Disturbance and stability dynamics in microbial communities for environmental biotechnology applications

Microbial communities are corner stones of environmental biotechnology, driving essential processes such as waste degradation, pollutant removal, and nutrient cycling, all fundamental to industrial bioprocesses and sustainability. The structure and functions of these communities are influenced by environmental disturbances, which can arise from changes in operational conditions. Understanding disturbance-stability dynamics, including the roles of rare taxa and gene potential, is crucial for optimizing processes such as wastewater treatment, bioenergy production, and environmental bioremediation. This review highlights recent theoretical, technical, and experimental advances - including ecological theory, multiscale approaches, and the use of machine learning and artificial intelligence - to predict community responses to disturbances. Together, these insights offer a valuable outlook for developing scalable and robust biotechnology applications.

Dissecting resilience curve archetypes and properties in human systems facing weather hazards

Resilience curves have been widely used for conceptualizing and representing specific aspects of resilience behavior during hazard events; however, their use has often remained conceptual with limited data-driven characterization and empirical grounding. While broader community resilience encompasses multiple social, economic, and infrastructure dimensions, targeted analyses of specific systems can provide valuable insights into resilience patterns. Empirical characterizations of resilience curves provide essential insights regarding the manner in which differently impacted systems of communities absorb perturbations and recover from disruptions. To address this gap, this study examines human mobility resilience patterns following multiple weather-related hazard events in the United States by analyzing more than 2000 empirical resilience curves constructed from high-resolution location-based mobility data. These empirical resilience curves are then classified into archetypes using k-means clustering based on various features (e.g., residual performance, disruption duration, and recovery duration). Three main archetypes of human mobility resilience are identified: Type I, with rapid recovery after mild impact; Type II, exhibiting bimodal recovery after moderate impact; and Type III, showing slower recovery after severe impact. The results also reveal critical thresholds, such as the bimodal recovery breakpoint at a 20% impact extent (i.e., function loss), at which the recovery rate decreases, and the critical functional threshold at a 60% impact extent, above which recovery rate would be rather slow. The results show that a critical functional recovery rate of 2.5% per day is necessary to follow the bimodal resilience archetype when impact extent exceeds 20%. These findings provide novel and important insights into different resilience curve archetypes and their fundamental properties. Departing from using resilience curves as a mere concept and visual tool, the data-driven specification of resilience curve archetypes and their properties improve our understanding of the resilience patterns of human systems of communities and enable researchers and practitioners to better anticipate and analyze ways communities bounce back in the aftermath of disruptive hazard events.

Microbial community structure and causal analysis in sediments of shallow eutrophic freshwater lakes under heavy metal compound pollution

Heavy metals, due to their toxicity, persistence, and non-biodegradability, have become some of the most severe environmental pollutants globally. Their accumulation in lake sediments can significantly impact aquatic ecosystems' biogeochemical cycles by altering the ecological dynamics of microbial communities. To further elucidate the mechanisms underlying microbial responses to complex heavy metal pollution in lake sediments, sediment samples were collected from Nan Yi Lake, and their physicochemical properties and microbial composition were systematically analyzed. The results demonstrated that the sediments of Nan Yi Lake were significantly contaminated with heavy metals, which were identified as the predominant factors shaping microbial community structure. Heavy metals influenced microbial richness and distribution patterns along sediment depth gradients, driving the establishment of optimal ecological niches. Meanwhile, other physicochemical factors indirectly affected microbial communities by modulating the concentration of heavy metals. Furthermore, the microbial co-occurrence network was closely associated with the concentrations of Fe and As, with sediment particle size also playing a contributing role. This study highlights the intricate interactions between physicochemical factors and microorganisms, offering critical insights into the multifaceted impacts of heavy metal compound pollution on lake ecosystems. It provides a scientific foundation for effective management of lake environmental pollution and ecological restoration efforts.

Species asynchrony, species stability, and compositional stability jointly stabilize, while bryophyte cover destabilizes plant communities across Japanese moorlands

Given the benefits that human society derives from the functions and services provided by diverse ecosystems, it is imperative to gain insight into the underlying mechanisms of community stability in naturally assembled communities. Despite the potential of subalpine and boreal moorland ecosystems for global carbon sequestration and climate regulation, research on biodiversity-stability relationships and their underlying mechanisms in these ecosystems is lacking. Here, an extensive vegetation dataset collected from subalpine and boreal moorlands across Japan was used to analyze the relationships between plant species richness, species asynchrony, species stability, compositional stability, bryophyte cover, and the temporal stability of community cover. The results revealed that species asynchrony, species stability, and compositional stability were the primary drivers stabilizing moorland community. The positive indirect effect of species richness on community stability, through increased species asynchrony, was largely offset by its negative indirect effect on stability via decreased species stability. Bryophyte cover had a negative effect on species asynchrony, which, in turn, reduced moorland community stability. Vascular plants in bryophyte mats, including sedges and dwarf shrubs, may respond synchronously to fluctuating soil moisture conditions, depending on how Sphagnum mosses react to increased temperatures. We thus provide general empirical evidence that species asynchrony, species stability, and compositional stability jointly stabilize, while bryophyte cover destabilizes moorland community stability. Given that plant communities in subalpine and boreal moorland ecosystems in Japan are increasingly threatened by the expansion of woody species and the reduction of areas occupied moorlands, our study underscores the importance of proactive conservation strategies targeting dominant species with habitat specificity in moorlands and the pivotal role that biodiversity plays in maintaining species asynchrony.

Legacies of temperature fluctuations promote stability in marine biofilm communities

The increasing frequency and intensity of extreme climate events are driving significant biodiversity shifts across ecosystems. Yet, the extent to which these climate legacies will shape the response of ecosystems to future perturbations remains poorly understood. Here, we tracked taxon and trait dynamics of rocky intertidal biofilm communities under contrasting regimes of warming (fixed vs. fluctuating) and assessed how they influenced stability dimensions in response to temperature extremes. Fixed warming enhanced the resistance of biofilm by promoting the functional redundancy of stress-tolerance traits. In contrast, fluctuating warming boosted recovery rate through the selection of fast-growing taxa at the expense of functional redundancy. This selection intensified a trade-off between stress tolerance and growth further limiting the ability of biofilm to cope with temperature extremes. Anticipating the challenges posed by future extreme events, our findings offer a forward-looking perspective on the stability of microbial communities in the face of ongoing climatic change.

Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake

Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO4 2-and PO4 3-, rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00256-8.

Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome

Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures. This study developed a machine-learning approach that integrates the properties of chemical structures with the diversity of soil bacteria and functions to predict the impact of heterocyclic compounds on the microbial community and improve the design of eco-friendly heterocyclic compounds. We screened the key chemical structures of heterocyclic compounds─particularly those with topological polar surface areas (<74.2 Å2 or 111.3-154.1 Å2), carboxyl groups, and dissociation constant, which maintained high soil bacterial diversity and functions, revealing threshold effects where specific structural parameters dictated microbial responses. These eco-friendly compounds stabilize communities and increase beneficial carbon and nitrogen cycle functions. By applying these design parameters, we quantitatively assessed the eco-friendliness scores of 811 heterocyclic compounds, providing a robust foundation for guiding future applications. Our study disentangles the critical chemical structure-related properties that influence the soil microbial community and establishes a computational framework for designing eco-friendly compounds with ecological benefits from an ecological perspective.

Reduced primary productivity and notable resilience of phytoplankton community in the coastal water of southern China under a marine heatwave

Increasing frequency, intensity and duration of marine heatwaves (MHWs) are supposed to affect coastal biological production in different regions to different extents. To understand how MHWs impact coastal primary productivity and community succession of phytoplankton and assess the changes in resilience of phytoplankton communities, we conducted a mesoscale enclosure experiment simulating a MHW in the coastal water of southern China. After 8 days of the MHW (+3 °C) treatment, community biomass was significantly lower than the control's, and primary productivity per volume of water was reduced by about 56%. Nevertheless, the phytoplankton community retrieved its biomass and primary productivity after the temperature was subsequently reset to that of the control. Although the MHW treatment decreased the abundance of diatom and increased the percentages of Synechococcus and Prasinophytes, the main phytoplankton functional types showed positive resilience that allowed the recovery of the phytoplankton community after the MHW. Our results indicate that key phytoplankton functional types in the southern coastal waters of China exhibited significant resilience, recovery, and temporal stability under the influence of the marine MHW by 3 °C rise. However, reduced primary productivity during the MHW period, along with decreased biomass density, might significantly influence secondary producers. In addition, the altered phytoplankton community structure may affect coastal food web processes at least during the MHW period.

The spatiotemporal stability of plant diversity is disconnected from biomass stability in response to human activities in a South American temperate grassland

Human activities alter biomass, nutrient availability, and species dominance in grasslands, impacting their richness, composition, and biomass production. Stability (invariability in time or space) can inform the predictability of plant communities in response to human activities. However, this measure has been simplistically analyzed for temporal (interannual) changes in live biomass, disregarding their spatial stability and the temporal stability of other plant community attributes. Moreover, the simultaneous analysis of temporal and spatial stabilities of plant communities has been scarcely assessed. Here, we test how biomass removal and nutrient addition simultaneously modify the temporal and spatial stabilities of plant richness (α diversity), composition dissimilarity (β diversity), aboveground live biomass, and the role of plant species dominance in the stability responses. We conducted a factorial experiment of biomass removal (grazing, mowing, or intact -no removal-) and nutrient addition (unfertilized or fertilized with nitrogen, phosphorus, and potassium) in a temperate grassland of Argentina, South America. We replicated the experiment in 6 blocks over 10 years to estimate the temporal and spatial stabilities of the plant community. The spatiotemporal stability of plant richness and composition dissimilarity decreased in the intact grassland, while the temporal stability of live biomass increased, compared to the grazed and mowed grasslands. Nutrient addition reduced the spatiotemporal stability of live biomass and the spatial stability of plant richness. The stabilities of species richness as well as that of composition dissimilarity were negatively associated with plant dominance, while the live biomass stability was not. Our results suggest that simplifying the effect of biomass removal and nutrient addition on grassland stability is not feasible, as plant diversity stability responses are not surrogates for biomass stability. The contrasting spatiotemporal stability responses of plant diversity and biomass represent a step forward in predicting human activities' impact over time and across space in temperate grasslands.

Variability of functional and biodiversity responses to perturbations is predictable and informative

Perturbations such as climate change, invasive species and pollution, impact the functioning and diversity of ecosystems. However diversity has many meanings, and ecosystems provide a plethora of functions. Thus, on top of the various perturbations that global change represents, there are also many ways to measure a perturbation's ecological impact. This leads to an overwhelming response variability, which undermines hopes of prediction. Here, we show that this variability can instead provide insights into hidden features of functions and of species responses to perturbations. By analysing a dataset of global change experiments in microbial soil systems we first show that the variability of functional and diversity responses to perturbations is not random; functions that are mechanistically similar tend to respond coherently. Furthermore, diversity metrics and broad functions (e.g. total biomass) systematically respond in opposite ways. We then formalise these observations to demonstrate, using geometrical arguments, simulations, and a theory-driven analysis of the empirical data, that the response variability of ecosystems is not only predictable, but can also be used to access useful information about species contributions to functions and population-level responses to perturbations. Our research offers a powerful framework for understanding the complexity of ecological responses to global change.

