Stability of ecological communities and the architecture of mutualistic and trophic networks

Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability

Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

Global effects of land-use intensity and exotic plants on the structure and phylogenetic signal of plant-herbivore networks

Interactions between plants and herbivorous insects are often phylogenetically structured, with closely related insect species using similar sets of species or lineages of plants, while phylogenetically closer plants tend to share high proportions of their herbivore insect species. Notably, these phylogenetic constraints in plant-herbivore interactions tend to be more pronounced among internal plant-feeding herbivores (i.e., endophages) than among external feeders (i.e., exophages). In the context of growing human-induced habitat conversion and the global proliferation of exotic species, it is crucial to understand how ecological networks respond to land-use intensification and the increasing presence of exotic plants. In this study, we analyzed plant-herbivore network data from various locations of the World to ascertain the degree to which land-use intensity and the prevalence of exotic plants induce predictable changes in their network topology - measured by levels of nestedness and modularity - and phylogenetic structures. Additionally, we investigated whether the intimacy of plant-herbivore interactions, contrasting endophagous with exophagous networks, modulate changes in network structure. Our findings reveal that most plant-herbivore networks are characterized by significant phylogenetic and topological structures. However, neither these structures did not show consistent changes in response to increased levels of land-use intensify. On the other hand, for the networks composed of endophagous herbivores, the level of nestedness was higher in the presence of a high proportion of exotic plants. Additionally, for networks of exophagous herbivores, we observed an increase in the phylogenetic structure of interactions due to exotic host dominance. These results underscore the differential impacts of exotic species and land-use intensity on the phylogenetic and topological structures of plant-herbivore networks.

Local and regional processes drive distance decay in structure in a spatial multilayer plant-pollinator network

Understanding spatial variation in species distribution and community structure is at the core of community ecology. Nevertheless, the effect of distance on metacommunity structure remains little studied. We examine how plant-pollinator community structure changes across geographical distances at a regional scale and disentangle its underlying local and regional processes. We use a multilayer network to represent linked plant-pollinator communities as a metacommunity in the Canary Islands. We used modularity (i.e. the extent to which the community is partitioned into groups of densely interacting species) to quantify distance decay in structure across space. In multilayer modularity, the same species can belong to different modules in different communities, and modules can span communities. This enabled quantifying how similarity in module composition varied with distance between islands. We developed three null models, each controlling for a separate component of the multilayer network, to disentangle the role of species turnover, interaction rewiring and local factors in driving distance decay in structure. We found a pattern of distance decay in structure, indicating that islands tended to share fewer modules with increasing distance. Species turnover (but not interaction rewiring) was the primary regional process triggering distance decay in structure. Local interaction structure also played an essential role in determining the structure similarity of communities at a regional scale. Therefore, local factors that determine species interactions occurring at a local scale drive distance decay in structure at a regional scale. Our work highlights the interplay between local and regional processes underlying community structure. The methodology, and specifically the null models, we developed provides a general framework for linking communities in space and testing different hypotheses regarding the factors generating spatial structure.

Temporal shifts in the phytoplankton network in a large eutrophic shallow freshwater lake subjected to major environmental changes due to human interventions

Phytoplankton communities are crucial components of aquatic ecosystems, and since they are highly interactive, they always form complex networks. Yet, our understanding of how interactive phytoplankton networks vary through time under changing environmental conditions is limited. Using a 29-year (339 months) long-term dataset on Lake Taihu, China, we constructed a temporal network comprising monthly sub-networks using "extended Local Similarity Analysis" and assessed how eutrophication, climate change, and restoration efforts influenced the temporal dynamics of network complexity and stability. The network architecture of phytoplankton showed strong dynamic changes with varying environments. Our results revealed cascading effects of eutrophication and climate change on phytoplankton network stability via changes in network complexity. The network stability of phytoplankton increased with average degree, modularity, and nestedness and decreased with connectance. Eutrophication (increasing nitrogen) stabilized the phytoplankton network, mainly by increasing its average degree, while climate change, i.e., warming and decreasing wind speed enhanced its stability by increasing the cohesion of phytoplankton communities directly and by decreasing the connectance of network indirectly. A remarkable shift and a major decrease in the temporal dynamics of phytoplankton network complexity (average degree, nestedness) and stability (robustness, persistence) were detected after 2007 when numerous eutrophication mitigation efforts (not all successful) were implemented, leading to simplified phytoplankton networks and reduced stability. Our findings provide new insights into the organization of phytoplankton networks under eutrophication (or re-oligotrophication) and climate change in subtropical shallow lakes.

Does warming erode network stability and ecosystem multifunctionality?

Environmental warming is thought to alter food web stability and functioning, but whether warming reduces food web resistance and resilience to further climatic events remains surprisingly unexplored. Warming experiments that superimpose acute disturbances are urgently needed to understand how extreme events further threaten the stability and multifunctionality of ecological networks.

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.

