessive nutrient loads reduce ecosystem resilience, resulting in fundamental changes in ecosystem structure and function when exceeding a certain threshold. However, quantitative analysis of the processes by which nutrient loading affects ecosystem resilience requires further exploration. Food web stability is at the heart of ecosystem resilience. In this study, we simulated the dynamics of the food web under different phosphorus loads for Lake Baiyangdian using the PCLake model and calculated the food web stability. Our results showed that there was a good correspondence between the food web stability and ecosystem state response to phosphorus loads. This relationship confirmed that food web stability could be regarded as a signal for the state transition in a real lake ecosystem. Moreover, our estimates suggested that food web stability was influenced only by several functional groups and their interaction strength. Diatoms and zooplankton were the key functional groups that affected food web stability. Phosphorus loads alter the distribution of functional group biomass, which in turn affects energy delivery and, ultimately, the stability of the food web. Corresponding to functional groups, the interactions among zooplankton, diatoms and detritus had the greatest impact, and the interaction strength of the three was positively correlated with food web stability. Overall, our study explained that food-web stability was critical to characterize ecosystem resilience response to external disturbances and can be turned into a scientific tool for lake ecosystem management.

Impacts of extreme climatic events on trophic network complexity and multidimensional stability

Untangling the relationship between network complexity and ecological stability under climate change is an arduous challenge for theoretical and empirical ecology. Even more so, when considering extreme climatic events. Here, we studied the effects of extreme climatic events (heatwaves) on the complexity of realistic freshwater ecosystems using topological and quantitative trophic network metrics. Next, we linked changes in network complexity with the investigation of four stability components (temporal stability, resistance, resilience, and recovery) of community's functional, compositional, and energy flux stability. We found reduction in topological network complexity to be correlated with reduction of functional and compositional resistance. However, temperature-driven increase in link-weighted network complexity increased functional and energy flux recovery and resilience, but at the cost of increased compositional instability. Overall, we propose an overarching approach to elucidate the effects of climate change on multidimensional stability through the lens of network complexity, providing helpful insights for preserving ecosystems stability under climate change.

Stabilization through self-coupling in networks of small-world and scale-free topology

Mechanisms that ensure the stability of dynamical systems are of vital importance, in particular in our globalized and increasingly interconnected world. The so-called connectivity-stability dilemma denotes the theoretical finding that increased connectivity between the components of a large dynamical system drastically reduces its stability. This result has promoted controversies within ecology and other fields of biology, especially, because organisms as well as ecosystems constitute systems that are both highly connected and stable. Hence, it has been a major challenge to find ways to stabilize complex systems while preserving high connectivity at the same time. Investigating the stability of networks that exhibit small-world or scale-free topology is of particular interest, since these topologies have been found in many different types of real-world networks. Here, we use an approach to stabilize recurrent networks of small-world and scale-free topology by increasing the average self-coupling strength of the units of a network. For both topologies, we find that there is a sharp transition from instability to asymptotic stability. Then, most importantly, we find that the average self-coupling strength needed to stabilize a system increases much slower than its size. It appears that the qualitative shape of this relationship is the same for small-world and scale-free networks, while scale-free networks can require higher magnitudes of self-coupling. We further explore the stabilization of networks with Kronecker-Leskovec topology. Finally, we argue that our findings, in particular the stabilization of large recurrent networks through small increases in the unit self-regulation, are of practical importance for the stabilization of diverse types of complex systems.

Effects of diversity on thermal niche variation in bird communities under climate change

Climate change alters ecological communities by affecting individual species and interactions between species. However, the impacts of climate change may be buffered by community diversity: diverse communities may be more resistant to climate-driven perturbations than simple communities. Here, we assess how diversity influences long-term thermal niche variation in communities under climate change. We use 50-year continental-scale data on bird communities during breeding and non-breeding seasons to quantify the communities' thermal variability. Thermal variability is measured as the temporal change in the community's average thermal niche and it indicates community's response to climate change. Then, we study how the thermal variability varies as a function of taxonomic, functional, and evolutionary diversity using linear models. We find that communities with low thermal niche variation have higher functional diversity, with this pattern being measurable in the non-breeding but not in the breeding season. Given the expected increase in seasonal variation in the future climate, the differences in bird communities' thermal variability between breeding and non-breeding seasons may grow wider. Importantly, our results suggest that functionally diverse wildlife communities can mitigate effects of climate change by hindering changes in thermal niche variability, which underscores the importance of addressing the climate and biodiversity crises together.