Declined nutrients stability shaped by water residence times in lakes and reservoirs under climate change

Water quality stability in lakes and reservoirs is essential for drinking water safety and ecosystem health, especially given the frequent occurrence of extreme climate events. However, the relationship between water quality stability and water residence time (WRT) has not been well elucidated. In this study, we explored the relationship based on nitrogen (N) and phosphorus (P) concentrations data in 11 lakes and 49 reservoirs in the Yangtze-Huaihe River basin from 2010 to 2022. Additionally, we examined the effects of hydrometeorological characteristics, the geomorphology of water bodies and catchments, and land use on the WRT, establishing a link between climate change and the stability of N and P in these water bodies. The results showed that a significant correlation between the stability of N and P in lakes and reservoirs and their WRT. The longer WRT tends to coincide with decreased stability and higher nutrient concentrations. Hydrometeorological factors are the primary factors on the WRT, with precipitation exerting the greatest effect, particularly under extreme drought. In recent years, extreme climatic events have intensified the fluctuations of WRT, resulting in a renewed increase in N and P concentrations and deterioration in stability. These findings highlight the importance of incorporating meteorological and hydrological factors alongside reinforcing ecological restoration into lake and reservoir management strategies, and providing a scientific basis for future efforts aimed at enhancing lake and reservoir water quality stability and safeguarding aquatic ecosystems.

Litter Removal Counteracts the Effects of Warming on Soil Bacterial Communities in the Qinghai-Tibet Plateau

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence strategies remain unclear. In this study, we used a fiberglass open-top chamber to simulate global change, and moderate grazing in winter was simulated by removing above-ground litter from all plants in the Qinghai-Tibet Plateau, China, to investigate the effects of warming, litter removal, and interactions on soil microbial communities. The treatments included (1) warming treatment (W); (2) litter removal treatment (L); (3) the combined treatment (WL); and (4) control (CK). The results show that compared with the control treatment, warming, litter removal, and the combined treatments increased bacterial Shannon diversity but reduced fungal Shannon diversity, and warming treatment significantly changed the bacterial community composition. Warming, litter removal, and the combined treatments reduced the colinear network connectivity among microorganisms but increased the modularity of the network, and the average path distance and average clustering coefficient were higher than those in the control group. Stochastic processes played a more important role in shaping the microbial community composition, and soil-available phosphorus and soil ammonium contributed more to the βNTI of the bacterial community, while total phosphorus and NAG enzyme in the soil contributed more to the βNTI of the fungal community. Notably, litter removal counteracts the effects of warming on bacterial communities. These results suggest that litter removal may enhance bacterial community stability under warming conditions, providing insights for managing alpine meadow ecosystems in the context of climate change.

Variation in the intestinal bacterial community composition under different water temperature culture conditions in largemouth bass (Micropterus salmoides)

AIMS

This study aimed to investigate the impact of temperature on the intestinal microbiota of largemouth bass using 16S rRNA gene amplicon sequencing, focusing on the under-explored role of abiotic factors in shaping the gut microbial community.

METHODS AND RESULTS

Five water temperature groups (20.0 ± 0.2°C, 25.0 ± 0.2°C, 28.0 ± 0.2°C, 31.0 ± 0.2°C, and 35.0 ± 0.2°C) were established, each with three replicates. Significant variations in intestinal bacterial community composition were observed across these conditions. Elevated temperatures (31.0 ± 0.2°C and 35.0 ± 0.2°C) led to an increase in opportunistic pathogens such as OTU180 Vibrio and OTU2015 Vogesella (P < 0.05). Species correlation network analysis showed a shift toward more positive relationships among intestinal microbes at higher temperatures (P < 0.05). Ecological process analysis highlighted a greater role of ecological drift in microbial community structure at 31.0 ± 0.2°C and 35.0 ± 0.2°C (P < 0.05).

CONCLUSIONS

The study suggests that higher temperatures may predispose largemouth bass to opportunistic pathogens by altering their intestinal microbiota. Effective water temperature management is crucial for largemouth bass aquaculture to mitigate pathogen risks and maintain a balanced intestinal microbiota. This research provides critical insights into the temperature-microbiota relationship and offers practical recommendations for aquaculture practices.

Enhancing the natural absorbing capacity of rivers to restore their resilience

Resilience, which can also be described as absorbing capacity, describes the amount of change that a system can undergo in response to disturbance and maintain a characteristic, self-sustaining regime of functions, processes, or sets of feedback loops. Rivers exhibit varying levels of resilience, but the net effect of industrialized anthropogenic alteration has been to suppress river resilience. As changing climate alters the inputs to rivers and human modification alters the morphology and connectivity of rivers, restoration increasingly considers how to enhance resilience. Characteristics that underpin river absorbing capacity include natural regimes, connectivity, physical and ecological integrity, and heterogeneity. River management emphasizing channel stabilization and homogenization has reduced river absorbing capacity. We propose that the paths to restoring rivers include defining relevant measures of absorbing capacity and understanding the scales of restoration and the sociopolitical elements of river restoration. We provide a conceptual framing for choosing measures that could be used to assess river absorbing capacity.

Shifts in foundation species dominance and altered interaction networks after compounding seismic uplift and extreme marine heatwaves

Seismic activity, erosion, sedimentation, and extreme temperatures can cause compounding large-scale disturbances to marine organisms, like large intertidal foundational seaweeds. In November 2016, a 7.8 Mw earthquake uplifted 130 km of coastline by 0.5-6 m near Kaikōura, New Zealand and thereby increased intertidal desiccation, aerial temperatures, reef erosion, and water turbidity. Furthermore, stress on uplifted intertidal species was compounded by unprecedented marine heatwaves over the summer of 2017/18. Here we documented altered dominances of large foundational seaweed and possible flow-on effects on seaweed-associated flora and fauna, following the uplift and heatwaves. These compounding disturbances caused instant high canopy loss of the dominant primary foundation species - the large perennial canopy-forming southern bull kelp Durvillaea antarctica - and no post-disturbance recovery, suggesting a maintenance threshold has been exceeded. After canopy loss of the primary foundation species, alternative foundation species - i.e., subordinate competitors under pre-disturbance conditions (the perennial canopy-forming fucoids Carpophyllum maschalocarpum, Cystophora scalaris, and Hormosira banksii) increased in abundance. Furthermore, field observations of attachment interaction networks demonstrated that the primary and alternative foundation species facilitated different sessile and mobile taxa. For example, the smaller and more morphologically complex C. maschalocarpum, H. banksii, and C. scalaris, supported more novel attachment associations, whereas the larger Durvillaea supported longer attachment chains. Overall, our results highlight abrupt and potentially long-lasting ecological changes after compounding disturbances, which altered dominance hierarchies. Alternative foundation species are now more common than the pre-disturbance primary foundation species, with flow-on effects on wider communities that depend on biogenic habitats.