Typical alien invasive aquatic-plant species changed the stability rather than the diversity of plankton community in fresh water

Alien invasive aquatic-plant (AIA) species are severely threatening the aquatic ecosystems worldwide, especially biodiversity. Although plankton have been used to monitor and address biodiversity, some gaps remain in understanding of the relationships between plankton communities and AIA species. Here, the effects of two typical AIA species (Pistia stratiotes and Eichhornia crassipes) on plankton communities in freshwater with a native plant Vallisneria natans were investigated using a 50-d microcosm experiment. Results showed that AIA species significantly decreased water pH and dissolved oxygen while increased oxidation-reduction potential (p < 0.05). AIA species, especially P. stratiotes, significantly inhibited dry biomass accumulation in V. natans by an average rate of 39.0 %, decreased water pH by up to 14.62 %, and increased aboveground lengths and chlorophyll contents of V. natans by up to 36.2 % and 63.7 % (p < 0.05), respectively. These species further modified the growth strategy of V. natans from dry biomass accumulation to aboveground elongation. Although the AIA species did not alter plankton diversity (p > 0.05), but they changed their dominant species, functional communities (e.g., Groups D and TB), and co-occurrence networks. P. stratiotes decreased the average degree of the networks by 12.37-19.02 % and the graph density by 10.53-14.47 %, while E. crassipes decreased the modularity of the networks by 10.24 % compared with the control (without AIA species), respectively. Overall, AIA species inhibited the growth of V. natans and decreased the stability of plankton communities and their resistance to environmental disturbances. These findings enhance our understanding of how AIA species affect the growth of native plants and variations in plankton communities, thereby providing a theoretical basis for improving the ecological function and safety of freshwater.

The structure of bacteria-fungi bipartite networks along elevational gradients in contrasting climates

Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change.

Community connectivity and local heterogeneity explain animal species co-occurrences within pond communities

Metacommunity processes have the potential to determine most features of the community structure. However, species diversity has been the dominant focus of studies. Nestedness, modularity and checkerboard distribution of species occurrences are main components of biodiversity organisation. Within communities, these patterns emerge from the interaction between functional diversity, spatial heterogeneity and resource availability. Additionally, the connectivity determines the pool of species for community assembly and, eventually, the pattern of species co-occurrence within communities. Despite the recognised theoretical expectations, the change in occurrence patterns within communities along ecological gradients has seldom been considered. Here, we analyse the spatial occurrence of animal species along sampling units within 18 temporary ponds and its relationship with pond environments and geographic isolation. Isolated ponds presented a nested organisation of species with low spatial segregation-modularity and checkerboard-and the opposite was found for communities with high connectivity. A pattern putatively explained by high functional diversity in ponds with large connectivity and heterogeneity, which determines that species composition tracks changes in microhabitats. On the contrary, nestedness is promoted in dispersal-limited communities with low functional diversity, where microhabitat filters mainly affect richness without spatial replacement between functional groups. Vegetation biomass promotes nestedness, probably due to the observed increase in spatial variance in biomass with the mean biomass. Similarly, the richness of vegetation reduced the spatial segregation of animals within communities. This result may be due to the high plant diversity of the pond that is observed similarly along all sampling units, which promotes the spatial co-occurrence of species at this scale. In the study system, the spatial arrangement of species within communities is related to local drivers as heterogeneity and metacommunity processes by means of dispersal between communities. Patterns of species co-occurrence are interrelated with community biodiversity and species interactions, and consequently with most functional and structural properties of communities. These results indicate that understanding the interplay between metacommunity processes and co-occurrence patterns is probably more important than previously thought to understand biodiversity assembly and functioning.

Stability, resilience and eco-evolutionary feedbacks of mutualistic networks to rising temperature

Ecological networks comprising of mutualistic interactions can suddenly transition to undesirable states, such as collapse, due to small changes in environmental conditions such as a rise in local environmental temperature. However, little is known about the capacity of such interaction networks to adapt to a rise in temperature and the occurrence of critical transitions. Here, combining quantitative genetics and mutualistic dynamics in an eco-evolutionary framework, we evaluated the stability and resilience of mutualistic networks to critical transitions as environmental temperature increases. Specifically, we modelled the dynamics of an optimum trait that determined the tolerance of species to local environmental temperature as well as to species interaction. We then evaluated the impact of individual trait variation and evolutionary dynamics on the stability of feasible equilibria, the occurrence of threshold temperatures at which community collapses, and the abruptness of such community collapses. We found that mutualistic network architecture, that is the size of the community and the arrangement of species interactions, interacted with evolutionary dynamics to impact the onset of network collapses. Some networks had more capacity to track the rise in temperatures than others and thereby increased the threshold temperature at which the networks collapsed. However, such a result was modulated by the amount of heritable trait variation species exhibited, with high trait variation in the mean optimum phenotypic trait increasing the environmental temperature at which networks collapsed. Furthermore, trait variation not only increased the onset of temperatures at which networks collapsed but also increased the local stability of feasible equilibria. Our study argued that mutualistic network architecture interacts with species evolutionary dynamics and increases the capacity of networks to adapt to changes in temperature and thereby delayed the occurrence of community collapses.

Identifying habitat modification by Chinese pangolin in subtropical forests of southern China

The excavation of Chinese pangolin (Manis pentadactyla) is expected to alter habitat heterogeneity and thus affect the functioning and structure of forest ecosystems. In this study, the bioturbation of Chinese pangolin on forest soils in three regions (Heping, Tianjingshan, and Wuqinzhang) across Guangdong province was quantified. Overall, a mean of 2.66 m3·ha-1 and 83.1 m2·ha-1 of burrows and bare mounds, respectively, was excavated by Chinese pangolin; the disturbed soils had significantly lower water content and P, C, available N concentrations, but higher bulk density, pH, and microbial abundance than those undisturbed soils. The unevenness of habitat heterogeneity improvement was mainly ascribed to the stronger soil disturbance caused in resting burrows by pangolins. Patterns of altering habitat heterogeneity were site-specific, with high-intensity soil disturbance occurring most in shrubs, meadows, steep habitats at high elevations, and mountain tops in Heping, while in broad-leaved, coniferous and mixed coniferous and broad-leaved forests away from human settlements in Tianjingshan and upper mountains at high elevations far away from roads and human settlements in Wuqinzhang. Road networks are the main interference for the burrow distribution in Heping and Wuqinzhang and should be programmed.