High seed diversity and availability increase rodent community stability under human disturbance and climate variation

The relationship between diversity and stability is a focus in community ecology, but the relevant hypotheses have not been rigorously tested at trophic and network levels due to a lack of long-term data of species interactions. Here, by using seed tagging and infrared camera tracking methods, we qualified the seed-rodent interactions, and analyzed the associations of rodent community stability with species diversity, species abundance, and seed-rodent network complexity of 15 patches in a subtropical forest from 2013 to 2021. A total of 47,400 seeds were released, 1,467 rodents were marked, and 110 seed-rodent networks were reconstructed to estimate species richness, species abundance, and seed-rodent network metrics. We found, from younger to older stands, species richness and abundance (biomass) of seeds increased, while those of rodents decreased, leading to a seed-rodent network with higher nestedness, linkage density, and generality in older stands, but higher connectance in younger stands. With the increase of temperature and precipitation, seed abundance (biomass), rodent abundance, and the growth rate of rodent abundance increased significantly. We found rodent community stability (i.e., the inverse of rodent abundance variability) was significantly and positively associated with seed diversity, seed availability, linkage density and generality of seed-rodent networks, providing evidence of supporting the Bottom-Up Diversity-Stability Hypotheses and the Abundant Food Diversity-Stability Hypothesis. Our findings highlight the significant role of resource diversity and availability in promoting consumers' community stability at trophic and network levels, and the necessity of protecting biodiversity for increasing ecosystem stability under human disturbance and climate variation.

Perturbation responses in co-evolved model meta-communities

A spatially explicit eco-evolutionary model assembles simulated meta-communities which are subjected to species and community perturbation experiments to determine factors affecting the stability of the global ecosystem. Spatial structure and resource variety increase the persistence of the ensembles against the removal of an individual species, yet they remain vulnerable to re-invasion by an existing member of the meta-community if it is introduced to all patches with minimal population. Optimal reserve placement strategies are identified for maximally preserving global biodiversity from the effects of sequences of patch disruption, and targeted reserve placement that shields the most or the rarest biodiversity is usually effective. However, if disturbed populations are permitted to re-settle in neighboring patches, then reserves should also be situated remotely to isolate their residents from invasion.

Coexistence in diverse communities with higher-order interactions

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, two species may interactively affect the growth of a focal species. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. Here we analytically predict and numerically confirm how the variability and strength of higher-order interactions affect species coexistence. We found that as higher-order interaction strengths became more variable across species, fewer species could coexist, echoing the behavior of pairwise models. If interspecific higher-order interactions became too harmful relative to self-regulation, coexistence in diverse communities was destabilized, but coexistence was also lost when these interactions were too weak and mutualistic higher-order effects became prevalent. This behavior depended on the functional form of the interactions as the destabilizing effects of the mutualistic higher-order interactions were ameliorated when their strength saturated with species' densities. Last, we showed that more species-rich communities structured by higher-order interactions lose species more readily than their species-poor counterparts, generalizing classic results for community stability. Our work provides needed theoretical expectations for how higher-order interactions impact species coexistence in diverse communities.

Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change

Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO₃^- contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.

Soil pH Determines the Spatial Distribution, Assembly Processes, and Co-existence Networks of Microeukaryotic Community in Wheat Fields of the North China Plain

Soil microeukaryotes play a pivotal role in soil nutrient cycling and crop growth in agroecosystems. However, knowledge of microeukaryotic community distribution patterns, assembly processes, and co-existence networks is greatly limited. Here, microbial eukaryotes in bulk and rhizosphere soils of the North China Plain were investigated. The results showed that soil pH was the driving factor for the microeukaryotic community composition in the bulk and rhizosphere soils. The soil microeukaryotic community could significantly differ between alkaline and acidic soils. The results indicated that the soil pH had a stronger effect than niche differences on community composition. Partial Mantel tests showed that soil pH and spatial distance had similar effects on the microeukaryotic community composition in the bulk soil. However, in the rhizosphere soil, spatial distance had a stronger effect than soil pH. Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) analysis revealed that drift was the most important process driving microeukaryotic community assembly, with an average relative importance of 37.4-71.1%. Dispersal limitation displayed slightly greater importance in alkaline rhizosphere than in alkaline bulk soils. Meanwhile, the opposite trend was observed in acidic soils. In addition, the contribution of each assembly process to each iCAMP lineage "bin" varied according to the acidic or alkaline conditions of the soil and the niche environment. High proportions of positive links were found within the four ecological networks. Alkaline soil networks, especially the alkaline bulk soil network, showed greater complexity than the acidic soil networks. Natural connectivity analysis revealed that the rhizosphere community had a greater stability than the bulk soil community in alkaline soil. This study provides a foundation for understanding the potential roles of microbial eukaryotes in agricultural soil ecosystem functioning.

Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities

With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.

Forecasting in the face of ecological complexity: Number and strength of species interactions determine forecast skill in ecological communities

The potential for forecasting the dynamics of ecological systems is currently unclear, with contrasting opinions regarding its feasibility due to ecological complexity. To investigate forecast skill within and across systems, we monitored a microbial system exposed to either constant or fluctuating temperatures in a 5-month-long laboratory experiment. We tested how forecasting of species abundances depends on the number and strength of interactions and on model size (number of predictors). We also tested how greater system complexity (i.e. the fluctuating temperatures) impacted these relations. We found that the more interactions a species had, the weaker these interactions were and the better its abundance was predicted. Forecast skill increased with model size. Greater system complexity decreased forecast skill for three out of eight species. These insights into how abundance prediction depends on the connectedness of the species within the system and on overall system complexity could improve species forecasting and monitoring.