Ecological debts induced by heat extremes

Heat extremes have become the new norm in the Anthropocene. Their potential to trigger major ecological responses is widely acknowledged, but their unprecedented severity hinders our ability to predict the magnitude of such responses, both during and after extreme heat events. To address this challenge we propose a conceptual framework inspired by the core concepts of ecological stability and thermal biology to depict how responses of populations and communities accumulate at three response stages (exposure, resistance, and recovery). Biological mechanisms mitigating responses at a given stage incur associated costs that only become apparent at other response stages; these are known as 'ecological debts'. We outline several scenarios for how ecological responses associate with debts to better understand biodiversity changes caused by heat extremes.

Compound hot-dry events greatly prolong the recovery time of dryland ecosystems

Compound hot-dry events cause more severe impacts on terrestrial ecosystems than dry events, while the differences in recovery time (ΔRT) between hot-dry and dry events and their contributing factors remain unclear. Both remote sensing observations and eddy covariance measurements reveal that hot-dry events prolong the recovery time compared with dry events, with greater prolongation of recovery time in drylands than in humid regions. Random forest regression modeling demonstrates that the difference in vapor pressure deficit between hot-dry and dry events, with an importance score of 35%, is the major factor contributing to ΔRT. The severity of stomatal restriction exceeds that of non-stomatal limitation, which restricts the vegetation productivity that is necessary for the recovery process. These results emphasize the negative effect of vapor pressure deficit on vegetation recovery during hot-dry events and project an extension of drought recovery time considering elevated vapor pressure deficit in a warming world.

Constructing cropland ecological stability assessment method based on disturbance-resistance-response processes and classifying cropland ecological types

The cropland ecosystem stability (CES) has received increasing attention, especially in ecologically fragile areas, because of its impact on cropland quality, agricultural production and its ability to resist external disturbances. In this study, we first introduced the concepts of resilience and resistance, proposed the ecosystem disturbance-resistance-response process, and established a framework for evaluating the spatial and temporal dynamics of the CES based on RS data, and innovatively combined the RS assessment results of CES with soil field samples data to further classify cropland ecological types (CET) in a key agricultural areas of the Qinghai-Tibetan Plateau, which can effectively identify those croplands in need of priority ecological protection. Results indicate that the combined interactions of disturbance, resistance and response systems affect CES, forming a complex process with significant fluctuations and spatial variations. We also conclude that the disturbance system is positively influenced by topography and precipitation, while slope negatively affects resistance system. Hydrothermal conditions positively influence resistance system, while the response system is influenced by environmental factors at a lower intensity in six periods. It was interesting to note that soil α-biodiversity indicators are significantly and positively correlated with CES at the end of the study period. Therefore, based on the CES assessment results, we further combined the soil α-biodiversity indicators to classify the type of spatial pattern of CET and found that the eastern and northern areas have better quality, which implied an increase in the CES and a higher level of soil biodiversity, which was ideal for cropland expansion. On the contrary, we concluded that the ecosystem maintenance of the Huangshui headwaters and the northern mountainous areas needs to be strengthened in order to reverse the ecological fragility here and safeguard the cropland productive capacity.

Rodent disturbance reduces ecosystem stability through regulating plant and soil functions in Hulun Buir steppe

Brandt's vole (Lasiopodomys brandtii), a typical rodent in the eastern Eurasian Steppe, has unclear impacts on ecosystem stability. In our field study in the Hulun Buir steppe, a multifunctional grazing ecosystem in this region, we used burrow entrance area and burrow density as alternative disturbance indices to derive a Disturbance Index (DI) for quantifying disturbance levels from rodents, and employed generalized linear mixed-effects model and the N-dimensional hypervolume framework to assess the influence of Brandt's vole disturbance on plant and soil functions, and then on the ecosystem functional stability. Our findings unequivocally illustrate that various plant functions including vegetation cover (Cover), aboveground biomass (ABG) and shoot carbon (ShootC) significantly declined with increasing disturbance, while shoot nitrogen (ShootN) and root nitrogen (RootN) show significantly positive responses. Soil functions such as soil nitrogen (SoilN), soil phosphorus (SoilP) and soil organic carbon (SoilC) showed significantly negative responses. Notably, the burrow entrance area exerts a more pronounced impact on both plant and soil functions in comparison to burrow density. Additionally, both disturbance indicators have a more significant influence on plant functions than on soil functions. Overall, the ecosystem functional stability progressively decreases with intensified disturbance, with varying response patterns for plant and soil functions, the former exhibited heightened stability as disturbance intensified, while the latter proved more stable at moderate disturbance levels. Our findings suggest that plant functions were more susceptible to disturbance by Brandt's vole compared to soils. Additionally, an ecosystem destabilization was synchronized with increasing Brandt's vole disturbance, although alterations in the functional stability of plants and soil show a different pattern.

Disturbance theory for ecosystem ecologists: A primer

Understanding what regulates ecosystem functional responses to disturbance is essential in this era of global change. However, many pioneering and still influential disturbance-related theorie proposed by ecosystem ecologists were developed prior to rapid global change, and before tools and metrics were available to test them. In light of new knowledge and conceptual advances across biological disciplines, we present four disturbance ecology concepts that are particularly relevant to ecosystem ecologists new to the field: (a) the directionality of ecosystem functional response to disturbance; (b) functional thresholds; (c) disturbance-succession interactions; and (d) diversity-functional stability relationships. We discuss how knowledge, theory, and terminology developed by several biological disciplines, when integrated, can enhance how ecosystem ecologists analyze and interpret functional responses to disturbance. For example, when interpreting thresholds and disturbance-succession interactions, ecosystem ecologists should consider concurrent biotic regime change, non-linearity, and multiple response pathways, typically the theoretical and analytical domain of population and community ecologists. Similarly, the interpretation of ecosystem functional responses to disturbance requires analytical approaches that recognize disturbance can promote, inhibit, or fundamentally change ecosystem functions. We suggest that truly integrative approaches and knowledge are essential to advancing ecosystem functional responses to disturbance.

Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks

BACKGROUND

Antibiotic exposure can occur in medical settings and from environmental sources. Long-term effects of brief antibiotic exposure in early life are largely unknown.

RESULTS

Post a short-term treatment by ceftriaxone to C57BL/6 mice in early life, a 14-month observation was performed using 16S rRNA gene-sequencing technique, metabolomics analysis, and metagenomics analysis on the effects of ceftriaxone exposure. Firstly, the results showed that antibiotic pre-treatment significantly disturbed gut microbial α and β diversities (P < 0.05). Both Chao1 indices and Shannon indices manifested recovery trends over time, but they didn't entirely recover to the baseline of control throughout the experiment. Secondly, antibiotic pre-treatment reduced the complexity of gut molecular ecological networks (MENs). Various network parameters were affected and manifested recovery trends over time with different degrees, such as nodes (P < 0.001, R2 = 0.6563), links (P < 0.01, R2 = 0.4543), number of modules (P = 0.0672, R2 = 0.2523), relative modularity (P = 0.6714, R2 = 0.0155), number of keystones (P = 0.1003, R2 = 0.2090), robustness_random (P = 0.79, R2 = 0.0063), and vulnerability (P = 0.0528, R2 = 0.28). The network parameters didn't entirely recover. Antibiotic exposure obviously reduced the number of key species in gut MENs. Interestingly, new keystones appeared during the recovery process of network complexity. Changes in network stability might be caused by variations in network complexity, which supports the ecological theory that complexity begets stability. Besides, the metabolism profiles of the antibiotic group and control were significantly different. Correlation analysis showed that antibiotic-induced differences in gut microbial metabolism were related to MEN changes. Antibiotic exposure also caused long-term effects on gut microbial functional networks in mice.

CONCLUSIONS

These results suggest that short-term antibiotic exposure in early life will cause long-term negative impacts on gut microbial diversity, MENs, and microbial metabolism. Therefore, great concern should be raised about children's brief exposure to antibiotics if the results observed in mice are applicable to humans. Video Abstract.

Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

Speed and degree of functional and compositional recovery varies with latitude and community age

Rates at which a community recovers after disturbance, or its resilience, can be accelerated by increased net primary productivity and recolonization dynamics such as recruitment. These mechanisms can vary across biogeographic gradients, such as latitude, suggesting that biogeography is likely important to predicting resilience. To test whether community resilience, informed by functional and compositional recovery, hinges on geographic location, we employed a standardized replicated experiment on marine invertebrate communities across four regions from the tropics to the subarctic zone. Communities assembled naturally on standardized substrate while experiencing distinct levels of biomass removal (no removal, low disturbance, and high disturbance), which opened space for new colonizers, thereby providing a pulse of limited resource to these communities. We then quantified functional (space occupancy and biomass) and compositional recovery from these repeated pulse disturbances across two community assembly timescales (early and late at 3 and 12 months, respectively). We documented latitudinal variation in resilience across 47° latitude, where speed of functional recovery was higher toward lower latitudes yet incomplete at late assembly in the tropics and subtropics. The degree of functional recovery did not coincide with compositional recovery, and regional differences in recruitment and growth likely contributed to functional recovery in these communities. While biogeographic variation in community resilience has been predicted, our results are among the first to examine functional and compositional recovery from disturbance in a single large-scale standardized experiment.

Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes

Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.

Network Complexity and Stability of Microbes Enhanced by Microplastic Diversity

Microplastic mixtures are ubiquitously distributed in global ecosystems and include varying types. However, it remains unknown how microplastic diversity affects the biotic interactions of microbes. Here, we developed novel experiments of 600 microcosms with microplastic diversity ranging from 1 to 6 types and examined ecological networks for microbial communities in lake sediments after 2 months of incubation at 15 and 20 °C. We found that microplastic diversity generally enhanced the complexity of microbial networks at both temperatures, such as increasing network connectance and reducing average path length. This phenomenon was further confirmed by strengthened species interactions toward high microplastic diversity except for the negative interactions at 15 °C. Interestingly, increasing temperatures further exaggerated the effects of microplastic diversity on network structures, resulting in higher network connectivity and species interactions. Consistently, using species extinction simulations, we found that higher microplastic diversity and temperature led to more robust networks, and their effects were additionally and positively mediated by the presence of biodegradable microplastics. Our findings provide the first evidence that increasing microplastic diversity could unexpectedly promote the complexity and stability of microbial networks and that future warming could amplify this effect.

Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes

Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.

Opposing effects of warming on the stability of above- and belowground productivity in facing an extreme drought event

Climate warming, often accompanied by extreme drought events, could have profound effects on both plant community structure and ecosystem functioning. However, how warming interacts with extreme drought to affect community- and ecosystem-level stability remains a largely open question. Using data from a manipulative experiment with three warming treatments in an alpine meadow that experienced one extreme drought event, we investigated how warming modulates resistance and recovery of community structural and ecosystem functional stability in facing with extreme drought. We found warming decreased resistance and recovery of aboveground net primary productivity (ANPP) and structural resistance but increased resistance and recovery of belowground net primary productivity (BNPP), overall net primary productivity (NPP), and structural recovery. The findings highlight the importance of jointly considering above- and belowground processes when evaluating ecosystem stability under global warming and extreme climate events. The stability of dominant species, rather than species richness and species asynchrony, was identified as a key predictor of ecosystem functional resistance and recovery, except for BNPP recovery. In addition, structural resistance of common species contributed strongly to the resistance changes in BNPP and NPP. Importantly, community structural resistance and recovery dominated the resistance and recovery of BNPP and NPP, but not for ANPP, suggesting the different mechanisms underlie the maintenance of stability of above- versus belowground productivity. This study is among the first to explain that warming modulates ecosystem stability in the face of extreme drought and lay stress on the need to investigate ecological stability at the community level for a more mechanistic understanding of ecosystem stability in response to climate extremes.