Microbial communities assembly in wastewater treatment plants in China

Community assembly processes determine community structure. Deterministic processes are essential for optimizing activated sludge (AS) bioreactor performance. However, the debate regarding the relative importance of determinism versus stochasticity remains contentious, and the influencing factors are indistinct. This study used large-scale 16S rRNA gene data derived from 252 AS samples collected from 28 cities across China to explore the mechanism of AS community assembly. Results showed that the northern communities possessed lower spatial turnover and more significant dispersal limitation than those in the south, whereas the latter had more substantial deterministic processes than the former (14.46 % v.s. 9.12 %). Meanwhile, the communities in the south exhibited lower network complexity and stability. We utilized a structural equation model to explore the drivers of deterministic processes. Results revealed that low network complexity (r = -0.56, P < 0.05) and high quorum sensing bacteria abundance (r = 0.25, P < 0.001) promoted deterministic assembly, which clarifies why determinism was stronger in southern communities than northern ones. Furthermore, total phosphorus and hydraulic retention time were found to be the primary abiotic drivers. These findings provide evidence to understand the community deterministic assembly, which is crucial for resolving community structure and improving bioreactor performance.

The Potential of Co-Fermentation of Whole-Plant Cassava with Piper sarmentosum: A Comprehensive Study of Fermentation Quality, Antioxidant Activity, Bacterial Community Structure, and Microbial Ecological Networks in Novel Foods

The objective of this study was to explore the preservation of food products through the co-fermentation of whole-plant cassava and Piper sarmentosum (PS) without additives. We assessed fermentation quality, antioxidant activity, bacterial community structure, function profile, and microbial ecological network features. Our results demonstrate that co-fermentation of whole-plant cassava with 10% PS significantly improves food quality. The co-fermented samples exhibited enhanced lactic acid concentrations and increased antioxidant activity, with reduced pH values and concentrations of acetic acid, butyric acid, and ammonia-N(NH3-N) compared to whole-plant cassava fermented alone. In addition, PS addition also optimized microbial community structure by elevating the total abundance of lactic acid bacteria and influenced bacterial predicted functions. Furthermore, our analysis of co-occurrence networks reveals that co-fermentation impacts microbial network features, including module numbers and bacterial relative abundances, leading to altered complexity and stability of the networks. Moreover, out study also highlights the impact of ferment undesirable bacteria like Pseudomonas aeruginosa and unclassified_Muribaculaceae playing crucial roles in microbial network complexity and stability. These findings provide valuable insights into the anaerobic fermentation process and offers strategies for regulating food fermentation quality.

The persistence of bipartite ecological communities with Lotka-Volterra dynamics

The assembly and persistence of ecological communities can be understood as the result of the interaction and migration of species. Here we study a single community subject to migration from a species pool in which inter-specific interactions are organised according to a bipartite network. Considering the dynamics of species abundances to be governed by generalised Lotka-Volterra equations, we extend work on unipartite networks to we derive exact results for the phase diagram of this model. Focusing on antagonistic interactions, we describe factors that influence the persistence of the two guilds, locate transitions to multiple-attractor and unbounded phases, as well as identifying a region of parameter space in which consumers are essentially absent in the local community.

Exploring spatial segregation induced by competition avoidance as driving mechanism for emergent coexistence in microbial communities

This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge the sufficiency of mean-field pairwise interaction models, and we consider the impact of spatial dynamics. We developed an individual-based spatial simulation depicting bacterial movement through a pattern of random walks influenced by competition avoidance, leading to the formation of spatially segregated clusters. This model was integrated with a Lotka-Volterra metapopulation framework focused on competitive interactions. Our findings reveal that spatial segregation combined with low diffusion rates and high compositional heterogeneity among patches can lead to emergent coexistence in microbial communities. This reveals a novel mechanism underpinning the formation of stable, coexisting microbe clusters, which is nonetheless incapable of promoting coexistence in the case of isolated pairs of species. This study underscores the importance of considering spatial factors in understanding the dynamics of microbial ecosystems.

Understanding diversity-synchrony-stability relationships in multitrophic communities

Understanding how species loss impacts ecosystem stability is critical given contemporary declines in global biodiversity. Despite decades of research on biodiversity-stability relationships, most studies are performed within a trophic level, overlooking the multitrophic complexity structuring natural communities. Here, in a global analysis of diversity-synchrony-stability (DSS) studies (n = 420), we found that 74% were monotrophic and biased towards terrestrial plant communities, with 91% describing stabilizing effects of asynchrony. Multitrophic studies (26%) were representative of all biomes and showed that synchrony had mixed effects on stability. To explore potential mechanisms, we applied a multitrophic framework adapted from DSS theory to investigate DSS relationships in algae-herbivore assemblages across five long-term tropical and temperate marine system datasets. Both algal and herbivore species diversity reduced within-group synchrony in both systems but had different interactive effects on species synchrony between systems. Herbivore synchrony was positively and negatively influenced by algal diversity in tropical versus temperate systems, respectively, and algal synchrony was positively influenced by herbivore diversity in temperate systems. While herbivore synchrony reduced multitrophic stability in both systems, algal synchrony only reduced stability in tropical systems. These results highlight the complexity of DSS relationships at the multitrophic level and emphasize why more multitrophic assessments are needed to better understand how biodiversity influences community stability in nature.

Multiple interaction networks reveal that Lepidoptera larvae and adults prefer various host plants for diet and pollination

Plant-Lepidoptera interactions are often studied using the pollination or herbivore networks only. Lepidoptera species are involved in two types of plant-insect interactions because they are herbivores as larvae and pollinators as adults. The study of entangled networks is critical, since the interaction of different networks can affect the overall network and community stability. Here, we studied the interaction of plants and Lepidoptera on the Yongxing Island, South China Sea. A plant-lepidopteran pollination network and a plant-lepidopteran herbivore network were built by using data from flower-pollinator and leaf-herbivore interactions. We then combined the two networks into a single network. We measured plant composition similarity within each sub-network and across sub-networks for Lepidoptera species. Our findings indicate that the plant-Lepidoptera pollination network and the herbivory network share significant proportions of Lepidoptera but small proportions of plant assemblages. The pollination network had higher nestedness and connectance than the herbivore network. Agrius convolvuli was the most specialized species, while Zizina otis had the highest species strength in the pollination network. Most Lepidoptera species were highly specialized in the herbivore network and their importance positively correlated across the two networks. Furthermore, there was no dietary composition similarity between the two networks for most Lepidoptera species. Our findings highlight the visible structural difference between the pollination and the herbivore networks. Adult Lepidoptera selects different plants for oviposition and feeding, a strategy that may benefit their reproduction and survival by sustaining adequate resources for their two life stages and the diversity of both plants and insects in oceanic island communities.

The human touch: a meta-analysis of anthropogenic effects on plant-pollinator interaction networks

Background

Anthropogenic activities significantly impact natural ecosystems, leading to alterations in plant and pollinator diversity and abundance. These changes often result in shifts within interacting communities, potentially reshaping the structure of plant-pollinator interaction networks. Given the escalating human footprint on habitats, evaluating the response of these networks to anthropization is critical for devising effective conservation and management strategies.

Methods

We conducted a comprehensive review of the plant-pollinator network literature to assess the impact of anthropization on network structure. We assessed network metrics such as nestedness measure based on overlap and decreasing fills (NODF), network specialization (H2'), connectance (C), and modularity (Q) to understand structural changes. Employing a meta-analytical approach, we examined how anthropization activities, such as deforestation, urbanization, habitat fragmentation, agriculture, intentional fires and livestock farming, affect both plant and pollinator richness.

Results

We generated a dataset for various metrics of network structure and 36 effect sizes for the meta-analysis, from 38 articles published between 2010 and 2023. Studies assessing the impact of agriculture and fragmentation were well-represented, comprising 68.4% of all studies, with networks involving interacting insects being the most studied taxa. Agriculture and fragmentation reduce nestedness and increase specialization in plant-pollinator networks, while modularity and connectance are mostly not affected. Although our meta-analysis suggests that anthropization decreases richness for both plants and pollinators, there was substantial heterogeneity in this regard among the evaluated studies. The meta-regression analyses helped us determine that the habitat fragment size where the studies were conducted was the primary variable contributing to such heterogeneity.

Conclusions

The analysis of human impacts on plant-pollinator networks showed varied effects worldwide. Responses differed among network metrics, signaling nuanced impacts on structure. Activities like agriculture and fragmentation significantly changed ecosystems, reducing species richness in both pollinators and plants, highlighting network vulnerability. Regional differences stressed the need for tailored conservation. Despite insights, more research is crucial for a complete understanding of these ecological relationships.

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. Understanding PEx ecology is challenged by high inter-patient variability in airway microbial community profiles. We analyze bacterial communities in 880 CF sputum samples collected during an observational prospective cohort study and develop microbiome descriptors to model community reorganization prior to and during 18 PEx. We identify two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx show hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx display stochasticity and increased diversity. A simulation of antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.

Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay

Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.

Properties of vertebrate predator-prey networks in the high Arctic

Predation is an important ecological process that can significantly impact the maintenance of ecosystem services. In arctic environments, the relative ecological importance of predation is thought to be increasing due to climate change, partly because of increased productivity with rising temperatures. Therefore, understanding predator-prey interactions in arctic ecosystems is vital for the sustainable management of these northern regions. Network theory provides a framework for quantifying the structures of ecological interactions. In this study, we use dietary observations on mammalian and avian predators in a high arctic region, including isolated peninsulas on Ellesmere Island and north Greenland, to construct bipartite trophic networks. We quantify the complexity, specialization, and nested as well as modular structures of these networks and also determine if these properties varied among the peninsulas. Mammal prey remains were the dominant diet item for all predators, but there was spatial variation in diet composition among peninsulas. The predator-prey networks were less complex, had more specialized interactions, and were more nested and more modular than random expectations. However, the networks displayed only moderate levels of modularity. Predator species had less specialized interactions with prey than prey had with predators. All network properties differed among the peninsulas, which highlights that ecosystems often show complex responses to environmental characteristics. We suggest that gaining knowledge about spatial variation in the characteristics of predator-prey interactions can enhance our ability to manage ecosystems exposed to environmental perturbations, particularly in high arctic environments subject to rapid environmental change.