Divergent ecological responses to typhoon disturbance revealed via landscape-scale acoustic monitoring

Climate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenize ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawa's diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.

Quantifying forest resilience post forest fire disturbances using time-series satellite data

Quantification of forest resilience will help us to manage the sustainability of the forest environment and the safety of biodiversity. Measuring forest resilience is crucial for ensuring long-term health of the forest ecosystem in the face of ongoing environmental changes and disturbances. This study focuses on providing a framework to estimate forest resilience scores to assess the vegetation condition after a disturbance. The resilience calculation framework provided uses number of recovery days, the phenological performance level of vegetation in the year when the disturbance took place, long-term mean phenological performance, and greenness levels in subsequent year to calculate the final resilience score at each pixel. Recovery of forests using Landsat data with the help of Normalized Difference Vegetation Index or Normalized Burn Ratio poses a challenge for continuous monitoring of forested landscapes due to cloud cover and availability of scenes at continuous intervals in Landsat datasets. In this regard, MODIS 16-day EVI products were used in this study (2001 to 2020) for monitoring vegetation health before, during, and after the disaster. Bandhavgarh National Park (BNP) located in Madhya Pradesh, India is considered for this study as it witnessed major forest fire breakouts in the second half of March 2018. The objectives of the study are the following: (1) to estimate post-fire recovery days and (2) to formulate new resilience index. The study revealed that the northern part of BNP is more vulnerable and shows slow recovery. The relationship between occupation of people living inside and in the neighboring area with forest resilience is also investigated in this study.

Response trait diversity and species asynchrony underlie the diversity-stability relationship in Romanian bird communities

Biodiversity-stability relationships have frequently been studied in ecology, with the recent integration of traits to explain community stability over time. Classical theory underlying the biodiversity-stability relationship posits that different species' responses to the environment should stabilise community-level properties (e.g. biomass or abundance) through compensatory dynamics. However, functional response traits, which aim to predict how species respond to environmental change, are still rarely integrated into studies of ecological stability. Such traits should mechanistically drive community stability, both in terms of community abundance (functional variability) and composition (compositional variability). In turn, whether and how functional or compositional stability scales to affect temporal variation in functional effect traits (a proxy for ecosystem functioning) remains largely unknown, but is key to consistent ecosystem functioning under environmental change. Here, we explore the diversity-stability relationship in bird communities using annual survey data across 98 sites in central Romania, in combination with global trait databases and structural equation models. We show that higher response trait diversity promotes compositional variability directly, and functional variability indirectly via species asynchrony. In turn, functional variability impacts the temporal stability of effect trait diversity. Multiple facets of diversity and community stability differ between natural forests and agricultural or human-dominated survey sites, and the relationship between response diversity and functional variability is mediated by land cover. Further integration of response-and-effect trait frameworks into studies of community stability will enhance understanding of the drivers of biodiversity change, allowing targeted conservation decision-making with a focus on stable ecosystem functioning in the face of global environmental change.

Complex consequences of disturbance on canopy plant communities of world forests: a review and synthesis

Epiphytes and their associated biota are increasingly recognized as contributing to biodiversity and to filling critical ecosystem functions in world forests. However, the attributes that have made them successful in canopy environments also make them vulnerable to natural and human-induced disturbances. Drawing upon ecological frameworks to understand disturbance, I categorized and synthesized the drivers and the consequences of disturbances on epiphytic materials. Across all impacts, disturbance agents were significantly more likely to lead to negative, rather than positive, effects in both tropical and temperate locales. Significantly more studies reported negative effects on abundance, diversity, community composition and connectivity, but some studies showed that disturbances enhanced these attributes. Although particular disturbance agents did not differently influence individual consequences, they explained a significant portion of variation in aggregated totals. Surprisingly, relative to human disturbances, natural disturbances were more likely to lead to negative effects. Many studies provided recommendations for effective societal responses to mitigate negative impacts, such as retaining large, old trees in forestry operations, patch-clearing for epiphyte harvest, maximizing forest fragment size, using epiphytes as bioindicators of disturbance, and applying principles of community forestry to land management. Future actions should also include communication of these results to policymakers and land managers.

Multidimensional responses of grassland stability to eutrophication

Eutrophication usually impacts grassland biodiversity, community composition, and biomass production, but its impact on the stability of these community aspects is unclear. One challenge is that stability has many facets that can be tightly correlated (low dimensionality) or highly disparate (high dimensionality). Using standardized experiments in 55 grassland sites from a globally distributed experiment (NutNet), we quantify the effects of nutrient addition on five facets of stability (temporal invariability, resistance during dry and wet growing seasons, recovery after dry and wet growing seasons), measured on three community aspects (aboveground biomass, community composition, and species richness). Nutrient addition reduces the temporal invariability and resistance of species richness and community composition during dry and wet growing seasons, but does not affect those of biomass. Different stability measures are largely uncorrelated under both ambient and eutrophic conditions, indicating consistently high dimensionality. Harnessing the dimensionality of ecological stability provides insights for predicting grassland responses to global environmental change.

Breakdown in seasonal dynamics of subtropical ant communities with land-cover change

Concerns about widespread human-induced declines in insect populations are mounting, yet little is known about how land-use change modifies both the trends and variability of insect communities, particularly in understudied regions. Here, we examine how the seasonal activity patterns of ants-key drivers of terrestrial ecosystem functioning-vary with anthropogenic land-cover change on a subtropical island landscape, and whether differences in temperature or species composition can explain observed patterns. Using trap captures sampled biweekly over 2 years from a biodiversity monitoring network covering Okinawa Island, Japan, we processed 1.2 million individuals and reconstructed activity patterns within and across habitat types. Forest communities exhibited greater temporal variability of activity than those in more developed areas. Using time-series decomposition to deconstruct this pattern, we found that sites with greater human development exhibited ant communities with diminished seasonality, reduced synchrony and higher stochasticity compared with sites with greater forest cover. Our results cannot be explained by variation in regional or site temperature patterns, or by differences in species richness or composition among sites. Our study raises the possibility that disruptions to natural seasonal patterns of functionally key insect communities may comprise an important and underappreciated consequence of global environmental change that must be better understood across Earth's biomes.

Diversity-stability relationships across organism groups and ecosystem types become decoupled across spatial scales

The relationship between biodiversity and stability, or its inverse, temporal variability, is multidimensional and complex. Temporal variability in aggregate properties, like total biomass or abundance, is typically lower in communities with higher species diversity (i.e., the diversity-stability relationship [DSR]). At broader spatial extents, regional-scale aggregate variability is also lower with higher regional diversity (in plant systems) and with lower spatial synchrony. However, focusing exclusively on aggregate properties of communities may overlook potentially destabilizing compositional shifts. It is not yet clear how diversity is related to different components of variability across spatial scales, nor whether regional DSRs emerge across a broad range of organisms and ecosystem types. To test these questions, we compiled a large collection of long-term metacommunity data spanning a wide range of taxonomic groups (e.g., birds, fish, plants, invertebrates) and ecosystem types (e.g., deserts, forests, oceans). We applied a newly developed quantitative framework for jointly analyzing aggregate and compositional variability across scales. We quantified DSRs for composition and aggregate variability in local communities and metacommunities. At the local scale, more diverse communities were less variable, but this effect was stronger for aggregate than compositional properties. We found no stabilizing effect of γ-diversity on metacommunity variability, but β-diversity played a strong role in reducing compositional spatial synchrony, which reduced regional variability. Spatial synchrony differed among taxa, suggesting differences in stabilization by spatial processes. However, metacommunity variability was more strongly driven by local variability than by spatial synchrony. Across a broader range of taxa, our results suggest that high γ-diversity does not consistently stabilize aggregate properties at regional scales without sufficient spatial β-diversity to reduce spatial synchrony.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Extreme weather events threaten biodiversity and functions of river ecosystems: evidence from a meta-analysis

Both gradual and extreme weather changes trigger complex ecological responses in river ecosystems. It is still unclear to what extent trend or event effects alter biodiversity and functioning in river ecosystems, adding considerable uncertainty to predictions of their future dynamics. Using a comprehensive database of 71 published studies, we show that event - but not trend - effects associated with extreme changes in water flow and temperature substantially reduce species richness. Furthermore, event effects - particularly those affecting hydrological dynamics - on biodiversity and primary productivity were twice as high as impacts due to gradual changes. The synthesis of the available evidence reveals that event effects induce regime shifts in river ecosystems, particularly affecting organisms such as invertebrates. Among extreme weather events, dryness associated with flow interruption caused the largest effects on biota and ecosystem functions in rivers. Effects on ecosystem functions (primary production, organic matter decomposition and respiration) were asymmetric, with only primary production exhibiting a negative response to extreme weather events. Our meta-analysis highlights the disproportionate impact of event effects on river biodiversity and ecosystem functions, with implications for the long-term conservation and management of river ecosystems. However, few studies were available from tropical areas, and our conclusions therefore remain largely limited to temperate river systems. Further efforts need to be directed to assemble evidence of extreme events on river biodiversity and functioning.

Nitrogen addition and mowing alter drought resistance and recovery of grassland communities

Nitrogen enrichment and land use are known to influence various ecosystems, but how these anthropogenic changes influence community and ecosystem responses to disturbance remains poorly understood. Here we investigated the effects of increased nitrogen input and mowing on the resistance and recovery of temperate semiarid grassland experiencing a three-year drought. Nitrogen addition increased grassland biomass recovery but decreased structural recovery after drought, whereas annual mowing increased grassland biomass recovery and structural recovery but reduced structural resistance to drought. The treatment effects on community biomass/structural resistance and recovery were largely modulated by the stability of the dominant species and asynchronous dynamics among species, and the community biomass resistance and recovery were also greatly driven by the stability of grasses. Community biomass resistance/recovery in response to drought was positively associated with its corresponding structural stability. Our study provides important experimental evidence that both nitrogen addition and mowing could substantially change grassland stability in both functional and structural aspects. Our findings emphasize the need to study changes across levels of ecological organization for a more complete understanding of ecosystem responses to disturbances under widespread environmental changes.

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.

Short-term stability of rocky intertidal biofilm to nitrogen and phosphorus pulses

Coastal environments experience both natural and anthropogenic inputs of nitrogen (N) and phosphorus (P). Agricultural fertilisers, organic run-offs, and edaphic characteristics of coastal environments may generate mosaics of nutrient concentrations that ultimately influence the coastal primary productivity. Here, we experimentally assessed the effects of repeated pulses of N and P on multiple components of ecological stability (sensitivity, resilience, temporal stability and recovery) of phototrophic rocky intertidal biofilm. We performed a repeated-pulses factorial experiment crossing increasing N and P concentrations chosen to reflect a range of nutrient enrichment conditions, from oligotrophic to eutrophic. N and P, regardless of concentration or whether they occurred in isolation or combination, enhanced biofilm's sensitivity (increased biomass or physiological performance compared to controls) without altering resilience. Our experiment illustrates how the stability of an essential coastal primary producer responds to increasing N and P supply levels. Furthermore, notwithstanding the importance of decomposing the multiple dimensions of stability, the transitory increase of the sole sensitivity indicated that rocky shore biofilm is robust against a wide range of nutrient enrichment.

Environmental factors indirectly reduce phytoplankton community stability via functional diversity

The biodiversity-stability relationship is a fundamental subject of ecological research. Considerable evidence demonstrates that biodiversity can either increase or decrease stability. Most relevant research mainly focuses on grassland and forest ecosystems. The biodiversity-stability relationship in aquatic ecosystems and the underlying mechanisms remain poorly understood. To fill the gap, we conducted a year-long study on the phytoplankton of reservoir ecosystems in the Xiangxi Bay of Three Gorges Reservoir (TGR) to test the following hypotheses: (H1) phytoplankton species richness and functional diversity directly reduce phytoplankton community stability in reservoir ecosystems; (H2) nutrient enrichment and water temperature increasing directly reduce phytoplankton community stability; and (H3) nutrients and water temperature indirectly reduce phytoplankton community stability via biodiversity. The structural equation model (SEM) found that functional diversity (community-weighted means of traits and functional divergence) had significant negative correlations with phytoplankton community stability (p &lt; 0.05), while the species diversity had no significant correlation with phytoplankton community stability (p &gt; 0.05). This finding partially supported the hypothesis H1, which suggested that the functional diversity had a closer tie with stability than the species diversity. SEM did not find any direct effect of environmental factors on phytoplankton community stability, which rejected our hypothesis H2. Instead, SEM found that water temperature and phosphate decreased phytoplankton community stability by increasing the first principal component of the community-weighted means of traits (CWM_PC1), which supported hypothesis H3. Further analysis showed that the increased water temperature and phosphate concentration can promote “r-strategists” species (larger CWM_PC1), which are less resistant to environmental disturbances, therefore decreasing the phytoplankton community stability. Our study highlights the importance of functional diversity in maintaining the relationship between biodiversity and stability in the phytoplankton community, which may provide a mechanistic understanding of the biodiversity-stability relationships in aquatic ecosystems.

Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime

Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (i.e., robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (i.e., cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (i.e., bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities' assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake

At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.

Organic fertilization enhances the resistance and resilience of soil microbial communities under extreme drought

INTRODUCTION

The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought.

OBJECTIVES

This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers.

METHODS

In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes.

RESULTS

Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting.

CONCLUSION

Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning.

Spatial and Ecological Scaling of Stability in Spatial Community Networks

There are many scales at which to quantify stability in spatial and ecological networks. Local-scale analyses focus on specific nodes of the spatial network, while regional-scale analyses consider the whole network. Similarly, species- and community-level analyses either account for single species or for the whole community. Furthermore, stability itself can be defined in multiple ways, including resistance (the inverse of the relative displacement caused by a perturbation), initial resilience (the rate of return after a perturbation), and invariability (the inverse of the relative amplitude of the population fluctuations). Here, we analyze the scale-dependence of these stability properties. More specifically, we ask how spatial scale (local vs. regional) and ecological scale (species vs. community) influence these stability properties. We find that regional initial resilience is the weighted arithmetic mean of the local initial resiliences. The regional resistance is the harmonic mean of local resistances, which makes regional resistance particularly vulnerable to nodes with low stability, unlike regional initial resilience. Analogous results hold for the relationship between community- and species-level initial resilience and resistance. Both resistance and initial resilience are “scale-free” properties: regional and community values are simply the biomass-weighted means of the local and species values, respectively. Thus, one can easily estimate both stability metrics of whole networks from partial sampling. In contrast, invariability generally is greater at the regional and community-level than at the local and species-level, respectively. Hence, estimating the invariability of spatial or ecological networks from measurements at the local or species level is more complicated, requiring an unbiased estimate of the network (i.e., region or community) size. In conclusion, we find that scaling of stability depends on the metric considered, and we present a reliable framework to estimate these metrics.

Life history mediates the trade-offs among different components of demographic resilience

Accelerating rates of biodiversity loss underscore the need to understand how species achieve resilience-the ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 910 natural populations of animals and plants predicts their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species' pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, whilst those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.

Faunal communities mediate the effects of plant richness, drought, and invasion on ecosystem multifunctional stability

Understanding the stability of ecosystem multifunctionality is imperative for maintaining ecosystem health and sustainability under augmented global change. However it remains unknown whether and how biological communities mediate multifunctional stability in response to biodiversity loss and disturbances. Here, we conducted a 3-year experiment by exposing 270 plant communities of four plant richness levels, i.e., 1, 2, 4, or 8 species, to drought and exotic plant invasion disturbances. Then, the direct effects of plant richness, drought and invasion, and their indirect effects mediated by the stability of plant, litter-faunal, and soil-faunal communities on multifunctional stability were disentangled. We found that plant richness increased, while drought and invasion decreased ecosystem multifunctional stability, which were mediated by plant or faunal community stability. By incorporating the stability of communities into the complex ecological mechanisms, the completeness and goodness of ecological models for explaining and maintaining the stability of ecosystem multifunctionality will be improved.

Food web rewiring drives long-term compositional differences and late-disturbance interactions at the community level

Multiple anthropogenic disturbances affect the structure and functioning of communities. Recent evidence highlighted that, after pulse disturbance, the functioning a community performs may be recovered fast due to functional redundancy, whereas community multivariate composition needs a longer time. Yet, the mechanisms that drive the different community recovery times have not been quantified empirically. We use quantitative food-web analysis to assess the influence of species interactions on community recovery. We found species-interactions strength to be the main mechanism driving differences between structural and functional recovery. Additionally, we show that interactions between multiple disturbances appear in the long term only when both species-interaction strength and food-web architecture change significantly.

Ecological communities are constantly exposed to multiple natural and anthropogenic disturbances. Multivariate composition (if recovered) has been found to need significantly more time to be regained after pulsed disturbance compared to univariate diversity metrics and functional endpoints. However, the mechanisms driving the different recovery times of communities to single and multiple disturbances remain unexplored. Here, we apply quantitative ecological network analyses to try to elucidate the mechanisms driving long-term community-composition dissimilarity and late-stage disturbance interactions at the community level. For this, we evaluate the effects of two pesticides, nutrient enrichment, and their interactions in outdoor mesocosms containing a complex freshwater community. We found changes in interactions strength to be strongly related to compositional changes and identified postdisturbance interaction-strength rewiring to be responsible for most of the observed compositional changes. Additionally, we found pesticide interactions to be significant in the long term only when both interaction strength and food-web architecture are reshaped by the disturbances. We suggest that quantitative network analysis has the potential to unveil ecological processes that prevent long-term community recovery.