Structural dynamics of plant-pollinator mutualistic networks

The discourse surrounding the structural organization of mutualistic interactions mostly revolves around modularity and nestedness. The former is known to enhance the stability of communities, while the latter is related to their feasibility, albeit compromising the stability. However, it has recently been shown that the joint emergence of these structures poses challenges that can eventually lead to limitations in the dynamic properties of mutualistic communities. We hypothesize that considering compound arrangements-modules with internal nested organization-can offer valuable insights in this debate. We analyze the temporal structural dynamics of 20 plant-pollinator interaction networks and observe large structural variability throughout the year. Compound structures are particularly prevalent during the peak of the pollination season, often coexisting with nested and modular arrangements in varying degrees. Motivated by these empirical findings, we synthetically investigate the dynamics of the structural patterns across two control parameters-community size and connectance levels-mimicking the progression of the pollination season. Our analysis reveals contrasting impacts on the stability and feasibility of these mutualistic communities. We characterize the consistent relationship between network structure and stability, which follows a monotonic pattern. But, in terms of feasibility, we observe nonlinear relationships. Compound structures exhibit a favorable balance between stability and feasibility, particularly in mid-sized ecological communities, suggesting they may effectively navigate the simultaneous requirements of stability and feasibility. These findings may indicate that the assembly process of mutualistic communities is driven by a delicate balance among multiple properties, rather than the dominance of a single one.

Pollen analysis reveals the effects of uncovered interactions, pollen-carrying structures, and pollinator sex on the structure of wild bee-plant networks

Pollination networks are increasingly used to model the complexity of interactions between pollinators and flowering plants in communities. Different methods exist to sample these interactions, with direct observations of plant-pollinator contacts in the field being by far the most common. Although the identification of pollen carried by pollinators allows uncovering interactions and increasing sample sizes, the methods used to build pollen-transport networks are variable and their effect on network structure remains unclear. To understand how interaction sampling influences the structure of networks, we analyzed the pollen found on wild bees from eight communities across Mallorca Island and investigated the differences in pollen loads between bee body parts (scopa vs. body) and sexes. We then assessed how these differences, as well as the uncovered interactions not detected in the field, influenced the structure of wild bee-plant networks. We identified a higher quantity and diversity of pollen in the scopa than in the rest of the female body, but these differences did not lead to differences in structure between plant-pollination (excluding scopa pollen) and bee-feeding interaction (including scopa pollen) networks. However, networks built with pollen data were richer in plant species and interactions and showed lower modularity and specialization (H2'), and higher nestedness than visitation networks based on field observations. Female interactions with plants were stronger compared to those of males, although not richer. Accordingly, females were more generalist (low d') and tended to be more central in interaction networks, indicating their more key role structuring pollination networks in comparison to males. Our study highlights the importance of palynological data to increase the resolution of networks, as well as to understand important ecological questions such as the differences between plant-pollination and bee-feeding interaction networks, and the role of sexes in pollination.

A successional shift enhances stability in ant symbiont communities

Throughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affect stability during succession in complex communities is rarely studied in natural ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests. We determined the abundance of 16 functional groups within the symbiont community across 51 host nests in the beginning and end stages of succession. Nest age was the main driver of the compositional shifts: symbiont communities in old nests contained more even species abundance distributions and a greater proportion of specialists. Based on the abundance data, we reconstructed interaction matrices and food webs of the symbiont community for each nest. We showed that the enhanced community evenness in old nests leads to an augmented food web stability in all but the largest symbiont communities. Overall, this study demonstrates that succession begets stability in a natural ecological network by making the community more even.

Water quality drives the reconfiguration of riverine planktonic microbial food webs

The food web is a cycle of matter and energy within river ecosystems. River environmental changes resulting from human activities are increasingly threatening the composition and diversity of global aquatic organisms and the multi-trophic networks. How multiple environmental factors influence food web patterns among multi-trophic microbial communities in rivers remains largely unknown. Using water quality evaluation and meta-omics techniques, we investigated the composition, structure and interaction characteristics, and drivers of food webs of microorganisms (archaea, bacteria, fungi, protists, metazoa, viridiplantae and viruses) at multiple trophic levels in different water quality environments (Classes II, III, and IV). First, water quality deterioration led to significant changes in the composition of the microbial community at multiple trophic levels, which were represented by the enrichment of Euryarchaeota in the archaeal community, the increase of r-strategists in the bacterial community, and the increase of the proportion of predators in the protist community. Second, deteriorating water quality resulted in a significant reduction in the dissimilarity of community structure (homogenization of community structure in Class III and IV waters). Of the symbiotic, parasitic, and predatory networks, the community networks in Class II water all showed the most stable symbiotic, parasitic, and predatory correlations (higher levels of modularity in the networks). In Class III and IV waters, nutrient inputs have led to increased reciprocal symbiosis and decreased competition between communities, which may have the risk of a positive feedback loop driving a system collapse. Finally, inputs of phosphorus and organic matter could be the main drivers of changes in the planktonic microbial food web in the Fen River. Overall, the results indicated the potential ecological risks of exogenous nutrient inputs, which were important for aquatic ecosystem conservation.

DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities

There have been a growing number of computational strategies to aid in the design of synthetic microbial consortia. A framework to identify regions in parametric space to maximize two essential properties, evenness and stability, is critical. In this study, we introduce DyMMM-LEAPS (dynamic multispecies metabolic modeling-locating evenness and stability in large parametric space), an extension of the DyMMM framework. Our method explores the large parametric space of genetic circuits in synthetic microbial communities to identify regions of evenness and stability. Due to the high computational costs of exhaustive sampling, we utilize adaptive sampling and surrogate modeling to reduce the number of simulations required to map the vast space. Our framework predicts engineering targets and computes their operating ranges to maximize the probability of the engineered community to have high evenness and stability. We demonstrate our approach by simulating five cocultures and one three-strain culture with different social interactions (cooperation, competition, and predation) employing quorum-sensing-based genetic circuits. In addition to guiding circuit tuning, our pipeline gives an opportunity for a detailed analysis of pockets of evenness and stability for the circuit under investigation, which can further help dissect the relationship between the two properties. DyMMM-LEAPS is easily customizable and can be expanded to a larger community with more complex interactions.

Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks

Vibrios, a group of bacteria that are among the most abundant in marine environments, include several species such as Vibrio cholerae and Vibrio parahaemolyticus, which can be pathogenic to humans. Some species of Vibrio contain prophages within their genomes. These prophages can carry genes that code for toxins, such as the zonula occludens toxin (Zot), which contribute to bacterial virulence. Understanding the association between different Vibrio species, prophages and Zot genes can provide insights into their ecological interactions. In this study, we evaluated 4619 Vibrio genomes from 127 species to detect the presence of prophages carrying the Zot toxin. We found 2030 potential prophages with zot-like genes in 43 Vibrio species, showing a non-random association within a primarily modular interaction network. Some prophages, such as CTX or Vf33, were associated with specific species. In contrast, prophages phiVCY and VfO3K6 were found in 28 and 20 Vibrio species, respectively. We also identified six clusters of Zot-like sequences in prophages, with the ZOT2 cluster being the most frequent, present in 34 Vibrio species. This analysis helps to understand the distribution patterns of zot-containing prophages across Vibrio genomes and the potential routes of Zot-like toxin dissemination.

Local people enhance our understanding of Afrotropical frugivory networks

Afrotropical forests are undergoing massive change caused by defaunation, i.e., the human-induced decline of animal species,1 most of which are frugivorous species.1,2,3 Frugivores' depletion and their functional disappearance are expected to cascade on tree dispersal and forest structure via interaction networks,4,5,6,7 as the majority of tree species depend on frugivores for their dispersal.8 However, frugivory networks remain largely unknown, especially in Afrotropical areas,9,10,11 which considerably limits our ability to predict changes in forest dynamics and structures using network analysis.12,13,14,15 While the academic workforce may be inadequate to fill this knowledge gap before it is too late, local ecological knowledge appears as a valuable source of ecological information and could significantly contribute to our understanding of such crucial interactions for tropical forests.16,17,18,19,20,21 To investigate potential synergies between local ecological knowledge and academic knowledge,20,21 we compiled frugivory interactions linking 286 trees to 100 frugivore species from the academic literature and local ecological knowledge coming from interviews of Gabonese forest-dependent people. Here, we showed that local ecological knowledge on frugivory interactions was substantial and original, with 39% of these interactions unknown by science. We demonstrated that combining academic and local ecological knowledge affects the functional relationship linking frugivore body mass to seed size, as well as the network structure. Our results highlight the benefits of bridging knowledge systems between academics and local communities for a better understanding of the functioning and response to perturbations of Afrotropical forests.

Ecology: The fruits of local knowledge

Local and indigenous communities often have an intimate connection to nature that is reflected in their ecological knowledge and practices. A new study shows that local ecological knowledge can transform the scientific understanding of an ecological network.

Re-oligotrophication and warming stabilize phytoplankton networks

Phytoplankton taxa are strongly interconnected as a network, which could show temporal dynamics and non-linear responses to changes in drivers at both seasonal and long-term scale. Using a high quality dataset of 20 Danish lakes (1989-2008), we applied extended Local Similarity Analysis to construct temporal network of phytoplankton communities for each lake, obtained sub-network for each sampling month, and then measured indices of network complexity and stability for each sub-network. We assessed how lake re-oligotrophication, climate warming and grazers influenced the temporal dynamics on network complexity and stability of phytoplankton community covering three aspects: seasonal trends, long-term trends and detrended variability. We found strong seasonality for the complexity and stability of phytoplankton network, an increasing trend for the average degree, modularity, nestedness, persistence and robustness, and a decreasing trend for connectance, negative:positive interactions and vulnerability. Our study revealed a cascading effect of lake re-oligotrophication, climate warming and zooplankton grazers on phytoplankton network stability through changes in network complexity characterizing diversity, interactions and topography. Network stability of phytoplankton increased with average degree, modularity, nestedness and decreased with connectance and negative:positive interactions. Oligotrophication and warming stabilized the phytoplankton network (enhanced robustness, persistence and decreased vulnerability) by enhancing its average degree, modularity, nestedness and by reducing its connectance, while zooplankton richness promoted stability of phytoplankton network through increases in average degree and decreases in negative interactions. Our results further indicate that the stabilization effects might lead to more closed, compartmentalized and nested interconnections especially in the deeper lakes, in the warmer seasons and during bloom periods. From a temporal dynamic network view, our findings highlight stabilization of the phytoplankton community as an adaptive response to lake re-oligotrophication, climate warming and grazers.

Assessing mutualistic metacommunity capacity by integrating spatial and interaction networks

We develop a spatially realistic model of mutualistic metacommunities that exploits the joint structure of spatial and interaction networks. Assuming that all species have the same colonisation and extinction parameters, this model exhibits a sharp transition between stable non-null equilibrium states and a global extinction state. This behaviour allows defining a threshold on colonisation/extinction parameters for the long-term metacommunity persistence. This threshold, the 'metacommunity capacity', extends the metapopulation capacity concept and can be calculated from the spatial and interaction networks without needing to simulate the whole dynamics. In several applications we illustrate how the joint structure of the spatial and the interaction networks affects metacommunity capacity. It results that a weakly modular spatial network and a power-law degree distribution of the interaction network provide the most favourable configuration for the long-term persistence of a mutualistic metacommunity. Our model that encodes several explicit ecological assumptions should pave the way for a larger exploration of spatially realistic metacommunity models involving multiple interaction types.

Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services

Agricultural intensification at field and landscape scales, including increased use of agrochemicals and loss of semi-natural habitats, is a major driver of insect declines and other community changes. Efforts to understand and mitigate these effects have traditionally focused on ecological responses. At the same time, adaptations to pesticide use and habitat fragmentation in both insects and flowering plants show the potential for rapid evolution. Yet we lack an understanding of how such evolutionary responses may propagate within and between trophic levels with ensuing consequences for conservation of species and ecological functions in agroecosystems. Here, we review the literature on the consequences of agricultural intensification on plant and animal evolutionary responses and interactions. We present a novel conceptualization of evolutionary change induced by agricultural intensification at field and landscape scales and emphasize direct and indirect effects of rapid evolution on ecosystem services. We exemplify by focusing on economically and ecologically important interactions between plants and pollinators. We showcase available eco-evolutionary theory and plant-pollinator modelling that can improve predictions of how agricultural intensification affects interaction networks, and highlight available genetic and trait-focused methodological approaches. Specifically, we focus on how spatial genetic structure affects the probability of propagated responses, and how the structure of interaction networks modulates effects of evolutionary change in individual species. Thereby, we highlight how combined trait-based eco-evolutionary modelling, functionally explicit quantitative genetics, and genomic analyses may shed light on conditions where evolutionary responses impact important ecosystem services.

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities

The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO43--P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO43--P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.

Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed bacterial communities in 880 CF sputum samples and developed microbiome descriptors to model community reorganization prior to and during 18 PEx. We identified two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx showed hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx displayed stochasticity and increased diversity. A simulation of antimicrobial treatment predicted better efficacy for hierarchically organized communities. This link between PEx type, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.

Both local stability and dispersal contribute to metacommunity sensitivity to asynchronous habitat availability

The stability of isolated communities depends on the complexity of their foodwebs. However, it remains unclear how local stability interacts with dispersal in multitrophic metacommunities to shape biodiversity patterns. This lack of understanding is deeper in the more realistic frame of landscapes that exhibit non-trivial and time-varying structures. Therefore, in this study, we aim to evaluate the influence of local stabilizing factors versus dispersal in determining the sensitivity of metacommunity biodiversity to increasing asynchrony of site availability. Additionally, we assess the role of foodweb complexity and landscape structure as modulating factors. To accomplish our goals we developed a model based on random matrices for local communities, which are linked by stochastic dispersal over explicit dynamic landscapes. We ran numerical simulations and computed the effect sizes of foodweb temperature, self-limitation, dispersal ability, and all pairwise combinations, on the sensitivity of biodiversity to landscape asynchrony. In our experiments we explored gradients of species richness, foodweb connectance, number of sites, and landscape modularity. Our results showed that asynchrony among site availability periods reduced α -diversity and increased β -diversity. Asynchrony increased γ -diversity at high dispersal rates. Both local and regional stabilizing factors determined the sensitivity of metacommunities to landscape asynchrony. Local factors were more influential in landscapes with fewer sites and lower modularity, as well as in metacommunities composed of complex foodwebs. This research offers insights into the dynamics of metacommunities in dynamic landscapes, providing valuable knowledge about the interplay between local and regional factors in shaping ecological stability and species persistence.

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.

Interaction network rewiring and species' contributions to community-scale flexibility

The architecture of species interaction networks is a key factor determining the stability of ecological communities. However, the fact that ecological network architecture can change through time is often overlooked in discussions on community-level processes, despite its theoretical importance. By compiling a time-series community dataset involving 50 spider species and 974 Hexapoda prey species/strains, we quantified the extent to which the architecture of predator-prey interaction networks could shift across time points. We then developed a framework for finding species that could increase the flexibility of the interaction network architecture. Those "network coordinator" species are expected to promote the persistence of species-rich ecological communities by buffering perturbations in communities. Although spiders are often considered as generalist predators, their contributions to network flexibility vary greatly among species. We also found that detritivorous prey species can be cores of interaction rewiring, dynamically interlinking below-ground and above-ground community dynamics. We further found that the predator-prey interactions between those network coordinators differed from those highlighted in the standard network-analytical framework assuming static topology. Analyses of network coordinators will add a new dimension to our understanding of species coexistence mechanisms and provide platforms for systematically prioritizing species in terms of their potential contributions in ecosystem conservation and restoration.

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Dual species interaction and ecological community stability

How diverse species coexist in nature remains a challenging issue that is not yet resolved in ecology. The traditional approach to tackling this problem uses an ecological community network comprising various biological interaction links between species, such as predator-prey, mutualism, and competition. However, in nature, the interaction between any species pair is not limited to a singular interaction; instead, various interactions occur mostly in two ways, such as competition/facilitation in plants, mutualism/antagonism in consumer-resource mutualisms, and reciprocal predation. Here, using an ecological community model, I show that such so-called dual interactions play a key role in stabilizing ecological communities. Theory predicts that dual interactions can stabilize ecological communities through the balance of positive and negative effects, which behave as if the interactions disappear. Communities with dual interactions are inherently more stable than a classical random community with multiple types of singular interactions, suggesting that dual interactions are more widespread than expected in nature and help to maintain ecological communities.

Fungal complexity and stability across afforestation areas in changing desert environments

The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.

A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau

The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.

Land use is a stronger determinant of ecological network complexity than the number of trophic levels

Land modification causes biodiversity loss and ecosystem modification. Despite many studies on the impacts of this factor, there is little empirical evidence on how it affects the interaction networks of plants, herbivores and their natural enemies; likewise, there is little evidence on how those networks change due to differences in the complexity of the communities they comprise. We analyzed the effects of land use and number of trophic levels on the interaction networks of exotic legume species and their associated arthropods. We collected seedpods from five exotic legume species (one of them invasive) in four land use types (urbanization, roadside, L. leucocephala plantation, wooded pasture) on Santa Cruz Island in the Galapagos, and obtained all arthropods that emerged from the seeds. Then, we built and analyzed the interaction networks for each land use at two community scales, each with different numbers of trophic levels: (1) three levels: plant-seed beetle-parasitoid (PSP), and (2) more than three levels: plant-seed beetle-parasitoid-predator and other trophic guilds (PSPP). Land use was more relevant than number of trophic levels in the configuration of species interactions. The number of species and interactions was highest on roadsides at PSPP and lowest in plantations at PSP. We found a significant effect of land use on connectance and interaction evenness (IE), and no significant effect of number of trophic levels on connectance, diversity or IE. The simultaneous analysis of land use and number of trophic levels enabled the identification of more complex patterns of community structure. Comparison of the patterns we found among islands and between exotic and native legumes is recommended. Understanding the structure of the communities analyzed here, as well as the relative contribution of their determinants of change, would allow us to develop conservation plans according to the dynamics of these neo-ecosystems.

Positive associations fuel soil biodiversity and ecological networks worldwide

Microbial interactions are key to maintaining soil biodiversity. However, whether negative or positive associations govern the soil microbial system at a global scale remains virtually unknown, limiting our understanding of how microbes interact to support soil biodiversity and functions. Here, we explored ecological networks among multitrophic soil organisms involving bacteria, protists, fungi, and invertebrates in a global soil survey across 20 regions of the planet and found that positive associations among both pairs and triads of soil taxa governed global soil microbial networks. We further revealed that soil networks with greater levels of positive associations supported larger soil biodiversity and resulted in lower network fragility to withstand potential perturbations of species losses. Our study provides unique evidence of the widespread positive associations between soil organisms and their crucial role in maintaining the multitrophic structure of soil biodiversity worldwide.

Community assembly of organisms regulates soil microbial functional potential through dual mechanisms

Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the β-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.

Generalist and topologically central avian frugivores promote plant invasion unequally across land-bridge islands

Seed dispersal by frugivorous birds facilitates plant invasions, but it is poorly known how invasive plants integrate into native communities in fragmented landscapes. We surveyed plant-frugivore interactions, including an invasive plant (Phytolacca americana), on 22 artificial land-bridge islands (fragmented forests) in the Thousand Island Lake, China. Focusing on frugivory interactions that may lead to seed dispersal, we built ecological networks of studied islands both at the local island (community) and at landscape (metacommunity) levels. On islands with P. americana, we found that P. americana impacted local avian frugivory networks more on islands with species-poor plant communities and on isolated islands. Moreover, as P. americana interacted mainly with local core birds (generalists), this indicates reduced seed dispersal of native plants on invaded islands. At the landscape level, P. americana had established strong interactions with generalist birds that largely maintain seed-dispersal functions across islands, as revealed by their topologically central roles both in the regional plant-bird trophic network and in the spatial metanetwork. This indicates that generalist frugivorous birds may have facilitated the dispersal of P. americana across islands, making P. americana well integrated into the plant-frugivore mutualistic metacommunity. Taken together, our study demonstrates that the impact of plant invasion is context-dependent and that generalist native frugivores with high dispersal potential may accelerate plant invasion in fragmented landscapes. These findings highlight the importance of taking the functional roles of animal mutualists and habitat fragmentation into account when managing plant invasions and their impact on native communities.

Coexistence mechanism of ecological specialists and generalists based on a network dimension reduction method

As an ecological strategy for species coexistence, some species adapt to a wide range of habitats, while others specialize in particular environments. Such 'generalists' and 'specialists' achieve normal ecological balance through a complex network of interactions between species. However, the role of these interactions in maintaining the coexistence of generalist and specialist species has not been elucidated within a general theoretical framework. Here, we analyze the ecological mechanism for the coexistence of specialist and generalist species in a class of mutualistic and competitive interaction ecosystems based on the network dimension reduction method. We find that ecological specialists and generalists can be identified based on the number of their respective interactions. We also find, using real-world empirical network simulations, that the removal of ecological generalists can lead to the collapse of local ecosystems, which is rarely observed with the loss of ecological specialists.

Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes

As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains.